title: 12month_Ctrl

description: 10x Genomics

data_processing:
raw reads were aligned to mouse genome build mm10 using cellranger v6.1.2
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Filtered feature-barcode matrix from cellranger out with cell barcode as column name and gene feature as row name

extract_protocol:
Total backskin from mice of indicated age was dissociated with collagenase treatment followed by trypsinization, single cell suspesion was obtained to load onto 10x Genomics single cell transcriptome profiling platform.
scRNAseq libraries were constructed using 10x Genomics Single Cell 3' v3 protocol


title: HCC_adjacent_sample_S006_Pt3

status: Public on Jun 25 2023

type: genomic

city: Barcelona

first: Roser

last: Pinyol

address: C/Rosselló

country: Spain

institute: IDIBAPS

hyb_protocol: Following Illumina HumanOmniExpressExome-8v1_A kit-associated protocol.

data_processing:
Genomic DNA extracted from the samples was genotyped using HumanOmniExpressExome-8v1_A (Illumina).
Genotype: AA,AB,BB,or empty (no call)

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Hepatocellular carcinoma adjacent tissue

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed with the ChargeSwitch gDNA Mini Tissue Kits (Invitrogen, CS11204)

tag: disease state

value: Hepatocellular Carcinoma

tag: tissue

value: Liver adjacent


title: HCC_adjacent_sample_S004_Pt2

scan_protocol: Following Illumina HumanOmniExpressExome-8v1_A kit-associated protocol.


title: RAW_PRX_2

type: SRA

city: Nagoya

first: Michiko

last: Itoh

state: Aichi

address: Furo-cho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

library_source: transcriptomic

data_processing:
Low-quality reads and adapter sequences were trimmed using fastp software (doi: 10.1093/bioinformatics/bty560).
The reads were mapped to the mm10 reference genome using HISAT2 (doi: 10.1038/s41587-019-0201-4) followed by transcript assembly and quantification using StringTie (doi:10.1038/nbt.3122).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Mus musculus

growth_protocol: RAW264 macrophages were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was purified using RNeasy MiniElute Cleanup Kit (QIAGEN, Hilden, Germany).
RNA-seq libraries were constructed by NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB) and MGIEasy RNA Directional Library Prep Set (MGI), according to the manufacturer’s instruction.

treatment_protocol: Macrophages treated with cholesterol crystals (500 ug/ml) with or without β-cyclodextrin polyrotaxane (βCD-PRX, 1mM) for 24 hours.

tag: cell line

tag: cell type

value: macrophage

tag: treatment

value: betaCD-PRX


title: SJSA-1 cells overexpressing scramble shRNA rep5

city: Changsha

first: Jianlin

last: Zhou

state: Hunan

address: 36 Lushan road

department: College of Life Science

country: China

institute: Hunan Normal 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 Homo_sapiens.GRCh38.87 whole genome
Fragments per kilobase per million mapped fragments (FPKM) were calculated using a protocol from Trapnell, C. et al, Nature  biotechnology, 2010.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw and normalized read count

source_name: SJSA-1 cell

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human osteosarcoma cell

tag: knockdown

value: scramble shRNA


title: RAW_PRX_1


title: SJSA-1 cells overexpressing scramble shRNA rep6


title: HCC_tumor_sample_S003_Pt2

source_name: Hepatocellular carcinoma tumor tissue

label_protocol: Following Illumina HumanOmniExpressExome-8v1_A kit-associated protocol.

value: Liver tumor


title: RAW_veh_4

value: vehicle


title: 6month_Ctrl

city: Chicago

first: Rui

last: Yi

state: IL

address: 303 E. Chicago Avenue

country: USA

institute: Northwestern University

description: 10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

source_name: Skin

value: Skin

tag: age

value: 6 months

tag: genotype

value: Wildtype

value: No


title: SJSA-1 cells overexpressing scramble shRNA rep4


title: HCC_adjacent_sample_S001_Pt1


title: RAW_veh_3


title: Control #2

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: 10x Genomics Chromium Single Cell Gene Expression data

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-3.0.2).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference (GRCm38) and analyzed using "cellranger count".
Genome_build: mm10
Supplementary_files_format_and_content: cellranger generated unfiltered feature-barcode matrix file.

source_name: Single cells obtained from mouse placenta

extract_protocol:
Single cells were obtained from enzymatic digestion of one mouse E13.5 placenta per sample. Red blood cells were removed using Ter-119 antibody. Cell viability and concentration were measured by Countess II FL Automated Cell Counter (Life Technologies) targeting ≥75% cell viability. The cell emulsification is performed with the 10X Chromium Controller using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 (10X Genomics 1000092) and Chromium Chip B Single Cell Kit (10X Genomics 1000074).
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).

tag: genotype/variation

value: control

value: E13.5 Placenta


title: SJSA-1 cells overexpressing scramble shRNA rep3


title: GATA Pl1-KO #2

value: GATA Pl1-KO


title: SJSA-1 cells overexpressing scramble shRNA rep2


title: GATA Pl1-KO #1


title: P28 Ctrl

description: 10x Genomics

library_source: genomic single cell

data_processing:
Raw reads were aligned to mouse genome build mm10 using cellrange-atac v2.0.0
Assembly: refdata-cellranger-arc-mm10-2020-A-2.0.0
Supplementary files format and content: Filtered_peak_bc_matrix from cellranger-atac output with cell barcode as column name and peak as row name.

extract_protocol:
Total backskin from mice of indicated age was dissociated with collagenase treatment followed by trypsinization, single cell suspesion was obtained to load onto 10x Genomics single cell ATACseq profiling platform.
scATAC libraries were constructed following 10x Genomics single cell ATAC v1 protocol.


