title: HBMEC cells, normal human RBCs, TNF treatment, 24hr, biol rep 2


title: No2.NC.D0_No2.Plate3.B3

status: Public on Sep 30 2023

type: SRA

city: Sendai

first: Kota

last: Sato

state: Miyagi

address: 1-1, Seiryo-machi, Aoba-ku

department: Ophthalmology

country: Japan

institute: Tohoku University

library_source: transcriptomic single cell

data_processing:
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software. Trimmed reads were then mapped to the mouse GRCm38.p6 (mm10) genome with STAR software (version 2.7.2b). Reads on annotated genes were counted using featureCounts (version 1.6.1). FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: retina

extract_protocol:
Total RNA were directly extracted with lysis buffer inculding Rnase inhibitor from single cell sorted with FACS.
RNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology (GO) enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). cDNA synthesis and amplification of RNA derived from lysed cell was sequentially conducted in a same PCR tube. After purification, amplified cDNA was validated and quantified. Following tagmentation of cDNA, adapter addition and PCR amplification were conducted using Nextera XT DNA Library Prep Kit (Illumina).

tag: cell type

value: microglia

tag: tissue

value: retina

tag: genotype

tag: age

value: 20-22 month old

tag: treatment

value: no treatment

tag: strain background

tag: strain


title: FLAG-EED-K19R 0d rep2

city: Macau

first: Gang

last: Li

address: E12 Avenida da Universidade, Taipa, Macau

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

library_source: transcriptomic

data_processing:
Illumina RTA software was used for basecalling and Illumina bcl2fastq 2.17 software was used for demultiplexing.
Illumina Hiseq 2000 reads were quality checked with FastQC v0.11.7.
Reads were trimmed with TrimGalore v0.6.0 to remove low quality ends, adaptor sequence (--stringency5) and reads shorter than 50 bps (for paired end reads).
The pre-processed reads were aligned to the mm10 mouse reference genome using STAR v2.7.0c.
The raw count of genes was quantified using featureCounts v1.6.3 of Subread.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_genename_counts.txt: Tab-delimited text files include raw count values for each sample.

source_name: mouse embryonic stem cells

growth_protocol: Wildtype mESCs, FLAG-EED wildtype and FLAG-EED K19R mutant knock-in mESCs were cultured on gelatin-coated dishes in high-glucose DMEM supplemented with 15% FBS, 1mM sodium pyruvate (Gibco), 1x GlutaMAX (Gibco), 1x nonessential amino acids (NEAA, Gibco), 40 μM β-mercaptoethanol (Acros Organics), 1000 U/ml Leukemia Inhibitory Factor (LIF) (EMD Millipore), 1% Penicillin/Streptomycin (Gibco), with or without 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021) at 37°C in a humidified atmosphere with 5% (v/v) CO2. Embryoid bodies (EBs) were cultured on low-attachment surface plates in differentiation medium and placed in a rotary shaking incubator set to 50 rpm at 37°C with 5% (v/v) CO2 and 85% humidity. in suspension for up to 10 days with medium changes every 2 days.

extract_protocol:
Cells were harvested at desired time points for total RNA isolation using RNeasy Mini kit (Qiagen).
RNA-seq library was prepared using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina.

treatment_protocol: Wildtype mESCs were culture with LIF. FLAG-EED wildtype and FLAG-EED K19R mutant knock-in mESCs were cultured with LIF + 2i. EBs were cultured in differentiation medium without LIF and 2i.

value: embryonic stem cells

value: FLAG-EED K19R mutant

tag: developmental stage

value: day 0

value: culture with LIF + 2i


title: HBMEC cells, P. falciparum-iRBCs, TNF treatment, 8hr, biol rep 1

city: Seattle

first: Ying

last: Zheng

state: WA

address: 1400 NE Campus Parkway

department: Bioengineering

country: USA

institute: University of Washington

data_processing:
RNA-seq data were aligned to the hg38 human genome using TopHat and genes with > 4 rpm were kept for further analysis
Assembly: hg38
Supplementary files format and content: Tab-delimited text files

organism: Homo sapiens

source_name: Human brain microvascular endothelial cells, primary human red blood cells, IT4Var19 Plasmodium falciparum-infected red blood cells

growth_protocol: 3D HBMEC vessels were cultured under perfusion in Lonza EGM-2MV

extract_protocol:
RNA was harvested using RNAeasy micro kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMART-Seq v4 ultra low input RNA kit (Takarabio) following manufacturer instructions

treatment_protocol: Vessels were treated with 10ng/mL TNF for 18 hours prior to blood perfusion. Vessels were perfused with either normal or infected red blood cells for 1 hour following TNF treatment or control

value: Brain endothelial cells, red blood cells

tag: time

value: P. falciparum iRBCs, TNF


title: sn_p2_smrt2_R24

city: Vienna

first: Ruben

last: Gutzat

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute GmbH

description: 1 single nucleus

data_processing:
NextSeq 550 RTA software
data were processed with nf-core/rnaseq (https://github.com/nf-core/rnaseq)
deviation from default pipeline options (star_salmon): parameters for trimming samples 191-210: --clip_r1 19 --clip_r2 9 --three_prime_clip_r1 5 --three_prime_clip_r2 5
counts table was analysed with Deseq2 and p-Values calculated with Wald-test
Genome_build: Tair10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and transposon for every sample

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: seedlings were grown on soil at standard growth conditions (16h light/8h dark) and shoot apices harvested 7 days after germination.

extract_protocol:
nuclei were extracted according to (DOI: 10.1007/978-1-0716-0179-2_7) and either 50 (bulk), 0 (neg control) or 1 single nucleus sorted into a single well.
For samples 1-190: Smart-seq2 single cell protocol (DOI: 10.1038/nmeth.2639). For samples 191-210: Smart-seq3 single cell protocol (according to Hagemann-Jensen et. al, https://doi.org/10.1038/s41587-020-0497-0).

tag: ecotype

tag: developmental age

value: 7 days after germination

value: stem cells


title: No2.NC.D0_No2.Plate3.A5


title: HBMEC cells, normal human RBCs, no treatment, 8hr, biol rep 2


title: FLAG-EED-K19R 0d rep1


title: No2.NC.D0_No2.Plate3.A4


title: sn_p2_smrt2_R22

description: 1 single nucleus


title: No2.NC.D0_No2.Plate3.A3


title: HBMEC cells, normal human RBCs, no treatment, 24hr, biol rep 2


title: sn_p2_smrt2_R23

description: 1 single nucleus


title: FLAG-EED WT EB 10d rep2

source_name: mouse embryoid bodies

value: embryoid bodies

value: FLAG-EED wildtype

value: day 10

value: culture without LIF and 2i


title: HBMEC cells, normal human RBCs, no treatment, 24hr, biol rep 1


title: No2.NC.D0_No2.Plate3.A2


title: FLAG-EED WT EB 10d rep1


title: sn_p2_smrt2_R21

description: 1 single nucleus


title: sn_p2_smrt2_R20

description: 1 single nucleus


title: HBMEC cells, normal human RBCs, no treatment, 8hr, biol rep 1


title: No2.NC.D0_No2.Plate3.A1


title: sn_p2_smrt2_R19

description: 1 single nucleus


title: FLAG-EED WT EB 6d rep2

value: day 6


title: HBMEC cells, P. falciparum-iRBCs, TNF treatment, 24hr, biol rep 1


title: No2.NC.D0_No2.Plate2.C6

value: microglia


title: FLAG-EED WT EB 6d rep1


title: sn_p2_smrt2_R18

description: 1 single nucleus


title: No2.NC.D0_No2.Plate2.C5

value: retina


title: HBMEC cells, normal human RBCs, TNF treatment, 8hr, biol rep 2

value: TNF


title: HBMEC cells, normal human RBCs, TNF treatment, 24hr, biol rep 1


title: FLAG-EED WT EB 2d rep2

value: day 2


title: sn_p2_smrt2_R17

description: 1 single nucleus


title: sn_p2_smrt2_R16

description: 1 single nucleus


title: sn_p2_smrt2_R13

description: 1 single nucleus


title: No2.NC.D0_No2.Plate2.C3

value: 20-22 month old

value: no treatment


title: No2.NC.D0_No2.Plate2.C4


title: No2.NC.D0_No2.Plate2.C1


title: biopsy154P, SP

city: st louis

first: andrew

last: malone

state: MO

address: 4525 laclede ave

institute: Washington University

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

library_source: other

data_processing:
The Illumina NovaSeq S4 XP platform was used to generate paired end read sequence (2x150) on the S4 flow cell to a depth of 50,000 reads per cell for gene expression and 5,000 reads per cell for SP sequence. The Cellranger 6.0 pipeline was used to generate BAM files and gene expression matrices for each biopsy. Matrices were used to generate Seurat objects using Seurat v4
Assembly: GRCh38-2020
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)
Library strategy: CITE-seq

molecule: protein

source_name: kidney transplant biopsy

extract_protocol:
cDNA libraries were prepared per 10X Chromium standard protocol usig 5-prime kits
single cell CITE-seq

value: kidney transplant biopsy

tag: library type

value: ADT

tag: antibodies/tags

tag: diagnosis

value: TCMR


title: No2.NC.D0_No2.Plate2.B5


title: Wildtype mESCs rep1

value: embryonic stem cells

value: wildtype

value: undifferentiated

value: culture with LIF


title: sn_p2_smrt2_R11

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: sn_p2_smrt2_R15

description: 1 single nucleus


title: No2.NC.D0_No2.Plate2.B6


title: sn_p2_smrt2_R12

description: 1 single nucleus


title: Wildtype mESCs rep2


title: sn_p2_smrt2_R14

description: 1 single nucleus


title: FLAG-EED WT 0d rep1

value: FLAG-EED wildtype

value: day 0

value: culture with LIF + 2i


title: HBMEC cells, normal human RBCs, TNF treatment, 8hr, biol rep 1

value: Brain endothelial cells, red blood cells


title: FLAG-EED WT 0d rep2


title: sn_p2_smrt2_R10

description: 1 single nucleus


title: biopsy154E, SP


title: No2.NC.D0_No2.Plate2.C2

value: microglia

value: retina


title: FLAG-EED WT EB 2d rep1

value: embryoid bodies

value: day 2

value: culture without LIF and 2i


title: No2.NC.D0_No2.Plate2.B3

value: 20-22 month old

value: no treatment


title: biopsy143E, SP

value: kidney transplant biopsy

value: ADT

value: TCMR


title: HiC_JK06_1hrauxin_L3_rep1b [JK155b]

city: New York

first: Jun

last: Kim

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

library_source: genomic

data_processing:
ChIP-seq: Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 or its variants based on perturbation with default parameters (Langmead and Salzberg, 2012). Bam sorting and indexing was performed using samtools version 1.11 (Danecek et al., 2021). BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage and ChIP/Input ratios with a bin size of 10 bp and 200 bp read extension (Ramírez et al., 2016). Reads with a minimum mapping quality of 1 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed (Amemiya et al., 2019). For DPY27 ChIP-seq data, the ratio values are used to rescale the data such that autosomes have mean of 0 and X-chromosome has mean of 1.
Hi-C:  data was mapped to ce10 (WS220) reference genome or its variant that corrosponds to the perturbation using default parameters of the Juicer pipeline version 1.5.7 (Durand et al., 2016).
Assembly: WS220 or its variants based on rex insertion or chromosome fusion
Supplementary files format and content: ChIP-seq: input normalized bigwigs
Supplementary files format and content: Hi-C:  hic matrix files

