title: DRG CPIP+ETA seq2

city: Hangzhou

first: Boyu

last: Liu

address: Binwen Road

institute: Zhejiang Chinese Medical University

description: Library name: Sample6

data_processing:
The fragments were enriched by PCR amplification to construct a library ready for sequencing using BGISEQ-500 by BGI Group (Shenzhen, China).
Primary sequencing data produced by RNA-Seq (raw reads) were subjected to quality control (QC)..
Raw reads were filtered into clean reads by internal software SOAPnuke (version 1.5.2), followed by: Remove reads in which unknown bases (N) are more than 10%; Remove reads with adaptors; Remove low quality reads (we define the low quality read as the percentage of base which quality is less than 15 and greater than 50% in a read).
QC of alignment was performed to determine if re-sequencing was needed. If the alignment result passed QC, downstream analysis including gene expression, differentially expressed genes, cluster analysis, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, etc. was proceeded.
Assembly: GCF_000001895.5_Rnor_6.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: L4-6 DRG

growth_protocol: Rats were randomly allocated, and 5 rats were housed per cage(12 hour light–dark cycles and 24 ± 2 ℃). Food and water were provided ad libitum.

extract_protocol:
Ipsilateral L4-L6 DRG were surgically removed after modeling 7 days and enzymatically preserved in RNAlater (Thermal Fisher Scientific, USA). Total RNA was extracted from DRG with Trizol reagent (Thermal Fisher Scientific, USA). The concentrations and the purity of DRG samples were evaluated using NanoDrop Spectrophotometer. RNA integrity number (RIN) was determined by Agilent TapeStation System (Agilent Technologies, USA) and only RIN ≥ 8.0 and A260/230 ≥ 1.5 were used for RNA-Seq. Samples were sequenced by BGISEQ-500 from BGI Group (Shenzhen,China). Distances to expressed genes were calculated using the Euclidean method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats were anesthetized by intraperitoneal injection of 3% pentobarbital sodium (40 mg/kg). An O-ring (inner diameter 5.5 mm for male rats) was used to ligate hind limb at a position near ankle joint for 3 h. Three hours later, the O-ring was removed. The control group of rats was treated with the same anesthesia steps but without O-ring ligature.Etanercept or vehicle were applied via intrathecal injection (i.t.) daily after modeling 2 days.

value: L4-6 DRG

value: WT

value: ETA treatment


title: HLF treated with DMSO IP for H3K4me3 replicate 5

status: Public on Apr 07 2025

type: SRA

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

country: USA

institute: University of North Carolina Chapel Hill

description: Library name: 1059_JR934_HLF_H3K4me3_DMSO_1

library_source: genomic

data_processing:
trim_galore version 0.6.7 --paired
bowtie2 version 2.3.4.1 --very-sensitive-local -X 800
picard version 2.20.0 MarkDuplicates
samtools view -b -q 30
deeptools version 3.5.4  bamCoverage --binSize 30 --smoothLength 60 --extendReads --ignoreDuplicates --efectiveGenomeSize 2701495761
macs version 2.2.7.1 macs2 callpeak -g 2701495761 --call-summits -q .05
individual bigwig files were averaged using wiggle tools from ucsc tools wiggletools mean ${bws} |\\   awk '\$1 ~ /^chr[XY0-9]+\$/' |\\   wigToBigWig stdin ${chrom_sizes} group${group_avg}_mean.bw
individual narrowPeak files were used to generate consensus peaks using RMSPC  version 1.8
all data processing steps are implemented as  Nextflow pipeline at github.com/raab-lab/cut-n-run using the --mode cnr
Assembly: hg38
Supplementary files format and content: peak files produced from Macs2, consensus peak files across all samples generated using RMSPC, and bigwig files for individual replicates as well as average bigwig tracks for each treatment condition.
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Homo sapiens

source_name: liver cancer

growth_protocol: HLF cells were grown in DMEM + 10% FBS + penicillin and streptomycin

extract_protocol:
CUT&RUN was performed adapted from PMID: PMC6598765
Kapa Hyperprep DNA kit

treatment_protocol: 5uM SNDX-5613 for 24 hours

tag: tissue

value: liver cancer

tag: cell line

value: HLF

tag: cell type

tag: antibody

tag: treatment

value: DMSO


title: PE7SB [RNA-seq]

city: Seoul

first: Heesoo

last: Uhm

address: 103 Daehak-ro

country: South Korea

institute: Seoul National University

description:
Library name: RNAseq_HeLa_PE7SB
HeLa_PE7SB_Read_Count

library_source: transcriptomic

data_processing:
Raw reads obtained from the sequencer were preprocessed to remove low-quality sequences and adapter contamination before analysis. The processed reads were then aligned to the Homo sapiens (hg38) reference genome using HISAT v2.1.0. After alignment, StringTie v2.1.3b was used to assemble aligned reads into transcripts and estimate their abundance, providing relative expression levels as read count values for transcripts and genes in each sample.
Assembly: hg38
Supplementary files format and content: Comma-separated values text(.csv) file including raw counts for each sample

molecule: polyA RNA

source_name: HeLa

extract_protocol:
For each sample, an independent library was prepared with the SMARTer Ultra-Low Input RNA Sample Prep Kit. Poly-A-containing mRNA molecules were purified using poly-T-attached magnetic beads. The purified mRNA was then fragmented into small pieces using divalent cations under elevated temperature. The fragmented RNA was reverse-transcribed into first-strand cDNA using SMARTScribe reverse transcriptase and 3’ SMART CDS primers, followed by second-strand cDNA synthesis using DNA Polymerase I, RNase H, and dUTP.
The resulting cDNA fragments underwent end repair, the addition of a single ‘A’ base, and adapter ligation. The final cDNA library was purified and enriched via PCR. Indexed libraries were then sequenced on the Illumina NovaSeq platform with paired-end (2 × 100 bp) sequencing performed by Macrogen Incorporated.

value: HeLa

value: EP


title: DRG CPIP+ETA seq1

country: China

description: Library name: Sample5

molecule: total RNA

tag: genotype


title: Subclone D3 (ap2-g F1+F0), H3K9me3 IP

city: Barcelona

first: Alba

last: Pérez-Cantero

state: Barcelona

address: Rosselló, 153

country: Spain

institute: Barcelona Institute for Global Health (ISGlobal)

description: Library name: chip_D3_F1F0_me3

data_processing:
ChIP-seq reads were trimmed using the bbduk command from BBmap software (version July, 26 2018). 3' end was trimmed when quality score < 6. Reads shorter than 10 bp after trimming were discarded
Quality control of the reads was performed using FastQC (v0.11.9) checking reads contamination with FastqScreen (v0.14.0)
Reads were mapped using Bowtie2 (v2.4.5) using the following parameters different from the default ones --very-sensitive --local -5 4 -3 4 -I 50 -X 2000
SAMtools (v1.15) was used for compressing, sorting and filtering-out < 5 mapping quality reads from the alignment files
PCR duplicates were removed using GATK (v4.4.0.0) MarkDuplicates command
Tracks were generated using deepTools (v3.5.1). To generate individual coverage tracks the command bamCompare was used with a bin size of 10 bp and a smoothing length of 200 bp. To obtain the tracks normalized by input, the bamCompare command was used with this parameters: --outFileFormat bedgraph --scaleFactorsMethod None --normalizeUsing RPKM -bs 10 --smoothLength 200 --pseudocount 10 -of bedgraph
Assembly: Reference Plasmodium falciparum (3D7) genome retrieved from PlasmoDB (VEuPathDB). Manually edited for analysis of transgenic parasite lines.
Supplementary files format and content: bedgraph (tracks normalized by input)

organism: Plasmodium falciparum

source_name: Plasmodium falciparum

extract_protocol:
Chromatin extraction from cultures at the late trophozoite/schizont was carried out using the MAGnify chromatin immunoprecipitation system (Life Technologies) after saponin lysis and formaldehyde crosslinking. Samples were then sonicated using an M220 sonicator (Covaris) at 10% duty factor, 200 cycles per burst, 140 W of peak incident power for 10min. Immunoprecipitation was performed overnight at 4ºC with 2µg of chromatin and 4µg of antibodies against H3K9me3 or H3K9ac (Diagenode). Washing, de-crosslinking and elution were performed following the manufacturer instructions, but to avoid high temperatures that may result in denaturation of extremely AT-rich intergenic regions, steps were performed at 45ºC instead of 65ºC.
Libraries for Illumina sequencing were prepared from 5 ng of immunoprecipitated DNA using a protocol adapted for extremely AT-rich genomes.After end-repair and addition of 3′ A-overhangs, NEBNext Multiplex Oligos for Illumina (NEB, E7500) were ligated. Purification steps were performed with Agencourt AMPure XP beads (Beckman Coulter, A63880). Libraries were amplified using the KAPA HiFi PCR Kit (KAPA Biosystems, KK2103) in KAPA HiFi Fidelity Buffer with the following conditions: 95°C for 3 min; 9 cycles at 98°C for 20 s and 62°C for 2 min 30 s; and 62 °C for 5 min. Amplified libraries were purified using 0.9X AMPure XP beads to remove adapter dimers. The library size was analysed in a 4200 TapeStation System (Agilent Technologies) and 125 bp paired-end reads were obtained using the HiSeq2500 or the NextSeq 500 System (Illumina).

tag: Stage

tag: chip antibody

tag: genetic modification

value: pfap2-g deletion (-3522 to +992 bp from ATG) + integration of pfap2-g F1+F0 at PF3D7_1144400

value: Plasmodium falciparum


title: EDL_WT_Vehicle_4

type: genomic

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Infinium MouseMethylation array (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing:
Sesame package in R environment (v4.3.2)
Raw IDAT files from the mouse model MM285k arrays were pre-processed with the sesame package (v4.3.2) with the default "TQCDPB" preprocessing steps. Noob normalization was applied to all samples to derive beta values.  Noob normalized beta values

label: Cy5 and Cy3

organism: Mus musculus

source_name: muscle

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from muscle fiber samples using DNeasy Blood & Tissue Kit (Qiagen) according to standard instructions

value: muscle

tag: disease state

value: wt

tag: Sex

value: male

value: wild type RyR1

value: no


title: DRG CPIP+Veh seq2

description: Library name: Sample4

value: CPIP model


title: PE7 [RNA-seq]

description:
Library name: RNAseq_HeLa_PE7
HeLa_PE7_Read_Count


title: Dnuc-1 0mM phosphate 4h Experiment 2 Replicate 2

city: Ithaca

first: Lori

middle: B

last: Huberman

state: NY

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

institute: Cornell University

description: Library name: Dnuc-1_0mM_Phosphate_4h_Exp2_Rep2

data_processing:
Illumina Casava1.8 software used for base calling
Sequenced reads were trimmed for adaptor sequence and aligned to the predicted transcripts from the N. crassa OR74A genome (v12) and TPMs were quantified with Salmon v. 1.4.0 with the --validateMappings setting.
Assembly: Neurospora crassa OR74A NC12
Supplementary files format and content: tab-deliminated text file with TPM values for each sample

organism: Neurospora crassa

source_name: Mycelia

growth_protocol: N. crassa conidia were inoculated into 3ml of Vogel's minimal media + 2% sucrose and incubated at 25C in constant light with constant shaking at 200rpm for 24h.

extract_protocol:
Mycelia were filtered using Whatman paper #1 and flash frozen using liquid nitrogen. RNA was isolated by beading beating in Trizol reagent and then cleaned up using the Qiagen RNeasy kit.
RNA were prepared for sequencing using poly-A enrichment and standard Illumina protocols

treatment_protocol: Mycelia were washed in 3ml Fries minimal media with 7mM phosphate (for 7mM phosphate) or Fries minimal media with 0mM phosphate (for 0mM phosphate) three times and then transferred to 3ml Fries minimal media with 7mM phosphate or 0mM phosphate as indicated and incubated at 25C in constant light with constant shaking at 200rpm for either 4h or 12h as indicated prior to harvesting for RNAseq.