title: SJSA-1 cells overexpressing scramble shRNA rep1


title: Patient 2 (PDAC2), scRNAseq

city: Stony Brook

first: Scott

last: Powers

state: NY

address: 101 Nicolls Rd

department: Pathology

institute: Stony Brook University School of Medicine -  - Stony Brook, NY

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: MTX - Sparse matrix format with genes and rows from Cell Ranger

source_name: Pancreas Tumor

extract_protocol:
Freshly resected human PDAC tissue was acquired in the grossing room immediately following resection via Whipple or distal pancreatectomy. Bulk tissue specimen was rapidly dissociated into single cell suspension to reduce transcriptional artifacts of handling and time. Subsequent lysis and single cell prep was performed as detailed previously
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Pancreas

value: Pancreas Tumor

tag: Sex

value: M

tag: location

value: Head

tag: tnm

tag: staging

value: III

tag: pathologic diagnosis

value: mod. Diff. PDAC


title: RAW_veh_2

value: macrophage


title: Patient 1 (PDAC1), scRNAseq

description: 10x Genomics

value: F

value: Body & Tail


title: P38_Ctrl

description: 10x Genomics


title: HCC_tumor_sample_S002_Pt1

value: Hepatocellular Carcinoma

value: Liver tumor


title: cmt3b-Sperm-1

status: Public on Jun 24 2023

city: wuhan

first: zhu

last: bo

state: beijing

address: shi zi shan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

data_processing:
Raw reads of all sequencing data were trimmed using fastp (v0.20.1)
Clean read was then matched to the MSU7.0 rice reference genome using hisat2 software. FeatureCounts were used for quantitative analysis and the differentially expressed genes (Fold change > 2,q < 0.01) were calculated by DESeq2.
Clean reads were mapped to the MSU7.0 rice genome. Bismark(v0.22.3) software was used to match, deduplicate and extract methylation sites.
Supplementary files format and content: bigwig files for BS-seq, RNA-seq count files
Supplementary files format and content: bigwigs were derived from combining sample replicates and are linked to the first replicate

organism: Oryza sativa Japonica Group

source_name: Sperm

extract_protocol:
Rice sperms, meiocytes and unicellular microspores were isolated from anthers of Cas9-free transgenic plants and tissue culture-regenerated wild type plants. For sperm isolation, mature anthers were soaked in 45% (w/v) sucrose and then transferred into 15% (w/v) sucrose to release sperm pairs. For isolation of meiocytes, panicles of about 5 cm length were chosen and middle parts of the panicles were collected. Intact anthers were carefully selected using dissecting needles, placed onto an RNAase-free slide, and suspended in a PBS solution containing 1% proteinase inhibitors. The outer wall of anthers was then removed by capillary to release meiocytes. For isolation of unicellular microspores, panicles of about 8 cm length were harvested and the middle parts of the panicles were collected. Anthers were dissected out and make a hole with a capillary tube in the same solution as used for meiocyte isolation. Squeeze gently from the opposite side of the hole to release unicellular microspore. All isolated cells were collected by a micromanipulator system (Eppendorf, TransferMan® 4r).Rice eggs and unicellular zygotes were isolated from ovules before and after fertilization of Cas9-free transgenic plants and tissue culture-regenerated wild type (Zhou et al., 2019; Zhou et al., 2021). Briefly, ovaries of non-pollinated and pollinated florets (about 6.5 h after pollination) were manually collected in RNAase-free water under a dissection microscope. The collected ovules were transferred to a solution containing 0.53 M mannitol and 1% proteinases inhibitors to release eggs or zygotes. All isolated cells were stained by FDA (Fluoresceinc diacetate, Sangon, 596-09-8) and collected by a micromanipulator system (Eppendorf, TransferMan® 4r).
For RNA-seq library construction, mRNA isolated from different types of cells were reverse transcribed and amplified by utilizing SMART-Seq® v4 Ultra® Low Input RNA Kit (TAKARA, Cat. No.634889). cDNAs were sheared into 200-400 bp DNA fragments followed by purification using Agencourt AMPure Beads (Beckman Coulter, USA A63881). The rest steps were performed using the Truseq ChIP DNA library preparation kit (Illumina. IP-202-1012). About 3000 sperm cells and 400 meiocytes were used to construct the transcriptome libraries. Fifty cells of egg or unicellular zygote were used for each replicate of the transcriptome library construction. BS-seq libraries were constructed using reported protocol (Clark et al., 2017). About 300-400 cells were pooled for each replicate for sperm, meicoyte and unicellular microspore bisulfite seq library construction and fifty cells of egg or unicellular zygote were used to construct bisulfite seq library.