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C. L3 worms were kept on plates with or without auxin prior to collection.

extract_protocol:
ChIP-seq: L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
Hi-C: Crosslinked worms were resuspended in 20 ul of PBS per 50ul of worm pellet then dripped into liquid nitrogen containing mortar. The worms were grounded with pestle until fine powder. Grounded worms were crosslinked again in 2% formaldehyde using the TC buffer as described by the Arima High Coverage Hi-C kit, which uses four 4-base cutters. The Arima manufacturer’s protocol was followed.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.
Hi-C: Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.


title: biopsy143P, SP


title: HiC_JK06_1hrauxin_L3_rep1a [JK155a]


title: HiC_JK06_1hrauxin_L3_rep2 [JK181]


title: biopsy150P, SP

value: mixed rejection


title: No2.NC.D0_No2.Plate2.B4


title: biopsy142, SP


title: sn_p2_smrt2_R9

description: 1 single nucleus

value: 7 days after germination


title: HiC_JK05_1hrauxin_L3_rep2 [JK180]


title: biopsy140, SP

value: ABMR


title: sn_p2_smrt2_R8

description: 1 single nucleus

value: stem cells


title: No2.NC.D0_No2.Plate2.B2


title: sn_p2_smrt2_R7

description: 1 single nucleus


title: No2.NC.D0_No2.Plate2.A6


title: biopsy138, SP


title: biopsy154P, GEX

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

molecule: polyA RNA

value: mRNA


title: No2.NC.D0_No2.Plate2.A4


title: No2.NC.D0_No2.Plate2.A5


title: sn_p2_smrt2_R5

description: 1 single nucleus


title: sn_p2_smrt2_R6

description: 1 single nucleus


title: biopsy150P, GEX


title: HiC_JK05_1hrauxin_L3_rep1 [JK153]


title: NF-κB1C59S  rep2

city: Guangzhou

first: Tan

middle: xiao

last: Zhang

address: Huang pu street

country: China

institute: First Affiliated Hospital of Jinan University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp 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 ploy-N 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.
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.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: kidney

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: kidney

value: NF-KB1C59S (inactivated)


title: NF-κB1C59S  rep3


title: sn_p2_smrt2_R4

description: 1 single nucleus


title: biopsy150E, GEX


title: sn_p2_smrt2_R3

description: 1 single nucleus


title: No2.NC.D0_No2.Plate2.A3

value: microglia


title: biopsy154E, GEX


title: NF-κB1C59S  rep1


title: FABP7 KO mice with MC38 metastatic

first: shaowan

last: xu

state: Guangdong

address: Jingxi

institute: southern medical university

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Ensembl release 104
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

growth_protocol: MC38 cells were maintained at 37 °C and 5% CO2

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA).
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina NovaSeq 6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: 500,000 MC38 cells were splenic injection into WT and FABP7 KO mice in 100ul PBS, and at day 10 post-inoculation, the macrophages were isolated from the liver of WT and FABP7 KO mice with metastatic.

value: liver

value: macrophage

value: FABP7 knockdown

value: MC38 metastatic


title: WT mice with MC38 metastatic

value: WT


title: No2.NC.D0_No2.Plate2.B1

value: retina

value: 20-22 month old

value: no treatment


title: sn_p2_smrt2_R2

description: 1 single nucleus


title: biopsy143P, GEX

value: kidney transplant biopsy

value: TCMR


title: No2.NC.D0_No2.Plate2.A1


title: NF-κB1C59A  rep3

value: NF-KB1C59A (activated)


title: biopsy150E, SP

value: ADT

value: mixed rejection


title: biopsy143E, GEX

value: mRNA


title: No2.NC.D0_No2.Plate1.C6


title: sn_p1_smrt2_R93

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: sn_p2_smrt2_R1

description: 1 single nucleus


title: biopsy142, GEX


title: No2.NC.D0_No2.Plate2.A2

value: microglia


title: No2.NC.D0_No2.Plate1.C5


title: No2.NC.D0_No2.Plate1.C4


title: WT rep3

value: kidney


title: NF-κB1C59A  rep1


title: No2.NC.D0_No2.Plate1.C3


title: biopsy138, GEX


title: WT rep2


title: sn_p1_smrt2_R91

description: 1 single nucleus


title: sn_p1_smrt2_R92

description: 1 single nucleus


title: No2.NC.D0_No2.Plate1.C2


title: biopsy140, GEX

value: ABMR


title: WT rep1


title: sn_p1_smrt2_R90

description: 1 single nucleus


title: biopsy118, SP

data_processing:
The Illumina NovaSeq platform was used to generate paired end read sequence (2x150) on the S4 flow cell to a depth of 50,000 reads per cell for gene expression and 5,000 reads per cell for SP sequence. The Cellranger 4.0 pipeline was used to generate BAM files and gene expression matrices for each biopsy. Matrices were used to generate Seurat objects using Seurat v4
Assembly: GRCh38-2020
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)
Library strategy: CITE-seq

tag: time post transplant

value: abmr


title: sn_p1_smrt2_R89

description: 1 single nucleus


title: No2.NC.D0_No2.Plate1.C1


title: NF-κB1C59A  rep2


title: sn_p1_smrt2_R87

description: 1 single nucleus


title: biopsy117, SP


title: No2.NC.D0_No2.Plate1.B6


title: biopsy116p, SP


title: No2.NC.D0_No2.Plate1.B5


title: sn_p1_smrt2_R86

description: 1 single nucleus


title: biopsy116e, SP


title: No2.NC.D0_No2.Plate1.B4


title: sn_p1_smrt2_R85

description: 1 single nucleus


title: No2.NC.D0_No2.Plate1.B3


title: biopsy103e, SP

value: non-rejection


title: sn_p1_smrt2_R83

description: 1 single nucleus


title: No2.NC.D0_No2.Plate1.B2


title: biopsy119, GEX


title: biopsy103p, SP


title: PyMT_Yohan_1

city: France

first: Julie

last: Helft

email: gerber.helft@gmail.com, julie.helft@inserm.fr, jason.cosgrove@curie.fr, yoann.missolo-koussou@curie.fr, yohan.gerber@curie.fr

address: 26 Rue D'ulm

country: France

institute: Institut Curie

description:
HSPC_SC_counts.csv
HSPC_SC_metadata.csv

data_processing:
[scRNAseq] The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0.
[Bulk RNAseq] Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore!
[Bulk RNAseq] The raw sequencing data was initially aligned on the murine reference genome mm10, using STAR aligner (v2.5.3a) (Dobin et al., 2013). Raw read counts matrix was made with STAR (using the parameter –quantMode Gene- Counts).
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes metadata and cluster informations

source_name: BONE MARROW

extract_protocol:
RNA was extracted and isolated using the Single Cell RNA purification kit (Norgen) according to the manufacturer’s instructions for bulk RNAseq experiments. For single cell experiments, sorted cells were loaded on a Chromium Controller using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 according to manufacturer’s instructions.
RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech/Takara) for bulk RNAseq and  Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v2 or v3 Reagent Kit (10x Genomics) according to manufacturer’s protocol.

value: BONE MARROW

value: Hematopoietic stem and progenitor cells

value: WT mouse


title: PyMT cells

value: Bone marrow stromal cells

value: PyMT mouse


title: PyMT_Yohan_3

description:
HSPC_SC_counts.csv
HSPC_SC_metadata.csv


title: No2.NC.D0_No2.Plate1.B1

value: retina

value: 20-22 month old

value: no treatment


title: WT cells


title: sn_p1_smrt2_R82

description: 1 single nucleus


title: PyMT_Yohan_2

description:
HSPC_SC_counts.csv
HSPC_SC_metadata.csv


title: biopsy119, SP

value: kidney transplant biopsy

value: ADT


title: No2.NC.D0_No2.Plate1.A6


title: biopsy118, GEX

value: mRNA


title: MSC_Py230_3

value: Mesenchymal stem cells

value: Tumor-bearing


title: sn_p1_smrt2_R81

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: MSC_Py230_4


title: biopsy117, GEX

value: abmr


title: biopsy116p, GEX


title: MSC_Py230_1


title: No2.NC.D0_No2.Plate1.A4

value: microglia


title: No2.NC.D0_No2.Plate1.A5


title: MSC_Py230_2

value: BONE MARROW


title: sn_p1_smrt2_R80

description: 1 single nucleus


title: sn_p1_smrt2_R79

description: 1 single nucleus


title: biopsy116e, GEX


title: No2.NC.D0_No2.Plate1.A3


title: sn_p1_smrt2_R78

description: 1 single nucleus


title: biopsy103p, GEX

value: non-rejection


title: No2.NC.D0_No2.Plate1.A2


title: MSC_Ctrl_4

value: Tumor-free


title: MSC_Ctrl_3


title: sn_p1_smrt2_R77

description: 1 single nucleus


title: biopsy103e, GEX


title: MSC_Ctrl_2


title: No2.NC.D0_No2.Plate1.A1


title: sn_p1_smrt2_R76

description: 1 single nucleus


title: HDMEC, DFU, sample4

first: Hengyu

last: Du

address: Huangpu Road West 601

institute: Department of Plastic Surgery of the First Affiliated Hospital of Jinan University

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China).
Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for DEGs in each Sample

source_name: skin

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: skin

value: HDMECs

tag: disease state

value: diabetic foot ulcer


title: sn_p1_smrt2_R75

description: 1 single nucleus


title: PA->SED HSCs (biol rep2) [12]

city: WORCESTER

first: Lyne

last: Khair

state: MA

address: 368 PLANTATION STREET

department: SURGERY

institute: UMASS MEDICAL SCHOOL

description: DEBrowser data PA and PA-SED (4,6,P4,11,12,PS4) .csv

data_processing:
DEBrowser v1.22.5a
Sequence reads were trimmed for adaptor sequence/low-quality sequence using DEBrowser
Trimmed sequence reads were mapped to mm10 using DEBrowser genomic benchwork
Read count extraction and normalization were performed using DEBrowser genomic benchwork
Assembly: mm10
Supplementary files format and content: csv files include read counts for each sample and list gene names

source_name: hematopoietic stem cells

extract_protocol:
RNA was isolated from freshly sorted HSCs using the RNAqueous™-Micro Total RNA Isolation Kit (Invitrogen) according to manufacturer’s instructions.
RNA was extracted from mouse mammary tumors using the TRIzol method.
Library preparation was performed using TruSeq Stranded mRNA Sample Prep Kit (Cat# 20020594, Illumina) according to manufacturer’s instruction.

