title: BLISS HU Dox BI8626 rep3

data_processing:
Breaks Labeling In Situ and Sequencing (BLISS)
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0. Reads were demultiplexed according to sample-barcode with UMI-tools v1.0.1. barcodes used as following: A1: CATCACGC, A2: GTCGTTCC, A3: TGATGATC, A4: ACGACATC
reads were aligned with Bowtie2 v2.3.4.1 to hg19 and filtered with bedtools intersect v2.26.0. Reads were counted for specific regions using the R package exomeCopy v1.18.0
Assembly: hg19
Supplementary files format and content: bedgraph

extract_protocol:
blunting of DSB, adapter ligation, DNA purification and fragmentation, in vitro transcription, fragmentation
libraries were prepared for sequencing using a modified NEBNext Small RNA library preperation protocol

value: U-2 OS MYC-tet-on

value: Dox inducible overexpression of MYC


title: Gallus gallus utricle, cell-155

status: Public on Sep 07 2022

type: SRA

city: South San Francisco

first: Daniel

middle: C

last: Ellwanger

state: CA

address: 1120 Veterans Blvd

department: Genome Analysis Unit

country: USA

institute: Amgen Inc

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the NCBI Gallus gallus v6.0 (GCF_000002315.6) reference genome and gene expression values were quantified with a customized STAR-RSEM pipeline for single-cell data.
FastQC and Scater were used for quality control.
Low-quality cells, ERCC spike-in transcripts, and low-level expressed genes were removed.
Assembly: NCBI Gallus gallus v6.0 (GCF_000002315.6) reference genome
Supplementary files format and content: Tab-separated values file reporting counts

molecule: total RNA

organism: Gallus gallus

source_name: Utricle sensory epithelia

extract_protocol:
Utricles were dissected in ice-cold Medium 199, otolithic membranes were mechanically removed, and tissue was incubated in thermolysin (0.5 mg/mL M199 medium) for 20 minutes at 37°C. Thermolysin activity was attenuated with 10% FBS in M199. The sensory epithelia were carefully peeled off from the underlying stromal cells using a 30- gauge 1⁄2-inch hypodermic needle attached to a 1 mL syringe. For each experiment, we pooled 4-8 sensory epithelia. The epithelia were dissociated using 1X Accutase for 20 minutes at 37°C, followed by mild mechanical trituration, and washed twice with PBS using a centrifugation step (300 x g, 5 min, room temperature (RT)). Viable single cells were isolated with a Becton Dickinson FACSAria Fusion flow cytometer (Ellwanger et al., 2018). Two independent batches of 270 cells were deposited into individual wells of 96-well plates, prefilled with 4 μl of a premade lysis solution with 1 U/μl of recombinant RNase inhibitor, 0.1% Triton X-100, 2.5 mM dNTP mix, 2.5 μM oligo d(T)30 VN (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT). Plates containing sorted cells were immediately sealed, frozen on dry ice, and stored at −80°C.
Single-cell RNA-seq was performed via Picelli and colleagues’ method (Picelli et al., 2014) using SMARTscribe for reverse transcription followed by 22 amplification cycles. Amplified cDNAs were purified by AMPure Beads cleanup using a Biomek FX automated platform and assessed with a fragment analyzer (Agilent) for quantitation and quality assurance. Barcoded libraries were synthesized using a scaled-down Nextera XT protocol (Mora-Castilla et al., 2016) in a total volume of 4 μl. A total of 384 libraries were pooled, and paired-end sequenced (2 x 150 bp) on a NextSeq 500/550 High Output flow cell.

tag: tissue

value: Utricle sensory epithelia

tag: genotype

value: Wildtype

tag: age

value: Posthatch day 7 (P7)

tag: well plate

tag: plate position


title: Gallus gallus utricle, cell-165


title: Gallus gallus utricle, cell-154


title: Gallus gallus utricle, cell-161


title: 59-1

type: RNA

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

hyb_protocol: RNA was hybridized to Affymetrix GeneChip HT HG-U219 arrays, and processed in a Gene Titan Platform (Affymetrix, Santa Clara, USA).

data_processing: The resulting CEL files were pre-processed using the RMA algorithm as implemented in Affymetrix Power Tools, including a log2 transformation step (version 1.16.1) [cite 12925520]. The probes were summarized using custom CDF files remapped to Ensembl genes (Brain array) [PMID 16284200].

label: biotin

molecule: polyA RNA

organism: Homo sapiens

source_name: ileum

growth_protocol: Human samples, no growth protocol

extract_protocol: All intestinal biopsies were placed immediately in RNAlater (Qiagen) stored in a refrigerator and later transferred to a -80ºC freezer for long time storage until RNA extraction. The biopsy tissue was transferred into a tube and homogenized with Ultra Turrax (IKA, Staufen, Germany), together with 700µl Qiazol reagent (company ref). The quality and concentration of the purified total RNA was investigated on a Bioanalyzer 2100  (Agilent) using the RNA 6000 Nano Labchip kit (Agilent technologies, Santa Clara, CA), and all RNA sample concentrations were measured on a ND-8000 NanoDrop (Thermo Fisher Scientific, Waltham, MA).  RNA quality was evaluated based on the 28S/18S ratio RIN (RNA integrity number. The RIN value from the human biopsy materials varied but all values above 7 were used for Array. RNA was stored at -80°C until use.

treatment_protocol: Mucosal biopsies were obtained from patients with chronic inflammatory bowel disease (IBD), ulcerative colitis (UC) or Crohn’s disease (CD) diagnosed according to generally accepted standard (Lennard-Jones PMID 2617184). Consecutively included were IBD patients followed at the IBD clinic Northsealand Hospital and referred to colonoscopy or sigmoidoscopy due to clinical activity of at least 14 days duration. As control patients were included persons referred to endoscopy for reasons other than IBD revealing normal endoscopy. Exclusion criteria were for IBD patients and controls: age below 18 years, any gastrointestinal disease other than IBD, malignant disease, or known autoimmune disease not associated to IBD. Totally 109 biopsy donors were included, 53 UC, 25 CD, and 28 controls.

tag: patient

tag: biopsy

tag: diagnosis

value: CD

tag: gastroscopy

value: FALSE

tag: inflammation

value: non

value: ileum


title: 6-4

scan_protocol: RNA was hybridized to Affymetrix GeneChip HT HG-U219 arrays, and processed in a Gene Titan Platform (Affymetrix, Santa Clara, USA).

source_name: sigmoideum

value: Control

value: sigmoideum


title: 4sU-seq U-2 OS MYC-AID Kless rep3

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

library_source: transcriptomic

data_processing:
library strategy: 4sU-seq
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For 4sU-seq, reads were mapped to hg19 with  Bowtie2, reads mapping to rRNA,exons and blacklist regions were removed, and then normalized based on read depth.
Assembly: hg19
Supplementary files format and content: bw

source_name: Bone Marrow

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
total RNA
4sU-RNA was used for library preparation with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep kit. The libraries were amplified with 10-14 PCR cycles depending on the input RNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq500 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

treatment_protocol: Treatment as indicated

value: Bone Marrow

tag: cell line

value: U-2 OS MYC-AID

tag: cell type

value: osteosarcoma cell line

value: Dox inducible overexpression of Kless-MYC

tag: treatment

value: Auxin, 6H + Dox, 1µg/ml, 24 h

tag: molecule subtype

value: nascent RNA


title: Gallus gallus utricle, cell-153


title: 31-2

label_protocol: RNA was hybridized to Affymetrix GeneChip HT HG-U219 arrays, and processed in a Gene Titan Platform (Affymetrix, Santa Clara, USA).

value: UC

value: yes


title: 59-2

source_name: coecum

value: coecum


title: 113-1

source_name: transversum

value: transversum


title: Gallus gallus utricle, cell-152

value: Utricle sensory epithelia

value: Wildtype

value: Posthatch day 7 (P7)


title: 116-3

source_name: rectum

value: CD

value: FALSE

value: non

value: rectum


title: Gallus gallus utricle, cell-150


title: BLISS HU rep3

library_source: genomic

molecule: genomic DNA

value: Bone Marrow

value: U-2 OS MYC-tet-on

value: Dox inducible overexpression of MYC


title: Gallus gallus utricle, cell-148


title: BLISS HU Dox BI8626 rep2

value: osteosarcoma cell line


title: 4sU-seq U-2 OS MYC-AID Kless rep1

value: U-2 OS MYC-AID

value: Dox inducible overexpression of Kless-MYC

value: Auxin, 6H + Dox, 1µg/ml, 24 h


title: Gallus gallus utricle, cell-147


title: 11-3

value: Control


title: Gallus gallus utricle, cell-146


title: 109-4

value: UC


title: Gallus gallus utricle, cell-145


title: 35-1

value: ileum


title: 59-7


title: BLISS HU Dox rep3

value: HU, 3.5mM, 4h+ Dox, 1µg/ml, 24 h


title: BLISS HU Dox rep2


title: Gallus gallus utricle, cell-144

value: Utricle sensory epithelia

value: Wildtype


title: BLISS HU BI8626 rep2


title: Gallus gallus utricle, cell-142

value: Posthatch day 7 (P7)


title: 11-4

source_name: descendens

value: FALSE

value: descendens


title: Gallus gallus utricle, cell-141


title: Gallus gallus utricle, cell-143


title: BLISS HU rep2


title: Gallus gallus utricle, cell-149


title: Gallus gallus utricle, cell-140


title: Gallus gallus utricle, cell-151


title: Gallus gallus utricle, cell-139


title: BLISS HU BI8626 rep3


title: BLISS HU Dox BI8626 rep1


title: Gallus gallus utricle, cell-137


title: Gallus gallus utricle, cell-138


title: 31-1

value: non

value: sigmoideum


title: BLISS HU Dox rep1

value: Bone Marrow

value: U-2 OS MYC-tet-on


title: Gallus gallus utricle, cell-136


title: 59-5

value: CD


title: 107-2


title: Gallus gallus utricle, cell-135


title: Gallus gallus utricle, cell-134


title: BLISS HU BI8626 rep1

value: osteosarcoma cell line

value: Dox inducible overexpression of MYC


title: 11-2

source_name: ascendens

value: ascendens


title: Gallus gallus utricle, cell-133


title: Gallus gallus utricle, cell-132


title: BLISS HU rep1


title: Gallus gallus utricle, cell-131


title: RNAseq_HybNeo3_2

city: Edinburgh

first: Catherine

last: Naughton

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description:
Chinese hamster/human hybrid retaining the following human chromosomes ; 4, 6, 8, 11, 13, 18 ,X and a 3 carrying a neocentromere (Neo3).
HybNeo3_RNAseq_norm.bdg

data_processing:
RNA-seq reads were aligned to the human reference genome (hg19) using TopHat v2 and processed with Samtools v1.6 and the deepTools “bamCoverage” tool with RPKM normalisation across Human chromsome 3 and with a 200bp bin size.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files of combined replicates for human chromosome 3 only, with RPKM normalisation and binsize of 200bp.

organism:
Homo sapiens
Cricetulus griseus

source_name: Somatic cell hybrid

growth_protocol: Human/Hamster hybrid cell lines GM10253A and HybNeo3 were grown in RPMI 1640 with L-Glutamine, 10% FCS and penicillin and streptomycin. Human parenral lymphoblastoid cell line was grown in RPMI 1640 with L-Glutamine, 20% FCS and penicillin and streptomycin.

extract_protocol:
Total RNA was extracted from cells using RNeasy mini kit (Qiagen) with on-column DNase I digestion (RNAse-Free DNase Set, Qiagen). Ribosomal RNA was depleted using Illumina® Ribo-Zero Plus rRNA Depletion Kit (Illumina, 20040526) following the manufacturer’s instructions.
Libraries for RNA-seq were prepared and indexed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645L) and NEBNext Singleplex Oligos for Illumina (NEB #E7335, E7500) following the manufacturer’s instructions. Single-end RNA-seq of 50-bp read length was performed on Illumina Hi-Seq 2000.

