title: genomic DNA from whole blood CKD 2

description:
Sample was bisulfite-converted and hybridized to the array following the manufacturer's protocol
SAMPLE 2


title: A_TT_H3K27_input_rep2

status: Public on May 10 2023

type: SRA

city: 天津市

first: Xinyue

last: Lei

state: 天津市

address: 天津市和平区气象台路22号天津医科大学

country: China

institute: 天津医科大学

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Data were filtered using Trimmomatic
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2-2.3.5
Determination of the normalized factor using deeptools
peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: A549 cells

growth_protocol: A549 cells  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°

extract_protocol:
1 × 10^7 cells were washed with PBS and fixed with 37 °C pre-heated 10% FBS MEDIA/1% formaldehyde at room temperature for 10 min, and quenched with 0.125 M glycine (V900144, Sigma) for 5 min, and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

tag: cell line

value: A549 cells

tag: cell type

value: lung cancer

tag: genotype

value: TT

tag: treatment

value: homozygous mutation

tag: chip antibody


title: DKTKRO_108_HNSCC_tumor_HPV-positive

type: RNA

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

hyb_protocol: According to the manufacturer's protocol.

data_processing: Text files were imported into R using the AgiMicroRna Bioconductor package. After quality filtering using Agilent quality filters and removing non-human miRNAs from the data set scanned intensities were background corrected, quantile normalized. The resulting expressions were log2-transformed after averaging signals determining expression of the same miRNA.

molecule: total RNA

source_name: head and neck tumor

growth_protocol: Formalin-fixed paraffin-embedded tumour specimens were derived from treatment-naive surgically resected tumour tissues. Haematoxylin-eosin-stained tissue sections were histopathologically reviewed by a pathologist (DKTK-ROG: KS; LMU-KKG: CW/AW), the tumour area was defined and micro-dissected whereby only samples with at least 60% tumour cells were included.

extract_protocol: Total RNA including the small RNA fraction was extracted using the Qiagen miRNeasy FFPE (DKTK-ROG) or the AllPrep DNA/RNA FFPE Kit (LMU-KKG) according to the manufacturer's protocols (Qiagen, Hilden, Germany).

treatment_protocol: not applicable

tag: hpv-status

value: positive


title: DKTKRO_107_HNSCC_tumor_HPV-positive

scan_protocol: According to the manufacturer's protocol.


title: A_TT_H3K27_input_rep1

address: 天津市和平区气象台路22号天津医科大学


title: RPE1 core essential_tumor suppressor multiSPAS(opAsCas12a) Screen Replicate 1

city: Frankfurt am Main

first: Martin

last: Wegner

state: Hessen

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry II

institute: University Hospital Frankfurt am Main, Germany

description: genomic DNA

data_processing:
Read counts of individual gRNA combinations were determined using cutadapt 2.8 and Bowtie 2.3.0 31,32.
Reads were trimmed with cutadapt in paired-end mode to the length of the respective library sequences using the constant regions upstream of the gRNA.
Cutadapt was set up with an error tolerance of 0.1 and to discard untrimmed reads.
The obtained sequences were then aligned to the respective gRNA library using Bowtie2 in local mode using a seed length of 11, a seed mismatch value of 1, and the interval function ‘S,1.0,0.75’.
Supplementary files format and content: Read counts
Library strategy: CRISPR screen

source_name: Eye; Pigmented epithelium; Retina

growth_protocol: hTERT-RPE1 cells were cultured in DMEM: Nutrient Mixture F-12 (DMEM/F12, Thermo Fisher Scientific, 11320-074) supplemented with 10% FBS, 1% penicillin-streptomycin and 0.01 mg/ml hygromycin B (Capricorn Scientific, HYG-H)) at 37°C with 5% CO2. Mycoplasma contamination testing was performed immediately after the arrival of the cells and regularly during the experiments by using Venor®GeM Classic (Minerva Biolabs GmbH, 11-1025) according to the manufacturer’s protocol.

extract_protocol: Cells were lysed in 12 mL of TEX buffer (10 mM Tris-HCl, pH 7.5; 1 mM EDTA, pH 7.9; 0.5 % SDS) containing ribonuclease A (RNase, 20 mg/mL, Carl Roth GmbH, 7156.2) and proteinase K (20 mg/mL, Carl Roth GmbH, 7528.6) and incubated overnight at 37°C under constant agitation. The next day after complete lysis, 4 mL of 5 M NaCl was added, and the mixture was shaken vigorously and incubated at 4°C for 1 hour. The tube was centrifuged at 15,000 g for 1 hour at 4° C. The supernatant containing the DNA was transferred into a new tube. 24 mL of ice-cold absolute ethanol was added, and mixed and the solution was incubated overnight at -20°C. The next day, the tube was centrifuged at 15,000 g for 1 hour at 4°C. The supernatant was removed and the DNA pellet was washed with 10 mL of ice-cold 70% ethanol and mixed very well. The mixture was centrifuged at 15,000 g for 1 hour at 4°C and the supernatant was removed. Air-dried DNA pellets were resuspended in 1 mL of sterile water.

treatment_protocol: CRISPR libraries were screened in hTERT-RPE1-SpCas9-enAsCas12a or SpCas9-opAsCas12a cell line with 100-fold coverage, each with two technical replicates. The total cell number for each screen was calculated by multiplying library complexity and the coverage of 100. Cells were transduced with respective library with MOI of 0.5. Cells were selected with puromycin (1 µg/ml) two days after transduction. Cells were subcultured and seeded at a cell number maintaining library diversity (library complexity x screening coverage) when they reached 80% confluency. Cells were harvested 14 days after transduction for subsequent gDNA extraction.

tag: tissue

value: Eye; Pigmented epithelium; Retina

value: hTERT RPE-1

value: Epithelial cell

value: WT

value: core essential_tumor suppressor CRISPR screen

tag: time

value: Day 14


title: RPE1 core essential_tumor suppressor multiSPAS(opAsCas12a) Screen Replicate 2

description: genomic DNA


title: skin tissues, healthy,Year3_1, smallRNA

city: Ya'an

first: Yu

middle: jing

last: Li

state: Sichuan

address: Xinkang street num 46

department: Department of Zoology, College of Life  Science

institute: Sichuan Agricultural University

description: sample 10

library_source: transcriptomic

data_processing:
DNBSEQ-G400 was used for sequencing.
Sequence reads were trimmed for adaptor reads,low-quality reads and reads whose N content was greater than 5% .
Trimmed sequence reads were mapped to the reference genome and transcriptome using bowtie2.
LncRNA and mRNA used RSEM to calculate the expression levels of genes and transcripts; miRNA used specific molecular tags (UMI) for relevant gene expression calculations; and we calculated the expression of circRNA based on the number of back-spliced reads compared to both ends of the circRNA and used two software programs(CIRI and find_circ), and the final back-spliced read number is the average of the two results.
Assembly: Reference Genome Version: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: tar.gz. files include all processed data

organism: Sus scrofa

source_name: forehead skin

extract_protocol:
The TRIzol Reagent (Invitrogen, CA, USA) was used to extract the total RNA, which was subsequently treated with DNase and purified by using the RNeasy Mini Kit (Qiagen, CA, USA).  The quality, concentration, and integrity of RNA were checked using a nanodrop photometer and an agilent 2100 bioanalyzer.
RNA libraries were prepared for sequencing using DNBSEQ protocols, including LncRNA library (mRNAs and lncRNAs), smallRNA library (miRNAs), and circRNA library (circRNAs).

value: forehead skin

tag: breed

value: Chenghua pig

tag: Sex

value: female

tag: disease state

value: healthy


title: skin tissues, healthy,Year3_2, smallRNA

description: sample 11


title: skin tissues, healthy,Year3_3, smallRNA

description: sample 12


title: Fe3_S3

city: State College

first: Aswathy

last: Sebastian

address: University Park

country: USA

institute: PennState

data_processing:
Data was trimmed using fastp
Trimmed data was mapped  to the reference genome using hisat2
Gene-level raw read counts were obtained using featureCounts
Differential expression was performed with DESeq2
Assembly: PlasmoDB-55_Pyoeliiyoelii17X_Genome
Supplementary files format and content: Tab delimited file with gene-level raw read counts for each sample

organism: Plasmodium yoelii

source_name: Female Gametocyte

growth_protocol: Plasmodium yoelii 17XNL parasites were grown in swiss webster mice, with ex vivo culture of zygotes.

extract_protocol:
RNA was purified by a Qiagen Rneasy kit with in-solution DNaseI digestion
Library preparation was via the Illumina stranded mRNA kit for 150nt single end reads.

treatment_protocol: Female gametocytes and zygotes were purified by flow cytometry

tag: strain

value: Female Gametocyte

value: WT with pylap4 promoter driving GFP expression


title: RPE1 core essential_tumor suppressor multiSPAS(enAsCas12a) Screen Replicate 2

description: genomic DNA


title: skin tissues, healthy,Day180_3, smallRNA

description: sample 9


title: skin tissues, healthy ,Day180_2, smallRNA

description: sample 8


title: A_CC_H3K4_IP_rep1

address: 天津市和平区气象台路22号天津医科大学

value: A549 cells

value: CC

value: H3K4me3 (ab8580, Abcam)


title: RPE1 core essential_tumor suppressor multiSPAS(enAsCas12a) Screen Replicate 1

description: genomic DNA


title: A_CC_H3K4_IP_rep2

address: 天津市和平区气象台路22号天津医科大学

value: lung cancer

value: homozygous mutation


title: A_CC_H3K4_input_rep2

address: 天津市和平区气象台路22号天津医科大学


title: DKTKRO_105_HNSCC_tumor_HPV-positive

label_protocol: According to the manufacturer's protocol.

value: positive


title: skin tissues, healthy,Day180_1, smallRNA

description: sample 7


title: DKTKRO_104_HNSCC_tumor_HPV-positive


title: core essential_tumor suppressor multiSPAS Library

description: plasmid DNA

value: Eye; Pigmented epithelium; Retina

value: hTERT RPE-1


title: A_CC_H3K4_input_rep1

address: 天津市和平区气象台路22号天津医科大学


title: DKTKRO_103_HNSCC_tumor_HPV-negative

value: negative


title: skin tissues, healthy,Day90_3, smallRNA

description: sample 6


title: DKTKRO_102_HNSCC_tumor_HPV-positive


title: DKTKRO_106_HNSCC_tumor_HPV-positive


title: RPE1 core essential_tumor suppressor CHyMErA.v2 Screen Replicate 2

description: genomic DNA

value: Epithelial cell

value: WT

value: core essential_tumor suppressor CRISPR screen


title: DKTKRO_101_HNSCC_tumor_HPV-positive


title: core essential_tumor suppressor CHyMErA.v2 Library

description: plasmid DNA

value: Day 14


title: skin tissues, healthy,Day90_1, smallRNA

description: sample 4

value: forehead skin

value: Chenghua pig

value: female


title: A_TT_H3K4_IP_rep1

address: 天津市和平区气象台路22号天津医科大学

value: TT


title: RPE1 core essential_tumor suppressor CHyMErA.v2 Screen Replicate 1

description: genomic DNA


title: DKTKRO_100_HNSCC_tumor_HPV-positive


title: A_TT_H3K4_IP_rep2

address: 天津市和平区气象台路22号天津医科大学

value: A549 cells


title: skin tissues, healthy,Day90_2, smallRNA

description: sample 5

value: healthy


title: A_TT_H3K4_input_rep2

address: 天津市和平区气象台路22号天津医科大学


title: skin tissues, healthy,Day3_3, smallRNA

description: sample 3

value: Day 3


title: A_TT_H3K4_input_rep1

address: 天津市和平区气象台路22号天津医科大学

value: lung cancer


title: DKTKRO_99_HNSCC_tumor_HPV-positive


title: DKTKRO_98_HNSCC_tumor_HPV-positive


title: DKTKRO_97_HNSCC_tumor_HPV-positive


title: skin tissues, healthy,Year3_3, lncRNA

description: sample 12


title: core essential_tumor suppressor enAsCas12a(dual-gRNA) Library

description: plasmid DNA


title: RPE1 core essential_tumor suppressor CHyMErA Screen Replicate 2

description: genomic DNA


title: RPE1 core essential_tumor suppressor enAsCas12a(dual-gRNA) Screen Replicate 1