value: hematopoietic stem cells

value: MMTV-PyMT

value: Sedentary transplanted with cells from physically active mouse


title: PA->SED HSCs (biol rep3) [PS4]


title: MSC_Ctrl_1


title: HDMEC, DFU, sample3


title: sn_p1_smrt2_R74

description: 1 single nucleus


title: HDMEC, DFU, sample2


title: PA->SED HSCs (biol rep1) [11]


title: Nrp1low ILC2s-3

city: Tianjin

first: Jie

last: Zhou

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: lung

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: lung

value: Nrp1low ILC2s

value: wild type

value: IL-33 treatment


title: Nrp1low ILC2s-2


title: sn_p1_smrt2_R73

description: 1 single nucleus

value: 7 days after germination


title: PA HSC week12 (biol rep3) [P4]

description: DEBrowser data SED and PA (1,3,S4,4,6,P4) .csv

value: Physically active

value: Week 12


title: HDMEC, DFU, sample1


title: sn_p1_smrt2_R72

description: 1 single nucleus

value: stem cells


title: Nrp1low ILC2s-1


title: Nrp1high ILC2s-3

value: Nrp1high ILC2s


title: PA HSC week12 (biol rep2) [6]


title: HDMEC, Control, sample4

value: non-diabetic


title: sn_p1_smrt2_R71

description: 1 single nucleus


title: HDMEC, Control, sample3


title: Nrp1high ILC2s-2


title: HDMEC, Control, sample2


title: SED HSC week12 (biol rep3) [S4]

value: Sedentary


title: sn_p1_smrt2_R70

description: 1 single nucleus


title: PyMT_Yohan_4

description:
HSPC_SC_counts.csv
HSPC_SC_metadata.csv

value: BONE MARROW

value: Hematopoietic stem and progenitor cells

value: PyMT mouse


title: Nrp1high ILC2s-1


title: HDMEC, Control, sample1

value: skin

value: HDMECs


title: sn_p1_smrt2_R69

description: 1 single nucleus


title: SED HSC week12 (biol rep2) [3]

value: hematopoietic stem cells

value: MMTV-PyMT


title: leukemia cell line FTY720 (5uM) 24hr biol rep3

city: London

first: Maria Teresa

last: Esposito

address: Holybourne Avenue

department: School of life and health

country: United Kingdom

institute: Centre for integrated research in  life and health

data_processing:
The RNA seq in FTY720 vs vehicle treated THP1 was performed by Novogene. Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software. Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5) [18 ]. STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads. HTSeq v0.6.1 was used to count the read numbers mapped of 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, Reads Per Kilobase of exon model per Million mapped reads, 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 [19]. Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3) [20, 21]. 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(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor [22]. Differential expression analysis of two conditions was performed using the edgeR R package (3.16.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 1 were set as the threshold for significantly differential expression. The Venn diagrams were prepared using the function venn Diagram in R based on the gene list for different group. Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the cluster Profiler R package, in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes.  KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/) [23]. We used cluster Profiler R package to test the statistical enrichment of differential expression genes in KEGG pathways [24]. PPI analysis of differentially expressed genes was based on the STRING database, which contained known and predicted Protein-Protein Interactions. For the species existing in the database (like human and mouse), we constructed the networks by extracting the target gene lists from the database.
Supplementary files format and content: Counts, differential gene expression FTY720 vs DMSO.

source_name: peripheral blood

growth_protocol: RPMI 1620 +10% FSB+ 1% pen/strept

extract_protocol:
extraction of total RNA by column Bioline kit
mRNA library preparation (polyA enrichment)

treatment_protocol: 5 uM FTY720 or DMSO for 24hr

value: peripheral blood

tag: cell line

value: monocyte

value: KMT2A translocation


title: SED HSC week12 (biol rep1) [1]

tag: cell type


title: HC

city: Beijing

first: Jia

last: Song

state: China

address: Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
The Cell ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 3.2.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 4000 or less than 600, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with NormalizeData function.
Harmony algorithm was used to integrate data.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: lymph node

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

tag: tissue

value: lymph node

value: Murine CD8+ T cells


title: sn_p1_smrt2_R67

description: 1 single nucleus

value: 7 days after germination


title: sn_p1_smrt2_R66

description: 1 single nucleus

value: stem cells


title: leukemia cell line FTY720 (5uM) 24hr biol rep2

tag: genotype


title: MP PA tumor week18 (biol rep3) [P18-3]

description: DEBrowser data S18-P18.csv

source_name: mammary tumor

value: mammary tumor

value: Physically active

value: Week 18


title: leukemia cell line FTY720 (5uM) 24hr biol rep1


title: MP PA tumor week18 (biol rep2) [P18-2]

description: DEBrowser data S18-P18.csv


title: MP PA tumor week18 (biol rep1) [P18-1]

description: DEBrowser data S18-P18.csv


title: PA HSC week12 (biol rep1) [4]

value: Week 12


title: leukemia cell line vehicle (DMSO) 24hr biol rep3

value: vehicle


title: sn_p1_smrt2_R64

description: 1 single nucleus


title: sn_p1_smrt2_R65

description: 1 single nucleus


title: leukemia cell line vehicle (DMSO) 24hr biol rep2


title: MP SED tumor week18 (biol rep3) [S18-3]

description: DEBrowser data S18-P18.csv

value: Sedentary


title: sn_p1_smrt2_R63

description: 1 single nucleus


title: HLF_KO_28Mono

city: Tübingen

first: Nikita

last: Popov

address: Otfried-Müller-Str 14

department: Clinical Tumor Biology

country: Germany

institute: University Hospital Tübingen

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 instrument (1 x 100 bp)
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2).
Reads were aligned to human genome (hg19) with STAR (2.5.4) and differentially expressed genes were determined using EdgeR (3.26.8).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files (EdgeR output) include differential expression (log2FC) and average logCPM values for each pair of samples

source_name: HLF

growth_protocol: HLF cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1% non-essential amino acids and 1% Pen-Strep in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRIzol reagent (Sigma). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following manufacturer's protocol.

value: HLF

value: hepatocellular carcinoma

value: Ctrl

value: sgUsp28, pRRL-Usp28-Mono


title: leukemia cell line vehicle (DMSO) 24hr biol rep1

value: peripheral blood


title: sn_p1_smrt2_R62

description: 1 single nucleus


title: sn_p1_smrt2_R68

description: 1 single nucleus


title: MP SED tumor week18 (biol rep2) [S18-2]

description: DEBrowser data S18-P18.csv

value: MMTV-PyMT


title: MP SED tumor week18 (biol rep1) [S18-1]

description: DEBrowser data S18-P18.csv


title: WT3-M2

city: shanghai

first: jiang

last: qi

address: No. 320 Yueyang Road, Xuhui District

institute: university of chinese academy of sciences

data_processing:
Original sequence data statistics and quality control.
Comparison with reference genomes.
Expression quantity analysis.
Differentially expression analysis.
GO and KEGG enrichment analysis of differential genes.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2 or DEGseq. DEGs with |log2FC| ≧ 1 and FDR≤ 0.05 (DESeq2) or FDR ≤0.001 (DEGseq) were considered to be significantly different expressed genes.
Assembly: not provided
Supplementary files format and content: Excel file includes TPM values.

source_name: peritoneal macrophages

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according to the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, > 1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The XX RNA-seq transcriptome library was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly, double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150bp read length).
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.

value: peritoneal macrophages

value: WT


title: cKO2-M2

value: Fbxo38 cKO


title: WT2-M2


title: cKO1-M2


title: sn_p1_smrt2_R61

description: 1 single nucleus

value: 7 days after germination


title: cKO3-M2


title: HLF_KO_28WT

value: sgUsp28, pRRL-Usp28-WT


title: NC

value: lymph node

value: Murine CD8+ T cells


title: sn_p1_smrt2_R60

description: 1 single nucleus

value: stem cells


title: HLF_KO_Ctrl

description:
HLF_KO_Usp28WT_Ctrl.txt
HLF_KO_Usp28Mono_Ctrl.txt

value: sgUsp28, pRRL-Ctrl


title: sn_p1_smrt2_R88

description: 1 single nucleus


title: sn_p1_smrt2_R59

description: 1 single nucleus


title: HLF_28KO


title: HLF_Ctrl

value: sgCtrl


title: sn_p1_smrt2_R58

description: 1 single nucleus


title: MP PA tumor week12 (biol rep1) [P12-1]

description: DEBrowser data S12-P12.csv

value: mammary tumor

value: Physically active

value: Week 12


title: WT1-M2


title: sn_p1_smrt2_R57

description: 1 single nucleus


title: D_V_05

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

data_processing:
Raw read data in FASTQ format were processed through fastp to remove adaptor sequences and low-quality sequences.
Trimmed sequence reads were mapped to the mouse genome mm10 using STAR (v2.5, mismatch=2) and quantified using HTSeq (v0.6.1, -m union).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including read counts of genes for each sample

source_name: aorta

extract_protocol:
RNA was extracted using Rneasy fibrous tissue mini kits (Qiagen, #74704). 1 ug of total RNA was used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA library prep kits for Illumina (NEB) following manufacturer's protocols.

treatment_protocol: Aortic samples were harvested from C57BL/6J mice administered with either water or BAPN for 1 week.