treatment_protocol: Normally growing cells

value: untreated


title: Gallus gallus utricle, cell-130


title: RNAseq_HybNeo3_1


title: RNAseq_GM10253A_2

description:
Chinese hamster/human hybrid retaining human chromosome #3
GM10253A_RNAseq_norm.bdg


title: Gallus gallus utricle, cell-128


title: 28-3

value: UC

value: yes

value: rectum


title: Gallus gallus utricle, cell-127

value: Utricle sensory epithelia


title: 101-2

value: transversum


title: 59-6


title: Gallus gallus utricle, cell-129

value: Wildtype

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-126


title: Gallus gallus utricle, cell-125


title: 11-1

value: Control

value: FALSE

value: coecum


title: RNAseq_GM10253A_1


title: Gallus gallus utricle, cell-123


title: TTseq_HybNeo3_ExoKD_2

description:
Chinese hamster/human hybrid retaining the following human chromosomes ; 4, 6, 8, 11, 13, 18 ,X and a 3 carrying a neocentromere (Neo3).
TTseq_HybNeo3_ExoKD_chr3_200.bw

data_processing:
50bp paired end reads had adapters removed (Trim Galore) and were aligned to a Human(hg38) /Hamster (GCA_003668045.1) hybrid reference genome using Bowtie2 and processed with Samtools v1.6, and the deepTools “bamCoverage” tool with RPKM normalisation across Human chromsome 3 and with a 200bp bin size.
Genome_build: Human(hg38) /Hamster (GCA_003668045.1) hybrid reference genome
Supplementary_files_format_and_content: Bigwig files of combined replicates for human chromosome 3 only,with RPKM normalisation and binsize of 200bp.

extract_protocol:
RNA extraction was performed with TRIzol (Invitrogen) following the manufacturers’ instructions. After DNase treatment (Turbo DNase, Thermo Fisher Scientific) RNA concentration and purity were determined using a NanoDrop. RNA (70 μg) was fragmented in 100 μl H20 to <1.5kb by 20 cycles of 30 seconds on/30 seconds off at high power in a Biorupter plus and RNA size assessed by agarose gel electrophoresis. Fragmented 4sU labelled RNA was biotinylated by adding 140 μl of EZ-Link Biotin-HPDP (1mg.ml-1 in dimethylformamide; Pierce, 21341), 70 μl of 10 x biotinylation buffer (100 mM Tris-HCl pH 7.5, 10 mM EDTA) and H20 to a final volume of 700 μl. This was incubated at room temperature for 1.5 h with rotation. Unincorporated biotin-HPDP was removed by two rounds of chloroform extraction with 2 ml Phase lock gel heavy tubes (Eppendorf). RNA was precipitated with 1/10 volume of 5M NaCl and an equal volume of Isopropanol. This was inverted to mix and incubated at room temperature for 10 min followed by centrifugation at 10,000g for 20 min at room temperature. RNA pellet was washed with 80% EtOH and centrifuged at 13,000 rpm for 10 min at 4°C. RNA was resuspended in 100 μl H20 and dissolved by heating to 40°C for 10 min with agitation. RNA was then immediately placed on ice and RNA concentration determined by Nanodrop spectrophotometer. Biotinylated 4sU labelled RNAs were then recovered using μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101) and separation on a μMACS Separator. For the concentration of total RNA in μg per sample an equal amount in μl of Streptavidin microbeads was added. This was incubated at room temperature for 15 min with rotation. μMacs columns were equilibrated with 900 μl room temperature washing buffer (100 mM Tris-HCl pH 7.5, 10 mM EDTA, 1 M NaCl, 0.1% Tween20). The RNA/streptavidin bead solution was then applied to the column followed by three washes with 900 μl of washing buffer at 65°C and three washes with 900 μl of washing buffer at room temperature. RNA was eluted with 2 x 100 μl of fresh elution buffer (100 mM dithiothreitol in RNase-free H20 ) directly into 2 ml lobind tubes (Eppendorf) containing 700μl Buffer RLT (RNeasy MinElute Cleanup Kit, Qiagen). 500 μl of 100% ethanol was added to the RNA solution, and mixed thoroughly by pipetting before RNA was purified through RNAeasy MinElute Spin Columns. RNA concentration was determined using a Nanodrop.
Libraries for RNA-seq were prepared and indexed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB #E7645L) and NEBNext Singleplex Oligos for Illumina (NEB #E7335, E7500) following the manufacturer’s instructions.

treatment_protocol: Nascent RNA was labelled by adding 500 μM 4-thiouridine (4sU)(Sigma, T4509) to untreated and siRNA (exosome) treated GM10253A and HybNeo3 cells and incubating at 37°C for 10 min. For siRNA treatment, cells (GM10253A and HybNeo3; 10%–20% confluent) were transfected with 10 nM Silencer Select Pre-designed siRNA targeting EXOSC3 (Ambion, Life Technologies) using Lipofectamine RNAi MAX (ThermoFisher) 24 h after seeding and again 48 h later. After a further 48 h exosome knockdown was confirmed by western blotting and TTseq was performed. Silencer Select RNA sequence for EXOSC3 were GAGATATATTCAAAGTTGA, part number s83102. The control RNA was Stealth RNAi siRNA Negative Control (ThermoFisher).

value: Exosome siRNA 48hr

value: nascent RNA


title: Gallus gallus utricle, cell-124


title: Gallus gallus utricle, cell-122


title: 99-1

value: non


title: Gallus gallus utricle, cell-120


title: Gallus gallus utricle, cell-121


title: Gallus gallus utricle, cell-119


title: TTseq_HybNeo3_ExoKD_1


title: TTseq_HybNeo3_2

description:
Chinese hamster/human hybrid retaining the following human chromosomes ; 4, 6, 8, 11, 13, 18 ,X and a 3 carrying a neocentromere (Neo3).
TTseq_HybNeo3_chr3_200.bw


title: 25-1

value: CD

value: ileum


title: Gallus gallus utricle, cell-118


title: 11-5

value: sigmoideum


title: Gallus gallus utricle, cell-116


title: Gallus gallus utricle, cell-115


title: Gallus gallus utricle, cell-117


title: Gallus gallus utricle, cell-114


title: TTseq_HybNeo3_1

value: untreated


title: TTseq_GM10253A_ExoKD_2

description:
Chinese hamster/human hybrid retaining human chromosome #3
TTseq_GM10253A_ExoKD_chr3_200.bw


title: 96-2


title: TTseq_GM10253A_ExoKD_1


title: Gallus gallus utricle, cell-112


title: 23-3

value: UC


title: 59-3

value: yes

value: ascendens


title: Gallus gallus utricle, cell-110

value: Utricle sensory epithelia


title: Gallus gallus utricle, cell-109


title: Gallus gallus utricle, cell-111


title: TTseq_GM10253A_1

description:
Chinese hamster/human hybrid retaining human chromosome #3
TTseq_GM10253A_chr3_200.bw


title: Gallus gallus utricle, cell-108


title: Gallus gallus utricle, cell-107


title: 65-1

value: descendens


title: 12-1


title: Gallus gallus utricle, cell-106

value: Wildtype


title: Gallus gallus utricle, cell-105

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-113


title: ES2_luteolin_1_2

city: 名古屋市昭和区

first: xuboya

last: chang

state: 愛知県

address: 日本愛知県名古屋市昭和区鶴舞町６５

country: Japan

institute: Nagoya University

data_processing:
Single-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R
Assembly: hg19
Supplementary files format and content: RNA-seq(TPM).txt

extract_protocol:
RNeasy® Mini Kit
cDNA libaries preparation and sequencing were performed by Rarevariant, Inc. (Tokyo, Japan)

value: ovarian cancer cell

value: WT

value: luteolin


title: ES2_luteolin_1_3

address: 日本愛知県名古屋市昭和区鶴舞町６５


title: ES2_luteolin_1_1

address: 日本愛知県名古屋市昭和区鶴舞町６５


title: 22-3

value: FALSE


title: Gallus gallus utricle, cell-103


title: ES2_DMSO_1_3

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: DMSO


title: 91-6

value: non

value: rectum


title: TTseq_GM10253A_2

value: nascent RNA


title: Gallus gallus utricle, cell-102


title: ES2_DMSO_1_2

address: 日本愛知県名古屋市昭和区鶴舞町６５


title: Gallus gallus utricle, cell-101


title: NK_Bach2 control_rep2

first: Shasha

last: Li

state: MO

address: 660 S Euclid Avenue

department: Rheumatology

institute: Washington University in St.Louis

data_processing:
Quality control of ATAC data was performed using the AIAP pipeline (v1.1). All libraries received the highest possible score (total_score = 10).
ATAC peaks for each sample were called as a part of the AIAP pipeline, using macs2 with FDR cutoff at 0.01. After manual inspection of the peaks called, we further filtered the resulting narrowPeak files for peaks with -log10FDR >= 9.
To call differentially accessible regions (DARs), we merged all overlapping peaks to create a union peakset. We then formed a peak-sample matrix with each entry corresponding to the number of Tn5 insertion sites in each peak for each sample. Tn5 insertion sites were also calculated as a part of the AIAP pipeline. DARs were called using DESeq2 (v1.26.0) with default parameters with the cutoff of “log2FoldChange >= 0.5 & FDR <= 0.05”.
Assembly: mm10
Supplementary files format and content: Counts_and_fold_change_of_differentially_accessible_regions.xlsx: Excel format, counts and fold change of the peaks between Bach2 knockout and control sample.

organism: Mus musculus

source_name: Primary splenic NK cells (CD3-CD19-NK1.1+NKp46+)

extract_protocol:
150k NK cells (CD3-CD19-NK1.1+NKp46+) from spleen were sorted out.
ATAC-seq libraries were generated using the omni-ATAC protocol.

value: wildtype

value: no treatment


title: NK_Bach2 control_rep1

value: Primary splenic NK cells (CD3-CD19-NK1.1+NKp46+)


title: NK_Bach2 cKO_rep1

value: Bach2 knockout


title: 52-5

value: CD

value: yes

value: sigmoideum


title: NK_Bach2 cKO_rep2


title: Gallus gallus utricle, cell-100

value: Utricle sensory epithelia

value: Wildtype


title: ES2_DMSO_1_1

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: ovarian cancer cell


title: 12-2

value: Control

value: ascendens


title: 52-2

value: FALSE


title: 48-2

value: UC


title: ES2_siVRK1_1_3

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: WT


title: Aldh 2.1 +/+ WT la6

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: GRCz11
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

organism: Danio rerio

source_name: whole larvae

growth_protocol: Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.

extract_protocol:
Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf, collected and snap frozen in liquid nitrogen in a clutch of 50.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

tag: developmental stage

value: larvae (120hpf)

value: whole larvae


title: Aldh 2.1 +/+ WT la5


title: Gallus gallus utricle, cell-104

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-099


title: Aldh 2.1 +/+ WT la3


title: ES2_siVRK1_1_1

address: 日本愛知県名古屋市昭和区鶴舞町６５


title: Gallus gallus utricle, cell-098


title: ES2_siVRK1_1_2

address: 日本愛知県名古屋市昭和区鶴舞町６５


title: 12-4

value: non

value: descendens


title: Aldh 2.1 +/+ WT la2


title: Gallus gallus utricle, cell-097


title: 12-3

value: transversum


title: Gallus gallus utricle, cell-095


title: 34-8

value: rectum


title: Aldh 2.1 -/- KO la6

value: aldh2.1 knockout


title: Gallus gallus utricle, cell-096


title: 120-5


title: 40-1

value: CD

value: ileum


title: ES2_siCont_1_3

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: siCtrl


title: ES2_siCont_1_1

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: ovarian cancer cell


title: Aldh 2.1 -/- KO la5


title: A2780_luteolin_1_3

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: luteolin


title: Aldh 2.1 -/- KO la3


title: Gallus gallus utricle, cell-094

value: Utricle sensory epithelia

value: Wildtype


title: Gallus gallus utricle, cell-093


title: 9-4

value: Control

value: FALSE


title: 50-2


title: A2780_luteolin_1_2

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: WT


title: Aldh 2.1 -/- KO la2

value: larvae (120hpf)

value: whole larvae


title: A2780_luteolin_1_1

address: 日本愛知県名古屋市昭和区鶴舞町６５


title: Gallus gallus utricle, cell-092

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-091


title: Aldh 2.1 +/+ WT la1


title: ES2_siCont_1_2

address: 日本愛知県名古屋市昭和区鶴舞町６５


title: A2780_DMSO_1_3

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: DMSO


title: 9-6

value: non

value: descendens


title: A2780_DMSO_1_2

address: 日本愛知県名古屋市昭和区鶴舞町６５


title: Gallus gallus utricle, cell-090


title: 39-1

value: UC

value: sigmoideum


title: 116-2

value: CD

value: rectum


title: 9-7


title: Gallus gallus utricle, cell-089


title: A2780_DMSO_1_1

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: ovarian cancer cell


title: A2780_siVRK1_1_3

address: 日本愛知県名古屋市昭和区鶴舞町６５


title: Aldh 2.1 -/- KO la1

value: aldh2.1 knockout


title: 113-2


title: 1:1_1

city: Seoul

first: Da-Hyun

last: Kim

address: 1 Gwanakro

country: South Korea

institute: Seoul National University

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012)
Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010)
The RC (Read Count) data were processed based on TMM+CPM normalization method using EdgeR within R (R development Core Team, 2020) using Bioconductor (Gentleman et al.,2004)
Assembly: RNA-seq reads were aligned to the reference genome (UCSC hg19).
Supplementary files format and content: matrix tables includes RPKM values for each sample

source_name: HepG2, HUVEC

growth_protocol: In this study, we prepared 3 types of spheroids: a HepG2 only spheroid and hybrid spheroid composed of HepG2 cells and HUVEC with different ratio (4:1 and 1:1). They were grown in a 96-well plate with U-shaped bottom wells (Sumitomo Bakelite, Tokyo, Japan). For suspension culture, EGM-2 medium was used for the cancer monoculture spheroid and the co-culture spheroid. All cell suspensions were prepared for total 5000 cells and mixed with 1% volume ratio of Matrigel in 200 μL of medium. After pre-culturing in a 96-well plate, a spheroid was introduced into the spheroid culture device. We used 4 to 6 days cultured spheroid for the experiments.