value: Mycelia

tag: strain

value: nuc-1::HygR mat a

value: 4h Fries minimal medium 0mM phosphate

tag: batch


title: Dnuc-1 0mM phosphate 4h Experiment 2 Replicate 1

description: Library name: Dnuc-1_0mM_Phosphate_4h_Exp2_Rep1


title: Subclone A3 (ap2-g F1+F0), input

description: Library name: chip_A3_F1F0_input


title: Subclone A3 (ap2-g F1+F0), H3K9me3 IP

description: Library name: chip_A3_F1F0_me3


title: MLH1dn [RNA-seq]

description:
Library name: RNAseq_HeLa_MLH1dn
HeLa_MLH1dn_Read_Count


title: Wild type 0mM phosphate 4h Experiment 2 Replicate 3

description: Library name: WT_0mM_Phosphate_4h_Exp2_Rep3

value: FGSC 2489

value: Wild type mat A


title: SB [RNA-seq]

description:
Library name: RNAseq_HeLa_SB
HeLa_SB_Read_Count


title: DRG Sham+Veh seq2

description: Library name: Sample2

value: L4-6 DRG

value: WT

value: sham-operated


title: DRG Sham+Veh seq1

description: Library name: Sample1


title: Subclone B11 (E5-AP2-G-DD), H3K9me3 IP

description: Library name: chip_B11_DD_me3

value: FKBP destabilization domain fused to PfAP2-G


title: PuroR [RNA-seq]

description:
Library name: RNAseq_HeLa_PuroR
HeLa_PuroR_Read_Count

value: HeLa

value: EP


title: Wild type 0mM phosphate 4h Experiment 2 Replicate 2

description: Library name: WT_0mM_Phosphate_4h_Exp2_Rep2


title: Lung, total, GEX

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

country: Germany

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, mapping, detection of intact cells as well as quantification of gene expression was performed using Cell Ranger’s count pipeline in default parameter settings with an expected number of 3,000 cells per sample and refdata-cellranger-mm10-1.2.0 as reference.
Assembly: mm10A
Supplementary files format and content: .h5 or .csv

source_name: lung

extract_protocol:
On day 17, lungs were removed and bronchial lymph nodes were dissected from the lung tissue under a stereo microscope. Single-cell suspensions from lung tissue were prepared using the Miltenyi gentleMACS Dissociator and digested with 0.5 mg/ml collagenase D and 20 mg/ml DNase I for 25 min at 37°C. Antigen-specific B cells were first enriched for CD45.1 expressing cells by magnetic sorting. For higher purity, cells were sorted on a Becton Dickinson ARIA II or ARIA Fusion cell sorter as DAPI- CD4- CD8- CD19+ CD45.1+ CD45.2- total B cells or additionally as CD138- CD38low GL7+ geminal center (GC) B cells.
Library construction was performed according to 10x Genomics instructions. For samples 1 and 2, the Chromium Next GEM Single Cell 3' v2 Kit was used. For samples 3-6, the Chromium Next GEM Single Cell 5' v2 kit in combination with the Single Cell Mouse BCR Amplification Kit was used.

treatment_protocol: 1.25 x 10e5 Smarta T cells were co-transferred with 5 x 10e5 follicular B1-8i B cells (expressing CD45.1 as congenic marker) into C57BL/6NCrl mice by intravenous injection. To induce lung inflammation, mice were repeatedly challenged intranasally with 10 µg of cognate antigen (Smarta peptide and iodinated nitrophenol (NIP) coupled to mouse serum album as non-immunogenic carrier) and 5 µg of LPS as adjuvant on days 0, 1, 10, and 13. For details of the mouse model see Bauer and Hutloff, Meth Mol Biol (2021) 2285:91-98.

value: lung

value: B cell


title: Wild type 0mM phosphate 4h Experiment 2 Replicate 1

description: Library name: WT_0mM_Phosphate_4h_Exp2_Rep1


title: Mock [RNA-seq]

description:
Library name: RNAseq_HeLa_Mock
HeLa_Mock_Read_Count


title: M2 macrophages

city: Jeongeup-Si

first: Hyoung-woo

last: Bai

address: 29 Geumgu-gil

institute: Korea Atomic Energy Research Institute (KAERI)

description: Library name: 3-1_1.fq.gz

data_processing:
Raw reads were trimmed using Trimmomatic v0.36 to remove adapter sequences and low-quality bases. Clean reads were aligned to the mm10 reference genome using HISAT2 v2.2.1. Read counts per gene were quantified using HTSeq-count v0.11.3 with GENCODE annotation.
Assembly: UCSC mm10
Supplementary files format and content: TXT/CSV files containing read count data for each gene across samples.
Supplementary files format and content: The read counts were generated using HTSeq-count (v0.11.3).

source_name: Bone marrow

growth_protocol: RAW 264.7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S). Cells were maintained at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted from polarized and irradiated macrophages using WelPrep™ Total RNA Isolation Reagent (Welgene, Gyeongsan, Korea) according to the manufacturer’s instructions.
Total RNA was fragmented, mRNA was enriched or depleted, followed by reverse transcription and second strand synthesis. After adapter ligation and PCR amplification, ssCircs were converted into DNA nanoballs (DNBs) for PE100/PE150 sequencing.

treatment_protocol: Macrophages were polarized into M1 (LPS 100 ng/mL + IFN-γ 20 ng/mL) or M2 (IL-4 20 ng/mL) phenotypes for 24 h. Polarized cells were then irradiated with 10 Gy using a Gammacell 40 Exactor (¹³⁷Cs source) and incubated at 37°C for an additional 24 h.

value: Bone marrow

value: Macrophage


title: Dnuc-1 0mM phosphate 4h Experiment 2 Replicate 3

description: Library name: Dnuc-1_0mM_Phosphate_4h_Exp2_Rep3


title: Treatment succinate, hours24, replicate 1

status: Public on Apr 06 2025

city: Larisa

first: Dimitrios

last: Karpouzas

address: Biopolis

department: Department of Biochemistry & Biotechnology

country: Greece

institute: University of Thessaly

description: Library name: 21078R-05Q1-34

data_processing:
The obtained RNA reads were subjected to quality trimming using fastp version 0.20.1 with mean Phred Q cutoff of 18 for the end trimming at a window of 4 bases (Chen et al., 2018) and alignment against the assembled genome of Paenarthrobacter sp. TA1.8 with STAR aligner version 2.6.1c (Dobin et al. 2013). The number of sequences per gene was determined with htseq version 2.0.3 (Putri et al. 2022). Differential gene expression analysis was performed with DESeq2 package, version 1.44.0 (Love et al., 2014), of the R language for statistical analysis version 4.4.0
Assembly: CP184287-CP184290
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Paenarthrobacter sp. TA1.8

source_name: Whole organism

extract_protocol:
RNA extraction using the Nucleospin RNA, (MACHEREY-NAGEL GmbH & Co. KG, Duren, Germany)
Downstream library preparation and RNA sequencing were undertaken by Admera Health (South Plainfield, NJ, USA). Prokaryotic RNA depletion was performed through the QIAseqFastSelect 5s/16s/23s rRNA removal kit (Qiagen, Hilden, Germany). High quality mRNA libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) and sequencing was performed with NovaSeq 6000, generating 250bp paired-end reads (Illumina, San Diego, CA, USA).

value: Whole organism

value: succinate

tag: time point


title: Treatment succinate, hours24, replicate 2

description: Library name: 21078R-05Q1-35


title: Treatment succinate, hours24, replicate 3

description: Library name: 21078R-05Q1-36


title: Treatment succinate, hours12, replicate 1

description: Library name: 21078R-05Q1-31


title: Treatment succinate, hours12, replicate 2

description: Library name: 21078R-05Q1-32


title: Subclone D7 (E5-AP2-G-DD), input

description: Library name: chip_D7_DD_input

value: Plasmodium falciparum


title: Treatment succinate, hours8, replicate 3

description: Library name: 21078R-05Q1-30


title: Treatment succinate, hours8, replicate 2

description: Library name: 21078R-05Q1-29


title: DRG CPIP+Veh seq1

description: Library name: Sample3

value: CPIP model


title: Treatment succinate, hours8, replicate 1

description: Library name: 21078R-05Q1-28


title: Treatment iprodione, hours24, replicate 3

description: Library name: 21078R-05Q1-27

value: iprodione


title: Treatment iprodione, hours24, replicate 1

description: Library name: 21078R-05Q1-25


title: Treatment iprodione, hours12, replicate 3

description: Library name: 21078R-05Q1-24


title: Treatment iprodione, hours24, replicate 2

description: Library name: 21078R-05Q1-26


title: Treatment iprodione, hours12, replicate 1

description: Library name: 21078R-05Q1-22


title: Treatment iprodione, hours8, replicate 3

description: Library name: 21078R-05Q1-21


title: Treatment iprodione, hours12, replicate 2

description: Library name: 21078R-05Q1-23


title: Treatment iprodione, hours8, replicate 2

description: Library name: 21078R-05Q1-20


title: CYC065 treated 4N replicate 3

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

description: Library name: 6_CYC_4N_S6_part_003

data_processing:
Illumina RTA v4.12.2software was used fro base calling, Bcl2fastq v2.17 was used for sample demultiplexing
Adapters from the samples were trimmed using Cutadapt 1.18 software
Genome mapping and transcript annotation were using STAR v2.7.0f with reference genome mm10 and gencode M21
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1
Assembly: mm10
Supplementary files format and content: gene count matrix in csv format

extract_protocol:
100 ng to 1µg was used as input to Illumina Stranded Totoal RNA prep kit according to the manufactures protocol
Illumina Stranded Total RNA lib prep ligation + RiboZero plus


title: Ln, total, GEX

description: 10x Genomics

source_name: tracheal lymph node

value: tracheal lymph node


title: CYC065 treated 4N replicate 1

description: Library name: 6_CYC_4N_S6_part_001


title: Treatment iprodione, hours8, replicate 1

description: Library name: 21078R-05Q1-19


title: CYC065 treated 2N replicate 2

description: Library name: 5_CYC2N_S5_part_002


title: CYC065 treated 4N replicate 2

description: Library name: 6_CYC_4N_S6_part_002


title: Vehicle treated 4N replicate 1

description: Library name: 4_Vehicle_4N_S4_part_001

value: vehicle


title: Vehicle treated 4N replicate 2

description: Library name: 4_Vehicle_4N_S4_part_002


title: Treatment succinate, hours12, replicate 3

description: Library name: 21078R-05Q1-33


title: Vehicle treated 2N replicate 2

description: Library name: 3_Vehicle2N_S3_part_002


title: Vehicle treated 2N replicate 3

description: Library name: 3_Vehicle2N_S3_part_003


title: CYC065 treated all cell replicate 3

description: Library name: 2_CYC065_S2_part_003


title: Vehicle treated 2N replicate 1

description: Library name: 3_Vehicle2N_S3_part_001


title: CYC065 treated all cell replicate 1

description: Library name: 2_CYC065_S2_part_001


title: Vehicle treated all cell replicate 3

description: Library name: 1_Vehicle_S1_part_003


title: Vehicle treated all cell replicate 2

description: Library name: 1_Vehicle_S1_part_002


title: CYC065 treated all cell replicate 2

description: Library name: 2_CYC065_S2_part_002


title: Vehicle treated all cell replicate 1

description: Library name: 1_Vehicle_S1_part_001


title: NS, WTRQ4, replicate 2

city: Bethesda

first: Mirit

middle: I

last: Aladjem

address: 37 convent drive

department: DTB

institute: NCI/NIH

description: Library name: NS_WTRQ4_S2.sorted.dedup.bam

data_processing:
*library strategy: NS-seq
Raw bam files were generated from fastq files of ChIP-seq or NS-seq after QC, trimmimming, QC, aligned to hg19 with BWA.
For ChIP-seq, narrow peaks were called using the no-IP control with MACS2. For nascent strand sequencing, broad peaks were called with the MACS2 algorithm.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: hg19
Supplementary files format and content: Bed file format showing: ChIP-seq peaks, NS-seq peaks
Supplementary files format and content: BigWig file format of ChIP-seq peaks and replication origin locations

source_name: Colon

growth_protocol: HCT116 are grown in RPMI medium with 10% FBS, Fibroblasts were grown in MEM medium, 15% FBS

extract_protocol:
For ChipSeq, DNA fragments were enriched using antibodies against proteins of interest, DNA was purified and processed as described in Thakur et al, NAR 2022. For NS-seq DNA from cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004.
Samples were eluted, and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB, E7335S and E7500S).
ChIP-seq (single-end sequencing) and NS-seq (Paired-end sequencing)

treatment_protocol: Aphidicolin (10uM) treated for 1hr, washed, and 1hr release by incubating with fresh media. For EX527 treatment cells were treated with 1uM for 48hr. HCT116 cells were synchronized with a double thymidine block, arresting them at G1/S. After recovery and a second thymidine treatment, samples were collected at various time points for analysis.