value: Water

value: aorta


title: D_V_03


title: MP SED tumor week12 (biol rep2) [S12-2]

description: DEBrowser data S12-P12.csv

value: Sedentary


title: D_V_02


title: D_V_04


title: HNRNPD_3FHBH_IP

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

description: HNRNPD bound RNA

data_processing:
For circRNA detection, we used CIRI2 (V2.0.6) pipeline to identify circRNAs. Adapters and low-quality reads were trimmed by trim_galore to obtain clean reads. Then we aligned the reads to the human reference genome (hg19) by bwa mem. The reads with continuous alignment to the reference genome were excluded, while the remaining reads were used for detecting circRNAs by CIRI2. Gencode.v19 was provided to CIRI2 to annotate circRNAs. EdgeR was used to identify differentially expressed circRNAs.
For HNRNPD binding sites analysis, we remove the universal adaptor sequences from the left side of reads with bbduk.sh. Furtherly, we used cutadapt to trim adaptor sequences from both sites of reads to get clean data. We then performed umi_tools to extract 12 nt from 3’ end of sequencing reads to assign as UMI (Unique Molecular Identifiers) tags for every read, accompanied by removing UMI sequences from reads. Reads with UMI tags were aligned to the Repbase database to remove suspicious reads that mapped to repetitive DNA. The remaining reads were aligned to the human genome (hg19) with STAR to get a bam format file. We next used dedup inside umi_tools to group PCR duplicates and deduplicate reads to yield one read per group. The clipper software was used to define binding peaks for HNRNPD. The peaks were annotated by Gencode.v19 with R.
For nascent circRNA detection, we used CIRI2 (V2.0.6) pipeline to identify circRNAs. Adapters and low-quality reads were trimmed by trim_galore to obtain clean reads. Then we aligned the reads to the human reference genome (hg19) by bwa mem. The reads with continuous alignment to the reference genome were excluded, while the remaining reads were used for detecting circRNAs by CIRI2. Gencode.v19 was provided to CIRI2 to annotate circRNAs. EdgeR was used to identify differentially expressed circRNAs.
For nascent mRNA visualization, sequencing reads were trimmed for adaptor sequence/low-quality sequence using trim_galore. Clean reads were mapped to the human reference genome (hg19) by hisat2 to get bam format files. Bam files from replicates were merged to get combined ones. We then used deeptools to convert bam format into bigWig format, normalizing IP samples with Input by bamCompare in both KO and WT, and finally visualize expression levels of parent mRNA of differentially expressed circRNA.
Assembly: hg19
Supplementary files format and content: bigWig, tab-delimited text files

extract_protocol:
For circRNA-sequencing, RNA was extracted with Trizol. For FLASH-sequencing, the HEK293T_HNRNPD_3FHBH cells were crosslinked by UV irradiation. After a series of operations (harvested, lysed, sonicated, and immunoprecipitated), the cells were fixed with 90% ethanol and linked up with azide-labeled biotin in the click reaction solution (DPBS, 2.5 mM biotin-azide, 3 mM CuSO4, 6 mM Tris(3-hydroxypropyltriazolymethyl) amine, 10 mM aminoguanidine and 50 mM sodium L-ascorbate). Then the cells were washed with DPBS (containing 0.5% Triton X-100 and 2 mM EDTA) and DPBS. Discarding the DPBS, the cells were transferred into a 1.5 ml tube and suspended with lysis buffer (20 mM Tris-Cl (pH 7.5), 500 mM LiCl, 1 mM EDTA, 0.5% lithium-dodecylsulfate, 5 mM DTT, and 0.1 U/µl RNase inhibitor) on the ice and homogenized through a syringe with a 0.4 mm diameter-needle 5 times. The nascent RNAs were immunoprecipitated with streptavidin-conjugated magnetic beads. Finally, the magnetic beads were washed with washing buffer and isolated from magnetic beads by RNA elution buffer (10 mM EDTA (pH 8.2) and 95% formamide), and digested with proteinase K. The nascent RNAs were extracted with Trizol reagent.
For circRNA detection, samples were digested by RNase R  to remove linear transcripts after ribosomal RNA (rRNA) depletion. Strand-specific libraries (also known as stranded/directional libraries) were prepared.    For FLASH-sequencing, the immunoprecipitated RNA-HNRNPD complex was digested by RNaseI and TURBO DNase, followed by dephosphorylation. The complex was ligated with an s-oligo using T4 RNA ligase I, which was also followed by dephosphorylation. The complex was resuspended with proteinase K digestion buffer to release crosslinked RNA, and column purification (Zymo DNA Clean and Concentrator). The purified RNA was executed reverse transcription with SuperScript III, and column purification. The cDNA was then circularized with CircLigase. The cyclized cDNA was the template of PCR reaction with NEBNext High-Fidelity Master Mix. Then the PCR products were cleaned up with l.5 X AM pure beads.  For RIP-sequencing, the Illumina Ribo-Zero Gold kit removed rRNA, and surplus RNA was purified for end repair and 50-adaptor ligation. Reverse transcription was performed with random primers containing 3’ adaptor sequences. Finally, the cDNAs were purified and amplified with PCR reactions. The products with lengths of 300-500 were purified and quantified. These libraries were utilized for 150 nt paired-end sequencing with an Illumina Nova seq 6000 system (Novogene, China).

value: Human Embryonic Kidney Cell

value: HNRNPD_3FHBH konck in


title: sn_p1_smrt2_R56

description: 1 single nucleus


title: MP SED tumor week12 (biol rep1) [S12-1]

description: DEBrowser data S12-P12.csv

value: MMTV-PyMT


title: GFP_3FHBH_IP

description: HNRNPD bound RNA

value: GFP_3FHBH overexpression


title: D_B_05

value: BAPN


title: UMSCC74B cells, FXR1 KD3

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_6

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (hg38 from UCSC). Human reference was used for gene annotation and counting (gencode M27). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: Human hg38
Supplementary files format and content: Input tables are included as tab separated files.

growth_protocol: UMSCC74B mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 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.

treatment_protocol: 25 MOI of lentiviral particles containing the control and FXR1 shRNAs were used to treat the cells for 18 hrs. Cells were washed after 18 hrs, kept for 72hrs more in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

value: Knockdown

value: mesenchymal cells

value: shRNA

value: 72 hrs


title: MP PA tumor week12 (biol rep3) [P12-3]

description: DEBrowser data S12-P12.csv


title: 200µM-Cu-treated for 4hrs, biological rep 3

city: Chicago

first: Matthew

middle: Oliver

last: Ross

state: United States

address: 929 E 57th St (loading dock behind 5741 S. Drexel Ave) GCIS E507

department: Chemistry

institute: University of Chicago

data_processing:
The fastqc (0.11.9) and trim-galore (0.6.7) packages were used for (i) quality control and (ii) to remove low-qualified bases and adapter-containing reads, respectively.
Paired end reads were mapped to reference HISAT2 (2.2.1) genomes generated from the hg38 genome build
Assembly: hg38
Supplementary files format and content: .csv, tables of read counts

extract_protocol:
Total RNA were extracted from cells by using Trizol reagent (Thermo, 15596026) and RCC-5 Kit (Zymo Research, R1013). Dynabeads® mRNA DIRECT™ Kit was used to enrich polyadenylated RNA (Thermo, 61011/61012).
RNA were used for library construction by using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs, E7760L).

value: lung adenocarcinoma

value: WT

value: 200µM CuCl2

value: 4 hours


title: D_B_04


title: MP PA tumor week12 (biol rep2) [P12-2]

description: DEBrowser data S12-P12.csv

value: mammary tumor

value: Physically active

value: Week 12


title: sn_p1_smrt2_R54

first: Ruben

last: Gutzat

address: Dr. Bohr-Gasse 3

institute: Gregor Mendel Institute GmbH

description: 1 single nucleus

data_processing:
NextSeq 550 RTA software
data were processed with nf-core/rnaseq (https://github.com/nf-core/rnaseq)
deviation from default pipeline options (star_salmon): parameters for trimming samples 191-210: --clip_r1 19 --clip_r2 9 --three_prime_clip_r1 5 --three_prime_clip_r2 5
counts table was analysed with Deseq2 and p-Values calculated with Wald-test
Genome_build: Tair10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and transposon for every sample

extract_protocol:
nuclei were extracted according to (DOI: 10.1007/978-1-0716-0179-2_7) and either 50 (bulk), 0 (neg control) or 1 single nucleus sorted into a single well.
For samples 1-190: Smart-seq2 single cell protocol (DOI: 10.1038/nmeth.2639). For samples 191-210: Smart-seq3 single cell protocol (according to Hagemann-Jensen et. al, https://doi.org/10.1038/s41587-020-0497-0).

value: 7 days after germination

value: stem cells


title: MP SED tumor week12 (biol rep3) [S12-3]

description: DEBrowser data S12-P12.csv

value: Sedentary


title: D_B_03

value: aorta


title: sn_p1_smrt2_R53

description: 1 single nucleus


title: UMSCC74B cells, FXR1 KD1

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_4


title: sn_p1_smrt2_R52

description: 1 single nucleus


title: D_V_01

value: Water


title: 200µM-Cu-treated for 4hrs, biological rep 1


title: 30µM-Cu-treated for 4hrs, biological rep 3

value: 30µM CuCl2


title: A_V_05


title: 30µM-Cu-treated for 4hrs, biological rep 2


title: sn_p1_smrt2_R50

description: 1 single nucleus


title: sn_p1_smrt2_R55

description: 1 single nucleus


title: UMSCC74B cells, Control 3

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_3

value: Control


title: sn_p1_smrt2_R51

description: 1 single nucleus


title: UMSCC74B cells, Control 1

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_1

value: mesenchymal cells


title: UMSCC74B cells, Control 2

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_2

value: shRNA


title: sn_p1_smrt2_R49

description: 1 single nucleus


title: 0µM-Cu-treated for 4hrs, biological rep 3

value: 0µM CuCl2


title: UMSCC74B cells, FXR1 KD2

description:
Bulk RNA-seq
Protocol 1
5107-MR-12_5

value: Knockdown

value: 72 hrs


title: A_V_03


title: 200µM-Cu-treated for 4hrs, biological rep 2

value: lung adenocarcinoma

value: WT

value: 200µM CuCl2


title: 0µM-Cu-treated for 4hrs, biological rep 2

value: 4 hours


title: HCT116-RAD-mAC-auxin-0h-Hi-C-Rep1

city: FARMINGTON

first: Yijun

last: Ruan

state: CT

address: 10 DISCOVERY DR

department: Ruan

institute: The Jackson Laboratory

description:
Sample 117
nuclear chromatin
Hi-C

data_processing:
Hi-C fastq files were mapped by our ChIA-PET processing pipeline, available in github (ChIA-PIPE; Lee et al., 2020).  2D contact map files (hic) were generated by Juicer Tools (Version 1.7.5) using chromatin interaction data.
Genome_build: hg38
Supplementary_files_format_and_content:
hic: 2D contact map file using all chromatin interactions , visualized by Juicebox software.

extract_protocol:
The chromatin was cut by restriction enzyme followind by biotin labeled dCTP fill in and blunt-end lligation.  Then the chromatin were sheared by sonicator. The  proximity ligated chromotin with biotin labeled were enriched with streptavidin beads .
We followed the protocol of KAPA HyperPrep kit for the library preparation.
The proximity ligated fratments were enriched by streptavidin beads and amplified.