extract_protocol:
Total RNA was extracted from spheroids by using TRIzol reagent (Invitrogen). 0.9 ug of RNA was used for constructing sequencing libraries.
Following the manufacturer’s instructions, the library was constructed by using a QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen, Austria).  Each total RNA were prepared and an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illuminacompatible linker sequence at its 5’ end. The double-stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components.

value: HepG2, HUVEC

value: Hepatocellular carcinoma, endothelial cell

value: spheroid formation with HepG2 cells and HUVECs in a 1:1 ratio


title: 1:1_2


title: Gallus gallus utricle, cell-087

value: Utricle sensory epithelia

value: Wildtype


title: A2780_siVRK1_1_2

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: WT


title: 4:1_3

value: spheroid formation with HepG2 cells and HUVECs in a 4:1 ratio


title: 4:1_2


title: Gallus gallus utricle, cell-086

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-088


title: A2780_siVRK1_1_1

address: 日本愛知県名古屋市昭和区鶴舞町６５


title: 4:1_1


title: 1:1_3


title: A2780_siCont_1_3

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: siCtrl


title: Gallus gallus utricle, cell-085


title: 40-2

value: FALSE

value: non

value: ascendens


title: Gallus gallus utricle, cell-084


title: HepG2 only_3

value: Hepatocellular carcinoma

value: spheroid formation with HepG2 cells


title: 50-1

value: CD

value: yes

value: ileum


title: HepG2 only_2


title: 51-3

value: UC

value: rectum


title: Gallus gallus utricle, cell-083


title: A2780_siCont_1_2

address: 日本愛知県名古屋市昭和区鶴舞町６５

value: ovarian cancer cell


title: 10-6

value: Control


title: A2780_siCont_1_1

address: 日本愛知県名古屋市昭和区鶴舞町６５


title: Gallus gallus utricle, cell-082

value: Utricle sensory epithelia

value: Wildtype


title: Gallus gallus utricle, cell-081


title: HepG2 only_1

value: WT


title: Sham2 [mRNA_expression_tissue]

city: Shenzhen

first: Xinjin

last: Chi

state: Guagndong

address: No. 628, Zhenyuan Road, Guangming New District

country: China

institute: he Seventh Affiliated Hospital of Sun Yat-Sen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp(version 0.20.0) softeware with default parameters in pair end mode.
The clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
The clean reads were mapped to reference of mouse mRNAs and lncRNAs using bowtie2(version 2.3.1) with parameters -q -L 16 --phred64 -p 6
TPM value and read counts of each transcript were obtained by eXpress(version 1.5.1) with parameters --no-update-check --rf-stranded.
Assembly: mm10
Supplementary files format and content: abundance measurements

source_name: Intestine

extract_protocol:
Total RNA of intestine samples was extracted respectively using the TRIzol (Thermo Scientific, USA) reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). A total amount of 1 µg RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Ribo-off™ rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme, China).
The sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA). The libraries were sequenced on an BGISEQ-500 platform.

tag: strain

value: C57BL/KsJ db/db

value: Intestine

value: 10～12 weeks old

value: Sham Operation


title: 11-6

value: FALSE

value: non


title: MLL-ENL_rearranged_PDX_1

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
CircRNAs were identified and quantified from RNA-seq data by CirComPara v0.3 using 6 backsplice detection method combinations.
Methods included in CircComPara v0.3: reads were  co-linearly mapped to reference genome with HISAT2 and processed with Cufflinks; co-linearly unmapped reads were analyzed with CIRI, CIRCexplorer and findcirc to detect circRNAs.
CircRNA annotation and all analyses were based on the Ensembl GRCh38 human genome and annotation v87.
Assembly: hg38
Supplementary files format and content: “circRNA_expression_per_sample.csv” file reports circRNA backsplice genomic coordinates, the overlapping gene(s) and the read count (as defined by CirComPara) for each sample, as a comma-separated table with circRNA IDs as rows and samples as columns.

source_name: bone marrow

growth_protocol: BCP-ALL blasts were isolated from the spleen of mice transplanted with patient derived cells by i.v. injection

extract_protocol:
RNA was exctracted with Trizol
Truseq Total RNA with Ribo Zero

treatment_protocol: No treatment

value: bone marrow

tag: sample type

value: Patient Derived Xenograft

value: bone marrow cells

tag: type of_leukemia

value: BCP-ALL

value: BCP-ALL cells isolated from patient-derived xenograft

tag: translocation


title: 43-1

tag: age

value: CD

tag: tissue

value: ileum


title: CLP2 [mRNA_expression_tissue]

value: CLP


title: 107-1

value: UC

value: ascendens


title: 51-2

value: yes

value: sigmoideum


title: BLISS HU R148KR389K rep2

data_processing:
library strategy: Breaks Labeling In Situ and Sequencing (BLISS)
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0. Reads were demultiplexed according to sample-barcode with UMI-tools v1.0.1. barcodes used as following: A1: CATCACGC, A2: GTCGTTCC, A3: TGATGATC, A4: ACGACATC
reads were aligned with Bowtie2 v2.3.4.1 to hg19 and filtered with bedtools intersect v2.26.0. Reads were counted for specific regions using the R package exomeCopy v1.18.0
Assembly: hg19
Supplementary files format and content: bedgraph

value: Bone Marrow

value: U-2 OS MYC-AID

value: osteosarcoma cell line

tag: genotype

value: Dox inducible overexpression of MYCK-R148KR389K

value: HU, 2.5mM, 4h+ Dox, 1µg/ml, 24 h + 6h IAA, 500 µM


title: Gallus gallus utricle, cell-079

value: Utricle sensory epithelia

value: Wildtype

value: Posthatch day 7 (P7)

tag: well plate

tag: plate position


title: CLP1 [mRNA_expression_tissue]

value: C57BL/KsJ db/db

value: Intestine

value: 10～12 weeks old


title: BLISS HU kless rep2

value: Dox inducible expression of kless MYC


title: MLL-ENL_rearranged_PDX_2

value: bone marrow

value: Patient Derived Xenograft

value: bone marrow cells

value: BCP-ALL

value: BCP-ALL cells isolated from patient-derived xenograft


title: Gallus gallus utricle, cell-078


title: 109-3

tag: patient

tag: biopsy

tag: diagnosis

value: UC

value: FALSE

value: non

value: sigmoideum


title: BLISS HU ctl rep2

value: Bone Marrow

tag: cell line

value: U-2 OS MYC-AID

value: osteosarcoma cell line


title: Gallus gallus utricle, cell-077

value: Utricle sensory epithelia

value: Wildtype

value: Posthatch day 7 (P7)


title: Sham1 [mRNA_expression_tissue]

value: C57BL/KsJ db/db

value: Intestine

value: 10～12 weeks old

value: Sham Operation


title: III-VI CNO 3

city: Kitakyushu-shi

first: Mitsuhiro

last: Yoshimura

state: Fukuoka

address: 1-12-8 Koshiki-hibikino, Wakamatsu-ku

institute: University of Occupational and Environmental Health, Japan

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver.10.1.1, Qiagen).
Reads were mapped to mouse reference genome (Rnor6) and quantified for 32623 genes.
Total counts were normalized by quantile method.
Differentially expressed genes were identified using Empirical Analysis of DGE tool in CLC Genomics Workbench.
Assembly: Rnor6
Supplementary files format and content: Microsoft Excel file format, containing gene name, raw read counts and normalized read counts.
Supplementary files format and content: Microsoft Excel file format, containing gene annotation.

organism: Rattus norvegicus

source_name: Dorsal horn (laminae III-VI)

extract_protocol:
Spinal cords were immediately removed, and frozen blocks containing L5 section were prepared using an ultra-low temperature freezer (PINO-600, Sakura Finetek, Osaka, Japan). Then, axial frozen spinal sections (12 µm) were made using a cryostat and mounted on RNase-free slide glasses with foil (Leica, Wetzlar, Germany). Glass slides were put into 100% ethanol for 1 min to fix spinal sections, thereafter, stained with 0.03 % Toluidin blue for 5 min. Slides were washed with DEPC water for 1 min, then put into 70 % ethanol for 1 min to dry. Specimens including laminae I-II and III-VI were collected separately into 0.5 ml PCR tubes using LMD 6 (Leica, Wetzlar, Germany). Finally, TRIzol® (Thermo Fisher Scientific, Waltham, MA, USA) was added into the PCR tube.
50ng total RNA for library prep with TAKARA SMART-Seq Stranded Kit (cat.634444)

value: Dorsal horn (laminae III-VI)

value: OT-hM3Dq-mCherry transgenic rat

value: 8 weeks

value: CNO


title: 12-5

value: Control

tag: gastroscopy

value: FALSE

tag: inflammation


title: BLISS HU WTMYC rep2

tag: cell type

value: Dox inducible expression of MYC

tag: treatment

value: HU, 2.5mM, 4h+ Dox, 1µg/ml, 24 h + 6h IAA, 500 µM


title: Gallus gallus utricle, cell-080


title: 51-1

value: UC

value: non

value: sigmoideum


title: 29-1

value: CD

value: transversum


title: Gallus gallus utricle, cell-076

value: Utricle sensory epithelia

value: Wildtype

value: Posthatch day 7 (P7)


title: III-VI CNO 2

tag: strain


title: 52-3

value: yes


title: III-VI CNO 1

value: Dorsal horn (laminae III-VI)


title: BLISS HU R148KR389K rep1

value: Bone Marrow

value: U-2 OS MYC-AID

value: osteosarcoma cell line

value: Dox inducible overexpression of MYCK-R148KR389K


title: 101-1

value: FALSE

value: ascendens


title: Gallus gallus utricle, cell-075


title: III-VI Saline 3

value: OT-hM3Dq-mCherry transgenic rat

value: 8 weeks

value: Saline


title: Gallus gallus utricle, cell-074


title: III-VI Saline 2


title: 12-6

value: Control

value: non

value: rectum


title: BLISS HU ctl rep1

value: Dox inducible expression of kless MYC


title: BLISS HU kless rep1

value: HU, 2.5mM, 4h+ Dox, 1µg/ml, 24 h + 6h IAA, 500 µM


title: III-VI Saline 1


title: 25-2

value: CD

value: ileum


title: Gallus gallus utricle, cell-073

value: Utricle sensory epithelia

value: Wildtype

value: Posthatch day 7 (P7)


title: 97-4

value: UC


title: BLISS HU WTMYC rep1

value: Bone Marrow

value: U-2 OS MYC-AID

value: osteosarcoma cell line

value: Dox inducible expression of MYC

value: HU, 2.5mM, 4h + Dox, 1µg/ml, 24 h + 6h IAA, 500 µM


title: 50-3

value: FALSE


title: 9-5

value: Control

value: descendens


title: Gallus gallus utricle, cell-072


title: I-II CNO 3

source_name: Dorsal horn (laminae I-II)

value: Dorsal horn (laminae I-II)

value: OT-hM3Dq-mCherry transgenic rat

value: 8 weeks

value: CNO


title: Gallus gallus utricle, cell-071

source_name: Utricle sensory epithelia


title: I-II CNO 2


title: Gallus gallus utricle, cell-070


title: Gallus gallus utricle, cell-069


title: RPE1, siTMED210, replicate 3

city: Lausanne

first: F.