value: Colon

value: colorectal carcinoma

value: NS, WTRQ4


title: RNAseA, cont, replicate 2

description: Library name: RNAseA_cont_S2.sorted.dedup.bam

value: RNAseA, cont


title: CYC065 treated 2N replicate 1

description: Library name: 5_CYC2N_S5_part_001


title: Vehicle treated 4N replicate 3

description: Library name: 4_Vehicle_4N_S4_part_003


title: NS, S89A, replicate 2

description: Library name: NS_S89A_S2.sorted.dedup.bam

value: NS, S89A


title: NS, WTRQ4, replicate 1

description: Library name: NS_WTRQ4_S1.sorted.dedup.bam


title: RNAseA, cont, replicate 1

description: Library name: RNAseA_cont_S1.sorted.dedup.bam


title: CYC065 treated 2N replicate 3

description: Library name: 5_CYC2N_S5_part_003


title: NS, S89A, replicate 1

description: Library name: NS_S89A_S1.sorted.dedup.bam


title: NS, KORQ4, replicate 2

description: Library name: NS_KORQ4_S2.sorted.dedup.bam

value: NS, KORQ4


title: WT, Treslin, replicate 1

description: Library name: WT_Treslin_rep1.sorted.dedup.bam

data_processing:
Raw bam files were generated from fastq files of ChIP-seq or NS-seq after QC, trimmimming, QC, aligned to hg19 with BWA.
For ChIP-seq, narrow peaks were called using the no-IP control with MACS2. For nascent strand sequencing, broad peaks were called with the MACS2 algorithm.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: hg19
Supplementary files format and content: Bed file format showing: ChIP-seq peaks, NS-seq peaks
Supplementary files format and content: BigWig file format of ChIP-seq peaks and replication origin locations

value: WT, Treslin


title: NS, KORQ4, replicate 1

description: Library name: NS_KORQ4_S1.sorted.dedup.bam


title: WTM2, tRQ4, replicate 2

description: Library name: WTM2_tRQ4_rep2.sorted.dedup.bam

value: WTM2, tRQ4


title: Genomic cont, replicate 2

description: Library name: Genomic_S2.sorted.dedup.bam

value: Genomic cont


title: WT, Treslin, replicate 2

description: Library name: WT_Treslin_rep2.sorted.dedup.bam


title: Genomic cont, replicate 1

description: Library name: Genomic_S1.sorted.dedup.bam


title: WTM2, tRQ4, replicate 1

description: Library name: WTM2_tRQ4_rep1.sorted.dedup.bam


title: WTM2, pS139, UT, replicate 2

description: Library name: WTM2_pS139_UT_rep2.sorted.dedup.bam

value: WTM2, pS139, UT


title: WTM2, pS139, Ex527, replicate 2

description: Library name: WTM2_pS139_Ex527_rep2.sorted.dedup.bam


title: WTM2, pS139, Ex527, replicate 1

description: Library name: WTM2_pS139_Ex527_rep1.sorted.dedup.bam


title: WTM2, pRQ4, replicate 1

description: Library name: WTM2_pRQ4_rep1.sorted.dedup.bam

value: WTM2, pRQ4


title: WTM2, MTBP, replicate 2

description: Library name: WTM2_MTBP_rep2.sorted.dedup.bam

value: WTM2, MTBP


title: WTM2, pS139, UT, replicate 1

description: Library name: WTM2_pS139_UT_rep1.sorted.dedup.bam


title: WTM2, pRQ4, replicate 2

description: Library name: WTM2_pRQ4_rep2.sorted.dedup.bam


title: WTM2, Ex527, tRQ4, replicate 2

description: Library name: WTM2_Ex527_tRQ4_rep2.sorted.dedup.bam

value: WTM2, Ex527, tRQ4


title: Veh, pRQ4, replicate 2

description: Library name: Veh_pRQ4_rep2.sorted.dedup.bam

value: Veh, pRQ4


title: Veh, pRQ4, replicate 1

description: Library name: Veh_pRQ4_rep1.sorted.dedup.bam


title: Veh, MTBP, replicate 2

description: Library name: Veh_MTBP_rep2.sorted.dedup.bam

value: Veh, MTBP


title: Veh, MTBP, replicate 1

description: Library name: Veh_MTBP_rep1.sorted.dedup.bam


title: S139A, pRQ4, replicate 1

description: Library name: S139A_pRQ4_rep1.sorted.dedup.bam

value: S139A, pRQ4


title: S139A, pRQ4, replicate 2

description: Library name: S139A_pRQ4_rep2.sorted.dedup.bam


title: S139A, MTBP, replicate 1

description: Library name: S139A_MTBP_rep1.sorted.dedup.bam

value: S139A, MTBP


title: S108A, tRQ4, replicate 1

description: Library name: S108A_tRQ4_rep1.sorted.dedup.bam

value: Colon

value: S108A, tRQ4


title: S108A, pS139, UT, replicate 2

description: Library name: S108A_pS139_UT_rep2.sorted.dedup.bam

value: colorectal carcinoma


title: S139A, MTBP, replicate 2

description: Library name: S139A_MTBP_rep2.sorted.dedup.bam


title: S108A, pS139, Ex527, replicate 2

description: Library name: S108A_pS139_Ex527_rep2.sorted.dedup.bam


title: S108A, tRQ4, replicate 2

description: Library name: S108A_tRQ4_rep2.sorted.dedup.bam


title: S108A, pS139, Ex527, replicate 1

description: Library name: S108A_pS139_Ex527_rep1.sorted.dedup.bam


title: Noc, 3hr, MTBP, replicate 2

description: Library name: Noc_3hr_MTBP_rep2.sorted.dedup.bam

value: Noc, 3hr, MTBP


title: S108A, Ex527, tRQ4, replicate 1

description: Library name: S108A_Ex527_tRQ4_rep1.sorted.dedup.bam


title: Noc, 3hr, Treslin, replicate 1

description: Library name: Noc_3hr_Treslin_rep1.sorted.dedup.bam

value: Noc, 3hr, Treslin


title: Noc, 3hr, Treslin, replicate 2

description: Library name: Noc_3hr_Treslin_rep2.sorted.dedup.bam


title: WTM2, MTBP, replicate 1

description: Library name: WTM2_MTBP_rep1.sorted.dedup.bam


title: Noc, 10hr, Treslin, replicate 1

description: Library name: Noc_10hr_Treslin_rep1.sorted.dedup.bam

value: Noc, 10hr, Treslin


title: Noc, 10hr, MTBP, replicate 1

description: Library name: Noc_10hr_MTBP_rep1.sorted.dedup.bam

value: Noc, 10hr, MTBP


title: Input, WTM2

description: Library name: Input_WTM2.sorted.dedup.bam

value: Input, WTM2


title: Noc, 10hr, MTBP, replicate 2

description: Library name: Noc_10hr_MTBP_rep2.sorted.dedup.bam


title: Noc, 10hr, Treslin, replicate 2

description: Library name: Noc_10hr_Treslin_rep2.sorted.dedup.bam


title: WTM2, Ex527, tRQ4, replicate 1

description: Library name: WTM2_Ex527_tRQ4_rep1.sorted.dedup.bam


title: Input, veh

description: Library name: Input_veh.sorted.dedup.bam

value: Input, veh


title: Input, Noc, 3hr

description: Library name: Input_Noc_3hr.sorted.dedup.bam

value: Input, Noc, 3hr


title: Input, Noc, 10hr

description: Library name: Input_Noc_10hr.sorted.dedup.bam

value: Input, Noc, 10hr


title: Input, Aph

description: Library name: Input_Aph.sorted.dedup.bam

value: Input, Aph


title: Input, 36hr

description: Library name: Input_36hr.sorted.dedup.bam

value: Input, 36hr


title: Input, S139A

description: Library name: Input_S139A.sorted.dedup.bam

value: Input, S139A


title: S108A, pS139, UT, replicate 1

description: Library name: S108A_pS139_UT_rep1.sorted.dedup.bam


title: S108A, Ex527, tRQ4, replicate 2

description: Library name: S108A_Ex527_tRQ4_rep2.sorted.dedup.bam


title: DTB, 8hr, Treslin, replicate 2

description: Library name: DTB_8hr_Treslin_rep2.sorted.dedup.bam

value: DTB, 8hr, Treslin


title: H3Y, Treslin, replicate 1

description: Library name: H3Y_Treslin_rep1.sorted.dedup.bam

value: H3Y, Treslin


title: DTB, 4hr, Treslin, replicate 2

description: Library name: DTB_4hr_Treslin_rep2.sorted.dedup.bam

value: DTB, 4hr, Treslin


title: DTB, 4hr, Treslin, replicate 1

description: Library name: DTB_4hr_Treslin_rep1.sorted.dedup.bam

value: Colon


title: DTB, 1hr, Treslin, replicate 2

description: Library name: DTB_1hr_Treslin_rep2.sorted.dedup.bam

value: DTB, 1hr, Treslin


title: DTB, 8hr, Treslin, replicate 1

description: Library name: DTB_8hr_Treslin_rep1.sorted.dedup.bam

value: colorectal carcinoma


title: H3Y, Treslin, replicate 2

description: Library name: H3Y_Treslin_rep2.sorted.dedup.bam


title: DTB, 1hr, Treslin, replicate 1

description: Library name: DTB_1hr_Treslin_rep1.sorted.dedup.bam


title: DTB, 0hr, Treslin, replicate 1

description: Library name: DTB_0hr_Treslin_rep1.sorted.dedup.bam

value: DTB, 0hr, Treslin


title: Noc, 3hr, MTBP, replicate 1

description: Library name: Noc_3hr_MTBP_rep1.sorted.dedup.bam

value: Noc, 3hr, MTBP


title: AS, Treslin, replicate 1

description: Library name: AS_Treslin_rep1.sorted.dedup.bam

value: AS, Treslin


title: AS, Treslin, replicate 2

description: Library name: AS_Treslin_rep2.sorted.dedup.bam


title: DTB, 0hr, Treslin, replicate 2

description: Library name: DTB_0hr_Treslin_rep2.sorted.dedup.bam


title: TXNIP overexpressed3

city: Daejeon

first: Eun Bok

last: Baek

address: 99 Daehak-ro

institute: Chungnam National University

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 mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: liver