tag: method

value: Hi-C

tag: antibody


title: sn_p1_smrt2_R48

description: 1 single nucleus

value: 7 days after germination


title: A_V_02

tag: treatment


title: D_B_02

value: BAPN


title: sn_p1_smrt2_R46

description: 1 single nucleus

value: stem cells


title: D_B_01

value: aorta


title: sn_p1_smrt2_R47

description: 1 single nucleus


title: A_V_04

value: Water


title: 30µM-Cu-treated for 4hrs, biological rep 1

value: 30µM CuCl2


title: HCT116-RAD-mAC-auxin-12h-RNA-seq-Rep2

description:
Sample 116
messenger RNA
RNA-seq

data_processing:
RNA-seq fastq files were mapped by STAR (version 2.5.3) and were de-duplicated by picard (version 2.0.1) using the MarkDuplicates command. Mapped reads are converted into strand-specific bedgraph files via samtools (version 1.5) and bedtools (version 2.27.0) using bamtobed and genomecov commands.  Fourth and fifth columns are amplified by 100.
Genome_build: hg38
Supplementary_files_format_and_content:
bedgraph: strand specific bedgraph format, forward strand in  fourth column and reverse strand in fifth column, representing the relative numer of reads mapped to the location in a strand-specific manner.

extract_protocol:
Total RNA were extracted by the Rneasy mini kit.
We followed the protocol of KAPA RNA HyperPrep Kits for the library construction.
The total mRNA was enriched and reverse transcripted to cDNA. The fragmented cDNA was ligated with adaptors compatiable with illumina sequencing platform.

value: RNA-seq


title: HCT116-RAD-mAC-auxin-6h-Hi-C-Rep1

description:
Sample 118
nuclear chromatin
Hi-C


title: 200µM-Cu-treated for 2hrs, biological rep 3

value: 2 hours


title: A_B_04


title: 200µM-Cu-treated for 2hrs, biological rep 1


title: 0µM-Cu-treated for 4hrs, biological rep 1


title: 200µM-Cu-treated for 2hrs, biological rep 2


title: A_V_01


title: HCT116-RAD-mAC-auxin-12h-RNA-seq-Rep1

description:
Sample 115
messenger RNA
RNA-seq


title: A_B_03


title: HCT116-RAD-mAC-auxin-9h-RNA-seq-Rep1

description:
Sample 113
messenger RNA
RNA-seq


title: sn_p1_smrt2_R43

description: 1 single nucleus


title: sn_p1_smrt2_R84

description: 1 single nucleus


title: sn_p1_smrt2_R42

description: 1 single nucleus


title: A_B_02


title: sn_p1_smrt2_R41

description: 1 single nucleus


title: A_B_05


title: A_B_01


title: HCT116-RAD-mAC-auxin-9h-RNA-seq-Rep2

description:
Sample 114
messenger RNA
RNA-seq


title: sn_p1_smrt2_R45

description: 1 single nucleus


title: 30µM-Cu-treated for 2hrs, biological rep 2


title: 30µM-Cu-treated for 2hrs, biological rep 1


title: sn_p1_smrt2_R44

description: 1 single nucleus


title: sn_p1_smrt2_R40

description: 1 single nucleus


title: 30µM-Cu-treated for 2hrs, biological rep 3


title: 0µM-Cu-treated for 2hrs, biological rep 3


title: cTEC, SCD1 knockout [KO_UEA1neg]

city: Shanghai

first: Mingyuan

last: Hu

address: 320, Yueyang Road

institute: Chinese Academy of Science

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: excel file includes raw counts for each Sample

source_name: Thymus

extract_protocol: RNA was harvested using standard protocol by Novogene. Briefly, NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used for generating sequencing libraries, and total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).

value: Thymus

value: Epithelial cells

value: SCD1 Knockout

tag: strain background


title: cTEC, Littermate control [WT_UEA1neg]


title: 0µM-Cu-treated for 2hrs, biological rep 2

value: 0µM CuCl2


title: HCT116-RAD-mAC-auxin-0h-RNA-seq-Rep2

description:
Sample 110
messenger RNA
RNA-seq


title: HCT116-RAD-mAC-auxin-6h-RNA-seq-Rep1

description:
Sample 111
messenger RNA
RNA-seq


title: HCT116-RAD-mAC-auxin-0h-RNA-seq-Rep1

description:
Sample 109
messenger RNA
RNA-seq


title: HCT116-input-ChIP-seq

description:
Sample 108
nuclear chromatin
Input-ChIP-seq

data_processing:
ChIP-seq fastq files were mapped by BWA (version 0.7.7) with mem command. DNA-binding protein coverage files (bedgraph) were generated by bedtools (version 2.26.0) with genomecov command. Coverage files were sorted by chromosome and coordinate. Peaks (broadPeak, bed file type) were called by SPP (version 1.13) with our input control file, (sample# 63, library ID: CHG0033 to produce peaks of samples# 94 and 95, GM12878, and sample# 108, library ID: CHH0020 to produce peaks of samples# 96 - 107, HCT116).
Genome_build: hg38
Supplementary_files_format_and_content:
bedgraph: bedgraph format, containing a DNA-binding protein coverage. broadPeak: broadPeak format, containing peaks called by SPP software.

extract_protocol:
The fixed cells were lysed. The chromatin was sonicated to generate DNA fragments averaging 200-500 bp in length .
We followed the protocol in the KAPA HyperPrep kit for the library preparation.
The adaptors were ligated at the two ends of DNA fragments. The DNA fragments with adaptors will be amplified.

value: Input-ChIP-seq


title: HCT116-RAD-mAC-auxin-6h-RNA-seq-Rep2

description:
Sample 112
messenger RNA
RNA-seq


title: mTEC cells, SCD1 knockout [KO_UEA1pos]


title: sn_p1_smrt2_R39

city: Vienna

description: 1 single nucleus

source_name: seedling


title: mTEC cells, Littermate control [WT_UEA1pos]

value: WT


title: sn_p1_smrt2_R38

description: 1 single nucleus


title: 0µM-Cu-treated for 2hrs, biological rep 1

value: lung adenocarcinoma


title: sn_p1_smrt2_R37

description: 1 single nucleus


title: Hmgb1ΔHepΔMye + Δ[O] HMGB1,CCl4#5

first: Xiaodong

last: Ge

state: IL

address: 909 South Wolcott Ave, COMRB 6140

department: Pathology

institute: The University of Illinois at Chicago

description: XG 6-5

data_processing:
Data were aligned using RNA-Seq Alignment v.2.0.1 in basespce
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count for each sample

source_name: Total liver

extract_protocol:
Total liver RNA was isolated with illustra™ RNAspin Mini RNA Isolation Kit; HSC RNA was isolated with Qiagen miRNeasy micro kit.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA library prep

treatment_protocol: Mice were injected with MO or CCl4 for 4 weeks and or regressed for 1 week, HSC was administrated with different HMGB1 isoforms for 6 hours

value: Total liver

value: Liver tissue lysate

value: 4 weeks

value: {delta}[O] HMGB1 + CCl4

tag: gender

value: Male


title: sn_p1_smrt2_R36

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: HCT116-RAD-mAC-auxin-9h-RNAPII-ChIP-seq-Rep1

description:
Sample 106
nuclear chromatin
RNAPII-ChIP-seq

value: RNAPII-ChIP-seq

value: RNAPII (BioLegend, catalog# 664912)


title: HCT116-RAD-mAC-auxin-6h-RNAPII-ChIP-seq-Rep1

description:
Sample 105
nuclear chromatin
RNAPII-ChIP-seq


title: Hmgb1ΔHepΔMye + Δ[O] HMGB1,CCl4#3

description: XG 6-3

tag: time


title: HCT116-RAD-mAC-auxin-12h-RNAPII-ChIP-seq-Rep1

description:
Sample 107
nuclear chromatin
RNAPII-ChIP-seq


title: Hmgb1ΔHepΔMye + Δ[O] HMGB1,CCl4#2

description: XG 6-2


title: HCT116-RAD-mAC-auxin-0h-RNAPII-ChIP-seq-Rep1

description:
Sample 104
nuclear chromatin
RNAPII-ChIP-seq


title: sn_p1_smrt2_R35

description: 1 single nucleus

tag: ecotype


title: Hmgb1ΔHepΔMye + Δ[O] HMGB1,CCl4#1

description: XG 6-1


title: sn_p1_smrt2_R34

description: 1 single nucleus

tag: developmental age


title: sn_p1_smrt2_R33

description: 1 single nucleus


title: Hmgb1ΔHepΔMye + Δ[O] HMGB1,MO#3

description: XG 5-3

value: {delta}[O] HMGB1 + MO


title: HCT116-RAD-mAC-auxin-12h-CTCF-ChIP-seq-Rep1

description:
Sample 103
nuclear chromatin
CTCF-ChIP-seq

value: CTCF-ChIP-seq

value: CTCF (Abclonal, catalog# A1133)


title: sn_p1_smrt2_R31

description: 1 single nucleus


title: Hmgb1ΔHepΔMye + Δ[O] HMGB1,MO#2

description: XG 5-2


title: HCT116-RAD-mAC-auxin-6h-CTCF-ChIP-seq-Rep1

description:
Sample 101
nuclear chromatin
CTCF-ChIP-seq


title: HCT116-RAD-mAC-auxin-9h-CTCF-ChIP-seq-Rep1

description:
Sample 102
nuclear chromatin
CTCF-ChIP-seq


title: sn_p1_smrt2_R30

description: 1 single nucleus


title: sn_p1_smrt2_R32

description: 1 single nucleus


title: HCT116-RAD-mAC-auxin-0h-CTCF-ChIP-seq-Rep1

description:
Sample 100
nuclear chromatin
CTCF-ChIP-seq


title: Hmgb1ΔHepΔMye + Δ[O] HMGB1,MO#1

description: XG 5-1


title: Hmgb1ΔHepΔMye + WT HMGB1,CCl4#5

description: XG 4-5

value: WT HMGB1 + CCl4


title: HCT116-RAD-mAC-auxin-12h-RAD21-ChIP-seq-Rep1

description:
Sample 99
nuclear chromatin
RAD21-ChIP-seq

value: RAD21 (Abcam, catalog# ab922)


title: Hmgb1ΔHepΔMye + WT HMGB1,CCl4#4

description: XG 4-4


title: HCT116-RAD-mAC-auxin-9h-RAD21-ChIP-seq-Rep1

description:
Sample 98
nuclear chromatin
RAD21-ChIP-seq


title: HCT116-RAD-mAC-auxin-6h-RAD21-ChIP-seq-Rep1

description:
Sample 97
nuclear chromatin
RAD21-ChIP-seq


title: Hmgb1ΔHepΔMye + WT HMGB1,CCl4#1

description: XG 4-1


title: Index_23._69

city: Sherbrooke

first: Sophie

last: Roux

state: Quebec

address: 3001, 12th avenue N

department: Division of Rheumatology

country: Canada

institute: Université de Sherbrooke

description: cDNA library generated with RNA-seq

data_processing:
Trimming of paired-end reads was performed using Trimmomatic v0.36 (parameters: ILLUMINACLIP:<fastaWithAdaptersEtc>:2:30:10) in order to remove adapters and low-quality reads.
FastQC v0.11.8 was used before and after trimming to assess the quality of the reads.
Alignment of reads to the reference human genome hg38 (v98) was performed using STAR v2.5.3a (parameters: --outFilterScoreMinOverLread = 0.3  --outFilterMatchNminOverLread = 0.4). The index needed to align reads was generated using STAR v2.5.3a, the reference human genome hg38 (v87) and the annotation file was taken from ENSEMBL (v98) and supplemented with missing miRNA information from mirbase.
Raw count gene expressions were obtained using CoCo v0.2.2.
Genome_build: hg38.98
Supplementary_files_format_and_content: Tabular-separated value (.tsv) file containing the raw count values of each sample for all the genes detected in the RNA-Seq.