description: genomic DNA


title: RPE1 core essential_tumor suppressor CHyMErA Screen Replicate 1

description: genomic DNA


title: skin tissues, healthy,Day3_1, smallRNA

description: sample 1


title: skin tissues, healthy,Day3_2, smallRNA

description: sample 2


title: DKTKRO_95_HNSCC_tumor_HPV-positive


title: RPE1 core essential_tumor suppressor enAsCas12a(dual-gRNA) Screen Replicate 2

description: genomic DNA


title: CC_H3K9me3_IP_rep2

address: 天津市和平区气象台路22号天津医科大学

source_name: H460 cells

growth_protocol: H460 (T/T) and H460 (C/C) cells  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°

extract_protocol:
1 × 107cells were washed with PBS and fixed with 37 °C pre-heated 10% FBS MEDIA/1% formaldehyde at room temperature for 10 min, and quenched with 0.125 M glycine (V900144, Sigma) for 5 min, and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: untreatment

value: H460 cells

value: H3K9me3 (ab8898, Abcam)


title: skin tissues, healthy,Year3_1, lncRNA

description: sample 10


title: CC_H3K9me3_IP_rep1

address: 天津市和平区气象台路22号天津医科大学


title: CC_H3K9me3_input_rep1

address: 天津市和平区气象台路22号天津医科大学


title: skin tissues, healthy,Year3_2, lncRNA

description: sample 11


title: TT_H3K9me3_IP_rep2

address: 天津市和平区气象台路22号天津医科大学


title: core essential_tumor suppressor CHyMErA Library

description: plasmid DNA

value: Eye; Pigmented epithelium; Retina


title: TT_H3K9me3_IP_rep1

address: 天津市和平区气象台路22号天津医科大学


title: skin tissues, healthy,Day180_3, lncRNA

description: sample 9


title: RPE1 core essential_tumor suppressor enAsCas12a Screen Replicate 1

description: genomic DNA

value: hTERT RPE-1


title: RPE1 core essential_tumor suppressor enAsCas12a Screen Replicate 2

description: genomic DNA


title: DKTKRO_96_HNSCC_tumor_HPV-positive

value: positive


title: DKTKRO_94_HNSCC_tumor_HPV-positive


title: DKTKRO_92_HNSCC_tumor_HPV-positive


title: DKTKRO_93_HNSCC_tumor_HPV-positive


title: CC_H3K9me3_input_rep2

address: 天津市和平区气象台路22号天津医科大学


title: skin tissues, healthy,Day180_1, lncRNA

description: sample 7


title: DKTKRO_91_HNSCC_tumor_HPV-positive


title: TT_H3K9me3_input_rep2

address: 天津市和平区气象台路22号天津医科大学


title: TT_H3K9me3_input_rep1

address: 天津市和平区气象台路22号天津医科大学


title: RPE1 core essential_tumor suppressor RPE1 SpCas9 Screen Replicate 2

description: genomic DNA

value: Epithelial cell


title: skin tissues, healthy,Day90_3, lncRNA

description: sample 6


title: DKTKRO_90_HNSCC_tumor_HPV-negative

value: negative


title: skin tissues, healthy,Day90_2, lncRNA

description: sample 5


title: CC_H3K27me3_IP_rep2

address: 天津市和平区气象台路22号天津医科大学

value: H3K27me3 (#9733, Cell signaling technology)


title: core essential_tumor suppressor SpCas9 Library

description: plasmid DNA

value: WT

value: core essential_tumor suppressor CRISPR screen

value: Day 14


title: skin tissues, healthy,Day90_1, lncRNA

description: sample 4

value: forehead skin

value: Chenghua pig

value: female


title: CC_H3K27me3_IP_rep1

address: 天津市和平区气象台路22号天津医科大学


title: DKTKRO_88_HNSCC_tumor_HPV-positive


title: skin tissues, healthy ,Day180_2, lncRNA

description: sample 8

value: healthy


title: CC_H3K27me3_input_rep2

address: 天津市和平区气象台路22号天津医科大学


title: core essential_tumor suppressor enAsCas12a Library

description: plasmid DNA


title: MCF10DCIS,P6,cHiC

city: Burlington

first: Joseph

middle: R

last: Boyd

state: Vermont

address: University of Vermont

department: Biomedical and Health Sciences

institute: University of Vermont

description: capture HiC

data_processing:
HiC-Pro (v 2.8.1_devel PMID: 26619908) was used to process and align reads (bowtie2 v 2.1.0 PMID: 22388286) to canonical chromosomes in hg38.
For visualization, .hic files were generated from allValidPairs files using the hicpro2juicebox.sh utility script included with HiC-pro to match resolutions in the hTERT-RPE1 and U2OS cells.
Supplementary files format and content: Supplementary file contains capture regions and compatible .hic files derived from HiC data in GSE98552 (ENCFF876OWE for hTERT-RPE1 and GSE141139 for USOS .hic files were also used but otherwise available).
Supplementary files format and content: .hic files were generated using HiC-Pro's hicpro2juicebox.sh script. They can be extracted using straw utility from JuiceBox software or strawr R package.

growth_protocol: MCF10DCIS were grown in DMEM/F12 (Corning 10-090-CV) supplemented with 5% horse serum (Gibco 16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882) + 20ng/ml hEGF (PeprotechAF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888), Pen/Strep, and L-Glutamine. MCF10CA1a were grown in DMEM/F12 (Corning 10-090-CV) supplemented with 5% horse serum (Gibco 16050 lot #1075876), Pen/Strep, and L-Glutamine. These cells were all grown in a humidified atmosphere with 5% CO2 at 37oC.

extract_protocol:
Hi-C was performed as previously described (Belton et al., 2012) and capture probes were designed in collaboration with Agilent. The capture procedure was performed as per the manufacturer's instructions.
Cells were fixed with 1% methanol free formaldehyde for 10′ at room temperature, treated with glycine on ice for 15 minutes, PBS rinsed, and snap frozen in liquid nitrogen. HINDIII restriction digested products were blunt ligated after incorporation of biotinylated dCTP. The DNA was sonicated and crosslinks were reversed. Beads were used to pull down biotinylated di-tags. Sheered ends were repaired, A-tailed, and barcoded adapters were ligated. High ligation efficiency was determined by nhel restriction digestion (blunt end formation creates a nheI site). The Belton et al., 2012 protocol was modified to increase the ligation step to 10 hours with a second spike-in of t4 ligase at hour 4. We found a dramatic increase in ligation efficiency using these conditions.

treatment_protocol: The media was changed on all cells 24 hours prior to harvesting and grown to ~90% confluence.

tag: replicate


title: MCF10DCIS,P3,cHiC

description: capture HiC


title: DKTKRO_86_HNSCC_tumor_HPV-positive


title: CC_H3K27me3_input_rep1

address: 天津市和平区气象台路22号天津医科大学


title: TT_H3K27me3_IP_rep2

address: 天津市和平区气象台路22号天津医科大学


title: skin tissues, healthy,Day3_3, lncRNA

description: sample 3

value: Day 3


title: skin tissues, healthy,Day3_1, lncRNA

description: sample 1


title: skin tissues, healthy,Day3_2, lncRNA

description: sample 2


title: DKTKRO_85_HNSCC_tumor_HPV-negative


title: DKTKRO_89_HNSCC_tumor_HPV-positive


title: DKTKRO_84_HNSCC_tumor_HPV-negative


title: skin tissues, healthy,Year3_3, circRNA

description: sample 12


title: RPE1 core essential_tumor suppressor RPE1 SpCas9 Screen Replicate 1

description: genomic DNA


title: TT_H3K27me3_IP_rep1

address: 天津市和平区气象台路22号天津医科大学

value: lung cancer


title: DKTKRO_83_HNSCC_tumor_HPV-negative


title: TT_H3K27me3_input_rep2

address: 天津市和平区气象台路22号天津医科大学

value: H460 cells


title: skin tissues, healthy,Year3_2, circRNA

description: sample 11


title: TT_H3K27me3_input_rep1

address: 天津市和平区气象台路22号天津医科大学


title: hT1 in MG004, Replicate C

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using with Trim Galore v0.4.4_dev
Trimmed sequence reads were mapped to GrCM38/mm10 for mouse samples and GRCh38/hg38 for human samples using STAR aligner v2.5.3a
Read count extraction was preformed with HOMER's analyzeRepeats.pl
Supplementary files format and content: tab-delimited text files include raw counts for each file.

source_name: pancreas

growth_protocol: Organoids were cultured as previously described (Tiriac et al 2018, Boj et al 2015)

extract_protocol:
RNA was harvested using Trizol reagent and an RNeasy Mini Kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq RNA Library Prep Kit (Illumina)

treatment_protocol: Organoids were cultured in Matrigel lot 04, Matrigel lot 01, Cultrex lot 83, Cultrex lot 87, or UltiMatrix lot 96 for 3 days (72 h) before harvesting of RNA.

tag: genome assembly

tag: organoid

value: pancreas


title: hT1 in Ultimatrix, Replicate B

value: Ultimatrix


title: hT1 in Ultimatrix, Replicate C


title: DKTKRO_82_HNSCC_tumor_HPV-negative


title: skin tissues, healthy,Year3_1, circRNA

description: sample 10


title: DKTKRO_87_HNSCC_tumor_HPV-positive


title: hT1 in MG004, Replicate B


title: DKTKRO_81_HNSCC_tumor_HPV-negative


title: CC_H3K27ac_IP_rep2

address: 天津市和平区气象台路22号天津医科大学

value: H3K27ac (ab4729, Abcam)


title: hT1 in MG004, Replicate A


title: skin tissues, healthy,Day180_3, circRNA

description: sample 9


title: CC_H3K27ac_IP_rep1

address: 天津市和平区气象台路22号天津医科大学


title: skin tissues, healthy ,Day180_2, circRNA

description: sample 8


title: hT1 in MG001, Replicate C


title: DKTKRO_80_HNSCC_tumor_HPV-negative


title: CC_H3K27ac_input_rep2

address: 天津市和平区气象台路22号天津医科大学


title: hT1 in Ultimatrix, Replicate A


title: skin tissues, healthy,Day180_1, circRNA

description: sample 7


title: DKTKRO_79_HNSCC_tumor_HPV-negative


title: hT1 in MG001, Replicate B


title: skin tissues, healthy,Day90_3, circRNA

description: sample 6


title: hT1 in MG001, Replicate A


title: skin tissues, healthy,Day90_2, circRNA

description: sample 5


title: hT1 in Cultrex187, Replicate C


title: DKTKRO_78_HNSCC_tumor_HPV-negative


title: DKTKRO_77_HNSCC_tumor_HPV-negative


title: hT1 in Cultrex187, Replicate B


title: skin tissues, healthy,Day90_1, circRNA

description: sample 4


title: DKTKRO_76_HNSCC_tumor_HPV-negative


title: TT_H3K27ac_IP_rep1

address: 天津市和平区气象台路22号天津医科大学


title: skin tissues, healthy,Day3_3, circRNA

description: sample 3


title: TT_H3K27ac_IP_rep2

address: 天津市和平区气象台路22号天津医科大学


title: DKTKRO_74_HNSCC_tumor_HPV-negative


title: DKTKRO_75_HNSCC_tumor_HPV-negative


title: skin tissues, healthy,Day3_2, circRNA

description: sample 2


title: hT1 in Cultrex183, Replicate C


title: hT1 in Cultrex187, Replicate A


title: DKTKRO_73_HNSCC_tumor_HPV-negative


title: CC_H3K27ac_input_rep1

address: 天津市和平区气象台路22号天津医科大学


title: CC_H3K4me3_IP_rep2

address: 天津市和平区气象台路22号天津医科大学

value: H3K4me3 (ab8580, Abcam)