value: Sperm


title: Control #1


title: cmt3b-Zygote-3

source_name: Zygote

value: Zygote

value: 6-8 hours after fertilization


title: cmt3b-Zygote-1


title: cmt3a-Egg-1

source_name: Egg

value: Egg


title: cmt3b-Sperm-3


title: cmt3b-Meiocyte-3

source_name: Meiocyte

value: Meiocyte


title: ZH11-Zygote-3

value: wild type


title: cmt3b-Egg-1


title: cmt3b-Egg-2


title: cmt3a-Egg-2


title: cmt3b-Zygote-2


title: cmt3b-Sperm-2


title: cmt3b-Meiocyte-1


title: ZH11-Zygote-2


title: RAW_veh_1

value: vehicle


title: ZH11-Egg-3


title: ZH11-Sperm-2


title: ZH11-Egg-2


title: ZH11-Egg-1


title: ZH11-Meiocyte-3


title: ZH11-Sperm-1


title: ZH11-Meiocyte-1


title: ZH11-Meiocyte-2


title: BS-J67-Sperm-2

library_source: genomic


title: cmt3b-Meiocyte-2


title: BS-J67-Meiocyte-2


title: BS-J67-Meiocyte-1


title: ZH11-Zygote-1


title: BS-cmt3b-UM-2

source_name: Unicellular microspores

value: Unicellular microspores


title: BS-cmt3b-Sperm-2


title: BS-cmt3b-Meiocyte-2


title: BS-cmt3b-Zygote-2


title: BS-cmt3b-UM-1


title: BS-cmt3b-Zygote-1


title: BS-cmt3b-Egg-1


title: BS-cmt3a-Meiocyte-2


title: BS-cmt3a-Sperm-2


title: BS-cmt3b-Egg-2


title: BS-cmt3a-Meiocyte-1


title: BS-cmt3a-Sperm-1


title: BS-cmt3b-Sperm-1


title: BS-cmt3b-Meiocyte-1


title: BS-cmt3a-Egg-2


title: BS-cmt3a-Egg-1


title: BS-ZH11-UM-2


title: BS-ZH11-seedling-2

source_name: Seedling

value: Seedling


title: BS-ZH11-seedling-1


title: BS-ZH11-UM-1


title: BS-J67-Sperm-1


title: BS-ZH11-Meiocyte-2


title: BS-ZH11-Meiocyte-1


title: BS-ZH11-Sperm-2


title: BS-ZH11-Zygote-1


title: BS-ZH11-Sperm-1


title: BS-ZH11-Egg-2


title: BS-ZH11-Egg-1


title: ADSCs, isolated from the chest region adipose tissue,scRNAseq 2

city: tianjin

first: xiaoxi

last: song

address: pudongjiedao

institute: tasly

description:
healthy
10x Genomics

data_processing:
The demultiplexing ,barcoded processing,gene counting and aggreation were made using the CellRanger software(7.00.version)
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: adipose

extract_protocol:
pADSCs were isolated from Bama miniature pigs as follows: Approximately 5 g (1 mm3) adipose tissue was harvested from the chest region after sterilization from anesthetized animals by aseptic surgery. pADSCs were isolated following a procedure described previously [29, 30]. The isolated pADSCs were propagated for 3 generations within 14 days, and the propagated pADSCs were cryopreserved until the use of in vivo application.
Library were performed Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 on the Chromium Controller.(10X Genomics)

value: adipose

value: ADSCs

value: Bama miniature pigs


title: ADSCs, isolated from the chest region adipose tissue,scRNAseq 1

description:
healthy
10x Genomics


title: Old Veh 5 Hi5

city: South San Francisco

first: Oliver

last: Hahn

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Sciences, LLC

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7, parameters: --paired --length 25). Trimmed sequences were aligned using STAR (v2.5.3a). Multi-mapped reads were filtered. Data visualization and analysis was performed using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: Deseq2 (Love et al., 2014), topGO (Alexa and Rahnenfuhrer, 2010) and org.Mm.eg.db.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file including raw counts for each sample

source_name: Hippocampus

extract_protocol:
RNeasy Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.
Unstranded mRNA-seq

value: Hippocampus

value: Male

value: Veh


title: Old Veh 8 Hi8


title: Old Veh 6 Hi6


title: Old Veh 12 Hi12


title: Old Veh 3 Hi3


title: Old Veh 11 Hi11


title: Old Veh 10 Hi10


title: Old PF4 9 Hi21


title: Old PF4 8 Hi20


title: Old PF4 3 Hi15


title: Old PF4 7 Hi19


title: Old PF4 2 Hi14


title: Old PF4 6 Hi18


title: Old PF4 1 Hi13


title: Old PF4 11 Hi23


title: Old PF4 10 Hi22


title: Old Veh 9 Hi9


title: Young Veh 8 Hi34


title: Young Veh 7 Hi32


title: Young Veh 6 Hi31


title: Young Veh 5 Hi29


title: Young Veh 9 Hi36


title: Young Veh 4 Hi27


title: Old Veh 7 Hi7


title: Old Veh 1 Hi1


title: Old Veh 2 Hi2


title: Young Veh 3 Hi26


title: Old Veh 4 Hi4


title: Old PF4 5 Hi17


title: Young Veh 2 Hi25


title: Young Veh 11 Hi38


title: Young Veh 13 Hi43


title: Young Veh 10 Hi37


title: Young Veh 12 Hi42


title: Young PF4 8 Hi44


title: Young Veh 1 Hi24


title: Young PF4 6 Hi40


title: Young PF4 3 Hi33


title: Young PF4 5 Hi39


title: Young PF4 4 Hi35


title: Young PF4 1 Hi28


title: Young PF4 12 Hi48


title: Young PF4 9 Hi45


title: Young PF4 7 Hi41


title: Young PF4 11 Hi47


title: Young PF4 10 Hi46


title: Young PF4 2 Hi30


title: PBMC120-4_S1Hi-C

city: Novosibirsk

first: Andrey

last: Popov

address: Academician Lavrentiev Avenue, 10

country: Russia

institute: Institute of Cytology and Genetics, SB RAS

description: patient confidential information

data_processing:
Datasets were aligned to the hg38 human genome assembly using BWA v.0.7.17-r1188.
Bam file sorting and indexing was performed using samtools.
BigWig files containing cut site coverage were generated using bamCoverage from deeptools with the options --OffSet 1 --binSize 1.
Merged_nodups were obtained using hg19 and modified version of the Juicer 1.6 (https://github.com/genomech/juicer1.6_compact)
Assembly: hg38 (for bigwigs), hg19 (for merged_nodups)
Supplementary files format and content: BigWig
Supplementary files format and content: Merged_nodups

source_name: blood

growth_protocol: Human K562 cells were grown in RPMI-1640 medium with 10% FBS and a penicillin/streptomycin mix

extract_protocol:
Extraction protocol was performed as described in (Gridina. et. al 2021).
K562S1 and PBMCS1 were processed by S1 and then a NGS library was prepared. For all other samples, a Hi-C library construction protocol was applied similar to the performed as described in (Gridina. et. al 2021) with some adaptions (see the paper for detailed protocol)
NGS (K562S1 and PBMCS1), Hi-C (for all other samples)

value: blood

value: PMBC


title: PBMC120-7_S1Hi-C

description: patient confidential information


title: PBMC120-3_S1Hi-C

description: patient confidential information


title: PBMC120-2_S1Hi-C

description: patient confidential information


title: PBMC120-9_S1Hi-C

description: patient confidential information


title: PBMC120-1_S1Hi-C

description: patient confidential information


title: PBMC121-9_S1Hi-C

description: patient confidential information


title: Root, 221, N9416, nanoP+Th

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

data_processing:
reads were quality filterred by rcorrector and Trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Arabidopsis thaliana, TAIR10 cds library, version 20101214
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Arabidopsis thaliana