source_name: cell culture (blood)

extract_protocol:
Total RNA was extracted at the end of the cultures by lysing the cells in Qiazol (Qiagen) and stored at -80°C until the experiment. The miRNeasy Micro Kit 217084 was used for RNA extraction.
The library was performed using NEBNext small RNA libraries E7330 protocol.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were differentiated into osteoclasts in 3-week in-vitro cultures in the presence of M-CSF and RANKL.

tag: disease

value: Paget's Disease of Bone

tag: Sex

value: male

tag: age


title: Index_23.84

description: cDNA library generated with RNA-seq

value: female


title: sn_p1_smrt2_R28

description: 1 single nucleus


title: HCT116-RAD-mAC-auxin-0h-RAD21-ChIP-seq-Rep1

description:
Sample 96
nuclear chromatin
RAD21-ChIP-seq


title: sn_p1_smrt2_R25

description: 1 single nucleus


title: sn_p1_smrt2_R27

description: 1 single nucleus


title: GM12878-RAD21-ChIP-seq

description:
Sample 95
nuclear chromatin
RAD21-ChIP-seq


title: Index_22.77

description: cDNA library generated with RNA-seq


title: Hmgb1ΔHepΔMye + WT HMGB1,MO#3

description: XG 3-3

value: Total liver

value: WT HMGB1 + MO


title: DCRT-KO-RIP-F-3

city: WUHAN

first: heng

middle: zhi

last: du

address: 1095 Jiefang Dadao, Wuhan City, Hubei Province, China

institute: Wuhan Tongji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt (Version 1.2.1) (Martin M, 2011) was used to remove 3' end joints, at least 10 bp Overlap (AGATCGGAAG), and 20% base error rate was allowed.
Reads per kilobase of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Ensembl 38.85
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: AC16 cells

growth_protocol: AC16 cells (ScienCell research laboratories, Carlsbad, CA) were from a single fetal donor, not pooled, and were maintained in medium (ScienCell research laboratories, Cat. #6201), according to the instruction manual.   medium consists of basal medium, foetal bovine serum (FBS),  AC16 cells growth supplement, and penicillin/streptomycin solution.

extract_protocol:
RNA was harvested using Trizol reagent following the instructions.
All of our RNA-seq projects used strand specific kits to construct the libraries.By using next-generation sequencing (NGS) technology, paired-end (PE) sequencing of these libraries was performed based on Illumina HiSeq sequencing platform

value: heart

value: AC16 cells

value: cardiomyocytes

value: DCRT-KO

tag: rip antibody


title: DCRT-KO-RIP-F-1


title: DCRT-KO-RIP-F-2


title: WT-RIP-F-3

value: WT


title: WT-RIP-F-1


title: WT-RIP-F-2


title: sn_p1_smrt2_R24

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: Hmgb1ΔHepΔMye + WT HMGB1,MO#1

description: XG 3-1

value: Liver tissue lysate

value: 4 weeks

value: Male


title: Hmgb1ΔHepΔMye + WT HMGB1,MO#2

description: XG 3-2


title: sn_p1_smrt2_R23

description: 1 single nucleus


title: Index_22._63

description: cDNA library generated with RNA-seq


title: GM12878-CTCF-ChIP-seq

description:
Sample 94
nuclear chromatin
CTCF-ChIP-seq

value: CTCF-ChIP-seq

value: CTCF (Abclonal, catalog# A1133)


title: HCT116-RAD-mAC-auxin-6h-RNAPII-ChIA-PET-Rep2-2

description:
Sample 93
nuclear chromatin
RNAPII-ChIA-PET

data_processing:
Library strategy: ChIA-PET
ChIA-PET fastq files were mapped by our ChIA-PET processing pipeline, available in github (ChIA-PIPE; Lee et al., 2020). DNA-binding protein coverage files (bedgraph) were generated by bedtools (version 2.26.0) with genomecov command. Coverage files were sorted by chromosome and coordinate. ChIA-PET loop files (bedpe) were generated by our ChIA-PET processing pipeline, available in github (ChIA-PIPE). Peaks (broadPeak, bed file type) were called by SPP (version 1.13) with our input control file (sample# 63, library ID: CHG0033 to produce peaks of sample# 75, GM12878, and sample# 108, library ID: CHH0020 to produce peaks of samples# 76-93, HCT116). 2D contact map files (hic) were generated by Juicer Tools (Version 1.7.5) using chromatin interaction data.
Genome_build: hg38
Supplementary_files_format_and_content:
BE3: bedpe format, containing ChIA-PET loops (long-range interactions), filtered out low PET count score, collecting only bigger than or equal to PET count score 3.  bedgraph: bedgraph format, containing a DNA-binding protein coverage. broadPeak: broadPeak format, containing peaks called by SPP software. hic: 2D contact map file using all chromatin interactions , visualized by Juicebox software.

extract_protocol:
The overall chromatin sample preparation for ChIA-PET is very similar to in situ Hi-C, except the proximity ligation step with biotin marked linkers and finally ligated chromatin enriched by interested protein factors (such as CTCF, cohesin, and RNAPII)  in ChIA-PET.
Nextera DNA library prepration kit and corresponding protocol was used for the library prepation.
We applied Tn5 transponase in the Nextera DNA library preparation kit to cut chromatin DNA and paste the linker sequence to the DNA ends simutaneously. Then the ligated chromatin with biotin marked linkers will be enriched by streptavidin beads.

value: RNAPII-ChIA-PET

value: RNAPII (BioLegend, catalog# 664912)


title: Alz_vs_WT_R1

type: RNA

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

description: Replicate 1 of 4: APPswe/PS1dE9 mutant  vs. WT NPCs

hyb_protocol: Agilent Gene Expression Hybridization Kit were used and labeled targets were incubated to na Agilent SurePrint G3 Mouse GE 8x60K Microarray enclosed in Agilent Microarray Hybridization Chamber. After hybridization, slides were washed sequentially.

scan_protocol: Agilent Feature Extraction Software (v 9.5)

data_processing: Four biological replicates were assessed with dye swap. gProcessedSignal and rProcessedSignal values were used to calculate log2 Alz/WT ratios. Only the probes with significantly greater expression (as determined via the 2-sided t-test) compared with the corresponding background level (flag ‘IsWellAboveBG’) in 3 of the 4 control sample replicates were defined as expressed and further analysed.

source_name: APPswe/PS1dE9 cells

label_protocol: 100 ng of total RNA were DNAse-treated and amplified and labeled using Agilent Low RNA Input Fluorescent Linear Amplification Kit following manufacturer's instructions.

growth_protocol: NPCs were isolated from embryo telencephalon (day 13) of wild-type or APPswe/PSldE9 C57BL/6 mice. All animal experiments were performed according to protocols approved by the ethics committee (authorization number: 10/2013). Isolated telencephalons were mechanically and enzymatically dissociated. A concentration of 2×105 cells/ml was seeded in 2% B-27 (Life Technologies, Carlsbad, CA), Dulbecco's modified Eagle's medium (DMEM) with Ham's F-12, antibiotics (100 units/ml penicillin and 100 g/ml streptomycin), 20 ng/ml EGF and 20 ng/ml FGF2 (Sigma-Aldrich, St Louis, MO) and cultured at 37 °C in a water-saturated atmosphere with 5% of CO2. Cultures were grown for 5 days until formation of neurospheres was observed. Neurospheres were washed twice with DMEM/F12 at 300 r.p.m for 3 min.

extract_protocol: Total RNA from APPswe/PS1dE9 and WT neurospheres was extracted using the RNAspin Mini Kit (GE Healthcare, UK), according to the manufacturer instructions. The RNA was treated with DNAse.

treatment_protocol: For neural differentiation, neurospheres were seeded on poly-L-lysine and laminin-precoated plastic flasks and cultured with DMEM/F-12, 2% B-27 in the absence of FGF-2 and EGF. Progenitor cells were differentiated for 7 days, with half of the medium changed every 2 days.