title: DKTKRO_72_HNSCC_tumor_HPV-negative


title: skin tissues, healthy,Day3_1, circRNA

description: sample 1


title: CC_H3K4me3_IP_rep1

address: 天津市和平区气象台路22号天津医科大学


title: Brd4 fl/fl Prx1-cre

city: Shenzhen

first: Wenhui

last: Yu

address: Shennan middle road #3025

department: Department of Orthopedics

institute: The Eighth Affiliated Hospital of Sun Yat-sen University

data_processing:
Raw reads were filtered and trimmed to remove sequencing adaptors and low-quality reads
Clean reads were mapped to the human genome version hg38 using Bowtie2 (v2.5.1)
Peaks were called using MACS2 (v.2.1.1) and normalization (reads per kilobase per million or RPKM) of the ChIP-seq data and heatmap plotting were performed using deepTools (v2.3.6.0)
The normalized ChIP-seq data were visualized on Integrative Genomics Viewer (IGV)
Assembly: Grch38
Supplementary files format and content: bw files were generated by deepTools (v2.3.6.0)
Library strategy: CUT&Tag

organism: Mus musculus

source_name: Mesenchymal stem cells

extract_protocol:
The DNA fragments were extracted using phenol chloroform.
The CUT&Tag assay was performed using NovoNGS® CUT&Tag 2.0 High-Sensitivity Kit (for Illumina®) (Novoprotein Scientific Inc., Cat# N259-YH01-01A) according to the manufacturer’s instructions. Briefly, cells were harvested with trypsin and enriched by ConA-magnetic beads. A total of 50,000 cells were re-suspended and washed twice with 100 μL Dig-wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM spermidine; 1× protease inhibitor cocktail; 0.05% digitonin). The samples were incubated with primary BRD4 antibody (1:100, 4°C, 18 h) and secondary antibody (1:200, 25°C, 1 h). After incubation, the beads were washed three times in Dig-Hisalt Buffer (0.05% digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× protease inhibitor cocktail). Cells were incubated with the protein A-Tn5 transposome at 25°C for 1 h and washed three times in Dig-Hisalt buffer to remove unbound protein A-Tn5. The cells were re-suspended in 50 μL Tagmentation buffer (10 mM MgCl2 in Dig-Hisalt Buffer) and incubated at 37°C for 1 h. The tagmentation was terminated with the addition of 1 μL of 10% SDS at 55°C for 10 min.
Cleavage under targets and tagmentation (CUT&Tag)

value: Mesenchymal stem cells

value: Brd4 fl/fl Prx1-cre


title: hT1 in Cultrex183, Replicate B


title: hT1 in Cultrex183, Replicate A


title: Brd4 fl/fl

value: Brd4 fl/fl


title: CC_H3K4me3_input_rep2

address: 天津市和平区气象台路22号天津医科大学


title: TT_H3K27ac_input_rep2

address: 天津市和平区气象台路22号天津医科大学


title: DKTKRO_71_HNSCC_tumor_HPV-negative

value: negative


title: TT_H3K27ac_input_rep1

address: 天津市和平区气象台路22号天津医科大学


title: JQ1_BRD4

value: JQ1 treatment


title: CC_H3K4me3_input_rep1

address: 天津市和平区气象台路22号天津医科大学


title: hM1F in Ultimatrix, Replicate B


title: DKTKRO_69_HNSCC_tumor_HPV-negative


title: TT_H3K4me3_IP_rep2

address: 天津市和平区气象台路22号天津医科大学


title: DKTKRO_68_HNSCC_tumor_HPV-negative


title: DKTKRO_67_HNSCC_tumor_HPV-negative


title: OB5

data_processing:
The sequencing data were filtered with SOAPnuke (v1.5.2)11 by (1) removing reads containing sequencing adaptors; (2) removing reads whose low-quality base ratio (base quality less than or equal to 5) was more than 20%; and (3) removing reads whose unknown base ('N' base) ratio was more than 5%
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5)13 was used to align the clean reads to the reference coding gene set, and then the expression level of the gene was calculated by RSEM (v1.2.12)
Differential expression analysis was performed using DESeq2 (v1.4.5)15 with a Q value ≤ 0.05
Grch38
Genome_build: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow

growth_protocol: MSCs were seeded in 12-well plates at a density of 5×104/well and cultured with DMEM (1000 mg/L glucose) with 10% FBS

extract_protocol:
Total RNA was extracted from MSCs using TRIzol (Invitrogen), and 1 μg of isolated RNA was the construction of sequencing libraries.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was  generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end  repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on  the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the  final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300  copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Culture medium was changed to osteogenic medium (OM) to induce osteogenic differentiation, consisting of DMEM (glucose 1000 mg/L) with 10% FBS, 100 IU/mL penicillin, 100 IU/mL streptomycin, 0.1 μM dexamethasone, 10 mM β-glycerol phosphate, and 50 μM ascorbic acid (Sigma-Aldrich). The OM was changed every 3 days thereafter for 7 days

tag: group

value: Osteogenesis


title: TT_H3K4me3_input_rep2

address: 天津市和平区气象台路22号天津医科大学


title: OB4


title: hM1F in MG004, Replicate C


title: hM1F in MG004, Replicate B


title: OB3


title: DKTKRO_70_HNSCC_tumor_HPV-negative


title: hM1F in MG004, Replicate A


title: DKTKRO_66_HNSCC_tumor_HPV-negative


title: hM1F in Ultimatrix, Replicate C


title: DKTKRO_65_HNSCC_tumor_HPV-negative


title: TT_H3K4me3_input_rep1

address: 天津市和平区气象台路22号天津医科大学


title: OB2


title: Pg infected donor bone marrow, western diet fed

city: Edmonton

first: Maria

last: Febbraio

state: AB

department: Dentistry

country: Canada

institute: University of Alberta

data_processing:
The original images obtained from Illumina HiSeq were transformed into sequencing reads by base calling, and these reads were called as  raw data or raw reads, which were saved in fastq format files. These files contain reads information and the corresponding sequencing quality information. Each read has four lines  described in details as follows: The first line begins with a "@", and then illumina sequence identifier as well as other descriptive information (optional). The second line represents read sequence. The third line begins with a "+", and then illumina sequence identifier as well as other descriptive information (optional). In the fourth line, each character's ASCII minus 33 equals base quality of the corresponding read bases.
The raw data high-through sequencing technology was qualified to guarantee the downstream bioinformatics analysis. Novogene uses FastQC to get a basic statistics of the raw reads. To obtain the qualified clean data, raw reads were trimmed to filter out the contaminated adapter sequence and low-quality reads. Trimmomatic is a flexible read trimming tool for Illumina NGS data and the selection of trimming steps and their associated parameters were performed as follows: (1) SLIDINGWINDOW:4:15: A 4-base sliding window trimming, cutting once the average quality within the window falls below a threshold of 15; (2) LEADING:3 and TRAILING:3: Cut bases off the start and end of a read, if below a threshold quality of 3 or containing N. (3) ILLUMINACLIP:2:30:10: Cut adapter and other illumina-specific sequences from the read. Modes: 1. a total 10-base alignment to adapter sequence with 2 mismatches allowed. 2.Palindrome Clip cut the non-overlapped region when the alignment score of overlap part of the read pairs rises above than 30;  (4) MINLEN:36: the minimum read length to be kept is specified as 36 nt; (5) The unpaired reads after trimming are discarded. FastQC was performed on the clean data obtained from trimming.
Bismark software (Krueger, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome. C is transformed to T and G is transformed to A (reverse complementary) in sequence reads and reference genome via Bismark, and then these sequencing reads were aligned to similarly converted versions of the genome separately. The process of Bismark performing alignment is as follows: (1) Perform C-to-T and G-to-A conversions for both sequencing reads and a reference genome; (2) Align converted reads to the converted genome; (3) Choose the best alignment from the parallel four alignment processes and consider it as the final result.
After alignment, Bismark (Krueger, 2011) is used to identify methyalted sites. Firstly, PCR duplicates were removed and then methylation state of cytosines was judged by comparison of reads base and the reference genome base at the same position. If the read base is C, it suggests that this cytosine was methylated; otherwise, it was unmethylated. For the methylated sites, the methylation level was calculated using the following formula: ML=mC/(mC+umC). ML represents the methylation level, and mc and umC represent the number of mythylated and unmethylated cytosines, respectively. Average methylation level of the whole genome in each sample was calculated. Average methylation level of all the covered cytosine sites on each chromosome was calculated. The average methylated level in different cytosine contexts was calculated in different functional genomic regions such as promoter, exon, intron, CGI, CGI shore, repeat (Promoter region defined as the 2kb region upstream of the transcription start site (TSS), 5’UTR, Exon and Intron are obtained from the ensemble structure annotation files).
Supplementary files format and content: bigWig: The raw signal file of all reads

source_name: elicited macrophages

extract_protocol:
DNA was extracted from macrophages using phenol:chloroform and thanol precipitation. DNA samples were tested for degradation and protein contamination by agarose gel electrophoresis and nanodrop, and quantified using Qubit.
After DNA testing for purity and quantification, negative control DNAs were added into the DNAs, and then they were fragmented into 200-300bp using Covaris S220. Next, terminal repairing, followed by A-ligation and then  ligation of methylation sequencing adapters  to the DNA fragments. The DNA library was subjected to Bisulfite treatment (EZ DNA Methylation Gold Kit,  Zymo Research). After bisulfite  treatment,  the fragments were size selected and amplified by PCR.
Library concentration was quantified by Qubit2.0, and then is diluted to 1 ng/ul before checking insert size on Agilent 2100 and then was quantified with more accuracy by Q-PCR(  effective concentration of library >2nM).
After passing Library testing, different libraries were pooled together and then fed into HiSeq devices according to effective concentration and expected data volume. The  sequencing strategy was paired-end sequencing.
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.