last: van der Goot

state: Vaud

address: Bâtiment AI, Station 19

department: SV

country: Switzerland

institute: EPFL – École Polytechnique Fédérale de Lausanne

data_processing:
Paired-end sequencing reads were aligned using STAR (version 2.7.9a) to the Human reference genome GRCh38 (gencode v36, Ensembl 102)
Quantification of uniquely mapped reads to the genes was performed with HTSeq counts (framework 'HTSeq' version 0.12.4).
Quality control was done with fastQC v0.11.9
Remaining processings (filtering, normalization, DEA analysis,…) were done using edgeR (v. 3.30.3) and DESeq2 package (v. 1.28.1).
Assembly: hg38
Supplementary files format and content: CSV file including cpm values for each sample.

source_name: Retina

growth_protocol: Cells were grown in complete medium for 72 hr.

extract_protocol:
RNA was extracted from RPE1 cells using the Qiagen RNAeasy kit and QIAshredder.
Illumina protocol

treatment_protocol: Media was supplemented with siRNA and transfection reagent.

value: Retina

value: Retina Epithelium


title: RPE1, siTMED210, replicate 2


title: I-II CNO 1


title: RPE1, siTMED210, replicate 1


title: RPE1, siControl, replicate 3


title: I-II Saline 3

value: Saline


title: Gallus gallus utricle, cell-068

value: Utricle sensory epithelia

value: Wildtype

value: Posthatch day 7 (P7)


title: I-II Saline 2


title: Gallus gallus utricle, cell-067


title: 96-1

source_name: ileum

value: CD

value: yes

value: ileum


title: 53-1

value: non


title: RPE1, siControl, replicate 2


title: 10-5

source_name: sigmoideum

value: FALSE

value: sigmoideum


title: 23-4

value: UC

value: rectum


title: I-II Saline 1

value: Dorsal horn (laminae I-II)

value: OT-hM3Dq-mCherry transgenic rat


title: RPE1, siControl, replicate 1

value: Control


title: Gallus gallus utricle, cell-066


title: ChIP-seq Exp66 MYC HU rep1

data_processing:
Sequencing libraries were subjected to Illumina NextSeq 500 and NextSeq 2000 sequencing according to the manufacturer’s instructions. After base calling with Illumina’s FASTQ Generation software v1.0.0 (NextSeq 500 sequencing), high quality PF-clusters were selected for further analyses and sequencing quality was ascertained using FastQC. ChIP samples were mapped to human hg19 and ChIP-Rx samples were mapped separately to the human hg19 and to the murine mm10 genome using Bowtie1 79 or Bowtie 2 80 with -N 1 parameters. For ChIP-Rx spike-in normalized reads were calculated by dividing the number of mapped reads mapped to hg19 by the number of reads mapped to mm10 for each sample and multiplying this ratio with the smallest number of reads mapped to mm10 for any sample.
CUT&RUN samples were mapped separately to the human hg19 and either to the murine mm10 genome using Bowtie 2 with -N 1 option. For CUT&RUN spike-in normalized reads were calculated by dividing the number of mapped reads mapped to hg19 by the number of reads mapped to mm10 for each sample and multiplying this ratio with the smallest number of reads mapped to mm10 for any sample.
Assembly: hg19
Supplementary files format and content: bw

source_name: Bone Marrow

extract_protocol:
ChIP-seqCells were treated with 1% formaldehyde for 5 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using Covaris. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used. CUT&RUN: cells were harvested using Accutase (Sigma) for cell detachement. Cells were counted and washed in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine). After washing, cells were coupled to ConA-coated magnetic beads (Polysciences Europe) and subsequently permeabilized and followed by addition of primary antibody in antibody binding buffer (wash buffer, 0.05% digitonin, 2 mM EDTA) over night at 4 °C. Cells were wased in Dig-Wash buffer (Wash buffer, 0.05% digitonin) and MNase (700ng/ml) was added to each sample for 1 hr at 4 °C. After washing with Dig-wash buffer and Low-salt Rinse buffer (20 mM HEPES pH 7.5, 0.5 mM Spermidinge, 0.05% digitonin) incubation buffer (3.5 mM HEPES pH 7.5, 10 mM CaCl2, 0.05% digitoin) was added for 30 min at 4°C. STOP buffer (170 mM NaCL, 20 mM EGTA, 0.05% digitonin, 20 ug/ml RMAse A, 25 ug/ml Glycogen was added to stop the MNase digestion. DNA fragments were released at 37 °C for 30 min and proteins digested for 1 h at 50 °C after adding 0.01 % SDS and 10 mg/ml Proteinase K followed by Phenol Chloroform extraction. Precipitated DNA was resuspended in 30 ul 0.1x TE buffer
ChIP-seq Libraries were prepared according to instructions accompanying the NEBNext Ultra™ II DNA Library Prep Kit for Illumina. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and eluted. DNA fragments were amplified by 12 to 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay. CUT&RUN: NEBnext Ultra II DNA Library Prep Kit (New England Biolabs) was used. Pre-PCR samples were purified using AmpureXP beads with a ratio of 1.75x. Then half of the eluted material was used with 12-17 PCR cycles. The libraries were cleaned using Agentcourt AMPure XP Beads (ratio 1.1x, Beckman Coulter), quality, quantity and fragment size assessed on the Fragment Analyzer (Agilent) using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent)

value: Bone Marrow

value: U-2 OS MYC-tet-on

value: osteosarcoma cell line

value: Dox inducible MYC overexpression

value: Dox 1ug/ml 8h, HU, 5mM 2h


title: EVO-3

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
Gene annotated in NCBI were quantified using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

growth_protocol: Human ESCC cell line Eca109 was cultured in Dulbecco’s modified Eagle’s medium or RPMI 1640 Medium (BasalMedia, Shanghai, China), containing 10% fetal bovine serum (FBS, Biochrom AG, Berlin, Germany) and 1% penicillin-streptomycin solution (Gibco, USA), at 37° C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was isolated using the Ultrapure RNA Kit (Com Win Biotech, Bei_x0002_jing, China) following the manufacturer's protocol.
RNA libraries were prepared for sequencing using polyA selection RNA-seq protocols

treatment_protocol: Evodiamine (99.86% purity, MedChem Express, Shanghai, China) was dissolved in dimethyl sulfoxide (DMSO, Sigma-Aldrich, Darmstadt, Germany). The purity of Evodiamine is 99.86%.Eca109 cells were treated with 1‰ DMSO or Evodiamine (1μM) for 24 h, and cells were harvested.

value: Esophageal squamous cell carcinoma cell line

value: WT

value: Evodiamine (1μM)


title: Gallus gallus utricle, cell-065

value: Utricle sensory epithelia

value: Wildtype

value: Posthatch day 7 (P7)


title: 91-5

value: FALSE

value: non

value: sigmoideum


title: EVO-2


title: Gallus gallus utricle, cell-064


title: ChIP-seq Exp66 MYC H2O rep1

value: Dox 1ug/ml 8h


title: 22-6

value: CD


title: EVO-1


title: Gallus gallus utricle, cell-063


title: DMSO-3

value: 1‰ DMSO


title: ChIP-seq Exp66 Input merge

value: Bone Marrow

value: merged


title: DMSO-2


title: Gallus gallus utricle, cell-062


title: DMSO-1


title: Gallus gallus utricle, cell-061


title: Gallus gallus utricle, cell-060


title: s10_CTAD

city: Moscow

first: Andrey

last: Zhelankin

address: Malaya Pirogovskaya 1a

country: Russia

institute: Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency

data_processing:
Sequence reads were trimmed for 3' adapter sequence (TGGAATTCTCGGGTGCCAAGG). 4N barcodes were then removed by trimming the first and last 4 bases from each read. Reads with length less than 16 and more than 28 were removed.
QuickMIRSeq pipeline was used for miRNA-seq analysis. Sequence reads were mapped to miRBase to obtain read counts and RPM values for each miRNA.
Assembly: miRBase, release 21
Supplementary files format and content: Comma-separated matrix table including miRNA read counts for each sample with filtering of noisy reads

source_name: plasma

extract_protocol:
Small RNA was extracted from 600 µl of plasma using NextPrep Magnazol cfRNA Isolation Kit (Perkin Elmer) following manufacturer's protocols.
miRNA libraries were prepared using NextFlex Small RNA-Seq Kit v3 (Perkin Elmer) with NextFlex tRNA/yRNA Blockers (Perkin Elmer) and with PAGE size selection and cleanup.

treatment_protocol:
Blood from 10 healthy participants (5 males and 5 females from 25 to 40 years old) was taken in Greiner Bio-One VACUETTE vacuum collection tubes with four different anticoagulants (ACD-B, Citrate, CTAD, and K2-EDTA). Volume of collection tubes was 3.5 ml or 4 ml.
Plasma samples were obtained by double centrifugation. First step: 1000 g for 10 min at 21°C in an Eppendorf 5702R swing-rotor centrifuge. After centrifugation, the upper plasma above the buffy coat was transferred into a 15 ml sterile conical tube.
Second step: 2500 g for 20 min at 21°C in the same centrifuge. After centrifugation, 600 µl aliquots of supernatant from each sample were transferred into 1.5 ml microcentrifuge tubes which were frozen and stored at -80°C until small RNA isolation.

value: plasma

tag: Sex

value: female

tag: anticoagulant type

value: CTAD


title: s10_Citrate

value: Sodium citrate, 3.2%


title: s09_EDTA


title: AD2121-R168H-RG-Pro-D7-14-OG1_biol rep 3

city: Parkville

first: Michael

last: See

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

country: Australia

institute: MCRI

data_processing:
Processing is automated using the RNAsik pipeline (https://doi.org/10.5281/zenodo.1403976). The workflow is as follows:
Reads are aligned using the STAR aligner (version 2.7.1b)
Aligned reads are sorted with Samtools (version 1.9) and marked duplicate with Picard (2.20.2)
Finally, reads assigned to features using featureCounts from SubRead (version 2.0.0)
Assembly: Ensembl GRCh38
Supplementary files format and content: Tab delimited files including features ID's and feature information

growth_protocol: iPSC were differentiated into kidney organoids following our differentiation protocol (Takasato et al, Nature 2016) and organoids glomeruli were harvested following our published protocol (Hale et al, Nat Commun, 2018)

extract_protocol:
RNA was harvested using PureLink RNA Mini Kit (Thermo Fisher Scientific, Cat No. 12183018A). 100 ng of mRNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA kit following manufacturer's protocols.

value: iPSC-derived organoid glomeruli

tag: time


title: Gallus gallus utricle, cell-058

data_processing:
Reads were aligned to the NCBI Gallus gallus v6.0 (GCF_000002315.6) reference genome and gene expression values were quantified with a customized STAR-RSEM pipeline for single-cell data.
FastQC and Scater were used for quality control.
Low-quality cells, ERCC spike-in transcripts, and low-level expressed genes were removed.
Assembly: NCBI Gallus gallus v6.0 (GCF_000002315.6) reference genome
Supplementary files format and content: Tab-separated values file reporting counts

extract_protocol:
Utricles were dissected in ice-cold Medium 199, otolithic membranes were mechanically removed, and tissue was incubated in thermolysin (0.5 mg/mL M199 medium) for 20 minutes at 37°C. Thermolysin activity was attenuated with 10% FBS in M199. The sensory epithelia were carefully peeled off from the underlying stromal cells using a 30- gauge 1⁄2-inch hypodermic needle attached to a 1 mL syringe. For each experiment, we pooled 4-8 sensory epithelia. The epithelia were dissociated using 1X Accutase for 20 minutes at 37°C, followed by mild mechanical trituration, and washed twice with PBS using a centrifugation step (300 x g, 5 min, room temperature (RT)). Viable single cells were isolated with a Becton Dickinson FACSAria Fusion flow cytometer (Ellwanger et al., 2018). Two independent batches of 270 cells were deposited into individual wells of 96-well plates, prefilled with 4 μl of a premade lysis solution with 1 U/μl of recombinant RNase inhibitor, 0.1% Triton X-100, 2.5 mM dNTP mix, 2.5 μM oligo d(T)30 VN (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT). Plates containing sorted cells were immediately sealed, frozen on dry ice, and stored at −80°C.
Single-cell RNA-seq was performed via Picelli and colleagues’ method (Picelli et al., 2014) using SMARTscribe for reverse transcription followed by 22 amplification cycles. Amplified cDNAs were purified by AMPure Beads cleanup using a Biomek FX automated platform and assessed with a fragment analyzer (Agilent) for quantitation and quality assurance. Barcoded libraries were synthesized using a scaled-down Nextera XT protocol (Mora-Castilla et al., 2016) in a total volume of 4 μl. A total of 384 libraries were pooled, and paired-end sequenced (2 x 150 bp) on a NextSeq 500/550 High Output flow cell.

tag: age


title: 10-2

data_processing: The resulting CEL files were pre-processed using the RMA algorithm as implemented in Affymetrix Power Tools, including a log2 transformation step (version 1.16.1) [cite 12925520]. The probes were summarized using custom CDF files remapped to Ensembl genes (Brain array) [PMID 16284200].