tag: strain

value: differentiated NPCs from APPswe/PS1dE9 embryo telencephalon

source_name: WT cells

value: differentiated NPCs from wild-type embryo telencephalon


title: sn_p1_smrt2_R29

description: 1 single nucleus


title: HCT116-RAD-mAC-auxin-6h-RNAPII-ChIA-PET-Rep2-1

description:
Sample 92
nuclear chromatin
RNAPII-ChIA-PET

tag: cell line


title: Alz_vs_WT_R2

description: Replicate 2 of 4: APPswe/PS1dE9 mutant  vs. WT NPCs

tag: cell type


title: WT, CCl4#4

description: XG 2-4

tag: tissue

value: Total liver


title: HCT116-RAD-mAC-auxin-6h-RNAPII-ChIA-PET-Rep1

description:
Sample 91
nuclear chromatin
RNAPII-ChIA-PET


title: WT, CCl4#3

description: XG 2-3

tag: genotype


title: sn_p1_smrt2_R22

description: 1 single nucleus


title: Index_20.62

description: cDNA library generated with RNA-seq

value: Paget's Disease of Bone

value: male


title: Index_21.76

description: cDNA library generated with RNA-seq

value: female


title: Index_21._56

description: cDNA library generated with RNA-seq


title: sn_p1_smrt2_R21

description: 1 single nucleus


title: HCT116-RAD-mAC-auxin-0h-RNAPII-ChIA-PET-Rep2-2

description:
Sample 90
nuclear chromatin
RNAPII-ChIA-PET

tag: method


title: sn_p1_smrt2_R20

description: 1 single nucleus


title: WT, CCl4#2

description: XG 2-2


title: Alz_vs_WT_R4

description: Replicate 4 of 4: APPswe/PS1dE9 mutant  vs. WT NPCs


title: WT, CCl4#1

description: XG 2-1


title: HCT116-RAD-mAC-auxin-0h-RNAPII-ChIA-PET-Rep2-1

description:
Sample 89
nuclear chromatin
RNAPII-ChIA-PET

tag: antibody


title: sn_p1_smrt2_R19

description: 1 single nucleus


title: Alz_vs_WT_R3

description: Replicate 3 of 4: APPswe/PS1dE9 mutant  vs. WT NPCs


title: sn_p1_smrt2_R18

description: 1 single nucleus


title: Index_19.61

description: cDNA library generated with RNA-seq


title: Index_18.59

description: cDNA library generated with RNA-seq


title: WT, MO#3

description: XG 1-3

tag: treatment

value: MO


title: Index_1.S-01

description: cDNA library generated with RNA-seq

value: control


title: HCT116-RAD-mAC-auxin-6h-CTCF-ChIA-PET-Rep2

description:
Sample 87
nuclear chromatin
CTCF-ChIA-PET

value: CTCF-ChIA-PET


title: HCT116-RAD-mAC-auxin-0h-RNAPII-ChIA-PET-Rep1

description:
Sample 88
nuclear chromatin
RNAPII-ChIA-PET


title: HCT116-RAD-mAC-auxin-6h-CTCF-ChIA-PET-Rep1

description:
Sample 86
nuclear chromatin
CTCF-ChIA-PET


title: WT, MO#1

description: XG 1-1

value: WT


title: Index_18.C-053

description: cDNA library generated with RNA-seq


title: sn_p1_smrt2_R16

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: Index_2.S-05

description: cDNA library generated with RNA-seq


title: Liver resolution+HMGB1Ab#3

description: XG#14 c-3-3

value: Liver tissue lysate

value: 1 week

value: Regress + HMGB1 Ab

value: Male


title: sn_p1_smrt2_R15

description: 1 single nucleus


title: Liver resolution+HMGB1Ab#2

description: XG#14 c-3-2


title: sn_p1_smrt2_R14

description: 1 single nucleus


title: Index_2.S-02

description: cDNA library generated with RNA-seq


title: Index_20.C-064

description: cDNA library generated with RNA-seq


title: Liver resolution+HMGB1Ab#1

description: XG#14 c-3-1


title: WT, MO#2

description: XG 1-2

value: 4 weeks


title: Index_6._50

description: cDNA library generated with RNA-seq


title: sn_p1_smrt2_R12

description: 1 single nucleus


title: sn_p1_smrt2_R13

description: 1 single nucleus


title: Index_7.S-011

description: cDNA library generated with RNA-seq


title: Liver resolution+[SO3] HMGB1#3

description: XG#14 c-2-3

value: Regress +[SO3] HMGB1


title: Liver resolution+[SO3] HMGB1#2

description: XG#14 c-2-2


title: HCT116-RAD21-ChIA-PET-Rep2-2

description:
Sample 83
nuclear chromatin
RAD21-ChIA-PET

value: RAD21 (Abcam, catalog# ab922)


title: HCT116-RAD-mAC-auxin-0h-CTCF-ChIA-PET-Rep1

description:
Sample 84
nuclear chromatin
CTCF-ChIA-PET

value: CTCF (Abclonal, catalog# A1133)


title: HCT116-RAD-mAC-auxin-0h-CTCF-ChIA-PET-Rep2

description:
Sample 85
nuclear chromatin
CTCF-ChIA-PET


title: sn_p1_smrt2_R11

description: 1 single nucleus


title: Index_4.S-04

description: cDNA library generated with RNA-seq


title: Hmgb1ΔHepΔMye + WT HMGB1,CCl4#3

description: XG 4-3

value: Total liver

value: WT HMGB1 + CCl4


title: Liver resolution+[SO3] HMGB1#1

description: XG#14 c-2-1


title: Index_3.S-03

description: cDNA library generated with RNA-seq

value: male


title: sn_p1_smrt2_R8

description: 1 single nucleus


title: Liver resolution+BSA#3

description: XG#14 c-1-3

value: Regress +BSA


title: sn_p1_smrt2_R7

description: 1 single nucleus


title: Cardiac Fibroblast, DMD 3

city: Toulouse

first: Nathalie

last: Pizzinat

address: 1 avenue du Pr Jean Poulhès

institute: INSERM

data_processing:
Fastq files were cleaned with hts pipeline using default parameters for hts_Stats, hts_SeqScreener, hts_SuperDeduper, hts_SeqScreener (with human rRNA), hts_AdapterTrimmer, hts_QwindowTrim, hts_Ntrimmer, hts_CutTrim, hts_Stats (version 1.3.2)
Cleaned fastq files were aligned with Salmon (v 1.9.0) with the –gcBias flag set
Counts table was generated with txImport (v 1.26.1) in R (v 4.3.2)
Assembly: Gencode v40 transcripts
Supplementary files format and content: Raw counts per sample in tab-delimited text format

source_name: hiPSC-derived cardiac fibroblasts

growth_protocol: Fibroblast growth medium 3

extract_protocol:
RNA were extracted with ReliaPrep RNA Cell Miniprep System (Promega).
Libraries were generated with TruSeq stranded mRNA Illumina and quantified on a Fragment analyzer

value: hiPSC-derived cardiac fibroblasts

value: DMD


title: sn_p1_smrt2_R9

description: 1 single nucleus


title: Cardiac Fibroblast, DMD 4


title: Liver resolution+BSA#1

description: XG#14 c-1-1

value: WT


title: Cardiac Fibroblast, DMD 2


title: Liver fibrosis+[O] HMGB1#3

description: XG#14 a-3-3

value: CCl4 +[O] HMGB1


title: sn_p1_smrt2_R6

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: HCT116-CTCF-ChIA-PET-Rep2

description:
Sample 77
nuclear chromatin
CTCF-ChIA-PET

value: CTCF-ChIA-PET


title: HCT116-RNAPII-ChIA-PET-Rep2

description:
Sample 79
nuclear chromatin
RNAPII-ChIA-PET

value: RNAPII-ChIA-PET

value: RNAPII (BioLegend, catalog# 664912)


title: HCT116-RNAPII-ChIA-PET-Rep1

description:
Sample 78
nuclear chromatin
RNAPII-ChIA-PET


title: HCT116-RAD21-ChIA-PET-Rep1-2

description:
Sample 81
nuclear chromatin
RAD21-ChIA-PET


title: HCT116-CTCF-ChIA-PET-Rep1

description:
Sample 76
nuclear chromatin
CTCF-ChIA-PET


title: sn_p1_smrt2_R10

description: 1 single nucleus


title: sn_p1_smrt2_R5

description: 1 single nucleus


title: HCT116-RAD21-ChIA-PET-Rep2-1

description:
Sample 82
nuclear chromatin
RAD21-ChIA-PET


title: Cardiac Fibroblast, DMD 1


title: HCT116-RAD21-ChIA-PET-Rep1-1

description:
Sample 80
nuclear chromatin
RAD21-ChIA-PET


title: Liver fibrosis+[O] HMGB1#2

description: XG#14 a-3-2

value: Liver tissue lysate

value: 4 weeks

value: Male


title: ARPE19-RAD21-ChIA-Drop-Rep6

description:
Sample 74
nuclear chromatin
RNAPII-ChIA-Drop
ARPE19-RAD21-pooled_comp.txt
ARPE19-RAD21-pooled.bedgraph
ARPE19-RAD21-pooled.hic

data_processing:
Library strategy: ChIA-Drop
ChIA-Drop fastq files were mapped by longranger (version 2.1.5, 10X Genomics) with wgs command. After mapping and identifying barcords of ChIA-Drop using longranger, our in-house processing pipeline (available in github, ChIA-DropBox) generated putative complexes. These data sets were further filtered by MIA-Sig (available in github), and then generated tab-delimited txt file. 2D contact map files (hic) were generated by Juicer Tools (Version 1.7.5) using chromatin interaction data using all pairwise interactions from each GEM.
Genome_build: hg38
Supplementary_files_format_and_content:
txt: tab-delimited text list, containing GEM_ID, GEM_coordinate, GEM_span, Fragment_number, List_of_fragment_coordinates. Each row represents one GEM. bedgraph: bedgraph format, containing a DNA-binding protein coverage. hic: 2D contact map file using all pairwise interactions from each GEM, visualized by Juicebox software

extract_protocol:
The overall chromatin sample preparation for ChIA-Drop is very similar to Hi-C, except without the proximity ligation step in ChIA-Drop.  Similarly, CTCF, cohesin, and RNAPII ChIA-Drop chromatin samples are prepared as they are for respective ChIA-PET experiments but omitting proximity ligation step.
Fragmented chromatin sample was mixed with BSA to prevent chromatin aggregation. About 0.5ng of chromatin DNA material was loaded to microfluidics device, Chromium Controller with reagents from Chromium Genome v2 Library Kit & Gel Bead Kit for partitioning of single chromatin complex into individual droplets with unique gel beads according to the manufacturer’s protocol with modification. The barcoded DNA amplicons of each chromatin complex were released from all droplets.The purified DNA fragments were subjected for end repair, A-tailing, adaptor ligation, Sample Index PCR and size selection.  The final ChIA-Drop library was sequenced (2× 150 bp) by NextSeq, HiSeq, or NovaSeq runs.
We applied microfluidics-based strategy for genome-wide analysis of multiplex chromatin interactions with single-molecule precision (ChIA-Drop). Here, individual chromatin complexes are isolated in droplets that contain a gel bead with unique DNA barcode, in which tethered chromatin DNA fragments are barcoded and amplified for sequencing and mapping to demarcate chromatin contacts.