value: elicited macrophages

value: Pg-infected

tag: antibodies/tags

value: methylation sequencing adapters


title: Sham-infected donor bone marrow, western diet fed

value: sham


title: OB1


title: DMSO_BRD4

value: DMSO treatment


title: hM1F in MG001, Replicate B


title: hM1F in Ultimatrix, Replicate A


title: DKTKRO_63_HNSCC_tumor_HPV-negative


title: DKTKRO_64_HNSCC_tumor_HPV-negative


title: NC5

value: Normal control


title: hM1F in MG001, Replicate A


title: TT_H3K4me3_IP_rep1

address: 天津市和平区气象台路22号天津医科大学

tag: cell line

value: H460 cells

value: lung cancer


title: M1,replicate 1, scRNAseq

city: Yangzhou

first: Tianfeng

last: Huang

address: 98 Nantong West Road

institute: Northern Jiangsu People's Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Postprocessing and quality control were performed using a 10× Cell Ranger package (v1.2.0; 10 × Genomics). Reads were aligned to the mm10 reference assembly (v1.2.0; 10 × Genomics). sn-RNA seq data (Cellranger_result) contains 4 samples (C1, C2, M1, M2).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: thalamus

extract_protocol:
0.1-0.3 g of brain tissue in each group was washed with 1xPBS (Thermo Fisher), minced and homogenized in a glass homogenizer containing 3 mL of Buffer A (250mM sucrose (Sangong), 10mg/mL BSA (Thermo Fisher), 5mM MgCI2 (Sinopharm), 0.12U/μL RNasin (Promega), 0.06U/mL SUPERasenTM RNase Inhibitor (ThermoFIsher), 1x Protease Inhibitor (CST)), and beat 10 times on ice with a large gap and a small gap pestle in turn. The mixture was filtered through a 100 um cell sieve filter, and the filter was washed twice with 1 mL and 750 uL of Buffer A. After the addition of Triton X-100 (Thermo Fisher), a non-ionic surfactant with a concentration of 0.5%, the mixture was further homogenized in a pestle and whipped 50 times. After the mixture passed through a 35um cell sieve membrane, following steps were performed in sequence: centrifuged at 500 g at 4°C for 5 min in turn, the supernatant was discarded, the pellet was resuspended in 1 mL of citric acid solution (0.25 M sucrose (Sangong), 25 mM citric acid (Sigma), 1ug/mL of Hoechst 33342 (Thermo Fisher)), centrifuged at 500 g at 4°C for 5 min, discarded the supernatant, centrifuged at 3000 g at 4°C for 5 min, resuspend the pellet in 1 mL Buffer B, and centrifuge, resuspended in 200uL Buffer B (320mM sucrose (Sangon), 10 mg/mL BSA (Thermo Fisher), 3mM CaCl2 (Sinopharm), 2mM MgAc2 (Sinopharm), 10mM Tris-HCl (Sigma), 0.1mM EDTA (Sigma), 1mM DTT (Invitrogen), 1 mM DTT (Invitrogen), 0.12U/μL RNasin (Promega), 0.06U/mL SUPERasenTM RNase Inhibitor (ThermoFIsher), 1xProtease Inhibitor (CST)), and centrifuged at 20.000g for 3 min at 4°C. Finally, the pellet was stained with trypan blue (Thermo Fisher) and counted by CountStar.
Single nucleus were run on a 10× Chromium system (10 × Genomics) and then through a library preparation by LC Sciences, following the recommended protocol for the Chromium Single Cell 30 Reagent Kit (v2 Chemistry). Libraries were run on the HiSeq4000 for Illumina sequencing.

treatment_protocol: Coll IV treatment applied to the M samples: Mice were anesthetized with evaporated isoflurane (5% induction, 2% maintenance) and placed in a stereotaxic framework. Under stereotactic guidance, animals were microinjected with Coll IV (Sigma-Aldrich Co., St. Louis, MO; 0.01U/10nl, dissolved in saline solution) into the right VPM and VPL of the thalamus (anterior-posterior-anterior-fontanel-0.82-2.30 mm: posterior 1.30-1.95 mm on the lateral side of the midline, and 3.01-4.25 mm on the ventral side of the skull surface). After administration, the glass micropipette was kept at this position for 10 minutes so that Coll IV could be completely dispersed. Slowly pull out the glass micropipette. After microinjection, the surgical area was perfused with sterile saline and iodophor and closed with a wound clip.

value: thalamus

tag: cell type

value: neuron,glia

value: WT

value: Coll IV


title: DKTKRO_61_HNSCC_tumor_HPV-negative


title: DKTKRO_62_HNSCC_tumor_HPV-negative


title: NC4

value: Mesenchymal stem cells


title: NC3


title: C2,replicate 2, scRNAseq

description: 10x Genomics

tag: genotype

value: saline


title: hM1F in MG001, Replicate C

value: pancreas

tag: treatment


title: hM1F in Cultrex187, Replicate B


title: C1,replicate 1, scRNAseq

description: 10x Genomics


title: NC2


title: NC1


title: zebrafish embryo, 6hpf, rep1

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

description: paired-end sequencing was ribosomal depleted while single-end was polyA selected

data_processing:
Sequence reads were trimmed for adaptor sequence using cutadapt
Trimmed sequence reads were mapped to GRCz11 using STAR
Read count extraction and NTR calculation were performed using GRAND-SLAM
Assembly: GRCz11/102
Supplementary files format and content: tab-delimited text file includes readcount and NTR (%new RNA) for each Sample
Library strategy: SLAM-seq

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA was isolated using tri reagent (Sigma T9424) and quantified using nanodrop
polyA+RNA: Indexed RNA-Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Inc.) according to the manufacturer’s protocol. Libraries were size-selected with SPRI beads and quantified by QuBIT (Life Technologies). Average size of 300 bp was determined by TapeStation (Agilent Technologies, USA). Libraries are then sequenced using an Illumina Nextseq500 sequencer. total-RNA: indexed RNA-Seq libraries for each sample were generated from total RNA using the Illumina RiboZero(Human/Mouse/Rat) kit following the manufacturer’s instructions. Libraries were size-selected with SPRI beads and quantified by QuBIT (Life Technologies). Libraries are then sequenced using an Illumina Novaseq sequencer.

treatment_protocol:
20mM 4sU injection at 1-cell stage
RNA was treated with Iodoacetamide to induce T to C conversions

value: whole embryo

value: AB/TL

value: 4sU injection


title: hM1F in Cultrex187, Replicate A


title: M2,replicate 2, scRNAseq

description: 10x Genomics


title: DKTKRO_57_HNSCC_tumor_HPV-negative

value: negative


title: DKTKRO_60_HNSCC_tumor_HPV-negative


title: DKTKRO_56_HNSCC_tumor_HPV-negative


title: hM1F in Cultrex183, Replicate C


title: zebrafish embryo, 1hpf, rep1


title: 10dpMNU 1

city: Fribourg

first: Anna

last: Jazwinska

address: Chemin du Musée 10

country: Switzerland

institute: University of Fribourg

data_processing:
Alignment, barcode assignation, and generation of cell-gene-count matrices were all performed using cellranger count from 10x genomics version 3.2.0
The GFP transcript sequence was added manually to the reference assembly.
Further processing was performed using Seurat v4 in R.
Assembly: GRCz11
Supplementary files format and content: gene-barcode expression matrix

source_name: retina

extract_protocol:
Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL.
Libraries for scRNA-seq were prepared using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10X Genomics).

value: adult retina

value: 1h treatment with MNU (150mg/L)


title: 10dpMNU 2


title: hM1F in Cultrex187, Replicate C


title: hF24 in Ultimatrix, Replicate C

value: Ultimatrix


title: DKTKRO_55_HNSCC_tumor_HPV-negative


title: hF24 in Ultimatrix, Replicate B


title: DKTKRO_59_HNSCC_tumor_HPV-negative


title: hF24 in Ultimatrix, Replicate A


title: 7dpMNU 2


title: 3dpMNU 2


title: 7dpMNU 1


title: DKTKRO_58_HNSCC_tumor_HPV-negative


title: DKTKRO_53_HNSCC_tumor_HPV-negative


title: hM1F in Cultrex183, Replicate B


title: DKTKRO_54_HNSCC_tumor_HPV-negative


title: DKTKRO_52_HNSCC_tumor_HPV-negative


title: hM1F in Cultrex183, Replicate A


title: hF24 in MG004, Replicate C


title: 3dpMNU 1


title: DKTKRO_51_HNSCC_tumor_HPV-negative


title: hF24 in MG004, Replicate B


title: uninjured 2

value: 1h treatment with heat-inactivated MNU


title: 160125_4400: Sinorhizobium meliloti JOE4400, biological rep3

city: Stanford

first: Melanie

middle: J

last: Barnett

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

hyb_protocol: Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees Celsius for 16 hours, as described by Barnett et al. (2004). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix Scanner 3000 7G

data_processing: The data were analyzed using Partek Genomics Suite 6.6 software, with the following settings: RMA for background correction; quantile normalization; log base 2 transformation; median polish summarization

label: biotin

organism: Sinorhizobium meliloti

source_name: Rm1021 strain expressing mutant JspA E148A from the taurine-inducible plasmid pJC555 (control strain)

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. (2004).

growth_protocol: Starter cultures were grown overnight in PYE medium with 0.5 ug ml-1 oxytetracycline; diluted to ~0.25 to ~0.30 OD-600 in 25 ml of the same medium with 10 mM taurine, in 125-ml flasks; and allowed to grow for 4.5 hours, shaken (250 rpm) at 30°C, to mid-exponential phase (~0.5 to ~0.7 OD-600), with replicates from a single experiment grown to within ~0.1 OD-600 units of each other, prior to harvest.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit, with modifications as described by Barnett et al. (2004) Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees Celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees Celsius until RNA extraction.

tag: genotype/variation


title: hF24 in MG004, Replicate A


title: DKTKRO_50_HNSCC_tumor_HPV-negative

tag: hpv-status


title: 160108_3200: Sinorhizobium meliloti JOE3200, biological rep2

source_name: Rm1021 strain carrying the empty vector, pCM130 (control strain)


title: 160108_4400: Sinorhizobium meliloti JOE4400, biological rep2

value: expressing mutant JspA E148A from the taurine-inducible plasmid pJC555 (control strain)


title: 160106_3200: Sinorhizobium meliloti JOE3200, biological rep1

value: carrying the empty vector, pCM130 (control strain)


title: 160125_3200: Sinorhizobium meliloti JOE3200, biological rep3


title: hF24 in MG001, Replicate C

tag: tissue


title: DKTKRO_49_HNSCC_tumor_HPV-negative


title: 160125_4140: Sinorhizobium meliloti JOE4140, biological rep3

source_name: Rm1021 strain expressing wild-type JspA from the taurine-inducible plasmid pJC535


title: 160106_4400: Sinorhizobium meliloti JOE4400, biological rep1


title: NPCT3

city: Xi’an city

first: Changgeng

last: Song

state: Shaanxi Province

address: 169 Changle Xi Road, Xincheng District

department: Department of Neurology, Xijing Hospital

institute: Fourth Militarty Medical University

data_processing:
Clustering and sequencing. After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase  and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.
Quality control. The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Novel transcripts prediction. The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level. The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis. Differential expression analysis groups was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: Rnor_6.0.97
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Fetus hippocampus

growth_protocol: Fetuses were collected on embryonic day 17 and hippocampi were dissected and placed in ice-cold Ca2+ and Mg2+ -free HEPES-buffered Hank’s salt solution. Dissociated cells were seeded at a density of 40,000 cells / cm2 on plates or cover glasses that had been coated with poly-D-lysine (0.1 mg/ml) and washed with H2O. Hippocampal neuronal cultures were maintained at 37℃ in a 5% CO2/95% air atmosphere and were grown in maintenance medium composed of neurobasal medium supplemented with 2% B27 , glutamine (2 Mm), and penicillin-streptomycin (100 U/ml). Maintenance medium was changed in half volume every other day.

extract_protocol:
RNA was harvested using with the aid of TRIzol reagent (Invitrogen). Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA.Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: Neurons in PCT1, PCT2, and PCT3 were incubated with 1 nM of human PCT for 24 h while neurons in NPCT1, NPCT2, NPCT3 were incubated with 1 nM human NPCT for 24h. Neurons in control1, control2, and control3 were treated with vehicle.

value: Fetus hippocampus

value: Primary hippocampal neurons

value: Stimulated with 1 nM NPCT for 24h at DIV7 and alterations in transcriptome were investigated


title: DKTKRO_48_HNSCC_tumor_HPV-negative


title: hF24 in MG001, Replicate B


title: 160106_4140: Sinorhizobium meliloti JOE4140, biological rep1

value: expressing wild-type JspA from the taurine-inducible plasmid pJC535


title: hF24 in MG001, Replicate A


title: 160108_4140: Sinorhizobium meliloti JOE4140, biological rep2


title: NPCT1

value: WT


title: NaCl+MT seeds, biol rep 2 (miRNA-Seq)

first: Rujia

last: Chen

address: Wenhui

institute: Yangzhou unversity

data_processing:
The generated reads were filtered using fastp, and then mapped onto the reference genome of maize using bowtie
HTSeq software was used to estimate the expression levels of genes
DESeq2 was used to detect differentially expressed miRNAs among three different comparisons.
Assembly: Maize B73 RefGen_v3
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

organism: Zea mays

source_name: seed

extract_protocol:
RNA was harvested using the RNA extraction kit (Tiangen Biotech). 1 ug of total RNA was used for the construction of sequencing libraries.
miRNA libraries for miRNA-seq were prepared using Small RNA Sample Pre Kit following manufacturer's protocols.