source_name: root

extract_protocol:
Protocol from Spectrum™ Plant Total RNA Kit (Sigma-Aldrich)
NEBNext Ultra II Directional RNA Library prep kit

value: root

value: nanoP+Th


title: Root, 216, N9416, mock+Th

value: mock+Th


title: Root, 214, N9416, mock+Th


title: Root, 224, N9416, nanoP

value: nanoP


title: Root, 225, N9416, nanoP


title: Root, 212, N9416, -P

value: -P


title: PBMC121-8_S1Hi-C

description: patient confidential information


title: Root, 215, N9416, mock+Th


title: Root, 218, N9416, mock

value: mock


title: Root, 220, N9416, nanoP+Th


title: Root, 222, N9416, nanoP+Th


title: Root, 223, N9416, nanoP


title: Root, 211, N9416, -P


title: Root, 219, N9416, mock


title: Root, 217, N9416, mock


title: Root, 210, N9416, -P+Th

value: -P+Th


title: Root, 209, N9416, -P+Th


title: PBMC120-5_S1Hi-C

description: patient confidential information


title: Root, 208, N9416, -P+Th


title: Root, 213, N9416, -P


title: PBMC121-5_S1Hi-C

description: patient confidential information


title: Root, 207, N8508, nanoP


title: Root, 206, N8508, nanoP


title: Root, 205, N8508, nanoP


title: Root, 204, N8508, nanoP+Th


title: Root, 201, N8508, mock


title: PBMC121-1_S1Hi-C

description: patient confidential information


title: Root, 199, N8508, mock


title: PBMC121-2_S1Hi-C

description: patient confidential information


title: PBMC121-3_S1Hi-C

description: patient confidential information


title: Root, 196, N8508, -P


title: Root, 202, N8508, nanoP+Th


title: Root, 200, N8508, mock


title: HeLa-RUNX3, Mock 2

city: Singapore

first: Vincent

last: oei

address: 14 Medical Dr, #12-01 Centre for Translational Medicine, Singapore

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. [1] Li R, Li Y, Kristiansen K, Wang J. (2008). SOAP: short oligonucleotide alignment program. Bioinformatics. 24(5):713-4
Assembly: you can refer the genome information in Dr. tom.
Supplementary files format and content: tab-delimited text files include Normalized gene counts for each sample.

source_name: Human cancer cell

growth_protocol: HeLa-RUNX3 was cultured in DMEM (Dulbecco’s Modified Medium, Nacalai Tesque) supplemented with 10% Tet-Free FBS (Fetal bovine serum, biowest) and penicillin (100 IU/ml), and streptomycin (100 µg/ml) (Thermo Fisher Scientific) at 37°C in a humidified 5% CO2 incubator. 500 ng/ml is the concentration of doxycycline added to the dox-treated samples. MKN28-RUNX3 was cultured in RPMI-1640 (Nacalai Tesque) supplemented with 10% Tet-Free FBS (Fetal bovine serum, biowest) and penicillin (100 IU/ml), and streptomycin (100 µg/ml) (Thermo Fisher Scientific) at 37°C in a humidified 5% CO2 incubator. 10 ng/ml is the concentration of doxycycline added to the dox-treated samples.

extract_protocol:
Cells were grown to 80% confluency before RNA-extraction. Total RNA from HeLa-RUNX3 and MKN28 RUNX3 Mock and Dox-treated cell lines were extracted using RNeasy Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq using MGIEasy RNA Directional Library Prep Set（1000006385，made in MGI）following manufacturer’s protocols.

treatment_protocol: For HeLa-RUNX3, 500 ng/ml is the concentration of doxycycline added to the dox-treated samples for 48 hours. For MKN28-RUNX3 samples, 10 ng/ml is the concentration of doxycycline added to the dox-treated samples for 48 hours.

value: Human cancer cell

value: Human Cervical cancer

value: Mock/Untreated (no induction)

value: no treatment


title: MKN28-RUNX3, Dox 1

value: Human Gastric cancer

value: Doxycycline-treated (Wild type RUNX3 induction)

value: Doxycycline


title: MKN28-RUNX3, Dox 3


title: MKN28-RUNX3, Mock 2


title: MKN28-RUNX3, Mock 1


title: MKN28-RUNX3, Mock 3


title: MKN28-RUNX3, Dox 2


title: Root, 195, N8508, -P+Th


title: PBMC121-4_S1Hi-C

description: patient confidential information


title: PBMC121-7_S1Hi-C

description: patient confidential information


title: Root, 198, N8508, -P


title: HeLa-RUNX3, Mock 1


title: Root, 193, N8508, -P+Th


title: HeLa-RUNX3, Dox 2


title: HeLa-RUNX3, Mock 3


title: Root, 197, N8508, -P


title: Root, 160, N8507, nanoP


title: HeLa-RUNX3, Dox 1


title: Root, 159, N8507, nanoP


title: Root, 158, N8507, nanoP


title: BS-ZH11-Zygote-2

value: Zygote

value: wild type

value: 6-8 hours after fertilization


title: Root, 203, N8508, nanoP+Th

value: root


title: JR_1

city: Beijing

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No 2

institute: Chinese Academy of Science

data_processing: featureCounts

organism: Glycine max

extract_protocol:
TRIzol reagent method (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT


title: Root, 157, N8507, nanoP+Th

value: nanoP+Th


title: Root, 156, N8507, nanoP+Th


title: JR_2


title: Root, 194, N8508, -P+Th


title: Root, 155, N8507, nanoP+Th


title: Root, 154, N8507, mock


title: Root, 153, N8507, mock


title: Root, 152, N8507, mock


title: HeLa-RUNX3, Dox 3


title: 34R_1

value: GmZF351 overexpressing


title: Root, 151, N8507, mock+Th

value: mock+Th


title: K40_1

city: Shenzhen

first: Yuqi

last: Liu

state: Guangdong

address: 66 Gongchang Road, Guangming District

institute: Sun yat-sen university

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
The alignment was performed using hisat2 against the reference Seriola dumerili Genome (Assembly: SAMD00083043_sdu_WGS.acclist.zip).
Gene counts were obtained using featureCounts.
Assembly: Seriola dumerili Genome (Assembly: SAMD00083043_sdu_WGS.acclist.zip)
Supplementary files format and content: One csv file containing raw count values for each sample

organism: Seriola dumerili

growth_protocol: Greater amberjack juveniles were raised in tanks at 22±1.0℃ at Donghai Island, Guangdong, China. All fish were fed a commercial diet twice a day. They were randomly assigned to twelve 1000 L cylindrical tanks (10 individuals per tank) with varying salinities of 40, 30, and 10 parts per thousand (ppt). The salines of 40, 30, and 10 ppt were made with commercial saltwater salty crystal and aerated tap water. The fish grown in natural seawater with a median saline concentration of 30 ppt were designated as the control group (CK). Every day, the water was changed (every 24 hours).

extract_protocol:
Total RNAs was extracted from the gills and kidneys of each fish using TRIzol.
Illumina libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: The fish of the same growth condition were selected and assigned into three experimental groups, where the first two groups were treated with 10 ppt and 40 ppt commercial seawater salty crystal and aerated tap water, and the rest one group was treated with the same amount of 30 ppt natural seawater as control (CK). After 72 hours treatment, six fishes were randomly selected from each group, and the gill and kideny tissues were taken from each individual of each group for RNA-seq.

tag: salinity

value: 40 ppt

value: kidney

value: 3 months

value: wt


title: JL_3

source_name: leaf

value: leaf


title: Root, 150, N8507, mock+Th


title: K30_2

value: 30 ppt


title: Root, 148, N8507, -P

value: -P


title: JL_2


title: JR_3


title: K30_1


title: JL_1


title: Root, 147, N8507, -P


title: Root, 146, N8507, -P


title: K10_3

value: 10 ppt


title: Root, 145, N8507, -P+Th

value: -P+Th


title: 34L_3


title: Root, 144, N8507, -P+Th


title: K40_2


title: Root, 143, N8507, -P+Th


title: 34L_2


title: K10_1


title: G40_2

value: gill


title: 34L_1


title: G40_1


title: Root, 140, Col-0, nanoP

value: nanoP


title: Root, 139, Col-0, nanoP+Th


title: LNCaP, RNASeq, 24hr, EPI-001, 25 µM, Rep 3

city: Berlin

first: Shaon

last: Basu

state: Germany

address: Ihnestrasse 63-73

department: Department of Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Paired end sequencing reads were first quality checked using FASTQC and then aligned to the Homo sapien genome build hg19 using STAR aligner v2.7.5a (Dobin et al., 2013) with standard settings.
Differential expression analysis between treatment conditions was conducted using the DESeq2 R/bioconductor v3.15 package, a statistical tool that uses shrinkage estimates to compute fold changes (Love et al. 2014). First, raw count matrices from sample libraries were merged into a single object using the ‘DESeqDataSetFromHTSeqCount’ function with the design set to the treatment condition (time, compound, and dosage). The merged count matrix was then fit to the DESeq statistical model using the ‘DESeq’ function.
Assembly: hg19
Supplementary files format and content: Excel spreadsheet ('SupplementTable3_ARcondensates_220531a'): read counts after fitting reverse strand reads from all sample libraries to the DESeq statistical model using 'DESeq' function from DESeq2 bioconductor package

source_name: LNCaP

extract_protocol:
LNCaP cells (Clone FGC, ATCC CRL-1740) in RPMI1640 5% FBS were seeded at a density of 300,000 cells / well in 6 well plates. 16 hours later, wells were refreshed with seeding media spiked with either EPI-001 or 1ae at the doses indicated and 0.5% v/v DMSO control. After 6 and 24 hours, media was removed and cells were harvested using 300 µL of TRIzol reagent (Thermo 15596026) for each well. RNA was then extracted using a Zymo DirectZol Micro kit (Zymo R2062) according to the manufacturer’s protocol.
Total RNA-seq libraries were then prepared using 1 µg of RNA from each sample and the KAPA RNA HyperPrep Kit with RiboErase (Roche KR1351) according to the manufacturer’s protocol with 10 amplification cycles.
Libraries were sequenced on a NovaSeq 6000 with paired-end reads of 100 base pairs, with a read depth of 50 million fragments / library. Three libraries from three corresponding biological replicates  were prepared for each treatment (time, dosage, and compound).