value: BMOL

value: progenitor cell line

value: cell line

value: TXNIP-expressing constructs


title: APH, recovery , 36hr, pRQ4, replicate 2

description: Library name: APH_rec_36hr_pRQ4_rep2.sorted.dedup.bam

value: APH, recovery , 36hr, pRQ4


title: APH, recovery , 36hr, pRQ4, replicate 1

description: Library name: APH_rec_36hr_pRQ4_rep1.sorted.dedup.bam


title: TXNIP overexpressed2


title: APH, recovery , 36hr, MTBP, replicate 2

description: Library name: APH_rec_36hr_MTBP_rep2.sorted.dedup.bam

value: APH, recovery , 36hr, MTBP


title: control3

value: vector control


title: APH, recovery , 36hr, MTBP, replicate 1

description: Library name: APH_rec_36hr_MTBP_rep1.sorted.dedup.bam


title: control2


title: TXNIP overexpressed1


title: APH, pRQ4, replicate 2

description: Library name: APH_pRQ4_rep2.sorted.dedup.bam

value: APH, pRQ4


title: APH, pRQ4, replicate 1

description: Library name: APH_pRQ4_rep1.sorted.dedup.bam


title: Aph, MTBP, replicate 2

description: Library name: Aph_MTBP_rep2.sorted.dedup.bam

value: Aph, MTBP


title: control1


title: IP_ifl_AP1_syd_rep2

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

description: Library name: Sample 6

data_processing:
Basecalls performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
MACS2 was used to identify ChIP-enriched peaks.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

organism: Arabidopsis thaliana

source_name: Arabidopsis inflorescences

growth_protocol: Arabidopsis seeds were sown on the Murahsige and Skoog (MS) medium and stratified at 4 ℃ for 2 days. Subsequently, they were grown under long-day conditions (16 h of light at 23 ℃ and 8 h of darkness at 22 ℃).  Whole plants of 12-day-old seedlings grown on MS medium or inflorescences of 4~5-week-old plants in soil were used for ChIP-seq experiments.

extract_protocol:
Arabidopsis inflorescences or seedlings were cross-linked by 1% formaldehyde. Chromatin were extracted from the sonicated nuclei and the protein-binding fragments were enriched by the corresponding antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp paired-end sequencing)

value: Arabidopsis inflorescences

value: Sigma, F1804


title: input_ifl_AP1_syd

description: Library name: Sample 4


title: IP_ifl_AP1_syd_rep1

description: Library name: Sample 5


title: APH, recovery, 8hr, pRQ4, replicate 1

description: Library name: APH_rec_8hr_pRQ4_rep1.sorted.dedup.bam

value: Colon

value: APH, recovery, 8hr, pRQ4


title: APH, recovery, 8hr, pRQ4, replicate 2

description: Library name: APH_rec_8hr_pRQ4_rep2.sorted.dedup.bam

value: colorectal carcinoma


title: IP_ifl_AP1_WT_rep2

description: Library name: Sample 3


title: IP_ifl_AP1_WT_rep1

description: Library name: Sample 2


title: APH, recovery, 8hr, MTBP, replicate 2

description: Library name: APH_rec_8hr_MTBP_rep2.sorted.dedup.bam

value: APH, recovery, 8hr, MTBP


title: APH, recovery, 8hr, MTBP, replicate 1

description: Library name: APH_rec_8hr_MTBP_rep1.sorted.dedup.bam


title: ifl_soc1_rep1

description: Library name: Sample 13

data_processing:
Basecalls performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
MACS2 was used to identify accessible regions.
DiffBind was used to identify differentially accessible regions of mutants and the wild type.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

growth_protocol: Arabidopsis seeds were sown on the Murahsige and Skoog (MS) medium and stratified at 4 ℃ for 2 days. Subsequently, they were grown under long-day conditions (16 h of light at 23 ℃ and 8 h of darkness at 22 ℃).  12-day-old seedlings or inflorescences of 4~5-week-old plants were used for ATAC-seq experiments.

extract_protocol:
Nucei of  Arabidopsis inflorescences or seedlings were extracted and the accessible chromatin regions were fragamented and tagged with adaptor DNA sequence by Tn5.
Sequencing libraries were built for ATAC-seq (the paired-end 150-bp strategy on the Illumina Novaseq 6000 platform).


title: ifl_soc1_rep2

description: Library name: Sample 14


title: APH, recovery, 4hr, pRQ4, replicate 1

description: Library name: APH_rec_4hr_pRQ4_rep1.sorted.dedup.bam

value: APH, recovery, 4hr, pRQ4


title: ifl_jag_rep2

description: Library name: Sample 12

value: jag-/-


title: APH, recovery, 4hr, MTBP, replicate 2

description: Library name: APH_rec_4hr_MTBP_rep2.sorted.dedup.bam

value: APH, recovery, 4hr, MTBP


title: APH, recovery, 4hr, MTBP, replicate 1

description: Library name: APH_rec_4hr_MTBP_rep1.sorted.dedup.bam


title: APH, recovery, 1hr, pRQ4, replicate 2

description: Library name: APH_rec_1hr_pRQ4_rep2.sorted.dedup.bam

value: APH, recovery, 1hr, pRQ4


title: ifl_jag_rep1

description: Library name: Sample 11


title: APH, recovery, 1hr, MTBP, replicate 2

description: Library name: APH_rec_1hr_MTBP_rep2.sorted.dedup.bam

value: APH, recovery, 1hr, MTBP


title: ifl_WT_forjagsoc1_rep1

description: Library name: Sample 9

value: wild type


title: APH, recovery, 1hr, pRQ4, replicate 1

description: Library name: APH_rec_1hr_pRQ4_rep1.sorted.dedup.bam


title: sdl_pifq_rep2

description: Library name: Sample 8

source_name: Arabidopsis 12-d seedlings

value: Arabidopsis 12-d seedlings


title: sdl_pifq_rep1

description: Library name: Sample 7


title: Aph, MTBP, replicate 1

description: Library name: Aph_MTBP_rep1.sorted.dedup.bam


title: APH, recovery, 1hr, MTBP, replicate 1

description: Library name: APH_rec_1hr_MTBP_rep1.sorted.dedup.bam


title: NSseq, WT, replicate 1

data_processing:
Raw bam files were generated from fastq files of ChIP-seq or NS-seq after QC, trimmimming, QC, aligned to hg19 with BWA.
For ChIP-seq, narrow peaks were called using the no-IP control with MACS2. For nascent strand sequencing, broad peaks were called with the MACS2 algorithm.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: hg19
Supplementary files format and content: Bed file format showing: ChIP-seq peaks, NS-seq peaks
Supplementary files format and content: BigWig file format of ChIP-seq peaks and replication origin locations
Library strategy: NS-seq

extract_protocol:
For ChipSeq, DNA fragments were enriched using antibodies against proteins of interest, DNA was purified and processed as described in Thakur et al, NAR 2022. For NS-seq DNA from cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004.
Samples were eluted, and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB, E7335S and E7500S).


title: NSseq, WT, APH, replicate 2


title: ifl_ap1_rep1

description: Library name: Sample 3


title: ifl_ap1_rep2

description: Library name: Sample 4


title: NSseq, WT, 8hr rel. from dThy, replicate 2


title: NSseq, WT, APH, replicate 1


title: input_ifl_AP1_WT

description: Library name: Sample 1


title: ifl_WT_forap1_rep2

description: Library name: Sample 2


title: NSseq, WT, 8hr rel. from dThy, replicate 1


title: sdl_WT_rep2

description: Library name: Sample 6


title: ifl_WT_forjagsoc1_rep2

description: Library name: Sample 10


title: NSseq, WT, 4hr rel. from dThy, replicate 2


title: NSseq, WT, 4hr rel. from dThy, replicate 1


title: sdl_WT_rep1

description: Library name: Sample 5


title: LEC1-ChIP-DE-endosperm R#2

city: Saskatoon

first: Jingpu

last: Song

address: 110 Gymnasium Pl

country: Canada

institute: NRC

description: Library name: AA8

data_processing:
Raw reads were uploaded to Galaxy (http://usegalaxy.org/). Sequences were trimmed with Trim Galore (Galaxy v 0.6.7) 41 before mapping to the Arabidopsis reference genome (TAIR10) with Bowtie2 42 for Illumina (Galaxy v 2.5.0) for DNA sequencing with pair end and other settings as default. Unmapped and PCR duplicates were filtered out using SAMtools 43, only uniquely and perfectly mapped reads were retained for further analysis. The bigwig format files were generated by bamCoverage with “bin size 10” and “normalize to RPKM (reads per kilobase per million)” in Deeptools 44 for visualization using Integrative Genomics Viewer 45. Peak calling was conducted using MACS2 (Galaxy v 2.2.7.1) with default parameters 46. Sequencing reads from Input-DNA were used as controls.
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: bed files of identified narrow peaks (LEC1-binding) for each sample

source_name: Endosperm

extract_protocol:
siliques were ground into fine powder in liquid nitrogen and resuspended in Honda buffer for 15 min at 4 ºC. The mixtures were filtered through miracloth (Millipore, MA) twice and lastly through a CellTrics strainer (30-mm) (Sysmex, Germany). Total nuclei were collected after centrifugation at 1500 g for 6 min at 4 ºC, followed by re-suspension in PBSB buffer. The suspension was incubated rotating with pre-blocked Dynabeads M-280 streptavidin beads (Invitrogen, Waltham, MA) for 2 h. After incubation, the beads were collected using a magnet rack, then gently resuspended in PBSBt buffer for 15 min at 4 ºC. To purify the biotin-labelled nuclei, the beads incubated with PBSBt buffer passed through the column-like separation system at a speed of ~2 ml/min. The purified nuclei with beads were resuspended in PBSB buffer and used directly for chromatin immunoprecipitation (ChIP) assays.Purified nuclei were fixed in 1% formaldehyde and incubated on ice for 8 min, followed by adding glycine for 5 min’s incubation. Beads were collected and resuspended in the nuclei lysis buffer, then the suspension was subjected to sonication. The sonicated chromatin solution was diluted with ChIP dilution buffer and was further split into the necessary number of portions. The aliquot was incubated with anti-GFP (Abcam, Cambridge, UK) overnight at 4 ºC with gentle rotation, followed by incubation with Dynabeads protein A (Invitrogen, Waltham, MA) for 2 h. The beads were collected with a magnetic rack and washed by low salt wash buffer, high salt wash buffer and TE buffer. ChIP-DNA was purified from the washed beads by using a Ipure Kit v2 (Diagenode, NJ).
The sequencing library was prepared using Accel-NGS 2S Plus DNA Library Kit (Swift, UK) and subsequently used for Illumina NOVAseq 6000 pair-end sequencing.

value: Endosperm

value: Columbia

tag: developmental stage

value: degenerateion (7 day after pollination)

value: PLL-ZIM


title: ifl_WT_forap1_rep1

description: Library name: Sample 1

value: Arabidopsis inflorescences


title: LEC1-ChIP-DE-endosperm R#1

description: Library name: AA7


title: LEC1-ChIP-CE-endosperm R#2

description: Library name: AA5

value: cellularization (5 day after pollination)


title: NSseq, WT, 1hr rel. from dThy, replicate 1

value: Colon


title: NSseq, WT, replicate 2


title: APH, recovery, 4hr, pRQ4, replicate 2

description: Library name: APH_rec_4hr_pRQ4_rep2.sorted.dedup.bam


title: LEC1-ChIP-CE-endosperm R#1

description: Library name: AA4


title: LEC1-ChIP-NP-endosperm R#2

description: Library name: AA2

value: nuclear proliferation  (1-3 day after pollination)

value: PLL-PIM


title: LEC1-ChIP-NP-endosperm R#1

description: Library name: AA1


title: NSseq, WT, 0hr rel. from dThy, replicate 1

value: colorectal carcinoma


title: NSseq, WT, 0hr rel. from dThy, replicate 2


title: NSseq, H3Y, replicate 1


title: NSseq, H3Y, replicate 2


title: IP_ifl_PMS2B_rep2

growth_protocol: Arabidopsis seeds were sown on the Murahsige and Skoog (MS) medium and stratified at 4 ℃ for 2 days. Subsequently, they were grown under long-day conditions (16 h of light at 23 ℃ and 8 h of darkness at 22 ℃).  Whole plants of 12-day-old seedlings grown on MS medium and inflorescences of 4~5-week-old plants in soil were used for ChIP-seq experiments.