value: seed

value: NaCl+MT

tag: Stage

value: seed germination


title: NaCl+MT seeds, biol rep 3 (miRNA-Seq)


title: NPCT2


title: NaCl+MT seeds, biol rep 1 (miRNA-Seq)


title: hF24 in Cultrex187, Replicate C

value: pancreas


title: DKTKRO_47_HNSCC_tumor_HPV-negative

source_name: head and neck tumor


title: NaCl seeds, biol rep 3 (miRNA-Seq)

value: NaCl


title: DKTKRO_46_HNSCC_tumor_HPV-negative

value: negative


title: uninjured 1

value: adult retina


title: DKTKRO_45_HNSCC_tumor_HPV-negative


title: hF24 in Cultrex187, Replicate B


title: PCT3

value: Stimulated with 1 nM PCT for 24h at DIV7 and alterations in transcriptome were investigated


title: PCT2


title: NaCl seeds, biol rep 2 (miRNA-Seq)


title: DKTKRO_44_HNSCC_tumor_HPV-negative


title: hF24 in Cultrex187, Replicate A


title: NaCl seeds, biol rep 1 (miRNA-Seq)


title: PCT1


title: CK seeds, biol rep 3 (miRNA-Seq)

value: CK


title: hF24 in Cultrex183, Replicate C


title: Control3

value: Vehicle control


title: hF24 in Cultrex183, Replicate A


title: CK seeds, biol rep 1 (miRNA-Seq)


title: Control2


title: CK seeds, biol rep 2 (miRNA-Seq)


title: Control1


title: DKTKRO_42_HNSCC_tumor_HPV-negative


title: hF24 in Cultrex183, Replicate B


title: mT69B in Ultimatrix, Replicate C

value: Ultimatrix


title: DKTKRO_41_HNSCC_tumor_HPV-negative


title: SOLINA, 14do, Night, Membrane, Rep3

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

data_processing:
Reads were adapter trimmed using Trim-galore v0.4.1
Mapping was performed using Bowtie2 v2.2.8.9 with normal paired reads and no errors were allowed
Read counts on defined genomic regions were determined using bedtools v.2.25.0
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Genome coverage per nucleotide is included for all the datasets in txt format

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Seeds were stratified in darkness at 4ºC for 48 hours, and for fourteen days-old plants, they grown on soil at 22ºC under white LED light (100 umol m-2 s-1) in 16h/8h day/night Cycle. For four days-old plants they were grown on 0.5X MS plates under continuous light (100 umol m-2 s-1).

extract_protocol:
Five grams of rosette leaves were harvested and rinsed 3 times with ultra-pure water to eliminate soil debris and homogenized in chloroplast enrichment buffer (0.33 M Sorbitol, 30 mM HEPES-KOH (pH 7.5), 0.001% beta-mercaptoethanol) using a blender. The homogenate was filtered through two layers of miracloth, and the flow-through was centrifuged at 1500 g for 5 minutes at 4ºC. The pelleted chloroplasts were resuspended in 1 ml of chloroplast enrichment buffer. Chloroplasts were crosslinked with 4 % Formaldehyde for 4 h
Sequencing libraries were prepared as reported (Bowman, et al. 2013, BMC Genomics, 14:466).

treatment_protocol: Day-treated plants were exposed to reported illumination cycle and collected 2 hours after light treatment. Night treated plants were exposed to total darkness for 24 h prior sample collection

value: Leaf

tag: ecotype

tag: organelle

value: Chloroplast

tag: sample type

value: Membrane

value: wild type

value: Night


title: S_shNAT10_2

city: Chongqing

first: yingfei

last: Long

address: Shuanghulu Street

department: The Third Clinical College

institute: Chongqing Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCh38.p13 human genome
Read count extraction and normalization were performed using RSEM software
GRCh38.p13
Assembly: tab-delimited text files include TPM values for each Sample

source_name: cervical cancer

extract_protocol:
RNA was harvested using Rneasy mini plus kit (VZ6). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: cervical cancer

value: Siha cells

value: knocking down NAT10 gene


title: S_shNC_2

value: control group


title: DKTKRO_40_HNSCC_tumor_HPV-negative

data_processing: Text files were imported into R using the AgiMicroRna Bioconductor package. After quality filtering using Agilent quality filters and removing non-human miRNAs from the data set scanned intensities were background corrected, quantile normalized. The resulting expressions were log2-transformed after averaging signals determining expression of the same miRNA.

extract_protocol: Total RNA including the small RNA fraction was extracted using the Qiagen miRNeasy FFPE (DKTK-ROG) or the AllPrep DNA/RNA FFPE Kit (LMU-KKG) according to the manufacturer's protocols (Qiagen, Hilden, Germany).


title: mT69B in Ultimatrix, Replicate A

value: pancreas


title: DKTKRO_39_HNSCC_tumor_HPV-positive

value: positive


title: DKTKRO_43_HNSCC_tumor_HPV-negative

value: negative


title: S_shNC_1


title: SOLINA, 14do, Night, Stroma, Rep2

value: Stroma


title: DKTKRO_38_HNSCC_tumor_HPV-negative


title: SOLINA, 14do, Night, Stroma, Rep3


title: DKTKRO_36_HNSCC_tumor_HPV-negative


title: SOLINA, 14do, Night, Membrane, Rep2


title: mT69B in Ultimatrix, Replicate B


title: S_shNAT10_1


title: mT69B in MG004, Replicate C


title: H_shNC_1

value: Hela cells


title: H_shNC_2


title: DKTKRO_35_HNSCC_tumor_HPV-negative


title: SOLINA, 14do, Night, Membrane, Rep1


title: mT69B in MG004, Replicate B


title: DKTKRO_37_HNSCC_tumor_HPV-negative


title: SOLINA, 14do, Night, Stroma, Rep1


title: H_shNAT10_2


title: SOLINA, 14do, Day, Membrane, Rep3

value: Day


title: mT69B in MG001, Replicate C


title: mT69B in MG004, Replicate A


title: H_shNAT10_1


title: mT69B in MG001, Replicate B


title: DKTKRO_34_HNSCC_tumor_HPV-negative


title: MCF10DCIS,input,rep1

description: NovaSeq S4-200 Xp

data_processing:
Single-end reads were aligned to hg38 using STAR (v 2.7.7a PMID: 23104886) with “--alignIntronMax 1” to disable spliced alignments. Resulting bam files were sorted using samtools sort (v 1.11 PMID: 33590861).
Peaks were called using cell line match input with MACS2 (v 2.1.1.20160309 PMID: 18798982), narrowPeaks for H3K4me3, H3K4me1 and CTCF and broadPeaks for H3K27ac, H3K27me3, and H3K9me3. Significant peaks were determined using q-value cutoff of 5e-3, with a broad-cutoff of 0.1 for broad peaks.
Fold-enrichment bigwig files were generated using macs2 bdgcmp and UCSC tools bedGraphToBigWig utility (v4 PMID: 20639541).
After pooling replicate bam files us “samtools merge”, peak calls and fold-enrichment bigwigs were also generated on pooled samples.
ChromHMM (v 1.2.4 PMID: 22373907) was used to binarize bam files and learn a 15 state model of the chromatin states using the 5 histone modifications.
Assembly: hg38
Supplementary files format and content: narrowPeak and broadPeak files contain areas of statistically significant enrichment and are produced by MACS2.
Supplementary files format and content: bigwig files contain fold-enrichment profiles.
Supplementary files format and content: chromHMM_model_15.tar contains a 15 state chromHMM model learned on this dataset. chromHMM gzipped bed files contain per cell line segmentation results for this model.

growth_protocol: MCF10A, MCF10AT1, and MCF10DCIS were grown in DMEM/F12 (Corning 10-090-CV) supplemented with 5% horse serum (Gibco 16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882) + 20ng/ml hEGF (PeprotechAF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888), Pen/Strep, and L-Glutamine. MCF10CA1a were grown in DMEM/F12 (Corning 10-090-CV) supplemented with 5% horse serum (Gibco 16050 lot #1075876), Pen/Strep, and L-Glutamine. These cells were all grown in a humidified atmosphere with 5% CO2 at 37oC.

extract_protocol:
ChIP-seq was performed as previously described (O’Geen et al., 2010). We performed independent replicates for MCF10A, MCF10AT1, MCF10DCIS and MCF10CA1a using H3K4me3 (ab8580), H3K4me1 (ab8895), H3K27ac (ab4729), H3K9me3 (ab8898), and H3K27me3 (ab6002).
ChIP-seq libraries were build using NEBNext Ultra II (E7645L) following the manufacturer's instructions.