value: LNCaP

value: human prostate adenocarcinoma

tag: time

value: 24 hours


title: Root, 142, Col-0, nanoP

value: root


title: Root, 149, N8507, mock+Th


title: Root, 141, Col-0, nanoP


title: LNCaP, RNASeq, 24hr, EPI-001, 25 µM, Rep 2


title: Root, 138, Col-0, nanoP+Th

value: nanoP+Th


title: Root, 136, Col-0, mock

value: mock


title: Root, 135, Col-0, mock


title: G30_2


title: LNCaP, RNASeq, 24hr, EPI-001, 25 µM, Rep 1


title: Root, 132, Col-0, -P


title: Root, 131, Col-0, -P


title: Root, 133, Col-0, -P


title: LNCaP, RNASeq, 24hr, EPI-001, 2.5 µM, Rep 2


title: Root, 128, Col-0, -P+Th


title: Root, 129, Col-0, -P+Th


title: Root, 137, Col-0, nanoP+Th


title: Sterlet sturgeon scute 68mm, replicate one

city: Pasadena

first: Jan

last: Stundl

state: California

address: 1200 E. California Blvd

institute: California Institute of Technology

description:
AR_scute_68mm_1
Sturgeon_scute_processed.txt

data_processing:
In brief, every sterlet/bichir protein sequence was queried locally against the zebrafish proteome, following which regions with the longest alignment were matched to the respective zebrafish proteins.
Using this alignment-based approach, proteins with highest alignment percentage score were identified as orthologues.
Sterlet/bichir scute/scale RNA sequencing libraries were aligned to the sterlet/bichir sequences, while the zebrafish scale RNA sequencing libraries were aligned to the zebrafish sequences using Bowtie23.
Transcript counts were calculated using featureCounts and differential gene expression analysis was performed using DESeq2.
Using zebrafish gene annotations as a reference, we added the transcript counts for duplicated orthologues found in the sterlet/bichir genome to calculate an ‘aggregated’ transcript count for each gene as described by Martik et al., 2019.
These aggregated transcript counts were then normalized using the formula: Zi=Ti−min(T)/max(T)−min(T) whereZiis the normalized transcript count andTiis the absolute transcript count.
A subset of genes previously identified as being part of the neural crest gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio.
Assembly: Sterlet sturgeon (Genome assembly ASM1064508v1)/ Senegal bichir (Genome assembly ASM1683550v1)/ zebrafish (Genome assembly GRCz11)
Supplementary files format and content: tab-delimited text files that includes featurecounts values for each sample

organism: Acipenser ruthenus

source_name: cells of scute

extract_protocol:
RNAqueous kit (Ambion), prepared according to the manufacturer's instructions.
The libraries were built according to Illumina Standard Protocols.

value: cells of scute

value: WT

tag: measure

value: 68 mm


title: Root, 130, Col-0, -P+Th


title: 34R_2

value: GmZF351 overexpressing


title: Sterlet sturgeon scute 68mm, replicate two

description:
AR_scute_68mm_2
Sturgeon_scute_processed.txt


title: LNCaP, RNASeq, 24hr, EPI-001, 2.5 µM, Rep 1


title: S528

city: Hefei

first: Jinghe

last: Zhang

state: Anhui

address: Huangshan Road 443

institute: University of Science and Technology of China

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18, then mapped to hg38 (Annotation: gencode.v30.annotation.gtf) whole genome using hisat2 v2.1.0 with default parameters.
Read counting were calculated using featureCounts v1.6.4 with parameters: "-T 24 -p --extraAttributes gene_type,gene_name"
Data was normalised to TPM use customized R script. Data was filtered to keep only genes with average TPM > 0.5 resulting in 32,229 expressed genes. Differential expression were performed using limma v3.42.2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Lung

extract_protocol:
The lung tissue was immobilized by formalin and the total RNA was obtained by TRIZOL.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

tag: disease state


title: LNCaP, RNASeq, 24hr, 1ae, 5 µM, Rep 3

value: 1ae, 5 uM, Rep 3


title: S527

tag: tissue


title: S523


title: LNCaP, RNASeq, 24hr, 1ae, 5 µM, Rep 2

tag: cell line

value: 1ae, 5 uM, Rep 2


title: Sterlet sturgeon scute 26mm, replicate two

description:
AR_scute_26mm_2
Sturgeon_scute_processed.txt

value: 26 mm


title: S519


title: Sterlet sturgeon scute 26mm, replicate one

description:
AR_scute_26mm_1
Sturgeon_scute_processed.txt


title: S59


title: LNCaP, RNASeq, 24hr, 1ae, 5 µM, Rep 1

tag: cell type

value: 1ae, 5 uM, Rep 1


title: Root, 134, Col-0, mock

tag: treatment


title: G10_2

value: 10 ppt

value: gill

value: 3 months

value: wt


title: LNCaP, RNASeq, 24hr, EPI-001, 2.5 µM, Rep 3

value: LNCaP

value: human prostate adenocarcinoma

value: 24 hours


title: G10_1


title: Sterlet sturgeon scute 22mm, replicate two

description:
AR_scute_22mm_2
Sturgeon_scute_processed.txt

value: 22 mm


title: C56

value: healthy


title: C55


title: LNCaP, RNASeq, 24hr, 1ae, 0.5 µM, Rep 3

value: 1ae, 0.5 uM, Rep 3


title: G30_1

value: 30 ppt


title: Sterlet sturgeon scute 22mm, replicate one

description:
AR_scute_22mm_1
Sturgeon_scute_processed.txt

value: cells of scute

value: WT


title: C5

value: lung


title: Bichir scale 88mm, replicate two

description:
PS_scale_88mm_2
Bichir_scale_processed.txt

organism: Polypterus senegalus

source_name: cells of ganoid scale

value: cells of ganoid scale

value: 88 mm


title: LNCaP, RNASeq, 24hr, 1ae, 0.5 µM, Rep 2

value: 1ae, 0.5 uM, Rep 2


title: Bichir scale 88mm, replicate one

description:
PS_scale_88mm_1
Bichir_scale_processed.txt


title: Bichir scale 65mm, replicate two

description:
PS_scale_65mm_2
Bichir_scale_processed.txt

value: 65 mm


title: PBMC120-8_S1Hi-C

description: patient confidential information

value: blood

value: PMBC


title: LNCaP, RNASeq, 24hr, DMSO, Rep 3

value: DMSO, Rep 3


title: Bichir scale 65mm, replicate one

description:
PS_scale_65mm_1
Bichir_scale_processed.txt


title: S52


title: LNCaP, RNASeq, 6hr, EPI-001, 25 µM, Rep 3

value: LNCaP

value: 6 hours


title: Bichir scale 60mm, replicate two

description:
PS_scale_60mm_2
Bichir_scale_processed.txt

value: 60 mm


title: Bichir scale 60mm, replicate one

description:
PS_scale_60mm_1
Bichir_scale_processed.txt


title: LNCaP, RNASeq, 24hr, 1ae, 0.5 µM, Rep 1

value: human prostate adenocarcinoma

value: 1ae, 0.5 uM, Rep 1

value: 24 hours


title: Zebrafish scale 30mm, replicate two

description:
DR_scale_2
Zebrafish_scale_processed.txt

organism: Danio rerio

source_name: cells of elasmoid scale

value: cells of elasmoid scale

value: 30 mm


title: LNCaP, RNASeq, 6hr, EPI-001, 25 µM, Rep 1


title: LNCaP, RNASeq, 24hr, DMSO, Rep 2

value: DMSO, Rep 2


title: Normal06

type: RNA

city: Sacramento

first: JAEHWAN

last: KIM

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor)

label: biotin

source_name: human skin biopsy

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer’s protocol.