value: RAD21 (Abcam, catalog# ab922)


title: sn_p1_smrt2_R4

description: 1 single nucleus


title: Liver fibrosis+[O] HMGB1#1

description: XG#14 a-3-1

value: Total liver


title: sn_p1_smrt2_R17

description: 1 single nucleus


title: GM12878-ActinomycinD-24h-RNAPII-ChIA-PET

description:
Sample 75
nuclear chromatin
RNAPII-ChIA-PET


title: ARPE19-RAD21-ChIA-Drop-Rep5

description:
Sample 73
nuclear chromatin
RNAPII-ChIA-Drop
ARPE19-RAD21-pooled_comp.txt
ARPE19-RAD21-pooled.bedgraph
ARPE19-RAD21-pooled.hic


title: Liver resolution+BSA#2

description: XG#14 c-1-2

value: 1 week


title: Cardiac Fibroblast, Control 4

value: Healthy


title: Cardiac Fibroblast, Control 3


title: Liver fibrosis+[H] HMGB1#3

description: XG#14 a-2-3

value: CCl4 +[H] HMGB1


title: Cardiac Fibroblast, Control 2

value: hiPSC-derived cardiac fibroblasts


title: sn_p1_smrt2_R3

description: 1 single nucleus


title: Liver fibrosis+[H] HMGB1#1

description: XG#14 a-2-1


title: ARPE19-RAD21-ChIA-Drop-Rep4

description:
Sample 72
nuclear chromatin
RNAPII-ChIA-Drop
ARPE19-RAD21-pooled_comp.txt
ARPE19-RAD21-pooled.bedgraph
ARPE19-RAD21-pooled.hic


title: ARPE19-RAD21-ChIA-Drop-Rep3

description:
Sample 71
nuclear chromatin
RNAPII-ChIA-Drop
ARPE19-RAD21-pooled_comp.txt
ARPE19-RAD21-pooled.bedgraph
ARPE19-RAD21-pooled.hic


title: Cardiac Fibroblast, Control 1


title: sn_p1_smrt2_R2

description: 1 single nucleus


title: Liver fibrosis+[H] HMGB1#2

description: XG#14 a-2-2


title: MDA-MB231 cells, no treatment

city: Oakland

first: Ravi

last: Sachidanandam

state: CA

address: 2945 Webster St

institute: Girihlet Inc.

data_processing:
Exact matches of the Reads (36 nt)  to the human genome (version hg19) were found, using a suffix-array based method. Using annotations of the genome from UCSC browser, genes were assigned counts. Longer reads in some of the experiments (72 nt), were split into two and mapped exactly.
Genome_build: hg19
Supplementary_files_format_and_content: csv file of read counts per gene (rows) in each experiment (columns)

source_name: breast cancer cell line

growth_protocol: A3250, MDA-MB231, HCC3153 and cells were cultured in high-glucose DMEM supplemented with 4 mM L-glutamine (Sigma, Cat. # D6429-500ML), 10% FBS (Corning, Cat. # 35-010-CV) and 1X antibiotics (100 U/ml penicillin, 100 U/ml streptomycin). The cells were plated in 10 cm dishes two days before RNA extraction (90% confluency at the time of RNA extraction)

extract_protocol: Total RNA was isolated from samples using TRIZOL reagent (Invitrogen) and RNeasy columns (Qiagen). cDNA was synthesized using random hexamers and ligated with bar-coded adaptors compatible with Illumina's NextSeq 500 (???).

treatment_protocol: A3250 cells were transduced with the VIRHD-EP lentiviral vector and selected with blasticidin (10 ug/ml).

value: Breast adenocarcinoma

value: no treatment


title: neg_p2_smrt2_R1

description: negative control


title: ARPE19-RAD21-ChIA-Drop-Rep1

description:
Sample 69
nuclear chromatin
RNAPII-ChIA-Drop
ARPE19-RAD21-pooled_comp.txt
ARPE19-RAD21-pooled.bedgraph
ARPE19-RAD21-pooled.hic


title: Liver fibrosis+BSA#2

description: XG#14 a-1-2

value: WT

value: CCl4 +BSA


title: bulk_p2_smrt2_R1

description: bulk of 50 stem cell nuclei

value: 7 days after germination

value: stem cells


title: neg_p2_smrt2_R2

description: negative control


title: GM12878-RNAPII-ChIA-PET-Rep2

description:
Sample 68
nuclear chromatin
RNAPII-ChIA-PET
LHG0035N_0035V_0045V.e500.clusters.cis.BE3
LHG0035N_0035V_0045V.for.BROWSER.sorted.bedgraph
LHG0035N_0035V_0045V.for.BROWSER.spp.z6.broadPeak
ChIA-PET_hg38_GM12878_RNAPII_LHG0035N_0035V_0045V_pooled_pairs.hic

data_processing:
Library strategy: ChIA-PET
ChIA-Drop fastq files were mapped by longranger (version 2.1.5, 10X Genomics) with wgs command. ChIP-seq fastq files were mapped by BWA (version 0.7.7) with mem command. ChIA-PET fastq files were mapped by our in-house ChIA-PET processing pipeline, available in github (ChIA-PIPE).
After mapping and identifying barcords of ChIA-Drop using longranger, our in-house processing pipeline (available in github, ChIA-DropBox) generated putative complexes. These data sets were further filtered by MIA-Sig (available in github), and then generated tab-delimited txt file.
DNA-binding protein coverage files (bedgraph) were generated by bedtools (version 2.26.0) with genomecov command. Coverage files were sorted by chromosome and coordinate.
ChIA-PET loop files (bedpe) were generated by our in-house ChIA-PET processing pipeline, available in github (ChIA-PIPE).
Peaks (broadPeak, bed file type) were called by SPP (version 1.13) with our input control file (sample# 63, library ID: CHG0033).
2D contact map files (hic) were generated by Juicer Tools (Version 1.7.5) using chromatin interaction data from ChIA-PET and ChIA-Drop. In ChIA-Drop, we used all pairwise interactions from each GEM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt format of ChIA-Drop, containing GEM_ID, GEM_coordinate, GEM_span, Fragment_number, List_of_fragment_coordinates. Each row represents one GEM.
Supplementary_files_format_and_content: bedgraph format of ChIA-Drop, ChIP-seq, and ChIA-PET, containing a DNA-binding protein coverage
Supplementary_files_format_and_content: bedpe format of ChIA-PET, containing ChIA-PET loop (long-range interaction data) data
Supplementary_files_format_and_content: broadPeak format of ChIP-seq and ChIA-PET, containing peaks called by SPP software
Supplementary_files_format_and_content: hic format of ChIA-Drop and ChIA-PET, 2D contact map file, visualized by Juicebox software

value: RNAPII-ChIA-PET


title: SUM-149 cells, shRNA ROR2, rep1

value: Inflammatory breast carcinoma

value: shRNA ROR2


title: Liver fibrosis+BSA#1

description: XG#14 a-1-1

value: Liver tissue lysate

value: 4 weeks


title: SUM-149 cells, shRNA control, rep2

value: shRNA control


title: Liver fibrosis+BSA#3

description: XG#14 a-1-3

value: Total liver

value: Male


title: GM12878-RAD21-ChIA-PET

description:
Sample 65
nuclear chromatin
RAD21-ChIA-PET
LHG0051H_0104V.e500.clusters.cis.BE3
LHG0051H_0104V.for.BROWSER.sorted.bedgraph
LHG0051H_0104V.for.BROWSER.spp.z6.broadPeak
ChIA-PET_hg38_GM12878_Cohesin_LHG0051H_0104V_pooled_pairs.hic

value: RAD21 (Abcam, catalog# ab922)


title: bulk_p1_smrt2_R1

description: bulk of 50 stem cell nuclei


title: GM12878-Input-ChIP-seq

description:
Sample 63
nuclear chromatin
Input-ChIP-seq
CHG0033.q30.nr.sorted.bedgraph

data_processing:
ChIA-Drop fastq files were mapped by longranger (version 2.1.5, 10X Genomics) with wgs command. ChIP-seq fastq files were mapped by BWA (version 0.7.7) with mem command. ChIA-PET fastq files were mapped by our in-house ChIA-PET processing pipeline, available in github (ChIA-PIPE).
After mapping and identifying barcords of ChIA-Drop using longranger, our in-house processing pipeline (available in github, ChIA-DropBox) generated putative complexes. These data sets were further filtered by MIA-Sig (available in github), and then generated tab-delimited txt file.
DNA-binding protein coverage files (bedgraph) were generated by bedtools (version 2.26.0) with genomecov command. Coverage files were sorted by chromosome and coordinate.
ChIA-PET loop files (bedpe) were generated by our in-house ChIA-PET processing pipeline, available in github (ChIA-PIPE).
Peaks (broadPeak, bed file type) were called by SPP (version 1.13) with our input control file (sample# 63, library ID: CHG0033).
2D contact map files (hic) were generated by Juicer Tools (Version 1.7.5) using chromatin interaction data from ChIA-PET and ChIA-Drop. In ChIA-Drop, we used all pairwise interactions from each GEM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt format of ChIA-Drop, containing GEM_ID, GEM_coordinate, GEM_span, Fragment_number, List_of_fragment_coordinates. Each row represents one GEM.
Supplementary_files_format_and_content: bedgraph format of ChIA-Drop, ChIP-seq, and ChIA-PET, containing a DNA-binding protein coverage
Supplementary_files_format_and_content: bedpe format of ChIA-PET, containing ChIA-PET loop (long-range interaction data) data
Supplementary_files_format_and_content: broadPeak format of ChIP-seq and ChIA-PET, containing peaks called by SPP software
Supplementary_files_format_and_content: hic format of ChIA-Drop and ChIA-PET, 2D contact map file, visualized by Juicebox software

value: Input-ChIP-seq


title: ARPE19-RAD21-ChIA-Drop-Rep2

description:
Sample 70
nuclear chromatin
RNAPII-ChIA-Drop
ARPE19-RAD21-pooled_comp.txt
ARPE19-RAD21-pooled.bedgraph
ARPE19-RAD21-pooled.hic


title: sn_p1_smrt2_R1

description: 1 single nucleus


title: Replicate 4, dura mater, wild-type, 2-month-old, female

city: Helsinki

first: Salli

last: Antila

state: Uusimaa

address: Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki, Wihuri Research Insitute

data_processing:
Data processing and analysis were performed using 10x Genomics Cell Ranger v3.0.1 pipelines.
The Sample libraries were sequenced on Illumina NovaSeq 6000 system using read lengths: 28bp (Read 1), 8bp (i7 Index), 0 bp (i5 Index) and 89bp (Read 2).
Assembly: Alignment was done against mouse genome mm10.
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Dura mater pooled from 4 individual mice

extract_protocol:
Dorsal dura mater from four different PBS-perfused mice were pooled as one sample. Freshly collected and cut tissues were dissociated with enzymatic digestion (Collagenase VIII and DNase I) and mechanical dissociation with pippeting. Cells were washed with Ca2+ and Mg2+ free HBSS and strained with 70-µm cell strainer. DAPI- viable singlets were sorted with FACS into 1.5 ml tube and kept in PBS with 0.04% BSA.
The Chromium Single Cell 3’RNAseq run and library preparation were done using the Chromium™ Single Cell 3' Reagent version 3 chemistry according to the manufacter’s instructions.

value: All DAPI- viable singlets

tag: cell target in loading / number of cells to be sequenced

value: 8000 cells

tag: sequencing depth (pe/cell)

value: wild-type

tag: genetic background

value: female


title: SUM-149 cells, shRNA control, rep1