tag: target

value: input

tag: antibody


title: SOLINA, 14do, Day, Membrane, Rep2


title: SOLINA, 14do, Day, Stroma, Rep3


title: mT69B in Cultrex187, Replicate C

tag: genome assembly


title: DKTKRO_33_HNSCC_tumor_HPV-negative


title: MCF10DCIS,H3K9me3,rep2

description: NovaSeq S4-200 Xp

tag: replicate


title: DKTKRO_32_HNSCC_tumor_HPV-negative


title: mT69B in MG001, Replicate A

tag: organoid


title: DKTKRO_30_HNSCC_tumor_HPV-negative


title: mT69B in Cultrex187, Replicate B


title: SOLINA, 14do, Day, Membrane, Rep1


title: SOLINA, 14do, Day, Stroma, Rep2


title: DKTKRO_29_HNSCC_tumor_HPV-negative


title: mT69B in Cultrex187, Replicate A


title: SOLINA, 14do, Day, Stroma, Rep1


title: SOLINA, 4do, sig6-1, Membrane, Rep3

source_name: Seedling

value: Seedling


title: mT69B in Cultrex183, Replicate C


title: SOLINA, 4do, sig6-1, Stroma, Rep3


title: MCF10DCIS,H3K4me3,rep1

description: NovaSeq S4-200 Xp


title: MCF10DCIS,H3K4me3,rep2

description: NovaSeq S4-200 Xp


title: MCF10DCIS,H3K9me3,rep3

description: NovaSeq S4-200 Xp


title: mT69B in Cultrex183, Replicate B


title: MCF10DCIS,H3K4me1,rep2

description: NovaSeq S4-200 Xp


title: MCF10DCIS,H3K4me1,rep1

description: NovaSeq S4-200 Xp


title: SOLINA, 4do, sig6-1, Stroma, Rep2


title: mT69B in Cultrex183, Replicate A


title: mT69A in Ultimatrix, Replicate C

value: Ultimatrix


title: SOLINA, 4do, sig6-1, Membrane, Rep2

value: Chloroplast


title: DKTKRO_31_HNSCC_tumor_HPV-negative


title: MCF10DCIS,H3K27me3,rep2

description: NovaSeq S4-200 Xp


title: DKTKRO_25_HNSCC_tumor_HPV-negative


title: DKTKRO_26_HNSCC_tumor_HPV-negative


title: DKTKRO_24_HNSCC_tumor_HPV-negative


title: mT69A in Ultimatrix, Replicate B


title: MCF10DCIS,H3K9me3,rep1

description: NovaSeq S4-200 Xp


title: DKTKRO_27_HNSCC_tumor_HPV-negative


title: MCF10DCIS,H3K27me3,rep1

description: NovaSeq S4-200 Xp


title: DKTKRO_28_HNSCC_tumor_HPV-negative


title: SOLINA, 4do, sig6-1, Membrane, Rep1

value: Membrane


title: SOLINA, 4do, sig6-1, Stroma, Rep1


title: DKTKRO_22_HNSCC_tumor_HPV-negative


title: DKTKRO_23_HNSCC_tumor_HPV-negative


title: MCF10DCIS,H3K27ac,rep2

description: NovaSeq S4-200 Xp


title: mT69A in Ultimatrix, Replicate A


title: SOLINA, 4do, sig2-2, Membrane, Rep3


title: MCF10DCIS,H3K27ac,rep1

description: NovaSeq S4-200 Xp


title: MCF10CA1a,input,rep1

description: NovaSeq S4-200 Xp


title: SOLINA, 4do, sig2-2, Stroma, Rep3


title: DKTKRO_21_HNSCC_tumor_HPV-negative


title: mT69A in MG004, Replicate B


title: SOLINA, 4do, sig2-2, Membrane, Rep2


title: DKTKRO_20_HNSCC_tumor_HPV-negative


title: mT69A in MG004, Replicate C


title: MCF10CA1a,H3K9me3,rep2

description: NovaSeq S4-200 Xp


title: mT69A in MG004, Replicate A


title: SOLINA, 4do, sig2-2, Stroma, Rep2


title: DKTKRO_19_HNSCC_tumor_HPV-negative


title: SOLINA, 4do, sig2-2, Membrane, Rep1


title: MCF10CA1a,H3K4me3,rep2

description: NovaSeq S4-200 Xp


title: SOLINA, 4do, sig2-2, Stroma, Rep1


title: MCF10CA1a,H3K9me3,rep1

description: NovaSeq S4-200 Xp


title: mT69A in MG001, Replicate C


title: mT69A in MG001, Replicate B


title: DKTKRO_18_HNSCC_tumor_HPV-negative


title: SOLINA, 4do, Col0, Membrane, Rep3

value: wild type


title: mT69A in Cultrex187, Replicate C


title: mT69A in MG001, Replicate A


title: MCF10CA1a,H3K4me3,rep1

description: NovaSeq S4-200 Xp


title: DKTKRO_14_HNSCC_tumor_HPV-negative


title: SOLINA, 4do, Col0, Stroma, Rep3


title: MCF10CA1a,H3K4me1,rep2

description: NovaSeq S4-200 Xp


title: mT69A in Cultrex187, Replicate B


title: DKTKRO_15_HNSCC_tumor_HPV-negative


title: mT69A in Cultrex187, Replicate A


title: MCF10CA1a,H3K4me1,rep1

description: NovaSeq S4-200 Xp


title: MCF10CA1a,H3K27me3,rep3

description: NovaSeq S4-200 Xp


title: mT69A in Cultrex183, Replicate C


title: MCF10CA1a,H3K27me3,rep2

description: NovaSeq S4-200 Xp


title: DKTKRO_17_HNSCC_tumor_HPV-negative


title: SOLINA, 4do, Col0, Membrane, Rep1


title: SOLINA, 4do, Col0, Stroma, Rep1


title: mT69A in Cultrex183, Replicate B


title: DKTKRO_16_HNSCC_tumor_HPV-negative


title: DKTKRO_12_HNSCC_tumor_HPV-negative


title: MCF10CA1a,H3K27me3,rep1

description: NovaSeq S4-200 Xp


title: mT69A in Cultrex183, Replicate A


title: DKTKRO_11_HNSCC_tumor_HPV-negative


title: MCF10CA1a,H3K27ac,rep2

description: NovaSeq S4-200 Xp


title: Chloroplast, input, Rep4

growth_protocol: Seeds were stratified in darkness at 4ºC for 48 hours, and for fourteen days-old plants, they grown on soil at 22ºC under white LED light (100 umol m-2 s-1) in 16h/8h day/night Cycle.

value: Leaf

tag: fraction


title: Chloroplast, input, Rep3


title: DKTKRO_10_HNSCC_tumor_HPV-negative


title: MCF10AT1,input,rep1

description: NovaSeq S4-200 Xp

tag: cell line


title: DKTKRO_13_HNSCC_tumor_HPV-negative


title: mT9 in Ultimatrix, Replicate A


title: SOLINA, 4do, Col0, Membrane, Rep2


title: mT9 in Ultimatrix, Replicate B


title: DKTKRO_09_HNSCC_tumor_HPV-negative


title: DKTKRO_08_HNSCC_tumor_HPV-negative


title: Chloroplast, input, Rep2


title: SOLINA, 4do, Col0, Stroma, Rep2


title: MCF10CA1a,H3K27ac,rep1

description: NovaSeq S4-200 Xp


title: MCF10AT1,H3K9me3,rep2

description: NovaSeq S4-200 Xp


title: MCF10AT1,H3K4me3,rep2

description: NovaSeq S4-200 Xp


title: DKTKRO_07_HNSCC_tumor_HPV-negative


title: DKTKRO_06_HNSCC_tumor_HPV-negative


title: mT9 in Ultimatrix, Replicate C


title: Chloroplast, IPOD, Rep3

value: IPOD


title: mT9 in MG004, Replicate A


title: DKTKRO_05_HNSCC_tumor_HPV-negative


title: MCF10AT1,H3K9me3,rep1

description: NovaSeq S4-200 Xp


title: mT9 in MG004, Replicate C


title: mT9 in MG004, Replicate B


title: Chloroplast, IPOD, Rep2


title: mT9 in MG001, Replicate C


title: MCF10AT1,H3K4me3,rep1

description: NovaSeq S4-200 Xp


title: Chloroplast, input, Rep1


title: MCF10AT1,H3K4me1,rep2

description: NovaSeq S4-200 Xp


title: DKTKRO_04_HNSCC_tumor_HPV-negative


title: Chloroplast, IPOD, Rep1


title: Chloroplast, Membrane, nox, Rep4

data_processing:
Reads were adapter trimmed using Trim-galore v0.4.1
Mapping and contact calling was made using Juicer
Matrices were generated using Juicer-tools
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Contact matrices are included together in simple triplet format in the txt file

extract_protocol:
Five grams of rosette leaves were harvested and rinsed 3 times with ultra-pure water to eliminate soil debris and homogenized in chloroplast enrichment buffer (0.33 M Sorbitol, 30 mM HEPES-KOH (pH 7.5), 0.001% beta-mercaptoethanol) using a blender. The homogenate was filtered through two layers of miracloth, and the flow-through was centrifuged at 1500 g for 5 minutes at 4ºC. The pelleted chloroplasts were resuspended in 1 ml of chloroplast enrichment buffer. Chloroplasts were crosslinked with 5 mM EGS for 45 min and 4 % Formaldehyde for 4 h
Sequencing libraries were prepared as reported (Bowman, et al. 2013, BMC Genomics, 14:466).

value: Non-crosslinked


title: MCF10AT1,H3K4me1,rep1

description: NovaSeq S4-200 Xp


title: DKTKRO_03_HNSCC_tumor_HPV-negative


title: mT9 in MG001, Replicate B


title: Chloroplast, IPOD, Rep4


title: mT9 in MG001, Replicate A


title: DKTKRO_02_HNSCC_tumor_HPV-negative


title: MCF10AT1,H3K27me3,rep2

description: NovaSeq S4-200 Xp


title: Chloroplast, Membrane, nox, Rep3


title: KKG_102_HNSCC_tumor_HPV-positive


title: mT9 in Cultrex187, Replicate C


title: DKTKRO_01_HNSCC_tumor_HPV-negative


title: Chloroplast, Membrane, nox, Rep2


title: MCF10AT1,H3K27me3,rep1

description: NovaSeq S4-200 Xp


title: mT9 in Cultrex187, Replicate B


title: mT9 in Cultrex187, Replicate A


title: MCF10AT1,H3K27ac,rep2

description: NovaSeq S4-200 Xp


title: Chloroplast, Membrane, nox, Rep1


title: MCF10AT1,H3K27ac,rep1

description: NovaSeq S4-200 Xp


title: KKG_101_HNSCC_tumor_HPV-positive


title: Chloroplast, Membrane, EGS, Rep4

value: EGS, Fa crosslinking


title: KKG_100_HNSCC_tumor_HPV-negative


title: mT9 in Cultrex183, Replicate C


title: Chloroplast, Membrane, EGS, Rep3


title: MCF10A,input,rep1

description: NovaSeq S4-200 Xp


title: KKG_99_HNSCC_tumor_HPV-positive


title: mT9 in Cultrex183, Replicate B


title: KKG_98_HNSCC_tumor_HPV-positive


title: MCF10A,H3K9me3,rep1

description: NovaSeq S4-200 Xp


title: Chloroplast, Membrane, EGS, Rep2


title: mT9 in Cultrex183, Replicate A


title: Chloroplast, Membrane, EGS, Rep1


title: MCF10A,H3K4me3,rep2

description: NovaSeq S4-200 Xp


title: RpoB, input, Night, Rep3

value: Night

tag: chip antibody


title: pancreatic islets_Sorcs2-/-_sample 3

city: Aarhus c

first: Per

last: Qvist

state: Danmark

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

data_processing:
Sequence data were aligned with the mouse genome using STAR version 2.7.8a and gene-level counts for cells in each sample were aggregated into a single count matrix.
Following pre-treatment, 8,846 cells, and 22106 genes were included in the analysis.
Data were normalized using Seurat and data corrected for batch effect using Limma. This was followed by dimensional reduction with UMAP.
Clusters of cells were identified using Seurat and cluster markers determined using Limma.
A multilayered matrix file (Kalnytska_et_al.loom) was exported containing all data.
Assembly: GRCm39
Supplementary files format and content: Loom file containing expression data (raw and normalized) along with cell cluster ID and other data

source_name: isolated pancreatic islets

extract_protocol:
Pancreatic islets from Sorcs2+/+ and Sorcs2-/- mice were isolated using collagenase dissociation method. Pancreatic islets were cultured overnight at 37°C and islets from 3 animals per genotype (~ 400-600 islets per sample) were collected in tubes. Single cell suspension was aquired by exposing pancreatic islet to Accutase with addition of 50 units/ml DNAse-1 for 10 min at 37°C.
scRNA-seq libraries were generated using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10X Genomics Inc., USA). Briefly, a droplet emulsion targeting 10.000 cells was generated in a microfluidic Next GEM Chip G, followed by barcoded cDNA generation inside the droplets. Purified and amplified cDNA was then subjected to library preparation and sequenced on a NovaSeq 6000 instrument (Illumina, USA) to a depth of 40.000 mean read pairs per cell.

value: isolated pancreatic islets

tag: strain

tag: genotype

tag: Sex

value: male


title: MCF10A,H3K4me3,rep1

description: NovaSeq S4-200 Xp


title: RpoB, input, Night, Rep2

tag: treatment


title: KKG_94_HNSCC_tumor_HPV-positive

first: Kristian

last: Unger

institute: LMU University Hospital

tag: hpv-status

value: positive


title: KKG_95_HNSCC_tumor_HPV-positive


title: KKG_96_HNSCC_tumor_HPV-positive


title: pancreatic islets_Sorcs2-/-_sample 1

tag: tissue


title: pancreatic islets_Sorcs2+/+_sample 3


title: MCF10A,H3K4me1,rep2

description: NovaSeq S4-200 Xp


title: MCF10A,H3K4me1,rep1

description: NovaSeq S4-200 Xp


title: RpoB, input, Day, Rep3

tag: ecotype


title: pancreatic islets_Sorcs2+/+_sample 2


title: MCF10A,H3K9me3,rep2

description: NovaSeq S4-200 Xp


title: RpoB, input, Day, Rep2

tag: organelle


title: KKG_93_HNSCC_tumor_HPV-negative

value: negative


title: MCF10A,H3K27me3,rep1

description: NovaSeq S4-200 Xp


title: KKG_97_HNSCC_tumor_HPV-positive


title: KKG_92_HNSCC_tumor_HPV-positive


title: RpoB, ptChIP, Night, Rep3

value: a-RpoB (PhytoAB Cat.:PHY1239 Lot:9321A5)


title: MCF10A,H3K27ac,rep2

description: NovaSeq S4-200 Xp


title: KKG_90_HNSCC_tumor_HPV-negative


title: KKG_91_HNSCC_tumor_HPV-positive


title: pancreatic islets_Sorcs2-/-_sample 2


title: RpoB, input, Day, Rep1

value: Day


title: RpoB, ptChIP, Night, Rep2


title: KKG_88_HNSCC_tumor_HPV-positive


title: WI_38_ETO_10_days

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Cells treated with 50 μM etoposide and collected 10 days later

data_processing:
Pre-processing of sequencing results and generation of count matrices was performed using the Cell Ranger version 5.0.0 (10x Genomics) with prebuilt annotation platform GRCh38.
Subsequent analysis was carried out using the R package Seurat, version 4.1.0 and Velocyto.py (version 0.17).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

growth_protocol: Human primary WI-38 fibroblasts (Coriell Institute) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% FBS, 1% antibiotics, and 1% non-essential amino acids (Gibco).  Cell cultures were maintained in an incubator at 37°C and 5% CO2.