value: skin

tag: disease

tag: lesional (ls) vs. nonlesional (nl) vs. normal

value: Normal

tag: psoriasis area and diseave severity index (pasi)

tag: scoring atopic dermatitis (scorad)

tag: eczema area and severity index (easi)

tag: sample relation with gse78097 (reanalysis)

value: Pretreatment


title: JWK-09-Th2-001_NL

value: Mixed

value: NL


title: JWK-09-Th2-001_LS

value: LS


title: Normal04


title: Normal03


title: Normal01


title: Normal05


title: Normal02


title: JWK-09-AD-303_LS


title: JWK-09-Ps-208_LS

value: Psoriasis


title: JWK-09-AD-302_LS


title: JWK-09-AD-303_NL


title: LNCaP, RNASeq, 6hr, EPI-001, 2.5 µM, Rep 3


title: JWK-09-Th2-013_LS


title: JWK-09-Th2-013_NL


title: Zebrafish scale 30mm, replicate one

description:
DR_scale_1
Zebrafish_scale_processed.txt

tag: genotype

value: WT


title: JWK-09-Th2-012_LS


title: LNCaP, RNASeq, 6hr, EPI-001, 2.5 µM, Rep 2

value: LNCaP


title: Experimental Mouse, Tomato+HIF-2 KO, irradiated, Day 14, Rep 3

city: Durham

first: Colleen

last: Wu

state: NC

address: 450 Research Drive

department: Orthopaedics

institute: Duke University

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

source_name: B6 mice, Bone marrow

extract_protocol:
RNA was collected using Qiagen RNAeasy kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: B6 mice, Bone marrow

value: LepR Tomato+ cells

value: Facs sorted Tomato+ Bone marrow stromal cells

value: LeprTomato+ HIF-2 KO

value: Irradiated


title: Experimental Mouse, Tomato+HIF-2 KO, irradiated, Day 14, Rep 2


title: LNCaP, RNASeq, 24hr, DMSO, Rep 1

value: human prostate adenocarcinoma

value: DMSO, Rep 1

value: 24 hours


title: JWK-09-Th2-011_LS

value: skin


title: LNCaP, RNASeq, 6hr, EPI-001, 2.5 µM, Rep 1

value: 6 hours


title: Experimental Mouse, Tomato+HIF-2 KO, irradiated, Day 14, Rep 1


title: Experimental Mouse, Tomato+HIF-2 KO, irradiated, Day 3, Rep 3


title: JWK-09-Th2-011_NL

value: Pretreatment


title: LNCaP, RNASeq, 6hr, 1ae, 5 µM, Rep 3

value: 1ae, 5 uM, Rep 3


title: LNCaP, RNASeq, 6hr, 1ae, 5 µM, Rep 2

value: 1ae, 5 uM, Rep 2


title: JWK-09-Th2-010_LS

value: Mixed

value: LS


title: LNCaP, RNASeq, 6hr, 1ae, 5 µM, Rep 1

value: 1ae, 5 uM, Rep 1


title: Experimental Mouse, Tomato+HIF-2 KO, irradiated, Day 3, Rep 2


title: Experimental Mouse, Tomato+HIF-2 KO, irradiated, Day 3, Rep 1


title: LNCaP, RNASeq, 6hr, 1ae, 0.5 µM, Rep 3

value: LNCaP

value: 1ae, 0.5 uM, Rep 3


title: JWK-09-Th2-009_LS


title: 34R_3

value: root

value: GmZF351 overexpressing


title: JWK-09-Th2-009_NL

value: NL


title: Experimental Mouse, Tomato+HIF-2 KO, no irradiation, Day 3, Rep 7

value: B6 mice, Bone marrow

value: LepR Tomato+ cells

value: Facs sorted Tomato+ Bone marrow stromal cells

value: LeprTomato+ HIF-2 KO

value: NO irradiation


title: JWK-09-Th2-008_LS

value: skin


title: JWK-09-Th2-012_NL

value: Pretreatment


title: JWK-09-Th2-007_LS


title: JWK-09-Th2-007_NL


title: JWK-09-Th2-006_NL


title: LNCaP, RNASeq, 6hr, 1ae, 0.5 µM, Rep 2

value: human prostate adenocarcinoma

value: 1ae, 0.5 uM, Rep 2

value: 6 hours


title: JWK-09-AD-302_NL


title: Experimental Mouse, Tomato+HIF-2 KO, no irradiation, Day 3, Rep 6


title: LNCaP, RNASeq, 6hr, 1ae, 0.5 µM, Rep 1

value: 1ae, 0.5 uM, Rep 1


title: Experimental Mouse, Tomato+HIF-2 KO, no irradiation, Day 3, Rep 5


title: JWK-09-Th2-010_NL

value: Mixed


title: LNCaP, RNASeq, 6hr, DMSO, Rep 3

value: LNCaP

value: DMSO, Rep 3


title: Experimental Mouse, Tomato+HIF-2 KO, no irradiation, Day 3, Rep 4


title: JWK-09-Th2-005_LS

value: LS


title: Experimental Mouse, Tomato+HIF-2 KO, no irradiation, Day 3, Rep 3


title: JWK-09-Th2-017_LS


title: LNCaP, RNASeq, 6hr, DMSO, Rep 2

value: DMSO, Rep 2


title: LNCaP, RNASeq, 6hr, DMSO, Rep 1

value: DMSO, Rep 1


title: JWK-09-Th2-003_LS


title: Experimental Mouse, Tomato+HIF-2 KO, no irradiation, Day 3, Rep 1

value: B6 mice, Bone marrow


title: P32

city: Guangzhou

first: lizhen

last: liu

address: Panyu

institute: Sun Yat-sen University cancer center

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by STAR instruction
RSEM were used for counting
R were used for visualization
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: NPC Patient_CR