extract_protocol:
Arabidopsis inflorescences were cross-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with GFP antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp paired-end sequencing)

value: Abcam, ab290


title: IP_ifl_PMS2B_rep1


title: WT, RQ4, replicate 2


title: input_ifl_PMS2B


title: WT, RQ4, replicate 1


title: IP_ifl_SWI3D_rep2


title: WT, pMCM2, replicate 2


title: IP_ifl_SWI3D_rep1


title: WT, pRQ4, replicate 2


title: IP_ifl_SWI3C_rep2


title: NSseq, WT, 1hr rel. from dThy, replicate 2


title: IP_ifl_SWI3C_rep1


title: WT, MTBP, replicate 1


title: WT, pMCM2, replicate 1


title: WT, APH, RQ4, replicate 2


title: WT, MTBP, replicate 2


title: input_ifl_SWI3D


title: WT, pRQ4, replicate 1


title: IP_sdl_PMS2B_rep1

source_name: Arabidopsis seedlings

value: Arabidopsis seedlings


title: WT, APH, RQ4, replicate 1


title: WT, APH, pRQ4, replicate 1


title: IP_sdl_SWI3D_rep2


title: input_sdl_SWI3D


title: WT, APH, pRQ4, replicate 2


title: IP_sdl_SWI3D_rep1


title: IP_sdl_SWI3C_rep2


title: WT, APH, pMCM2, replicate 2


title: WT, APH, MTBP, replicate 2


title: IP_sdl_SWI3C_rep1


title: WT, APH, MTBP, replicate 1


title: UT, pRQ4, replicate 2


title: input_ifl_SWI3C


title: UT, pRQ4, replicate 1


title: ifl_pms2ab_rep2

growth_protocol: Arabidopsis seeds were sown on the Murahsige and Skoog (MS) medium and stratified at 4 ℃ for 2 days. Subsequently, they were grown under long-day conditions (16 h of light at 23 ℃ and 8 h of darkness at 22 ℃).  Inflorescences of 4~5-week-old plants in soil were used for ATAC-seq experiments.

extract_protocol:
Nucei of  Arabidopsis inflorescencess were extracted and the accessible chromatin regions were fragamented and tagged with adaptor DNA sequence by Tn5.
Sequencing libraries were built for ATAC-seq (the paired-end 150-bp strategy on the Illumina Novaseq 6000 platform).


title: ifl_pms2ab_rep1


title: ifl_minu12_rep2


title: UT, MTBP, replicate 1


title: input_sdl_SWI3C


title: IP_sdl_PMS2B_rep2


title: ifl_sys123_rep2


title: UT, MTBP, replicate 2


title: ifl_sys123_rep1


title: ifl_minu12_rep1


title: S89A, pRQ4, UT, replicate 1


title: S89A, pRQ4, APH, replicate 2


title: S89A, pRQ4, APH, replicate 1


title: ifl_swi3d_rep1


title: S89A, MTBP, UT, replicate 2


title: input_sdl_PMS2B


title: ifl_syd_rep2

value: syd-/-


title: S89A, MTBP, UT, replicate 1


title: ifl_swi3d_rep2


title: ifl_syd_rep1


title: WT, APH, pMCM2, replicate 1


title: ifl_brm_rep2

value: brm-/-


title: S89A, MTBP, APH, replicate 1


title: S89A, MTBP, APH, replicate 2


title: S108A, pRQ4, replicate 2


title: S108A, pRQ4, replicate 1


title: ifl_WT_rep1


title: S89A, pRQ4, UT, replicate 2


title: S108A, Ex, pRQ4, replicate 2


title: S108A, MTBP, replicate 2


title: S108A, MTBP, replicate 1


title: RQ4, WT, pRQ4, APH, replicate 1


title: S108A, Ex, MTBP, replicate 2


title: S108A, Ex, pRQ4, replicate 1


title: RQ4, WT, MTBP, UT, replicate 2


title: S108A, Ex, MTBP, replicate 1


title: RQ4, WT, pRQ4, UT, replicate 2


title: RQ4, WT, pRQ4, UT, replicate 1


title: E9.5 rep2 WT

city: Edinburgh

first: Takuya

last: Azami

address: Crewe Road

department: Institute of Genetics and Cancer

country: United Kingdom

institute: The University of Edinburgh

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger
Assembly: mm10 with tdTomato
Supplementary files format and content: Count matrices and additional metadata

source_name: Whole embryo

extract_protocol:
chimeric embryos were collected at E7.5, E8.5, and E9.5 and pooled in 1.5 ml tube (~10 embryos for E7.5, ~ 4 embryos for E8.5, 1 embryo for E9.5). Embryos were dissociated into single-cell by TrypLE™ Express Enzyme and tdTomato+ and tdTomato- cells were sorted using a BD Influx sorter
Sequencing libraries were prepared following 10x Genomics manufacturers protocol using 10x Single Cell 3' v3 chemistry.

value: Whole embryo

value: WT

tag: embryo pool

tag: sampleID


title: RQ4, WT, pRQ4, APH, replicate 2

tag: tissue


title: E8.5 rep2 WT

description: 10x Genomics


title: RQ4, WT, MTBP, UT, replicate 1

tag: cell line


title: E9.5 rep2 Stat3null

description: 10x Genomics

value: Stat3 null


title: E7.5 rep2 WT

description: 10x Genomics


title: RQ4, WT, MTBP, APH, replicate 2

tag: cell type


title: RQ4, null, pRQ4, UT, replicate 2


title: E7.5 rep2 Stat3null

description: 10x Genomics


title: RQ4, null, pRQ4, UT, replicate 1


title: ifl_brm_rep1


title: CLIP-seq_NCL_rep2

city: Shenzhen

first: Tian

last: (Simon) Zhongyuan

state: Guangdong

address: 1088 Xueyuan Avenue

department: School of Life Sciences

institute: Southern University of Science and Technology (SUSTech)

data_processing:
(1) RDD and ChIA-PET data were processed using the ChIA-PIPE pipeline (https://github.com/TheJacksonLaboratory/ChIA-PIPE), involving steps like linker filtering, data alignment, coverage generation, interaction clustering, quality control, and data classification for visualization and analysis. (2) ChIP-seq and ATAC-seq data were processed using BWA (v0.7.17) to align the raw FASTQ files to the reference genome. Following alignment, SAMtools (v0.1.19) was used to filter the reads, ensuring that only high-quality, uniquely mapped reads were retained. This included de-duplication and selecting reads with a mapping quality (MAPQ) greater than 30, to ensure accuracy and reliability in the downstream analysis.. (3) RNA-seq and CLIP-seq data were mapped using STAR (v2.7.9a) and analyzed for differentially expressed genes (DEGs) using RSEM (v1.3.1) . SAMtools (v0.1.19) was then used to filter reverse-strand reads (‘-f 128’)  to generate a two-value BEDGRAPH file (one value for ‘strand+’, another value for ‘strand–’) for RNA-seq ‘Coverage’ in the BASIC Browser (https://github.com/TheJacksonLaboratory/basic-browser).
Assembly: hg38+EBV.B958
Supplementary files format and content: loop, bedgraph, gene_expression

growth_protocol: GM12878 and HEK293T cells was cultured following manufacture’s instruction.

extract_protocol:
(1) RDD: Dual-crosslinked cells undergo lysis to isolate and fragment nuclei. The ncRNA of interest is purified through hybridization with biotinylated probes and immobilized on streptavidin beads, with unbound sites blocked to prevent unwanted interactions. During proximity ligation, chromatin DNA contacts are captured using biotinylated linkers. The ligated products are then subjected to tagmentation and enriched for sequencing, allowing for the analysis of specific RNA-associated chromatin DNA–DNA interactions. (2) ChIA-PET: Using protein antibody instead of RNA probe in RDD method, other steps are same. (3) ChIP-seq: Crosslinked cells undergo lysis to isolate nuclei, which are then fragmented. The antibody of interest is used for immunoprecipitation to purify associated complexes. Finally, enriched DNA undergoes tagmentation and sequencing to analyze specific factor-associated chromatin DNA. (4) ATAC-seq: Collect cells and permeabilize. Resuspend lysed nuclei in a tagmentation mixture, then incubate. Purify the transposed DNA and proceed with PCR amplification and sequencing. (5) RNA-seq: Extract total RNA from cells and deplete ribosomal RNA. Prepare stranded RNA sequencing libraries according to guidelines, then sequence the libraries using a high-throughput sequencer with paired-end reads. (6) CLIP-seq: Using NCL antibody to capture chromatin complexes and extract RNA from the complextes, which is then transcribed into cDNA and subjected to libary contruction and sequencing.
The ligated DNA or cDNA was fragmented by using Tn5 transposase. Then the fragmented DNA contained bridge linker were captured with Streptavidin beads and used for PCR amplification. These PCR products were then performed double size-selection with AMPure beads to achieve the DNA fragments with size of 300-600 bp, then subjected for Illumina NovaSeq 6000 with paired-end sequencing at read lengths of 150 bp.
RDD, ChIA-PET, ChIP-seq, ATAC-seq, RNA-seq and CLIP-seq

treatment_protocol: For EBERs-KD (knockdown) cells, cells in the exponential growth phase are first infected with CRISPRi lentivirus, then with sgRNA lentiviral constructs (KD, NC), and subsequently selected and amplified using puromycin. For NCL-KD (knockdown) cells, the cells are transfected with siRNA.

tag: rna probe/chip_antibody

tag: biomaterial provider

value: human lymphoblastoid

value: NCL


title: ifl_WT_rep2

tag: genotype

value: wild type


title: RQ4, null, pRQ4, APH, replicate 2


title: E9.5 rep1 WT

description: 10x Genomics

tag: Stage


title: CLIP-seq_NCL_rep1


title: RNA-seq_EBERsKD_rep2

value: EBERsKD


title: RNA-seq_EBERsKD_rep1


title: RQ4, null, pRQ4, APH, replicate 1


title: RNA-seq_EBERsNC_rep2

value: EBERsNC


title: E9.5 rep1 Stat3null

description: 10x Genomics


title: ATAC-seq_EBERsKD_rep2


title: RQ4, null, MTBP, UT, replicate 1


title: RNA-seq_EBERsNC_rep1


title: E7.5 rep1 Stat3null

description: 10x Genomics


title: ATAC-seq_EBERsNC_rep2


title: RQ4, WT, MTBP, APH, replicate 1


title: E8.5 rep2 Stat3null

description: 10x Genomics


title: ATAC-seq_EBERsNC_rep3


title: RQ4, null, MTBP, APH, replicate 1


title: ATAC-seq_EBERsNC_rep1


title: RQ4, null, MTBP, APH, replicate 2


title: NCL_ChIP-seq_EBERsKD_rep2

value: anti-nucleolin (NCL) antibody (Abcam, Cat# ab22758; RRID:AB_776878)


title: NCL_ChIP-seq_EBERsKD_rep1


title: E9.5 rep4 Stat3null

description: 10x Genomics


title: MCM2, WT, pRQ4, replicate 2

value: Colon


title: NCL_ChIP-seq_EBERsNC_rep2


title: E7.5 rep1 WT

description: 10x Genomics


title: E8.5 rep1 WT

description: 10x Genomics


title: HSPA9_ChIP-seq_EBERsKD_rep2

value: anti-HSPA9 antibody (ABclonal, Cat# A0558; RRID:AB_2757264)


title: HSPA9_ChIP-seq_EBERsKD_rep1


title: RQ4, null, MTBP, UT, replicate 2


title: NCL_ChIP-seq_EBERsNC_rep1


title: ATAC-seq_EBERsKD_rep1


title: HSPA9_ChIP-seq_EBERsNC_rep1


title: MCM2, WT, MTBP, replicate 1


title: RNAPII_ChIA-PET_HEK293T_NCLKD_rep1

value: anti-RNAPII monoclonal antibody (8WG16, BioLegend, Cat# 664906; RRID:AB_2565554)

value: human embryonic kidney cells

value: NCLKD


title: E8.5 rep1 Stat3null

description: 10x Genomics


title: RNAPII_ChIA-PET_HEK293T_NCLKD_rep2


title: E9.5 rep3 WT

description: 10x Genomics


title: MCM2, WT, Ex, pRQ4, replicate 1

value: colorectal carcinoma


title: SVF_HFHS_2

city: Los Angeles

first: Yen-Wei

last: Chen

address: 650 Charles E. Young Dr. South  16-035 Center for Health Sciences

department: IDP Molecular Toxicology

institute: University of California, Los Angeles

data_processing:
Fastq files were converted to BAM format and cell and molecular barcodes were tagged. Reads corresponding to low quality barcodes were removed
Any occurrence of the Illumina adapter sequence or polyA tails found in the reads were trimmed. These cleaned reads were converted back to fastq format to be aligned to the mouse reference genome mm10 using STAR-2.5.0c.
Assembly: mm10
Supplementary files format and content: Matrix.mtx file with gene count information,  genes.tsv for gene information and barcodes.tsv for cell barcodes.