extract_protocol:
Collected cells were counted and single-cell suspensions and subjected to the 10x Genomics Chromium Controller Instrument, for generation of gel bead-in-emulsions (GEMs).
Single-cell libraries were prepared using Chromium Next GEM Single Cell 3ʹ Kits v3.1 with Chip G (10x Genomics).

treatment_protocol: To induce senescence by treatment with ionizing radiation (IR), proliferating (PDL 24) fibroblasts were exposed to 10 Gy, and incubated for an additional 10 days.  For etoposide (ETO)-induced senescence, cells were grown for 10 days in 50 µM etoposide media that was refreshed every 72 h.

tag: cell type

value: human female diploid lung fibroblasts

value: WT

value: Etoposide-induced senescent (50 microM, 10 days)


title: WI_38_ETO_7_days

description: Cells treated with 50 μM etoposide and collected 7 days later

value: Etoposide-induced senescent (50 microM, 7 days)


title: MCF10A,H3K27me3,rep2

description: NovaSeq S4-200 Xp

tag: target


title: MCF10A,H3K27ac,rep1

description: NovaSeq S4-200 Xp

tag: antibody


title: RpoB, ptChIP, Day, Rep3

value: Chloroplast


title: pancreatic islets_Sorcs2+/+_sample 1


title: E17.5_RNA_hs754-humanized_rep4

city: New Haven

first: James

middle: P.

last: Noonan

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University

data_processing:
For ChIP-seq: reads were mapped to either the wild type mouse genome (mm39), or a humanized version in which the mm39 genome was edited to contain the human sequence. Indexes for both genomes were generated from fasta files using bowtie2-build in Bowtie 2 (v2.4.2). ChIP-seq reads were aligned using Bowtie2 with --sensitive and --no-unal settings. Peaks were called using MACS2 (v2.2.7.1) with the default (narrow peak) setting for H3K27ac, H3K4me3, and CTCF, and the --broad setting for H3K27me3. Bigwig files were generated using bamCoverage from deepTools (v3.5.1) using the settings --effectiveGenomeSize 2309746861 --normalizeUsing CPM --binSize 10 --extendReads 300 --centerReads. Effective genome size was calculated using unique-kmers.py from deepTools. Signal in bigwig files represents counts per million (CPM) in 10 bp bins.
For RNA-seq: reads were mapped to mm39 using STAR (2.7.9a) using an index generated using --runMode genomeGenerate with gencode.vM31.basic.annotation.gtf. STAR was then run using --quantMode GeneCounts to output reads counts for each gene.
Assembly: For ChIP-seq: mm39 or hs754-humanized mm39; For RNA-seq: mm39
Supplementary files format and content: bigWig (.bw) files contain ChIP-seq signal data as counts per million in 10-bp bins; bed files (.bed.gz) contain peak coordinates for ChIP-seq experiments; gene count files output by STAR (.ReadsPerGene.out.tab.gz) contain counts per gene as annotated by Gencode (vM31 basic annotation). Counts in each column are unstranded, forward strand, reverse strand.

source_name: diencephalon

extract_protocol:
Tissue from E11.5 or E17.5 diencephalon was snap-frozen, then thawed and homogenized. Each replicate consists of tissue from 3 (at E17.5) or 6 (at E11.5) pooled embryos from the same litter. RNA was collected using the Qiagen miRNeasy Kit (#74106).
Libraries were prepared using polyA selection (Roche Kapa mRNA  Hyper Prep Cat# KR1352) and sequenced (2×150 bp) using standard Illumina protocols on an Illumina NovaSeq 6000.

tag: developmental stage

value: diencephalon


title: E17.5_RNA_wildtype_rep3

value: wild type


title: RpoB, ptChIP, Day, Rep2

value: Leaf


title: KKG_86_HNSCC_tumor_HPV-positive

city: Munich

address: Marchioninistr. 15


title: E17.5_RNA_wildtype_rep4


title: KKG_87_HNSCC_tumor_HPV-positive


title: RpoB, ptChIP, Day, Rep1


title: E17.5_RNA_wildtype_rep2


title: WI_38_ETO_2_days

description: Cells treated with 50 μM etoposide and collected 2 days later

value: Etoposide-induced senescent (50 microM, 2 days)


title: WI_38_ETO_1_days

description: Cells treated with 50 μM etoposide and collected 1 day later

value: Etoposide-induced senescent (50 microM, 1 day)


title: E17.5_RNA_wildtype_rep1


title: E17.5_RNA_hs754-humanized_rep3


title: WI_38_ETO_0_days

description: Cells untreated

value: Proliferating control (DMSO)


title: E17.5_RNA_hs754-humanized_rep1


title: KKG_85_HNSCC_tumor_HPV-positive


title: KKG_84_HNSCC_tumor_HPV-negative


title: WI_38_ETO_replicate_2

description: Cells treated with 50 μM etoposide and cultured for 10 days - replicate 2

value: Etoposide-induced senescent (50 microM)


title: KKG_89_HNSCC_tumor_HPV-positive


title: KKG_83_HNSCC_tumor_HPV-positive


title: E17.5_RNA_hs754-humanized_rep2


title: KKG_81_HNSCC_tumor_HPV-positive


title: E11.5_RNA_wildtype_rep4


title: WI_38_ETO_replicate_1

description: Cells treated with 50 μM etoposide and cultured for 10 days - replicate 1


title: WI_38_ETO_4_days

description: Cells treated with 50 μM etoposide and collected 4 days later

value: Etoposide-induced senescent (50 microM, 4 days)


title: KKG_82_HNSCC_tumor_HPV-positive

value: positive


title: Chloroplast, ATAC, Naked, Rep7

data_processing:
Reads were adapter trimmed using Trim-galore v0.4.1
Mapping was performed using Bowtie2 v2.2.8.9 with normal paired reads and no errors were allowed
Insertion site counts on defined genomic regions were determined using bedtools v.2.25.0
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Genome coverage per nucleotide is included for all the datasets in txt format

extract_protocol:
Five grams of rosette leaves were harvested and rinsed 3 times with ultra-pure water to eliminate soil debris and homogenized in chloroplast enrichment buffer (0.33 M Sorbitol, 30 mM HEPES-KOH (pH 7.5), 0.001% beta-mercaptoethanol) using a blender. The homogenate was filtered through two layers of miracloth, and the flow-through was centrifuged at 1500 g for 5 minutes at 4ºC. The pelleted chloroplasts were resuspended in 1 ml of chloroplast enrichment buffer. Chloroplasts were crosslinked with 4 % Formaldehyde for 4 h
Sequencing libraries were prepared with the Nextera Library-prep kit (Illumina)

value: Naked


title: E11.5_RNA_wildtype_rep3


title: Chloroplast, ATAC, Naked, Rep8


title: Chloroplast, ATAC, Naked, Rep6


title: KKG_79_HNSCC_tumor_HPV-negative

value: negative


title: KKG_80_HNSCC_tumor_HPV-positive


title: WI_38_IR_replicate_2

description: Cells exposed to 10 Gy IR and cultured for 10 days - replicate 2

value: IR-induced senescence (10 Gy)


title: E11.5_RNA_hs754-humanized_rep2


title: E11.5_RNA_hs754-humanized_rep4


title: KKG_78_HNSCC_tumor_HPV-negative


title: Chloroplast, ATAC, Naked, Rep4


title: E11.5_RNA_wildtype_rep2


title: Chloroplast, ATAC, Naked, Rep5


title: WI_38_RS_replicate_1

description: Untreated cells cultured until PDL 57 - replicate 1

value: human female diploid lung fibroblasts

value: Replicative senescence (PDL 57)


title: KKG_77_HNSCC_tumor_HPV-negative


title: Chloroplast, ATAC, Naked, Rep3


title: E11.5_RNA_hs754-humanized_rep3


title: E11.5_RNA_wildtype_rep1


title: A549CC_4C_rep2

city: 天津市

first: Xinyue

last: Lei

address: 天津市和平区气象台路22号天津医科大学

institute: 天津医科大学

data_processing:
The reduced genome was generated by extracting the sequences flanking the HindIII restriction sites (30 bp on each strand from the HindIII restriction sites to downstream) using the hg38 reference human genome, called 4C frag-ends. Non-unique frag-ends are discarded in subsequent analysis.
Subsequently, the highest covered frag-end was removed from the dataset in the normalization process and data are read-depth normalized to 1 million aligned intrachromosomal reads.
A Bioconductor package ‘r3Cseq’ with 2.5 kb sliding window was used to determine significant interactions and calculate interaction difference.
Assembly: hg38
Supplementary files format and content: bedGraph
Library strategy: 4Cseq

extract_protocol:
4C-seq was performed as previously described using EcoR I for the first digestion, and Csp6 I for the second digestion. In brief, cells were cross-linked in 2% formaldehyde for 10 min at room temperature, glycine (V900144, Sigma) was added to a final concentration of 0.2 M to quench the reaction. After crosslinking, cells were rinsed with cold PBS at room temperature twice and incubated in lysis buffer (50 mM Tris-Cl, pH 8.0, 150 mM NaCl, 5 mM EDTA, 0.5% CA630, 0.1% Triton X-100 and protease inhibitor cocktail (04693132001, Roche)) while tumbling for 1 h at 4 ℃. Cells were then pelleted, washed, and resuspended in EcoR I buffer. SDS was added to a final concentration of 0.3% for 1 h in a thermomixer at 37 °C and 900 rpm. Triton X-100 was then added to a final concentration of 1.8% and incubated in a thermomixer at 37 °C and 900 rpm for 3 h. 200 units EcoR I enzyme (New England Biolabs, R3101M) were added for a 4 h incubation in a thermomixer at 37 °C and 900 rpm; another 200 units EcoR I were added for overnight incubation. EcoR I was heat inactivated by incubating at 65 °C for 20 min. Cells were suspended in ligation buffer while 4,000 units of T4 ligase (New England Biolabs, M0202M) were added and incubated more than 8 h at 16 °C and 300 rpm. After ligation, 300 μg Proteinase K were added for overnight incubation at 65 °C and 400 rpm. DNA was purified and digested with 90 units Csp6 I (New England Biolabs, R0639S) and incubated for 5 h in a thermomixer at 25 °C and 500 rpm, followed by heat inactivation of enzyme at 65 °C for 20 min. DNA were then diluted with ligation buffer and 100 units T4 ligase were added for ligation overnight at 16 °C and 300 rpm. The second ligation circularized DNA were purified and amplified using bait-specific inverse primers (29 bp downstream of the rs1663689 and 55bp downstream of the EcoR I site to identify the allele at SNP and unknown DNA sequences interacting with the bait). Primers were extended with dangling Illumina adaptor sequences. After amplification, PCR products were pooled and purified. Sequencing reads were demultiplexed and trimmed of the primer sequence using sabre tool (https://github.com/najoshi/sabre), mapped to the human reference genome (hg38) with Bowtie2 (version 2.2.1) and converted to restriction fragment space. Interactions were called on single 4C experiments with peakC, using a sliding window of 21 fragments.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: lung cancer

value: CC

value: homozygous mutation


title: A549CC_4C_rep1

address: 天津市和平区气象台路22号天津医科大学


title: KKG_76_HNSCC_tumor_HPV-negative


title: Chloroplast, ATAC, Naked, Rep2

value: Chloroplast


title: E17.5_ChIP_input-for-H3K4me3-H3K27me3-CTCF_hs754-humanized_rep3

extract_protocol:
Crosslinked diencephalon tissue from E11.5 or E17.5 was used for nuclei isolation, sonication, and chromatin extraction. Each replicate consists of tissue from 3 (at E17.5) or 6 (at E11.5) pooled embryos from the same litter. Chromatin immunopecipitation was performed with H3K27ac (Active Motif #39133), H3K4me3 (Cell Signaling #9751S), H3K27me3 (Cell Signaling #9733S), or CTCF (Diagenode #C15410210-50) antibody-coated magnetic beads (Protein G Dynabeads, Invitrogen) as described in doi:10.1101/pdb.prot084848.
Libraries were prepared and sequenced (2×150 bp) using standard Illumina protocols on an Illumina NovaSeq 6000.