extract_protocol: All intestinal biopsies were placed immediately in RNAlater (Qiagen) stored in a refrigerator and later transferred to a -80ºC freezer for long time storage until RNA extraction. The biopsy tissue was transferred into a tube and homogenized with Ultra Turrax (IKA, Staufen, Germany), together with 700µl Qiazol reagent (company ref). The quality and concentration of the purified total RNA was investigated on a Bioanalyzer 2100  (Agilent) using the RNA 6000 Nano Labchip kit (Agilent technologies, Santa Clara, CA), and all RNA sample concentrations were measured on a ND-8000 NanoDrop (Thermo Fisher Scientific, Waltham, MA).  RNA quality was evaluated based on the 28S/18S ratio RIN (RNA integrity number. The RIN value from the human biopsy materials varied but all values above 7 were used for Array. RNA was stored at -80°C until use.

value: Control

tag: tissue

value: ascendens


title: Gallus gallus utricle, cell-059

value: Utricle sensory epithelia

tag: genotype

value: Wildtype


title: AD2121-R168H-RG-Pro-D7-14-OG2_biol rep 2


title: AD2118-R168H-RG-Pro-D7-14-OG2_biol rep 1


title: s10_ACD-B

value: ACD-B


title: s09_Citrate


title: AD2122-R168H-RG-Un-D7-14-OG1_biol rep 3


title: Gallus gallus utricle, cell-057

value: Posthatch day 7 (P7)

tag: well plate


title: 53-3

value: FALSE

value: non

value: sigmoideum


title: 22-7

source_name: rectum

value: CD

value: rectum


title: Gallus gallus utricle, cell-056

tag: plate position


title: s09_ACD-B


title: AD2122-R168H-RG-Un-D7-14-OG2_biol rep 2


title: s10_EDTA


title: 127-5

tag: patient

value: yes


title: s08_EDTA

value: plasma

value: male


title: 53-4

source_name: transversum

tag: biopsy

value: transversum


title: Gallus gallus utricle, cell-055


title: AD2119-R168H-RG-Un-D7-14-OG1_biol rep 1


title: 48-1

source_name: descendens

tag: diagnosis

value: UC

value: descendens


title: 91-3

source_name: ascendens


title: s08_CTAD

value: CTAD


title: 22-2

source_name: coecum

value: coecum


title: AD2131-R291W-D7-14-OG1_biol rep 3

tag: cell line

value: iPSC-derived organoid glomeruli


title: Gallus gallus utricle, cell-054

value: Utricle sensory epithelia

value: Wildtype


title: AD2127-R291W-D7-14-OG1_biol rep 2


title: 125-1

tag: gastroscopy


title: s08_Citrate

value: Sodium citrate, 3.2%


title: 123-5

value: FALSE

tag: inflammation


title: AD2052-R291W-D7-14-OG2_biol rep 1

tag: cell type


title: s07_EDTA

value: female


title: Gallus gallus utricle, cell-051

value: Posthatch day 7 (P7)


title: 91-4

value: non


title: 27-1

value: sigmoideum


title: s07_CTAD


title: s07_Citrate


title: AD2155-R168H-D7-14-OG1_biol rep 3


title: 91-2


title: Gallus gallus utricle, cell-050


title: AD2041-R168H-D7-14_biol rep 1


title: s07_ACD-B

value: ACD-B


title: 121-7

value: Control

value: rectum


title: 20-1


title: 37-2

value: yes


title: Gallus gallus utricle, cell-053


title: Gallus gallus utricle, cell-048


title: s06_CTAD

value: plasma


title: Gallus gallus utricle, cell-047


title: AD2110-R138Q-C83-D7-14-OG2_biol rep 3


title: 91-1

value: UC

value: ileum


title: Gallus gallus utricle, cell-052


title: AD2108-R138Q-C83-D7-14-OG1_biol rep 2


title: Gallus gallus utricle, cell-049


title: Gallus gallus utricle, cell-046


title: AD2145-R168H-D7-14-OG1_biol rep 2


title: 31-3


title: s08_ACD-B

value: male


title: s06_Citrate


title: 20-3

value: transversum


title: 90-3


title: Gallus gallus utricle, cell-044

value: Utricle sensory epithelia


title: s05_EDTA


title: s05_CTAD

value: CTAD


title: AD2048-P118L-D7-14_biol rep 2

value: iPSC-derived organoid glomeruli


title: Gallus gallus utricle, cell-045

value: Wildtype


title: Gallus gallus utricle, cell-043


title: 120-4

value: FALSE


title: 20-4

value: descendens


title: 36-1

value: non


title: Gallus gallus utricle, cell-041

value: Posthatch day 7 (P7)


title: AD2043-P118L-D7-14_biol rep 1


title: AD2050-R138Q-C83-D7-14_biol rep 1


title: s05_Citrate

value: Sodium citrate, 3.2%


title: AD2044-G92C-D7-14_biol rep 1


title: Gallus gallus utricle, cell-042


title: AD2126-G92C-D7-14-OG1_biol rep 3


title: 116-1

value: CD

value: sigmoideum


title: s04_CTAD


title: s05_ACD-B

value: ACD-B


title: Gallus gallus utricle, cell-039


title: 38-2


title: s04_Citrate

value: plasma


title: AD2124-G92C-D7-14-OG2_biol rep 2


title: AD2125-P118L-D7-14-OG1_biol rep 3


title: Gallus gallus utricle, cell-040


title: 19-1

value: yes

value: coecum


title: 112-1

value: UC


title: Gallus gallus utricle, cell-037


title: s04_EDTA

value: male


title: 90-2


title: 90-1


title: Gallus gallus utricle, cell-038

value: Utricle sensory epithelia


title: s03_EDTA


title: Gallus gallus utricle, cell-036


title: AD2141-808-5-CTL-D7-14-OG2_biol rep 1

value: WT


title: AD2112-808-3-CTL-D7-14_biol rep 3

value: iPSC-derived organoid glomeruli


title: s03_CTAD

value: CTAD


title: AD2156-808-5-CTL-D7-14-OG2_biol rep 3


title: Gallus gallus utricle, cell-035

value: Wildtype


title: s03_Citrate


title: Gallus gallus utricle, cell-034


title: AD2101-808-3-CTL-D7-14-OG2_biol rep 2


title: 109-2

value: FALSE


title: AD2101-808-3-CTL-D7-14-OG1_biol rep 1


title: 19-2

value: ileum


title: s03_ACD-B


title: 42-4

value: Control

value: non

value: descendens


title: AD2156-808-5-CTL-D7-14-OG1_biol rep 2


title: Gallus gallus utricle, cell-033

value: Posthatch day 7 (P7)


title: 89-2

value: rectum


title: Gallus gallus utricle, cell-032


title: COVID_19 lung autopsy sample 3

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human GRCh37 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Transcript abundances was estimated in Fragments Per Kilobase of exon per Million mapped reads (FPKM) by using Cufflinks v2.1.1 package.
Assembly: hg19
Supplementary files format and content: excel file storing expression FPKM values

source_name: Lung

extract_protocol:
Samples were lysed by Trizol. RNA ioslation protocol was followed the instruction of Trizol reagent.
RNAseq libraries were prepared using the TruSeq Stranded mRNA Library Preparation kit (Illumina) according to the manufacturer's instructions.

value: Lung

value: Lung cells

tag: disease state


title: s02_EDTA

value: plasma

value: female


title: 19-3

value: CD

value: ascendens


title: Gallus gallus utricle, cell-031

value: Utricle sensory epithelia


title: COVID_19 lung autopsy sample 2


title: s02_CTAD


title: s02_Citrate

value: Sodium citrate, 3.2%


title: 34-6

value: UC


title: Gallus gallus utricle, cell-030

value: Wildtype


title: PRIMARYCHON_CNR_7366_PBS_0180

city: Chapel Hill

first: Douglas

middle: H

last: Phanstiel

state: NC

address: 104 Manning Dr (Thurston Bowles Building), Rm 4019

institute: University of North Carolina at Chapel Hill

description:
Cut and run in primary human articular chondrocytes
MERGE_CHON_ATAC_ATAC_CND_PBS_0180_S_peaks.narrowPeak
MERGE_CHON_ATAC_ATAC_CND_PBS_0180_S.bw

data_processing:
In situ Hi-C datasets were processed using a modified version of the Juicer Hi-C pipeline (https://github.com/EricSDavis/dietJuicer) with default parameters as previously described (Durand et al., 2016). Reads were aligned to the hg19 human reference genome with bwa (v0.7.17) and MboI was used as the restriction enzyme. Four  replicates were aligned and merged to create a Hi-C mega map with a total of 2,779,816 Hi-C read pairs yielding 2,373,892,594 valid Hi-C contacts (85.40%).
Looping interactions were called with Significant Interaction Peak (SIP) caller (v1.6.2) and Juicer tools (v1.14.08) using the replicate-merged, mapq > 30 filtered hic file with the following parameters: “-norm KR -g 2.0 -min 2.0 -max 2.0 -mat 2000 -d 6 -res 5000 -sat 0.01 -t 2000 -nbZero 6 -factor 1 -fdr 0.05 -del true -cpu 1 -isDroso false”. Loop anchors were expanded to 20 Kb and loops with overlapping anchors were filtered out (14 loops). This resulted in 9,271 loops after filtering.
Cut and run data was processed by first trimming adaptors and low-quality reads from paired-end reads using Trim Galore! (v0.4.3). Reads were aligned to the hg19 genome with BWA mem (v0.7.17) and sorted with Samtools (v1.9). Duplicates were removed with PicardTools (v2.10.3) and mitochondrial reads were removed with Samtools idxstats. Samtools was also used to merge donors, and index BAM files. Peaks were called from the merged alignments using MACS2 with the following settings: -f BAM -q 0.01 -g hs --nomodel --shift 100 --extsize 200 --keep-dup all -B --SPMR (v2.1.1.20160309). Peaks were then merged using bedtools (v2.26), and multicov was used to extract counts from each replicate BAM file. Signal tracks were made from alignments using deeptools (v3.0.1).
Assembly: hg19
Supplementary files format and content: hic and bedpe files

source_name: Primary human articular chondrocytes

growth_protocol: Primary articular chondrocytes were isolated via enzymatic digestion from human femoral cartilage obtained from tissue donors without a history of arthritis, as previously described (Loeser et al. 2003). Two million primary articular chondrocytes from 2 donors were plated onto four 6cm plates in DMEM/F12 media supplemented with 10% fetal bovine serum, 0.1% penicillin streptomycin solution, 0.1% amphotericin B, and 0.04% gentamicin. Cells were serum-starved by treatment with serum-free DMEM/F12 media with 1% penicillin streptomycin solution, 1% amphotericin B, and 0.04% gentamicin for 2 h.