source_name: SVF

growth_protocol: Eight-week-old B6 male and female mice were treated with chow diet with water (control group), chow diet with water containing 15 % fructose (Fructose group) and a high fat high sucrose diet containing 16.8% kcal protein, 51.4% kcal carbohydrate, and 31.8% kcal fat with water (Research Diets- D12266B, NJ, USA; HFHS group) for 11 weeks. The diets were changed once a week and water or fructose drink were changed twice a week. Food and liquid were accessed ad libitum and the intake amount for each was measured. After 11 weeks, mice were sacrificed, and tissues including hypothalamus, gonadal adipose tissue, liver, and whole small intestine were collected for scRNAseq using Drop-seq.

extract_protocol:
Tissues were collected, cells were lysed, suspended and barcoded using optimized protocols for hypothalamus (n=2 control, 2 fructose, 2 HFHS samples)23, gonadal adipose stromal vascular fraction (SVF) (n=2 control, 2 fructose, 2 HFHS samples)25, small intestine (n=2 control, 2 fructose, 2 HFHS samples)26, liver non-parenchymal cells (NPCs) (n=3 control, 5 fructose, 4 HFHS samples)27 and hepatocytes (n=2 control, 4 fructose, 4 HFHS samples) (http://mouselivercells.com/procedure.html) and version 3.1 of the online Drop-seq protocol (http://mccarrolllab.com/download/905/).
Sequencing libraries were prepared according to the Drop-seq protocol and sequenced using Illumina HiSeq4000 with 50bp paired-end setting at 20-50k reads/cell.

value: male

value: Mouse adipose stromal vascular fraction (SVF)

tag: treatment

value: high fat high sucrose diet

tag: condition

value: HFHS

value: SVF


title: RNAPII_ChIA-PET_HEK293T_NCLNC_rep1

value: NCLNC


title: HSPA9_ChIP-seq_EBERsNC_rep2

value: human lymphoblastoid


title: E9.5 rep4 WT

description: 10x Genomics

value: Whole embryo

value: WT


title: RNAPII_ChIA-PET_NCLKD_rep1


title: RNAPII_ChIA-PET_HEK293T_NCLNC_rep2


title: NCL_ChIA-PET_EBERsKD_rep1

value: EBERsKD


title: SVF_Fruc_2

treatment_protocol: Eight-week-old B6 male and female mice were treated with chow diet with water (control group), chow diet with water containing 15 % fructose (Fructose group) and a high fat high sucrose diet containing 16.8% kcal protein, 51.4% kcal carbohydrate, and 31.8% kcal fat with water (Research Diets- D12266B, NJ, USA; HFHS group) for 11 weeks. The diets were changed once a week and water or fructose drink were changed twice a week. Food and liquid were accessed ad libitum and the intake amount for each was measured. After 11 weeks, mice were sacrificed, and tissues including hypothalamus, gonadal adipose tissue, liver, and whole small intestine were collected for scRNAseq using Drop-seq.

value: chow + 15% fructose drink

value: Fruc


title: SVF_HFHS_1_liver_mixed


title: NCL_ChIA-PET_EBERsNC_rep1

value: anti-nucleolin (NCL) antibody (Abcam, Cat# ab22758; RRID:AB_776878)

value: EBERsNC


title: MCM2, WT, pRQ4, replicate 1

value: Colon


title: MCM2, WT, Ex, MTBP, replicate 1


title: SVF_Fruc_1


title: RNAPII_ChIA-PET_EBERsKD_rep2

value: anti-RNAPII monoclonal antibody (8WG16, BioLegend, Cat# 664906; RRID:AB_2565554)


title: E9.5 rep3 Stat3null

description: 10x Genomics

value: Stat3 null


title: Input, WT, RQ, R1, 001

value: colorectal carcinoma


title: RNAPII_ChIA-PET_EBERsKD_rep1


title: MCM2, WT, MTBP, replicate 2


title: RNAPII_ChIA-PET_EBERsNC_rep2


title: SVF_Control_2

value: male

value: Mouse adipose stromal vascular fraction (SVF)

value: chow diet

value: Control


title: MCM2, WT, Ex, pRQ4, replicate 2


title: SVF_Control_1

value: SVF


title: RNAPII_ChIA-PET_EBERsNC_rep1

value: human lymphoblastoid


title: MALAT1_RDD_combined_rep3

data_processing:
(1) RDD and ChIA-PET data were processed using the ChIA-PIPE pipeline (https://github.com/TheJacksonLaboratory/ChIA-PIPE), involving steps like linker filtering, data alignment, coverage generation, interaction clustering, quality control, and data classification for visualization and analysis. (2) ChIP-seq and ATAC-seq data were processed using BWA (v0.7.17) to align the raw FASTQ files to the reference genome. Following alignment, SAMtools (v0.1.19) was used to filter the reads, ensuring that only high-quality, uniquely mapped reads were retained. This included de-duplication and selecting reads with a mapping quality (MAPQ) greater than 30, to ensure accuracy and reliability in the downstream analysis.. (3) RNA-seq and CLIP-seq data were mapped using STAR (v2.7.9a) and analyzed for differentially expressed genes (DEGs) using RSEM (v1.3.1) . SAMtools (v0.1.19) was then used to filter reverse-strand reads (‘-f 128’)  to generate a two-value BEDGRAPH file (one value for ‘strand+’, another value for ‘strand–’) for RNA-seq ‘Coverage’ in the BASIC Browser (https://github.com/TheJacksonLaboratory/basic-browser).
Assembly: hg38+EBV.B958
Supplementary files format and content: loop, bedgraph, gene_expression
Library strategy: RDD


title: RNAPII_ChIA-PET_NCLNC_rep1

value: NCLNC


title: MALAT1_RDD_combined_rep2

value: WT


title: Input, WT, APH, R1, 001


title: v-snoRNA1_RDD_combined_rep1


title: SI_HFHS_2

source_name: SI

value: Mouse small intestine

value: high fat high sucrose diet

value: HFHS

value: SI


title: Input, UT, 2, R1, 001


title: v-snoRNA1_RDD_combined_rep2


title: Input, WT, MCM2


title: miR-BART_RDD_combined_rep2

value: miR-BART


title: Input, UT, 1, R1, 001

value: Colon


title: miR-BART_RDD_combined_rep1


title: EBERs_RDD_combined_rep2

value: EBERs


title: MALAT1_RDD_combined_rep1


title: SI_Fruc_1

value: chow + 15% fructose drink

value: Fruc


title: SI_Fruc_2

value: male


title: Input, S89A, RQ, R1, 001

value: colorectal carcinoma


title: EBERs_RDD_combined_rep3


title: THP-1 cells, sh-CCT6A-Exo treated rep2

city: Wuhan

first: Minghe

last: Zhang

state: Hubei

address: Donghu Road

institute: WuHan University

data_processing:
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Excel file including raw counts for each Sample

extract_protocol:
Total RNA was extracted from the XXX(tissue) using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, sequencing was performed with an Illumina Novaseq 6000 instrument.

value: Exosomes derived from sh-CCT6A BxPC-3 cells


title: SI_Control_2

value: chow diet

value: Control


title: EBERs_RDD_combined_rep1

value: human lymphoblastoid


title: Input, H3Y, R1, 001


title: THP-1 cells, sh-CCT6A-Exo treated rep1


title: SI_Control_1


title: Input, WT, R1, 001


title: THP-1 cells, sh-NC-Exo treated rep2

value: Exosomes derived from sh-NC BxPC-3 cells


title: THP-1 cells, sh-CCT6A-Exo treated rep3


title: SI_HFHS_1


title: THP-1 cells, sh-NC-Exo treated rep3


title: Input, AS, R1, 001


title: high EPA+DHA, rep3

city: Qingdao

first: Qingyuan

last: Li

address: Haijun road 88

institute: IOCAS

description: Library name: G3

data_processing:
After the library was constructed, Qubit2.0 was used for preliminary quantification, and the library was diluted to 1ng/μl, and then the insert size of the library was detected using Agilent 2100 Bioanalyzer, and after the insert size was as expected, the effective concentration of the library was accurately quantified using Q-PCR (the effective concentration of the library was > 2nM). to ensure the quality of the libraries. After the library inspection, different libraries were pooled according to the effective concentration and the target downstream data volume, and then PE150 sequencing was performed using the Illumina platform to obtain 150bp bipartite sequencing reads.The raw image data files obtained by high-throughput sequencing were transformed into the original sequenced sequences by Base Calling analysis. The raw image data file obtained from high-throughput sequencing was analyzed by Base Calling and transformed into raw sequenced reads, which we call Raw Data or Raw Reads, and the results were stored in FASTQ (abbreviated as fq) file format, which contains the sequence information of the sequenced sequences (reads) as well as their corresponding sequencing quality information.
Assembly: No. GCA_011032805.1
Supplementary files format and content: tab-delimited text file

organism: Magallana gigas

source_name: mantle

extract_protocol:
Total RNA from tissues was extracted using Trizol; RNA samples were assayed for concentration and purity using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific); and RNA sample integrity was measured using an Agilent 2100 Bioanalyzer and 2100 RNA Nano 6000 Assay The integrity of RNA samples was checked using an Agilent 2100 Bioanalyzer and 2100 RNA Nano 6000 Assay Kit (Agilent Technologies).
The total RNA that passed the quality control was used as the starting sample, and the TIANSeq mRNA Capture Kit (TIANGEN Biotech) was used to enrich the eukaryotic total RNA with Poly-A structure, and then the library construction was performed with the captured RNA as the library starting sample using the TIANSeq Rapid RNA Library Construction Kit (Illumina platform) (TIANGEN Biotech). TIANGEN Biotech) for library construction. The transcriptome sequencing library was constructed through RNA fragmentation, cDNA one-strand/two-strand synthesis, end repair, A-tail addition, junction ligation and PCR library enrichment.