value: diencephalon

value: none (input control)


title: E17.5_ChIP_input-for-H3K4me3-H3K27me3-CTCF_wildtype_rep3

value: wild type


title: WI_38_RS_replicate_2

description: Untreated cells cultured until PDL 57 - replicate 2

value: WT


title: WI_38_CTRL_replicate_2

description: Untreated cells PDL 24 - replicate 2

value: Proliferating control (PDL 24)


title: E17.5_ChIP_input-for-H3K4me3-H3K27me3-CTCF_hs754-humanized_rep2


title: KKG_73_HNSCC_tumor_HPV-negative


title: KKG_74_HNSCC_tumor_HPV-negative


title: E17.5_ChIP_input-for-H3K4me3-H3K27me3-CTCF_wildtype_rep2


title: A549CC_3 (RNA-seq)

address: 天津市和平区气象台路22号天津医科大学

description: A549(CC) rep 3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie2.
HTseq was used to quantify gene count.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: A549 cells

growth_protocol: A549 (T/T) and A549 (C/C) cells  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA sequencing libraries were prepared using NovaSeq™ 6000 v1.5.

value: A549 cells


title: KKG_72_HNSCC_tumor_HPV-negative


title: E11.5_RNA_hs754-humanized_rep1


title: A549CC_2 (RNA-seq)

address: 天津市和平区气象台路22号天津医科大学

description: A549(CC) rep 2


title: A549TT_4C_rep2

address: 天津市和平区气象台路22号天津医科大学

value: TT


title: KKG_71_HNSCC_tumor_HPV-negative


title: KKG_75_HNSCC_tumor_HPV-positive

value: positive


title: E17.5_ChIP_input-for-H3K4me3-H3K27me3-CTCF_wildtype_rep1


title: KKG_70_HNSCC_tumor_HPV-negative


title: A549CC_1 (RNA-seq)

address: 天津市和平区气象台路22号天津医科大学

description: A549(CC) rep 1


title: E17.5_ChIP_input-for-H3K4me3-H3K27me3-CTCF_hs754-humanized_rep1


title: WI_38_IR_replicate_1

description: Cells exposed to 10 Gy IR and cultured for 10 days - replicate 1


title: Chloroplast, ATAC, Nucleoid, Rep7

value: Leaf

value: Nucleoid


title: Chloroplast, ATAC, Naked, Rep1

value: Naked


title: Chloroplast, ATAC, Nucleoid, Rep8


title: KKG_69_HNSCC_tumor_HPV-negative

value: negative


title: A549TT_4C_rep1

address: 天津市和平区气象台路22号天津医科大学


title: Chloroplast, ATAC, Nucleoid, Rep6


title: KKG_68_HNSCC_tumor_HPV-negative


title: A549TT_3 (RNA-seq)

address: 天津市和平区气象台路22号天津医科大学

description: A549(TT) rep 3


title: A549TT_2 (RNA-seq)

address: 天津市和平区气象台路22号天津医科大学

description: A549(TT) rep 2


title: E17.5_ChIP_CTCF_wildtype_rep3

value: CTCF (Diagenode #C15410210-50)


title: E17.5_ChIP_CTCF_hs754-humanized_rep2


title: KKG_67_HNSCC_tumor_HPV-negative


title: A549TT_1 (RNA-seq)

address: 天津市和平区气象台路22号天津医科大学

description: A549(TT) rep 1

value: lung cancer


title: Chloroplast, ATAC, Nucleoid, Rep4


title: Chloroplast, ATAC, Nucleoid, Rep3


title: Chloroplast, ATAC, Nucleoid, Rep5


title: KKG_65_HNSCC_tumor_HPV-negative


title: E17.5_ChIP_CTCF_wildtype_rep2


title: xmoo1_line_ctrl_3 [1862_21S001282]

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

institute: MPI of Immunobiology and Epigenetics

data_processing:
Bases were called on an Illumina NovaSeq 6000 platform
Reads were aligned with STAR 2.6.1b (Settings: --sjdbOverhang 74 --alignIntronMax 30000, otherwise default)
Cluster raw counts per sample were produced by counting all mapped reads within 15 bases of at least 1 base position with > 5 reads mapped in one replicate
Internal priming was mitigated by blacking out all genomic positions with more than 70% As in a 10-bp upstream window, or > 6 bp of poly-A immediately upstream (blackout sites were not applied for genomic positions within 200 bp of known ensembl TESs)
Assembly: Human GRCh38_ensembl Assembly; Annotation: Ensembl-release-91
Supplementary files format and content: raw cluster expression was observed, no differential expression was assessed

molecule: polyA RNA

source_name: 60 days-old iPSC-derived cerebral organoids

growth_protocol: iPSC-derived cerebral organoids were generated as described in (Giandomenico et al., 2021), with some modifications. Briefly, after dissociation into a cell suspension with accutase, 6,000 cells were seeded per one well of 96-well plates in 100 µl of embryoid body medium (EBM: DMEM/F12, 20% Knockout replacement serum, 1x Glutamax, 1x MEM-NEAA, 2% ESC FBS, 50µM ROCK Inhibitor, 10 µM bFGF). On day four, the medium was replaced with EBM without bFGF and ROCK inhibitor. On day five, the medium was replaced with a neural induction medium (NIM:  DMEM/F12, 1x N2 supplement, 1x Glutamax, 1x MEM-NEAA, 10µg/ml heparin solution). On day 7-9, the formed organoids were embedded into Matrigel (Corning, 356234) and kept in NIM for one day, and in 1:1 NIM: organoid differentiation medium (ODM: 1:1 DMEM/F12: Neurobasal, 1xN2 supplement, 1x B27- vitamin A supplement, insulin, 2-ME solution, Glutamax, MEM-NEAA) for one additional day, followed by four days in ODM. Next, the organoids were transferred to ultra-low attachment 6-well plates and cultured on an orbital shaker (85 rpm) in organoid maturation medium (OMM: 1:1 DMEM/F12: Neurobasal, N2 supplement, B27+ vitamin A supplement, insulin, 2-ME solution, Glutamax supplement, MEM-NEAA, Vitamin C solution, chemically defined lipid concentrate, BDNF, GDNF, cAMP, 1% Matrigel).

extract_protocol:
RNA was purified with TRIzol LS Reagent (Ambion 10296028) according to the manufacturer’s instructions.
Libraries were prepared with 10 ng of total RNA using QuantSeq 3’ mRNA-Seq Library Prep Kit REV (Lexogen) according to manufacturer’s instructions.

treatment_protocol: untreated

value: cerebral organoid

tag: age

value: 60 days


title: KKG_66_HNSCC_tumor_HPV-negative


title: xmoo1_line_ctrl_2 [1862_21S001281]

description: expression was observed, no differential expression was assessed


title: E17.5_ChIP_CTCF_wildtype_rep1


title: E17.5_ChIP_CTCF_hs754-humanized_rep3


title: Chloroplast, ATAC, Nucleoid, Rep2

value: Chloroplast


title: xmoo1_line_ctrl_1 [1862_21S001280]


title: E17.5_ChIP_H3K27me3_hs754-humanized_rep3

value: diencephalon

value: H3K27me3 (Cell Signaling #9733S)


title: H460_C3

address: 天津市和平区气象台路22号天津医科大学

description: H460(CC) rep 3

source_name: H460 cells

value: H460 cells

value: CC

value: homozygous mutation


title: Chloroplast, ATAC, Nucleoid, Rep1

value: wild type


title: KKG_64_HNSCC_tumor_HPV-negative


title: KKG_63_HNSCC_tumor_HPV-negative


title: WT-GFP-Rep2

city: Guangzhou

first: Liang

last: Zhenwei

state: Guangdong

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen University

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.01, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Assembly: TAIR10
Supplementary files format and content: bigwig

source_name: whole seedling

growth_protocol: Plants were grown in 1/2MS media with 22 degree in 16h light/8h dark

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
Two ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction.  Libraries were constructed by the VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (ND607), VAHTSTM DNA Adapters set3 - set6 for Illumina® (N805) and VAHTS® DNA Clean Beads (N411-02, Vazyme) according to the manufacturer’s protocol. protocol. Illumina Novaseq was used for high-throughput sequencing of the ChIP-seq library.

value: whole seedling

value: GFP (ab290, abcam)


title: E17.5_ChIP_H3K27me3_wildtype_rep3


title: KKG_62_HNSCC_tumor_HPV-negative


title: KKG_61_HNSCC_tumor_HPV-negative


title: H460_T3

address: 天津市和平区气象台路22号天津医科大学

description: H460(TT) rep 3

value: TT


title: H460_C2

address: 天津市和平区气象台路22号天津医科大学

description: H460(CC) rep 2


title: E17.5_ChIP_H3K27me3_hs754-humanized_rep2


title: H460_C1

address: 天津市和平区气象台路22号天津医科大学

description: H460(CC) rep 1


title: E17.5_ChIP_CTCF_hs754-humanized_rep1


title: WT-GFP-Rep1


title: E17.5_ChIP_H3K27me3_wildtype_rep2


title: H460_T2

address: 天津市和平区气象台路22号天津医科大学

description: H460(TT) rep 2


title: PKL-GFP val1 val2-IP-Rep1

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.05, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files

source_name: Young seedlings

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
1 ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction.  Libraries were constructed by the VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (ND607), VAHTSTM DNA Adapters set3 - set6 for Illumina® (N805) and VAHTS® DNA Clean Beads (N411-02, Vazyme) according to the manufacturer’s protocol. protocol. Illumina Novaseq was used for high-throughput sequencing of the ChIP-seq library.

tag: genotype/variation

value: val1 val2

tag: develomental stage

tag: condition

value: LD (long day)


title: WT-INPUT


title: H460_T1

address: 天津市和平区气象台路22号天津医科大学

description: H460(TT) rep 1

tag: cell line


title: E17.5_ChIP_H3K27me3_hs754-humanized_rep1

tag: chip antibody

tag: strain


title: PKL-GFP val1 val2-IP-Rep2


title: E17.5_ChIP_H3K27me3_wildtype_rep1

tag: genotype


title: PKL-GFP val1 val2-INPUT


title: E17.5_ChIP_H3K4me3_hs754-humanized_rep3

value: H3K4me3 (Cell Signaling #9751S)