extract_protocol: Primary chondrocytes were washed with 1X PBS and treated with trypsin-EDTA (0.25%) for 5 minutes. Trypsin was quenched and cells were pelleted at 4°C for 5 minutes at 1000g. Cells were resuspended in 1mL plain DMEM per million cells and crosslinked in 1% formaldehyde for 10 min with rotation before quenching in a final concentration of 125mM glycine for 5 min with rotation. Cells were pelleted by spinning at 1000g for 5 min at 4°C. Each 2 million cell pellet was washed in 1mL cold PBS prior to flash freezing in liquid nitrogen. Thawed pellets were resuspended in 1mL ice-cold nuclei isolation buffer (NE1 buffer; 20mM HEPES pH 7.5, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, 1X CPI added fresh) and incubated for 10 min at 4°C with rotation. Nuclear pellet was collected by centrifugation at 1000g for 5 min at 4°C, then resuspended in 1mL of ice-cold wash buffer (WB; 20mM HEPES pH 7.5, 0.2% Tween-20, 150mM NaCl, 150mM BSA, 0.5mM Spermidine, 10mM Na-Butyrate, 1X CPI added fresh). 10uL concanavalin A lectin beads washed and resuspended in binding buffer (BB; 20mM HEPES pH 7.5, 10mM KCl, 1mM CaCl2, 1mM MnCl2) were added to each sample and incubated for 10 min at RT. Beads were reclaimed and resuspended in 50uL antibody buffer (AbB; WB supplemented with 0.1% Triton X-100 and 2mM EDTA). 0.01ug/uL H3K27ac antibody in AbB was added to each sample and samples were incubated overnight at 4°C with mixing at 1000xRPM. Beads were reclaimed and washed with 1mL triton wash buffer (TwB; WB supplemented with 0.1% Triton X-100) without mixing. Beads were reclaimed and resuspended in 50uL AbB. 2.5uL CUTANA pAG-MNase (Epicypher, #15-1016) was added and samples were incubated for 1 h at 4°C on a metal block. Beads were reclaimed and washed twice with 1mL TwB before resuspension in 100uL TwB. To digest chromatin, 2uL 100mM CaCl2 was added and samples were incubated for 30 min at 4°C on a metal block. Digestion was halted by the addition of 100uL 2X STOP buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.1% Triton X-100, 50ug/mL RNAse A). Samples were incubated for 20 min at 37°C to release pA-MNase cleaved fragments from nuclei). Beads were placed on a magnet and the supernatant containing DNA fragments was transferred to a new tube. To reverse crosslinks, 2uL 10% SDS and 2uL 20mg/mL proteinase K were added to each sample and incubated for 1 h at 65°C. DNA was purified using the Zymo DNA Clean & Concentrator Kit according to manufacturer’s protocols using 5 volumes of DNA binding buffer. DNA was eluted in 55uL water. Sequencing libraries were prepared from CUT&RUN fragments using KAPA HyperPrep with library amplification kit (no. KK8504) following the manufacturer’s instructions. Post-ligation bead cleanup was performed with two rounds of 1.2X volumes of beads and DNA was eluted in a final volume of 25uL 10mM Tris-HCl pH 8. Library amplification was performed with 20uL of the adapter ligated DNA with 12 PCR cycles. One round post amplification cleanup was performed with 1.2X volumes of beads. The resulting libraries were then quantified by Qubit and Tapestation. A low depth sequence was performed first using the Miniseq sequencer system (Illumina) and analyzed using the Juicer pipeline to assess quality control. The resulting libraries underwent paired-end 2x150bp sequencing on an Illumina NextSeq sequencer.

tag: cell line/type

value: Primary human articular chondrocytes

tag: antibody

tag: donor

tag: treatment

value: PBS for 180 mins

tag: biological replicate

tag: technical replicate


title: s01_EDTA

tag: tissue

tag: age

tag: Sex

value: male

tag: anticoagulant type


title: Gallus gallus utricle, cell-029

first: Daniel

last: Ellwanger

institute: Amgen Inc

tag: genotype

tag: well plate

tag: plate position


title: Gallus gallus utricle, cell-027


title: 19-4

first: Lasse

last: Folkersen

institute: National Genome Center

tag: patient

tag: biopsy

tag: diagnosis

tag: gastroscopy

value: FALSE

value: non


title: 89-1

tag: inflammation

value: sigmoideum


title: 105-2

value: yes


title: s01_CTAD

value: CTAD


title: PRIMARYCHON_CNR_7365_PBS_0180

tag: cell line/type

tag: antibody

value: PBS for 90 mins


title: MOLM13_dIRF8_dTAG_4h_input_rep2_S10

city: PHILADELPHIA

first: Zhendong

last: Cao

state: PA

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania

data_processing:
Reads were aligned to human genome hg19 using Bowtie2 v2.3.5 , following parameters as previously suggested (Skene et al., 2018): --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -k1 -N1. Picard tools v1.96 was used to remove presumed PCR duplicates using the MarkDuplicates command. Bam files containing uniquely mapped reads were created using Samtools v1.1. Fragments of <40 bp or >1000 bp were filtered out. Blacklist regions defined by ENCODE, random chromosomes, and mitochondria were removed, and filtered bam files were used for downstream analysis. Read count per million (RPM)-normalized bigwig files were created by bedGraphToBigWig (UCSC).
Assembly: hg19
Supplementary files format and content: bigwig, gene track

source_name: human AML MOLM-13 cell line

growth_protocol: MOLM-13 cells were cultured in RPMI 1640-Media with 25mM HEPES supplemented with 10% Bovine Calf Serum (FCS) and 1% Penicillin/ Streptomycin.

extract_protocol:
For all the experiments, cells were collected in culture media, and crosslinked in 1% formaldehyde for 20 min at room temperature, and the reaction was sequestered with 0.125M Glycine in PBS for 10 min. The crosslinked cells were spun down, washed with PBS and freezed in -80°C until use. Ten million cells were used for H3K27ac and H3K4me1, and 50 million cells for the SPI1, respectively. Cell pellets were lysed in cell lysis buffer (10mM Tris pH 8.0, 10 mM NaCl, 0.2% NP-40) with protease inhibitor (Roche) and incubated for 15 min on ice. The cells were spun down for 30 seconds at 4,200 RPM and the buffer was removed. The cells were resuspended in 1ml nuclear lysis buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS) per 10 million cells, followed by a 10 min incubation on ice. The cells were sonicated with a bioruptor for 5 mins at 4°C and spun down at max speed for 15 mins at 4°C. Supernatants containing fragmented chromatins were collected, diluted with 7ml IP dilution buffer (20 mM Tris pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.01% SDS) per 10 million cells, and applied with respective antibodies (PU.1: 10 μg, CST#2266; H3K27ac: 2 μg, #ab4729, H3K4me1: 2μg, #ab8895). For each antibody, 30 μl of protein A magnetic beads (Invitrogen) were applied after washing with 0.5% BSA in TBS for 3 times and blocked at 4°C on a rotor for 2h. The mixture was incubated overnight at 4°C in rotation. The beads were washed once with IP wash I buffer (20 mM Tris pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.01% SDS), twice with high salt buffer (20 mM Tris pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP wash 2 buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate), and twice with 1xTE. The beads were incubated with 200 μl elution buffer (50mM Tris 8.0,10mM EDTA, 1%SDS), vortexed 3x for 5s, followed by shaking at 950 RPM at 65°C for 15 mins. Supernatants were collected, and reverse crosslinking was performed in 0.25M NaClat 65°C overnight. non-DNA content was eliminated with 2 μl RNase A for 1 hr at 37 °C, followed by 0.2 mg/ml Proteinase K for 2 hr at 42°C.
ChIP DNA was purified using QIAquick PCR purification kit according to manufacturer’s instructions, and eluted with 40 μl water. ChIP-seq libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645L), and the optimal cycle numbers were determined by NEBNext® Library Quant Kit for Illumina (E7630L). Library quality was assessed using the high sensitivity Bioanalyzer kit (Agilent) and libraries were pooled and single-end sequenced for 75 bp on the Nextseq 500 platform.

treatment_protocol: For targeted degradation, MOLM13-dIRF8 (cells derived from MOLM13 expressing degradable IRF8 via dTAG system with endogenous IRF8 depletion) cells were treated with either DMSO or 500 nM dTAG-47 compound and collected at 4h and 24h timepoints.

tag: cell line


title: 27-2


title: 100-6


title: MOLM13_dIRF8_DMSO_4h_input_rep2_S9


title: PRIMARYCHON_CNR_7365_PBS_0090

description:
Cut and run in primary human articular chondrocytes
MERGE_CHON_ATAC_ATAC_CND_PBS_0090_S_peaks.narrowPeak
MERGE_CHON_ATAC_ATAC_CND_PBS_0090_S.bw

data_processing:
library strategy: Cut&Run
In situ Hi-C datasets were processed using a modified version of the Juicer Hi-C pipeline (https://github.com/EricSDavis/dietJuicer) with default parameters as previously described (Durand et al., 2016). Reads were aligned to the hg19 human reference genome with bwa (v0.7.17) and MboI was used as the restriction enzyme. Four  replicates were aligned and merged to create a Hi-C mega map with a total of 2,779,816 Hi-C read pairs yielding 2,373,892,594 valid Hi-C contacts (85.40%).
Looping interactions were called with Significant Interaction Peak (SIP) caller (v1.6.2) and Juicer tools (v1.14.08) using the replicate-merged, mapq > 30 filtered hic file with the following parameters: “-norm KR -g 2.0 -min 2.0 -max 2.0 -mat 2000 -d 6 -res 5000 -sat 0.01 -t 2000 -nbZero 6 -factor 1 -fdr 0.05 -del true -cpu 1 -isDroso false”. Loop anchors were expanded to 20 Kb and loops with overlapping anchors were filtered out (14 loops). This resulted in 9,271 loops after filtering.
Cut and run data was processed by first trimming adaptors and low-quality reads from paired-end reads using Trim Galore! (v0.4.3). Reads were aligned to the hg19 genome with BWA mem (v0.7.17) and sorted with Samtools (v1.9). Duplicates were removed with PicardTools (v2.10.3) and mitochondrial reads were removed with Samtools idxstats. Samtools was also used to merge donors, and index BAM files. Peaks were called from the merged alignments using MACS2 with the following settings: -f BAM -q 0.01 -g hs --nomodel --shift 100 --extsize 200 --keep-dup all -B --SPMR (v2.1.1.20160309). Peaks were then merged using bedtools (v2.26), and multicov was used to extract counts from each replicate BAM file. Signal tracks were made from alignments using deeptools (v3.0.1).
Assembly: hg19
Supplementary files format and content: hic and bedpe files

tag: donor

tag: treatment

tag: biological replicate


title: s01_ACD-B

tag: tissue

value: plasma

tag: age

value: ACD-B


title: MOLM13_dIRF8_4h_dTAG_PU1_rep3_S16

value: PU.1 (Cell Signaling Technology (Cat #:2266)


title: COVID_19 lung autopsy sample 1

value: Lung

tag: cell type

value: Lung cells

tag: disease state


title: C28_HiC_1.4

description:
Hi-C in C-28/I2 cell line
C28_HiC_megaMap_inter_30.hic
C28_HiC_megaMap_SIP_20kb_loops.bedpe