value: mantle


title: THP-1 cells, sh-NC-Exo treated rep1


title: H3Y, RQ4, replicate 2


title: NPC_HFHS_Set2_1

value: Mouse liver non parenchymal cells


title: NPC_HFHS_Set2_3

value: high fat high sucrose diet


title: NPC_HFHS_Set2_2

value: HFHS


title: High-Neuron-3-3

city: Seoul

first: Jinsoo

last: Seo

address: 50 Yonsei-ro

department: Department of Systems Biology

institute: Yonsei University

data_processing:
The raw fastq data were aligned to human hg38 assembly using STAR 2.4.0 RNA-seq aligner
Gene raw counts were generated from the mapped data using featureCounts tool
The mapped reads were also processed DESeq2 1.26.0 package for differential expression analysis using negative binomial model.
Assembly: Human hg38
Supplementary files format and content: text file includes raw counts for each Sample

source_name: hiPSC-derived neural progenitor cells

growth_protocol: hiPSC-derived NPCs were cultured in media, which comprised DMEM/F-12 GlutaMAX (Gibco), Neurobasal (Gibco), 0.5x NEAA (Sigma-Aldrich), 0.5x GlutaMAX (Gibco), 5 µg/ml insulin (Sigma-Aldrich), 100 µM 2-mercaptoethanol (Sigma-Aldrich), 20 ng/mf FGF2 (Peprotech)

extract_protocol:
Cells were lysed using Ambion Trizol Reagent (Invitrogen) under RNase-free conditions for RNA extraction. The lysate was separated into an aqueous RNA phase using chloroform and centrifugation. The RNA pellet was washed with RNase-free 75% ethanol, air-dried, and resuspended in RNase-free water.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols

value: hiPSC-derived neural progenitor cells

tag: group

value: High


title: high EPA+DHA, rep2

description: Library name: G2


title: high EPA+DHA, rep1

description: Library name: G1


title: H3Y, pRQ4, replicate 2

value: Colon


title: High-Neuron-3-2


title: low EPA+DHA, rep3

description: Library name: L3


title: low EPA+DHA, rep2

description: Library name: L2


title: NPC_Fruc_Set2_3

tag: Sex


title: NPC_HFHS_Set1_1_SI_mixed

tag: strain


title: low EPA+DHA, rep1

description: Library name: L1


title: Low-Neuron-3-3

value: Low


title: NPC_Fruc_Set2_2

value: chow + 15% fructose drink

tag: batch


title: H3Y, pMCM2, replicate 1


title: H3Y, pMCM2, replicate 2


title: Low-Neuron-3-2


title: H3Y, MTBP, replicate 2


title: H3Y, RQ4, replicate 1


title: NPC_Fruc_Set2_1

value: Fruc


title: Low-Neuron-3-1


title: NPC_Fruc_Set1_2

value: male


title: brown adipose tissue, Female Vehicle, room temperature(25℃)

city: Tokyo

first: Kazutaka

last: Tsujimoto

address: 1-5-45 Yushima, Bunkyo-ku

country: Japan

institute: Institute of Science Tokyo

description: Library name: experimental2_ FemaleVeh

data_processing:
RNA-seq data processing was performed by Novogene (Beijing, China). Differentially expressed genes were identified based on a fold change >1.5.
Assembly: mm10
Supplementary files format and content: The processed data files are provided in CSV format.TPM (Transcripts Per Million) values are included for each gene across all samples.

source_name: brown adipose tissue

extract_protocol:
Total RNA was isolated using the RNeasy Plus Universal Mini Kit (Qiagen).
Sequencing libraries were prepared using the NEBNext Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, USA), following the manufacturer’s instructions. The libraries were sequenced on an Illumina NovaSeq 6000 platform, generating 150-bp paired-end reads.

value: brown adipose tissue

value: WT

value: Vehicle


title: brown adipose tissue, Female TMX, room temperature(25℃)

description: Library name: experimental2_ FemaleTMX

value: Tamoxifen


title: brown adipose tissue, Male TMX, room temperature(25℃)

description: Library name: experimental2_ MaleTMX


title: NPC_Fruc_Set1_1


title: H3Y, MTBP, replicate 1

value: colorectal carcinoma


title: High-NPC-3-2

value: Control


title: brown adipose tissue, Male Vehicle, room temperature(25℃)

description: Library name: experimental2_ MaleVeh


title: High-NPC-3-3


title: DTB, Input, 8hr, R1, 001


title: H3Y, pRQ4, replicate 1


title: High-Neuron-3-1


title: High-NPC-3-1


title: DTB, Input, 4hr, R1, 001


title: NPC_Control_Set2_1

value: chow diet


title: brown adipose tissue, Female PGC-1α knockout, room temperature(25℃)

description: Library name: experimental1_ Female_KO

value: PGC-1a knockout


title: DTB, Input, 1hr, R1, 001


title: Low-NPC-3-3


title: NPC_Control_Set1_1

value: Mouse liver non parenchymal cells


title: DTB, 8hr, pRQ4, replicate 2


title: Low-NPC-3-2


title: Hyp_HFHS_2

source_name: Hyp

value: Mouse hypothalamus

value: high fat high sucrose diet

value: HFHS

value: Hyp


title: brown adipose tissue, Male PGC-1α knockout, room temperature(25℃)

description: Library name: experimental1_ Male_KO


title: Low-NPC-3-1

value: hiPSC-derived neural progenitor cells

value: Low


title: Hyp_HFHS_1


title: Whole-NPC-3APP3

value: APPswe

value: Whole


title: Hyp_Fruc_2

value: male

value: chow + 15% fructose drink

value: Fruc


title: DTB, 8hr, pRQ4, replicate 1

value: Colon


title: NPC_Control_Set2_2


title: DTB, 8hr, pMCM2, replicate 1

value: colorectal carcinoma


title: Hyp_Fruc_1


title: brown adipose tissue, Female PGC-1a knockout, room temperature(25C)

description: Library name: experimental1_ Female_KO_ATAC

data_processing:
Reads were aligned to the reference genome using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, and only uniquely mapped, properly paired reads with a mapping quality score ≥1 were retained for further analysis.Alignments were extended in silico at their 3’-ends to 200 bp and assigned to 32-nt bins along the genome. Genomic signal maps were generated and stored in bigWig files. Peaks were identified using MACS 3.0.0 with a p-value cutoff of 1e-7, without a control file, and with the --nomodel option. Peaks overlapping the ENCODE blacklist of known false-positive regions were removed. Final signal maps and peak annotations were analyzed using Active Motif’s proprietary software to generate Excel tables containing sample comparisons, peak metrics, peak locations, and gene annotations.
Assembly: mm10
Supplementary files format and content: The processed data files are provided in CSV format and include peak-related information from ATAC-seq experiments, such as peak presence, peak values, and gene annotations across different conditions (male control, male KO, female control, female KO).

extract_protocol:
Flash-frozen tissues were sent to Active Motif to perform the ATAC-seq assay. The tissue was manually dissociated, and nuclei were isolated by mechanical disruption. Isolated nuclei were quantified using a hemocytometer. A total of 100,000 nuclei were used for downstream processing.
Nuclei were tagmented as previously described (Buenrostro et al., 2013), with modifications based on Corces et al. (2017), using the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif). Tagmented DNA was purified using the MinElute PCR purification kit (Qiagen), followed by amplification with 10 cycles of PCR. The amplified DNA was further purified using Agencourt AMPure SPRI beads (Beckman Coulter). The resulting libraries were sequenced using paired-end 42 bp reads (PE42) on the NovaSeq 6000 sequencer (Illumina).

value: brown adipose tissue


title: brown adipose tissue, Female Control, room temperature(25C)

description: Library name: experimental1_ Female_Control_ATAC

value: WT


title: Whole-NPC-3APP2


title: Hyp_Control_2

value: chow diet

value: Control


title: brown adipose tissue, Male PGC-1a knockout, room temperature(25C)

description: Library name: experimental1_ Male_KO_ATAC

value: PGC-1a knockout


title: DTB, 8hr, MTBP, replicate 2


title: Whole-NPC-3APP1


title: DTB, 8hr, MTBP, replicate 1


title: brown adipose tissue, Male Control, room temperature(25C)

description: Library name: experimental1_ Male_Control_ATAC


title: Hyp_Control_1

value: Mouse hypothalamus


title: brown adipose tissue, Female Control, room temperature(25℃)

description: Library name: experimental1_ Female_Control


title: Whole-NPC-3-2


title: DTB, 4hr, pRQ4, replicate 1


title: HEP_HFHS_Set2_2

value: Mouse liver hepatocytes

value: high fat high sucrose diet

value: HFHS


title: Whole-NPC-3-1

value: hiPSC-derived neural progenitor cells


title: brown adipose tissue, Male Control, room temperature(25℃)

description: Library name: experimental1_ Male_Control


title: DTB, 4hr, pRQ4, replicate 2


title: WT_EpiSC_8

data_processing:
Sequence reads were trimmed for adaptor sequence/low quality sequence using Trim Galore
Trimmed sequence reads were mapped to GRCm38/mm10 using HISAT2.
StringTie was used for gene counts.
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample

source_name: EpiSC

growth_protocol: EpiSCs were cultured in N2B27 supplemented with FGF2, Activin A, and XAV-939 on fibronectin coated plate.

extract_protocol:
For low in put RNA-sequencing, RNA was isolated from indibidual epiblast usisng PicoPure RNA extraction kit (Thermo). Total RNA was isolated using Rneasy Mini Kit (QIAGEN) from EpiSCs.
SMARTer® Stranded Total RNA-Seq Kit v2 was used for the library construction from epiblast sample. NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® was used for the library construction from EpiSCs sample.

value: EpiSC


title: HEP_HFHS_Set1_2


title: DTB, 4hr, pMCM2, replicate 2


title: DTB, 4hr, pMCM2, replicate 1


title: HEP_HFHS_Set2_1


title: DTB, 8hr, pMCM2, replicate 2


title: DTB, 4hr, MTBP, replicate 2


title: HEP_Fruc_Set2_2


title: Whole-NPC-3-3

value: Whole


title: E7.5_WT_9

source_name: postimplantation epiblast cell

value: postimplantation epiblast cell


title: DTB, 4hr, MTBP, replicate 1


title: HEP_HFHS_Set1_1

value: male


title: HEP_Fruc_Set1_2

value: chow + 15% fructose drink

value: Fruc


title: E7.5_WT_8


title: Stat3null_EpiSC_2

value: Stat3 null


title: HEP_Fruc_Set2_1


title: DTB, 1hr, pRQ4, replicate 1

value: Colon

value: colorectal carcinoma


title: E7.5_WT_7

value: WT


title: HEP_Fruc_Set1_1


title: E7.5_WT_6


title: HEP_Control_Set2_1

value: chow diet

value: Control


title: E7.5_WT_5


title: E7.5_WT_4


title: HEP_Control_Set1_1


title: DTB, 1hr, pMCM2, replicate 2


title: DTB, 1hr, MTBP, replicate 2


title: C_3

city: Tianjin

first: Gengyin

last: Huang

address: Jinjing road

institute: Tianjin Agricultural University

description: Library name: Sample 9

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Pacbio sequencing + Hi-C analysis
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mactra quadrangularis

source_name: hypoxic stress group

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: branchiae

value: hypoxic stress


title: C_2

description: Library name: Sample 8


title: DTB, 1hr, MTBP, replicate 1

data_processing:
Raw bam files were generated from fastq files of ChIP-seq or NS-seq after QC, trimmimming, QC, aligned to hg19 with BWA.
For ChIP-seq, narrow peaks were called using the no-IP control with MACS2. For nascent strand sequencing, broad peaks were called with the MACS2 algorithm.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: hg19
Supplementary files format and content: Bed file format showing: ChIP-seq peaks, NS-seq peaks
Supplementary files format and content: BigWig file format of ChIP-seq peaks and replication origin locations


title: DTB, 1hr, pRQ4, replicate 2


title: E7.5_WT_2


title: WT_EpiSC_13


title: DTB, 0hr, pRQ4, replicate 2


title: B_3

description: Library name: Sample 6


title: C_1

description: Library name: Sample 7


title: E7.5_WT_1


title: E7.5_Stat3null_3


title: DTB, 0hr, pMCM2, replicate 2


title: B_2

description: Library name: Sample 5


title: B_1

description: Library name: Sample 4


title: E7.5_Stat3null_1


title: DTB, 0hr, pMCM2, replicate 1


title: E7.5_Stat3null_2


title: DTB, 1hr, pMCM2, replicate 1


title: DTB, 0hr, MTBP, replicate 1


title: A_3

description: Library name: Sample 3

source_name: normal seawater control group

value: normal control


title: A_2

description: Library name: Sample 2


title: E6.5_WT_8


title: DTB, 0hr, MTBP, replicate 2

source_name: Colon


title: AS, pRQ4, replicate 2


title: E7.5_WT_3


title: E6.5_WT_9


title: A_1

description: Library name: Sample 1


title: E6.5_WT_7


title: AS, pRQ4, replicate 1


title: E6.5_WT_6


title: AS, pMCM2, replicate 2


title: E6.5_WT_5


title: DTB, 0hr, pRQ4, replicate 1


title: ifl_pms2ab_rep3

data_processing:
Zebracall software used for basecalling.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

growth_protocol: Arabidopsis seeds were sown on the Murahsige and Skoog (MS) medium and stratified at 4 ℃ for 2 days. Subsequently, they were grown under long-day conditions (16 h of light at 23 ℃ and 8 h of darkness at 22 ℃).  Inflorescences of 4~5-week-old plants in soil were used for RNA-seq experiments.