source_name: C-28/I2 cell line

extract_protocol: C-28/I2 cells were cultured in DMEM/F12 media with 10% fetal bovine serum, 0.1% penicillin streptomycin solution, 0.1% amphotericin B, and 0.04% gentamicin. Cells were treated with DMEM/F12 media with 1% ITS-Plus for 48 hours prior to experiments to promote the chondrocyte phenotype. Cells were then washed with 1X PBS and treated with trypsin-EDTA (0.25%) for 3 minutes. Trypsin was quenched and cells were pelleted at 4°C for 5 minutes at 300g. Cells were resuspended in 1mL DMEM/F12 per million cells and crosslinked in 1% formaldehyde for 10 min with rotation before quenching in a final concentration of 0.2M glycine for 5 min with rotation. Cells were pelleted at 300g for 5 min at 4°C. Pellets were washed with cold PBS and aliquoted into ~3 million cell aliquots. Pellets were flash frozen in liquid nitrogen and stored at -80°C. In situ Hi-C was performed as previously described42. Pellets were lysed in ice-cold Hi-C lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% IGEPAL CA630) with 50μL of protease inhibitors for 15 min on ice. Cells were pelleted and washed using the same buffer. Pellets were resuspended in 50μL 0.5% SDS and incubated at 62°C for 7 min. Reactions were quenched with 145μL water and 25μL 10% Triton X-100 at 37°C for 15 min. Chromatin was digested overnight with 25μL 10X NEBuffer2 and 100U MboI at 37°C with rotation. Reactions were incubated at 62°C for 20 min then cooled to RT. Fragment overhangs were repaired by adding 37.5μL 0.4mM biotin-14-dATP; 1.5μL each 10mM dCTP, dGTP, dTTP; 8μL 5U/μL DNA Polymerase I, Large (Klenow) Fragment and incubating at 37°C for 1.5 h with rotation. Ligation was performed by adding 673μL water, 120μL 10X NEB T4 DNA ligase buffer, 100μL 10% Triton X-100, 6μL 20mg/mL BSA, and 1μL 2000U/μL T4 DNA ligase and incubating at RT for 4 h with slow rotation. Samples were pelleted at 2500g, resuspended in 432μL water, 18μL 20mg/mL proteinase K, 50μL 10% SDS, and 46μL 5M NaCl, incubated at 55°C for 30 min, and then transferred to 68°C overnight. Samples were cooled to RT and 1.6x volumes of pure ethanol and 0.1x volumes of 3M sodium acetate pH 5.2 were added to each sample, prior to incubation at -80°C for over 4-6 h. Samples were spun at max speed at 2°C for 15 min and washed twice with 70% ethanol. Pellets were dissolved in 130μL 10mM Tris-HCl pH 8.0 and incubated at 37°C for 1-2 h. Samples were stored at 4°C overnight. DNA was sheared using the Covaris LE220 (Covaris, Woburn, MA) to a fragment size of 300-500bp in a Covaris microTUBE. DNA was transferred to a fresh tube and the Covaris microTUBE was rinsed with 70μL of water and added to the sample. A 1:5 dilution of DNA was run on a 2% agarose gel to verify successful shearing. Sheared DNA was size selected using AMPure XP beads. 0.55x volumes of 2X concentrated AMPure XP beads were added to each reaction and incubated at RT for 5 min. Beads were reclaimed on a magnet and the supernatant was transferred to a fresh tube. 30μL 2X concentrated AMPure XP beads were added and incubated for 5 min at RT. Beads were reclaimed on a magnet and washed with fresh 70% ethanol. Beads were dried for 5 min at RT prior to DNA elution in 300μL 10mM Tris-HCl pH 8. Undiluted DNA was run on a 2% agarose gel to verify successful size selection between 300-500 bp. 150μL 10mg/mL Dynabeads MyOne Streptavidin T1 beads were washed with 400μL 1X Tween washing buffer (TWB; 250μL Tris-HCl pH 7.5, 50μL 0.5M EDTA, 10mL 5M NaCl, 25μL Tween 20, 39.675μL water). Beads were then resuspended in 300μL 2X Binding Buffer (500μL Tris-HCl pH 7.5, 100μL 0.5M EDTA, 20mL 5M NaCl, 29.4mL water), added to the DNA sample, and incubated at RT for 15 min with rotation. DNA-bound beads were then washed twice with 600μL 1X TWB at 55°C for 2 min with shaking. Beads were resuspended in 100μL 1X NEBuffer T4 DNA ligase buffer, transferred to a new tube, and reclaimed. Sheared ends were repaired by resuspending the beads in 88μL 1X NEB T4 DNA Ligase Buffer with 1mM ATP, 2μL 25mM dNTP mix, 5μL 10U/uL NEB T4 PNK, 4uL 3U/uL NEB T4 DNA polymerase I, and 1uL 5U/uL NEB DNA polymerase 1, large (Klenow) fragment and incubating at RT for 30 min. Beads were washed two more times with 1X TWB for 2 min at 55°C with shaking. Beads were washed once with 100uL 1X NEBuffer 2, transferred to a new tube, and resuspended in 90uL 1X NEBuffer 2, 5uL 10mM dATP, and 5uL NEB Klenow exo minus, and incubated at 37°C for 30 min. Beads were washed two more times with 1X TWB for 2 min at 55°C with shaking. Beads were washed in 100uL 1X Quick Ligation Reaction Buffer, transferred to a new tube, reclaimed, and resuspended in 50uL 1X NEB Quick Ligation Reaction Buffer. 2uL NEB DNA Quick Ligase and 3uL of an appropriate Illumina indexed adapter (TruSeq nano) were added to each sample before incubating at RT for 15 minutes. Beads were reclaimed and washed twice with 1X TWB for 2 min at 55°C. Beads were washed in 100uL 10mM Tris-HCl pH 8, transferred to a new tube, reclaimed, and resuspended in 50uL 10mM Tris-HCl pH 8. Hi-C libraries were amplified directly off T1 beads with 8 cycles in 5uL PCR primer cocktail, 20uL Enhanced PCR mix, and 25uL of DNA on beads. The PCR settings were as follows: 3 min at 95°C followed by 4-12 cycles of 20s 98°C, 15s at 60°C, and 30s at 72°C. Samples were held at 72°C for 5 min before holding at 4°C. Amplified samples were transferred to a new tube and brought to 250uL in 10mM Tris-HCl pH 8. Beads were reclaimed and the supernatant containing the amplified library was transferred to a new tube. Beads were resuspended in 25uL 10mM Tris-HCl pH 8 and stored at -20°C. 0.7x volumes of warmed AMPure XP beads were added to the supernatant sample and incubated at RT for 5 min. Beads were reclaimed and washed with 70% ethanol without mixing. Ethanol was aspirated. Beads were resuspended in 100uL 10mM Tris-HCl pH 8, 70uL of fresh AMPure XP beads were added, and the solution was incubated for 5 min at RT. Beads were reclaimed and washed twice with 70% ethanol without mixing. Beads were left to dry and DNA was eluted in 25uL 10mM Tris-HCl pH 8. The resulting libraries were then quantified by Qubit and Tapestation. A low depth sequence was performed first using the Miniseq sequencer system (Illumina) and analyzed using the Juicer pipeline to assess quality. The resulting libraries underwent paired-end 2x150bp sequencing on an Illumina NovaSeq sequencer. Each replicate was sequenced to an approximate depth of 750 million reads. The full sequencing depth was 2.8 billion reads.

value: C-28/I2 cell line

tag: technical replicate


title: Gallus gallus utricle, cell-025

city: South San Francisco

address: 1120 Veterans Blvd

value: Utricle sensory epithelia

tag: genotype

value: Posthatch day 7 (P7)

tag: well plate

tag: plate position


title: Gallus gallus utricle, cell-024

value: Wildtype


title: C28_HiC_1.3

growth_protocol: C-28/I2 cells were cultured in DMEM/F12 media with 10% fetal bovine serum, 0.1% penicillin streptomycin solution, 0.1% amphotericin B, and 0.04% gentamicin. Cells were treated with DMEM/F12 media with 1% ITS-Plus for 48 hours prior to experiments to promote the chondrocyte phenotype.


title: 88-3

city: Copenhagen

address: Artellerivej

tag: patient

tag: biopsy

tag: diagnosis

value: UC


title: PRIMARYCHON_CNR_7366_PBS_0090

tag: cell line/type

value: Primary human articular chondrocytes

value: PBS for 180 mins


title: Gallus gallus utricle, cell-028


title: C28_HiC_1.2


title: Gallus gallus utricle, cell-023


title: MOLM13_dIRF8_4h_dTAG_PU1_rep2_S15

tag: antibody


title: s06_ACD-B

tag: Sex

value: female

tag: anticoagulant type


title: Gallus gallus utricle, cell-026


title: 97-3

tag: gastroscopy

value: FALSE

tag: inflammation

value: non

value: sigmoideum


title: C28_HiC_1.1

tag: biological replicate


title: Gallus gallus utricle, cell-022

tag: tissue

tag: age


title: P2D11-rep3

first: Ting

last: Zhang

address: 100 Haining Road

department: Department of Ophthalmology

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

data_processing:
Clean data were obtained from FastQ raw data by removing adapter, ploy-N sequences and low-quality reads.
The reads were mapped to the hg38 version of human genome using TopHat2 version 2.0.9 program.
We calculated fragment per kilobase per million (FPKM) as expression level using featureCounts (v1.5.0-p3). Genes with the FPKM>1.0 in at least one sample across all samples were retained for further analysis and the expression levels were transformed to log-space by using the log2 (FPKM+1).
Genome_build: hg38
Supplementary_files_format_and_content: excel files include FPKM values for each gene in each Sample

source_name: human ESC-derived RPE cells

growth_protocol: Human ESCs (H9) were differentiated into RPE by sequential exposure to various molecules as previously described.  To passage hESC-derived RPE, cells were dissociated with TryPLE and cultured in XVIVO-10 on matrigel-coated surface with the seeding density of 105 cells/cm2. The Passaged 1 (P1) RPE cells were further cultured in XVIVO-10 for 5 weeks before they were passaged to P2.

extract_protocol:
Total RNA was extracted with Trizol and mRNA was purified by using poly-T oligo-attached magnetic beads.
The RNA was reversed transcribed by using random hexamer primer and M-MuLV Reverse Transcriptase. The double-stranded cDNA was amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and purified using AMPure XP beads (Bechman Coulter). After quantification by Qubit2.0 Fluorometer, cDNA was applied to Bioanalyzer 2100 on a High-Sensitive DNA chip (Agilent Bioanalyzer) to check the library size distribution. All sample libraries were sequenced on Illumina NovaSeq 6000 to generate 150 bp paired-end reads.

tag: cell type

value: human ESC-derived RPE cells

tag: time of culture


title: MOLM13_dIRF8_4h_dTAG_H3K4me1_rep3_S8

tag: cell line


title: 22-1

value: CD

value: ileum


title: P2D11-rep2


title: Gallus gallus utricle, cell-019

tag: genotype

tag: well plate


title: P2D5-rep3


title: 18-2

tag: patient

value: yes

value: transversum


title: 18-3

tag: biopsy


title: Gallus gallus utricle, cell-020

tag: plate position


title: MOLM13_dIRF8_4h_dTAG_H3K27ac_rep3_S7


title: MOLM13_dIRF8_4h_dTAG_H3K27ac_rep2_S3


title: Gallus gallus utricle, cell-018


title: 88-2

tag: diagnosis


title: P2D5-rep2


title: MOLM13_dIRF8_4h_dTAG_input_rep3_S12

tag: antibody


title: MOLM13_dIRF8_4h_DMSO_PU1_rep3_S14

value: PU.1 (Cell Signaling Technology (Cat #:2266)


title: Gallus gallus utricle, cell-017


title: 20-2

value: ascendens


title: 92-6

value: rectum


title: Gallus gallus utricle, cell-021

value: Utricle sensory epithelia

value: Posthatch day 7 (P7)


title: 18-1

value: UC

value: coecum


title: MOLM13_dIRF8_4h_DMSO_PU1_rep2_S13


title: 88-1

value: descendens


title: Gallus gallus utricle, cell-016

value: Wildtype


title: P2D5-rep1


title: MOLM13_dIRF8_4h_dTAG_H3K4me1_rep2_S4


title: P2D11-rep1


title: MOLM13_dIRF8_4h_DMSO_input_rep3_S11


title: P1D35-rep2


title: 127-4

value: FALSE


title: 87-4

value: non


title: P1D35-rep1


title: MOLM13_dIRF8_4h_DMSO_H3K4me1_rep2_S2


title: Gallus gallus utricle, cell-014


title: MOLM13_dIRF8_4h_DMSO_H3K4me1_rep3_S6


title: bulk_K562_rep2

city: Beijing

first: Fuchou

last: Tang

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Biomedical Pioneering Innovation Center, Peking University

description: Bulk short-read ATAC-seq of K562

data_processing:
Raw Illumina paired-end reads were trimmed by cutadapt (v3.2) to remove adaptors, including 'AGATGTGTATAAGAGACAG' at 5' ends and 'CTGTCTCTTATACACATCT' at 3' ends. It also filtered reads with quality < 20 or length < 30bp at either end.
Trimmed paired-end reads were aligned to reference genome by Bowtie2 (v2.4.2) with `--no-unal` parameter to suppress reads failed to align recorded into bam. Reads with mapping quality less than 30 were filtered. Then duplicates in aligned reads were removed by `picard MarkDuplicates`, including both PCR duplicates and Illumina sequencing optical duplicates.
ATAC-seq peaks were called from bam files by `callpeak` function of MACS2 (v2.2.7.1). We set other macs2 parameters as `--nomodel --shift -75 --extsize 150` to adapt to ATAC-seq data. The false discovery rate of peak calling was controlled by setting `-q` parameter to 0.01.
Genome_build: hg38 for human; mm10 for mouse
Supplementary_files_format_and_content: Bigwig files recorded ATAC-seq signal strength tracks. Bed files recorded coordinates of ATAC-seq peaks.

growth_protocol: K526 cells were cultured in RPMI-1640 (Gibco; 11875093) supplemented with 10% fetal bovine serum (Gibco; 26140079). HEK293T and HFF1 cells were cultured in DMEM (Gibco; 11995040) supplemented with 10% fetal bovine serum.  GM12878 cells were cultured in RPMI-1640 supplemented with 15% fetal bovine serum. eHAP1 cells were cultured in IMDM (Gibco; 12440053) supplemented with 10% fetal bovine serum. Mouse embryonic stem cells (mESCs) were cultured without feeders in equal volume of Dulbecco’s modified eagle’s medium (DMEM/F-12, Gibco; 11320033) and Neurobasal Medium (Gibco; 21103049) supplemented with 1,000 U/ml leukemia inhibitory factor (LIF, Millipore, ESG1107), 0.5× N-2 (Gibco, 17502048), 0.5× B-27 (Gibco, 10889038), 50 μg/ml Bovine Serum Albumin (BSA, Sigma-Aldrich, A3311), 2 mM L-Glutamine (Gibco, 2503081), 0.1 mM β-Mercaptoethanol (Sigma-Aldrich, M7522), 1× MEM Non-Essential Amino Acids Solution (NEAA, Gibco, 11140050), 100 U/ml Penicillin and 0.1mg/ml Streptomycin (Gibco, 15140122).

extract_protocol:
Cells (100,000-200,000 cells before freezing) were quickly thawed at 37℃ and centrifuged at 500 g for 5 min at 4℃. Then nuclei were isolated with Omni-ATAC lysis buffer (10 mM Tris-HCl (pH 7. 4), 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA630, 0.1% Tween-20, 0.01% digitonin) and incubated on ice for 3-5 min.
Nuclei were isolated with Omni-ATAC protocol lysis buffer. Then nuclei were resuspended in 50 μl tagmentation mix with Tn5 from the NovoNGS DNA Library FlashPrep Kit for Illumina, Cat. No. N233. The tagmentation reaction was performed on a thermomixer at 800 rpm, 37 °C, 30 min. To stop the tagmentation reaction, 50 μl of tagmentation stop buffer (10 mM Tris-HCl, pH 8.0, 20 mM EDTA, pH 8.0) was added to tagged nuclei. Around 20,000 nuclei stained with DAPI was sorted into 200μl tubes by FACS. The nuclei were resuspended in lysis buffer and incubated at 65℃ for 30 minutes to release Tn5. Equal volume of 10% TWEEN-20 was added to ~30ng lysed product. 2X KAPA PCR Mix was added to perform library amplification PCR: 72℃ 10 minutes; 98℃ 5 minutes; [98℃ 10 seconds, 63℃ 30 seconds, 72℃ 20 seconds] x 15 cycle; 4℃ hold. Libraries were size selected(200bp-700bp) with 2% agarose gel and sequenced on Illumina NovaSeq 6000.


title: MOLM13_dIRF8_4h_DMSO_H3K27ac_rep3_S5


title: Gallus gallus utricle, cell-013


title: Gallus gallus utricle, cell-012


title: MOLM13_dIRF8_4h_DMSO_H3K27ac_rep2_S1


title: Gallus gallus utricle, cell-011


title: P1D35-rep3


title: bulk_K562_rep1

description: Bulk short-read ATAC-seq of K562


title: p6315_RNAseq

data_processing:
Sequencing reads were aligned to human genome hg19 using STAR Aligner. Raw read counts were generated via HTSeq-count.
RPM-normalized track files (bigwig) were generated with the bedGraphToBigWig tool.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: primary human AML samples #6315

extract_protocol:
Primary human samples were first washed with the Dead Cell Removal Kit (MACS) to remove dead cells. Total RNA was isolated from 1-3 million cells using Direct-zol RNA Miniprep Plus kit (ZYMO).
RNA-seq libraries were prepared  using NEBNext® Ultra II RNA Library Prep Kit for Illumina. One μg of total RNA was poly-A selected followed by fragmentation using the NEBNext® PolyA(A) mRNA Magnetic Isolation module. The selected RNA were subjected to a first and second strand cDNA synthesis. The libraries were end-repaired and linked with Illumina adaptors. The libraries were PCR amplified using 8 cycles, followed by sequencing using the Nextseq 500 platform with 75bp single-end reads or 2x42 paired-end reads.

tag: cell ine

value: primary human AML samples #6315


title: Gallus gallus utricle, cell-015

source_name: Utricle sensory epithelia


title: 124-4


title: bulk_HFF1_rep2

description: Bulk short-read ATAC-seq of HFF1


title: Gallus gallus utricle, cell-010


title: bulk_HFF1_rep1

description: Bulk short-read ATAC-seq of HFF1


title: p592_RNAseq_rep3


title: 87-3

value: sigmoideum


title: Gallus gallus utricle, cell-009


title: bulk_HEK293T_rep2

description: Bulk short-read ATAC-seq of HEK293T


title: Gallus gallus utricle, cell-007


title: 20-5


title: 20-6


title: p592_RNAseq_rep1

source_name: primary human AML sample #592

value: primary human AML sample #592


title: p6315_IgG

data_processing:
reads were aligned to hg19 using Bowtie2 v2.3.5 (Langmead and Salzberg, 2012), following parameters as previously described (Skene et al., 2018): --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -k1 -N1. Picard tools v1.96 (Broad Institute) was applied to displace presumed PCR duplicates using the MarkDuplicates command. Bam files with uniquely mapped reads retained were generated using Samtools v1.1(Li et al., 2009). Fragments between 40-1000 bp were kept. Blacklist regions defined by ENCODE (ref), random chromosomes, and mitochondria were removed, and filtered bam files were used for further analysis. Reads per kilobase per million mapped reads (RPKM)-normalized bigwig files were created using deeptools bamCoverage (Ramírez et al., 2016) with parameters -bs 10 --smoothLength 50 --normalizedUsing RPKM --skipNAs to visualize binding signals. Tracks were loaded to UCSC genome browser for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for binding signals

growth_protocol: MOLM-13 were cultured in RPMI 1640-Media with 25mM HEPES supplemented with 10% Bovine Calf Serum (FCS) and 1% Penicillin/ Streptomycin.

extract_protocol:
CUT&RUN experiments were slightly modified from a previous protocol (Skene et al., 2018). Concanavalin A-coated beads were washed with Binding buffer (20 mM HEPES-KOH, 10 mM KCl, 1 mM NaCl and 1 mM MnCl2) prior to use. Around 2x106 live cells were collected, washed twice in Wash buffer (150 mM NaCl, 20 mM HEPES-KOH pH 7.9, 0.5 mM Spermidine and protease inhibitor cocktail), and incubated in 1ml of Wash buffer containing 20 μl of Concanavalin A-coated beads for 5-10 min with rotation at room temperature. Cell-attached beads were then resuspended with 300 μl Antibody buffer (Wash buffer with 0.05% Digitonin and 2mM EDTA) in combination with 20 μl MEF2D antibody (Abcam, #ab32845) or 2 μl IgG overnight at 4°C with rotation. Based were washed once with Dig-wash buffer (Wash buffer with 0.05% Digitonin) and resuspended in 300 μl Dig-wash buffer with 700 ng/ml pA-MN purified protein at 4°C for 1 hr with rotation. Beads were then washed twice with Dig-wash buffer, resuspended in Dig-wash buffer and chilled on a heat block on ice. Chromatin digestion was conducted in the presence of CaCl2 for 30 min, and sequestered with an equal volume of 2x STOP solution (340 mM NaCl, 20 mM EDTA, 50 μg/mL RNase A, 4 mM EGTA, 0.02% Digitonin, 50 μg/mL Glycogen and 2 pg/mL heterogenous spike-in DNA) at 37°C for 10 min. The supernatant was collected and DNA was subject to Phenol-Chloroform extraction.
Sequencing libraries were constructed with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following a previously described method for TF. Adapters were diluted 50x and 10-12 cycles of PCR amplification were applied. Library quality was assessed using the high sensitivity Bioanalyzer kit (Agilent) and libraries were pooled and paired-end sequenced for 2x42bp on the Nextseq 500 platform.
CUT&RUN

value: IgG (Sigma I8140)


title: p592_RNAseq_rep2


title: Gallus gallus utricle, cell-008


title: 46-1


title: bulk_GM12878_rep2

description: Bulk short-read ATAC-seq of GM12878


title: bulk_HEK293T_rep1

description: Bulk short-read ATAC-seq of HEK293T


title: 45-2


title: Gallus gallus utricle, cell-006


title: 123-4


title: bulk_GM12878_rep1

description: Bulk short-read ATAC-seq of GM12878


title: Gallus gallus utricle, cell-004


title: 87-2

value: CD

value: yes


title: p6315_H3K27ac


title: Gallus gallus utricle, cell-005


title: Gallus gallus utricle, cell-003


title: Parental 6Gy 48hr - RNA-seq

city: London

first: HUGANG

last: FENG

address: Chester Beatty Laboratories, 237 Fulham Road

department: Cancer Biology

institute: The Institute of Cancer Research

data_processing:
Bcl2fastq software (v2.2.20, Illumina) was used for converting the raw basecalls to fastqs and to further demultiplex the sequencing data
The STAR alignment software (v.2.5.1b) was used to align reads to the reference genome
HTSeq-count (HTSeq v0.6.1) was used to count the number of reads mapping unambiguously to genomic features in each sample
Normalised count data was generated in R using the Bioconductor package DESeq2 (v1.14.1)
The normalised data was filtered further to remove all the rows where the row sum was less than 1
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Excel spreadsheet with normalised gene counts for every gene and every sample

source_name: Immortalised fibroblast cell line

growth_protocol: 1BR3-hTERT cells were cultured in DMEM medium with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Cell pellets were subjected to Trizol lysis and RNA extraction with ZYMO Direct-zol RNA purification kit
RNA libraries were prepared for sequencing using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: 6Gy X-ray ionising radiation for Sample 4-6

tag: cell strain

value: PBRM1 WT

tag: treatment

value: Untreated


title: PBRM1 KO5 Untreated - RNA-seq

value: PBRM1 Knockout

value: 48hr post 6Gy X-ray treatment


title: K562_sgMEF2D_1

data_processing:
Sequencing reads were aligned to human genome hg38 using STAR Aligner. Raw read counts were generated via HTSeq-count.
Genome_build: hg38
Supplementary_files_format_and_content: txt, raw read counts

source_name: human CML K562 cell line

growth_protocol: MOLM-13, MV4-11, THP1 and K562 were cultured in RPMI 1640-Media with 25mM HEPES supplemented with 10% Bovine Calf Serum (FCS) and 1% Penicillin/ Streptomycin.

extract_protocol:
Total RNA was isolated from 1~5 million cells using Direct-zol RNA Miniprep Plus kit (ZYMO) with DNase I treatment in column.
RNA-seq libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep Kit (Lexogen) with 0.5-2 µg of total RNA according to the manufacturer's protocol. Library quality was checked by High Sensitivity Bioanalyzer (Agilent) and libraries with different barcodes were pooled and sequenced on the Nextseq 500 platform with 75 or 150 bp single-end reads.

treatment_protocol: MOLM-13 cells were harvested on day 5 post-infection of sgRNA, MV4;11 and K562 cells were harvested on day 4 post-infection, and THP-1 cells were harvested on day 10 post-infection.

tag: post infection

value: day 4 after infection


title: 17-3

source_name: sigmoideum

growth_protocol: Human samples, no growth protocol

value: UC

tag: gastroscopy

tag: inflammation


title: 6_15_RLT_CD8

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

data_processing:
Illumina Casava1.7 software used for basecalling.
Transcript counts calculated from Fastq files using Kallisto.
Transcript counts summarized to gene counts using tximport.
Abundance (logTPM) and estimated count measures from tximport normalized using TMM and filtered for expressed genes.
Assembly: hg19

extract_protocol:
Tumor infiltrating immune cells (TIICs) were obtained from a non-necrotic tumor piece at approximately 2 cm in diameter that could be spared for research purpose after the clinical specimens were prioritized and were dissected by pathologist. RPMI-1640 media were used to resuspend all the cells after disruption and homogenization. The cell suspension was filtered with a 70Œºm cell strainer and a layer of mononuclear cells that contained TIICs were then isolated using the Ficoll density gradient centrifugation with Ficoll-Paque‚Ñ¢ PLUS (Cytiva) as described 39. TIICs were washed three times using 40 ml of the complete RPMI media each time. After the final wash with the RPMI media, isolated TIICs were cryopreserved in the liquid nitrogen freezer or subjected to cell sorting. Peripheral blood mononuclear cells were obtained from patient‚Äôs whole blood using the Ficoll-Paque‚Ñ¢ PLUS gradient centrifugation to serve as the FACS staining control. TIICs and peripheral blood mononuclear cells were stained with the Zombie Green viability dye (Biolegend), anti-CD4-PE-CF594 (Biolegend), anti-CD8-APC (Biolegend), anti-CD19-PE (Biolegend), and anti-CD11b-BV421 (Biolegend) antibodies. After sorting with the BD FACSAria IIu Cell Sorter (Biosciences), bulk tumor RNA was extracted by using the All Prep DNA/RNA Micro Kit (Qiagen) according to the manufacturer‚Äôs instruction and sent to a commercial vendor (BGI Genomics) for whole transcriptomic RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: arm

value: Control

tag: os

tag: cd66b gr_status

tag: treg status

tag: cd8 cd137_status

tag: m1 status

tag: m2 status

tag: jtm normcount_inc

value: Y

tag: jtm tpm_inc

value: N

tag: cancercell inc

tag: cd4 th17_status


title: Parental Untreated - RNA-seq

tag: genotype


title: 40-5

tag: patient

tag: biopsy

tag: age

tag: diagnosis

value: FALSE

tag: tissue


title: 6_15_RLT_CD4

tag: cell type

tag: arm


title: PBRM1 KO5 6Gy 48hr - RNA-seq

tag: cell strain

tag: treatment


title: p592_IgG

tag: cell line

tag: antibody


title: s04_ACD-B

source_name: plasma

value: plasma

tag: Sex

value: male

tag: anticoagulant type

value: ACD-B


title: PBRM1 KO3 6Gy 48hr - RNA-seq