extract_protocol:
Total RNA was extracted from Arabidopsis inflorescences with TRIzol reagent (Invitrogen, 15596018).
Sequencing libraries were built for RNA-seq (the single-end 50-bp strategy on the BGISEQ-500 platform).

value: Arabidopsis inflorescences


title: AS, MTBP, replicate 2


title: ifl_pms2ab_rep2


title: E6.5_WT_4


title: E6.5_WT_3


title: Stat3null_EpiSC_6


title: ifl_pms2ab_rep1


title: E6.5_WT_2


title: Tongue epithelial cells, ZT12

city: Hirakata

first: Toru

last: Matsu-ura

state: Osaka

address: 2-5-1 Shin-mach

department: Pathology

institute: Kansai Medical University

description:
Library name: sample2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene cunting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tongue epithelium

extract_protocol:
Tongue epithliums were isolated from mice at two different circadian times (ZT0 and ZT12). The epitheliums were minced and digested by TrypLE Express (Thermo Fisher). Isolated epithelial cells were washed, re-suspended in FACS buffer (PBS, 2% v/v FBS, 1 mM EDTA), and stained with viability dye (7-AAD). Alive tongue epithelial cells were sorted using a SH800S (Sony).
Library was performed according to the manufacture's instruction (single cell 3' v2 protocol, 10x Genomics). Briefly, tongue epithelial cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Tongue epithelium

value: Epithelial cells

tag: age

value: 8-12 weeks

value: Male

tag: host strain


title: HAP1 cells, SV3_CTRLB

city: Camperdown

first: Graham

middle: Gregory

last: Neely

state: NSW

address: John Hopkins Dr

country: Australia

institute: Charles Perkins Centre, The University of Sydney

description:
CtlvsSV3_9dayLow.rra.txt
CtlvsSV3_9dayLow.sgrra.txt

data_processing:
Data was analyzed using the MAGeCK (v05.9.2) pipeline
Assembly: GRCh37.p13
Supplementary files format and content: .txt file containing robust rank aggregation of genes
Supplementary files format and content: .txt file containing robust rank aggregation of inidividual sgRNAs
Library strategy: Amplicon sequencing

extract_protocol:
Genomic DNA was extracted from cell pellets with the ISOLATE II Genomic DNA Kit (Bioline). Samples of gDNA (25 μg for controls and 5 μg for selected samples) were added to NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs) along with the following primers to bind the sgRNA region: NGSCRISPRv2F1 5’-GGACAGCACAGATCCAGTTTGGT- 3’ and NGSCRISPRv2R1 5’-GAGCCAATTCCCACTCCTTTCAA-3’. A second PCR reaction with a staggered primer mix of P5 and P7 indexing primers unique to each sample was prepared. Reactions were isolated by gel electrophoresis.
Samples were sequenced with Novogene

value: control

value: Diversity control


title: Liver WT rep3 [LAB_338_06]

city: Tsukuba

first: Akihiro

last: Kuno

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

data_processing:
Sequencing reads were mapped to the Ensembl mouse genome (release GRCm38.102) using subread (version 2.0.2) (PMID:23558742) and the read counts  aligning to known genes were generated by featureCounts (PMID: 24227677).
The read counts were normalized with the iDEGES/edgeR method implemented in TCC (version 1.34.0) (PMID:12770646), and pairwise comparisons of gene expression between livers from WT control and Lmln KO were conducted with the edgeR (version 3.36.0) (PMID:19910308). The false discovery rate (FDR) adjustments (DOI:http://www.jstor.org/stable/2346101) were applied to correct for multiple testing, and differentially expressed genes (DEGs) were identified with an FDR cutoff of 0.05.
Assembly: GRCm38.102
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Total RNA from the liver was isolated using the TRIZOL reagent (Thermo Fisher Scientific). RNA quality was examined by RNA 6000 Pico kit (Agilent, Santa Clara, CA). An amount of 50 ng total RNA was used for RNA-seq library preparation with NEB NEBNext rRNA Depletion Kit and ENBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA); 2x36 base paired-end sequencing was performed with NextSeq500 (Illumina, San Diego, CA) by Tsukuba i-Laboratory LLP (Tsukuba, Ibaraki, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: post natal 46 weeks

value: wild type


title: Tongue epithelial cells, ZT0

description:
Library name: sample1
10x Genomics


title: MCM2, WT, Ex, MTBP, replicate 2

extract_protocol:
For ChipSeq, DNA fragments were enriched using antibodies against proteins of interest, DNA was purified and processed as described in Thakur et al, NAR 2022. For NS-seq DNA from cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004.
Samples were eluted, and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB, E7335S and E7500S).

value: Colon

value: colorectal carcinoma


title: ifl_minu12_rep3

source_name: Arabidopsis inflorescences


title: Liver WT rep2 [LAB_338_05]


title: E6.5_WT_1

value: postimplantation epiblast cell

value: WT


title: HAP1 cells, SV3_CTRLA


title: Liver WT rep1 [LAB_338_04]


title: HAP1 cells, SV3_B5ug

value: 5ug/mL of Naja nigricollis venom over a total of 9 days

value: Amplified sgRNA region to identify genes that sensitise or protect againt venom compared to diversity controls


title: Liver Lmln-KO rep3 [LAB_338_03]

value: post natal 39 weeks

value: Lmln-/-


title: ifl_minu12_rep1

value: Arabidopsis inflorescences


title: HAP1 cells, SV3_A5ug


title: AS, pMCM2, replicate 1


title: Liver Lmln-KO rep2 [LAB_338_02]


title: E6.5_Stat3null_6

value: Stat3 null


title: ifl_sys123_rep3


title: AS, MTBP, replicate 1


title: ifl_sys123_rep2


title: E6.5_Stat3null_5


title: HAP1 cells, SV1_CTRLB

description:
CtlvsSV1_5ug.rra.txt
CtlvsSV1_5ug.sgrra.txt


title: ifl_sys123_rep1


title: Liver Lmln-KO rep1 [LAB_338_01]


title: KI111_3

first: Zhiqiang

last: Peng

address: 38 Life Science Park Road

institute: State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics

description:
Library name: sample6
Column name in raw_counts_All_Samples.txt:KI111_3

data_processing:
CLC genomics workbench v11.0.1
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: embryo

extract_protocol:
RNA was harvested using  Oligo(dT) beads. RNA was diluted at 2 nM for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer’s protocols.

value: embryo

value: KI

tag: developmental stage

value: Embryonic development E7.5


title: HAP1 cells, SV1_CTRLA

value: control

value: Diversity control


title: E6.5_Stat3null_4


title: HAP1 cells, SV1_B5ug

value: 5ug/mL of Naja pallida venom over a total of 9 days


title: ifl_swi3d_rep3


title: E6.5_Stat3null_3


title: E6.5_Stat3null_8


title: ifl_swi3d_rep2


title: KI111_1

description:
Library name: sample4
Column name in raw_counts_All_Samples.txt:KI111_1


title: KI111_2

description:
Library name: sample5
Column name in raw_counts_All_Samples.txt:KI111_2


title: ifl_minu12_rep2


title: E6.5_Stat3null_7


title: E6.5_Stat3null_2


title: OE3 ATAC-seq

first: Zhenli

address: 1277 Jiefang Avenue,

institute: Huazhong University of Science and Technology

data_processing:
The library products were enriched, quantified and sequenced on a DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with the PE150 model.
The quality control of raw data was performed by FastQC (version v0.11.5). Raw sequencing data were filtered through the Trimmomatic (version 0.36) to remove the adaptor and low-quality reads, and were further treated with FastUniq (version 1.1) to eliminate PCR duplications.
The deduplicated clean data were mapped reads to the reference genome Homo_sapiens.GRCh38 (ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/) by bowtie2 software (version 2.2.6). RSeQC（version 2.6）was used to evaluate the mapped reads distribution, coverage uniformity, and strand specificity. MACS2 software（Version 2.1.1）was used for peak calling.
Peak annotation and peak distribution were analyzed by using BedTools (Version 2.25.0). Motif enrichment was calculated using HOMER (version 4.10).
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: xls files with raw gene counts for every gene and every sample

source_name: Peripheral blood

growth_protocol: Purified CD4+ T cells were isolated from the peripheral blood of healthy donors and cultured with X-VIVO15 supplemented with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
An ATAC assay was performed  to analyze CD4+GFP+ cell (50000 cells). Cells were treated with cell lysis buffer and nuclei were collected by centrifugation for 5min at 500×g.
The TruePrep DNA Library Prep Kit V2 for Illumina kit  was used for translocation and high-throughput DNA sequencing library construction.

treatment_protocol: Anti-CD3 mAb and anti-CD28 mAb were used to activate CD4+ T cells (1x106/mL), and IL-2 (10 ng/ml) was added into the medium for further culturing. After activation for 24 hours with anti-CD3/CD28 antibodies, CD4+ T cells were transfected with the SMAR1 lentivirus vector or empty vector carrying green fluorescent protein (GFP). GFP-positive cells were sorted by flow cytometry 5 days after transfection.

value: Peripheral blood

value: CD4+T cell

value: CD4+T cell were transfected with SMAR1 lentivirus vector


title: E6.5_Stat3null_1

value: postimplantation epiblast cell


title: ifl_swi3d_rep1


title: E5.5_WT_2

value: WT


title: OE2 ATAC-seq


title: ifl_syd_rep3

value: syd-/-


title: WT111_3

description:
Library name: sample3
Column name in raw_counts_All_Samples.txt:WT111_3


title: WT111_2

description:
Library name: sample2
Column name in raw_counts_All_Samples.txt:WT111_2


title: OE1 ATAC-seq


title: E5.5_WT_1


title: WT111_1

description:
Library name: sample1
Column name in raw_counts_All_Samples.txt:WT111_1


title: ifl_syd_rep2


title: Ctrl3 ATAC-seq

value: CD4+T cell were transfected with empty vector


title: E5.5_Stat3null_4


title: HAP1 cells, SV1_A5ug

value: Amplified sgRNA region to identify genes that sensitise or protect againt venom compared to diversity controls


title: Ctrl2 ATAC-seq


title: ifl_brm_rep3

value: brm-/-


title: ifl_syd_rep1

value: Arabidopsis inflorescences