growth_protocol: S26 P and S26 R cells were cultured in DMEM with 5% FBS, 1% P/S.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: S26 R cells were treated with 1μM pacritinib

value: nasopharyngeal carcinoma

tag: group

value: complete response

tag: agent

value: paclitaxel


title: P33


title: JWK-09-Th2-002_LS


title: JWK-09-Th2-006_LS


title: Experimental Mouse, Tomato+HIF-2 KO, no irradiation, Day 3, Rep 2

value: LepR Tomato+ cells

value: Facs sorted Tomato+ Bone marrow stromal cells

value: LeprTomato+ HIF-2 KO

value: NO irradiation


title: JWK-09-Th2-008_NL

value: skin

value: NL

value: Pretreatment


title: JWK-09-Th2-002_NL

value: Mixed


title: JWK-09-Th2-005_NL


title: JWK-09-Th2-003_NL


title: P31

source_name: NPC Patient_PR

value: partially response


title: Control mouse, Tomato+, irradiated,  Day 14, rep2

value: LeprTomato+ WT

value: Irradiated


title: Control mouse, Tomato+, irradiated,  Day 14, rep3


title: JWK-09-Th2-016_LS

value: LS


title: JWK-09-Ps-211_LS

value: Psoriasis


title: JWK-09-Th2-004_NL


title: JWK-09-Th2-004_LS


title: JWK-09-Th2-017_NL


title: Control mouse, Tomato+, irradiated,  Day 14, rep1

value: B6 mice, Bone marrow


title: P30

value: nasopharyngeal carcinoma


title: P28

value: complete response


title: P26

value: paclitaxel


title: JWK-09-Ps-211_NL


title: JWK-09-Th2-016_NL


title: HFD Epi B

city: Charlottesville

first: Brant

middle: E

last: Isakson

state: Virginia

department: Cardiovascular Research Center

institute: University of Virginia

data_processing:
Data from two separate experiments were analyzed in RStudio (2022.07.1) with the Seurat package (4.3.0). Sequencing yielded 17,164 cells with 54,100 features.  In order to ensure high quality data, cells were excluded if they contained less than 200 genes, more than 5000 genes, if their transcriptome was more than 5% mitochondrial, and more than 5% hemoglobin beta. Data was combined using SCTransform, normalized, and 3000 variable features were chosen. UMAPs were generated using 20 principal components. Clusters were generated using a resolution of 1. Non-endothelial cells were excluded based on low expression of Pecam1 and Cdh5 as well as high expression of non-endothelial markers (Col1a1, Acta2, Cd3g, Ptprc, Ccr5, Adipoq).
Assembly: mm10
Supplementary files format and content: tab seperated value files and matrix files
Supplementary files format and content: rds file of fully integrated seurat object

source_name: Epididymal Adipose

extract_protocol:
Mesentery, epididymal fat pads, and lungs were dissected and placed in ice cold FACS buffer (1% BSA, 3% FBS, 96% Ca2+ and Mg2+ free PBS) with 1 g/ml Actinomycin D (ThermoFisher BP606-5). After isolation, samples were moved to a digestion solution (0.2 mg/mlg Liberase TM in PBS (ThermoFisher 50-100-3280), 1 g/ml Actinomycin D). Samples were minced and incubated at 37 C for 1 hour or until adequately digested. The samples were further homogenized by passing through a 1 ml pipette tip and 19 G needle. The samples were incubated for 30 min at 37 C after which they were diluted to 14 ml with cold FACS buffer and placed on ice. The samples were centrifuged at 400 x g for 10 min. The supernatant was collected and centrifuged for 1000 x g for 10 min. Both pellets were recombined and resuspended in RBC lysis buffer (ThermoFisher 00-4333-57) and incubated for a maximum of 5 min. RBC lysis was stopped by addition of 10 ml FACS buffer. The cells were centrifuged at 800 x g for 8 min. The pellets were resuspended and filtered through 70 m filters. Tissues from 6 mice were combined in a single sample. The single cell suspensions were centrifuged at 800 x g for 8 min and resuspended in a solution of 3% non-acetylated BSA in PBS. Cell viability was determined with Sytox blue (1 l/ml; ThermoFisher S34857).  Cells were sorted on the Becton Dickinson Influx Cell Sorter with the assistance of UVA Flow Cytometry Core staff. Cells were gated as shown in Supplementary Figure 1. Lung from a Cre+ mouse and mesentery from a Cre- mouse were used as positive (YFP only) and negative (no color) controls respectively. This experiment was repeated twice to provide two independent replicates.
The generation of single cell indexed libraries was performed by the School of Medicine Genome Analysis and Technology Core, RRID:SCR_018883, using the 10X Genomics chromium controller platform and the Chromium Single Cell 3′ Library & Gel Bead Kit v3.1 reagent.  Briefly, around 5,000 cells were targeted per sample and loaded onto each well of a Chromium Single Cell G Chip to generate single cell emulsions primed for reverse transcription.  After breaking the emulsion, the single cell specific barcoded DNAs were subjected to cDNA amplification and QC on the Agilent 4200 TapeStation Instrument, using the Agilent D5000 kit.  Each of the four samples’ cDNA was used to prepare indexed libraries that were pooled prior to sequencing.  A QC run was performed on the Illumina Miseq using the nano 300Cycle kit (1.4 Million reads/run), to estimate the number of targeted cells per sample using the Cellranger 3.0.2 function.  The cell estimate enabled the core to re-balance the pooled sample prior to deep sequencing onto the NextSeq 2000, using the P3-100 cycle kit.  After run completion, the Binary base call (bcl) files were converted to fastq format using the Illumina bcl2fastq2 software, and data transferred to the Bioinformatics team for further analysis.

treatment_protocol: At 6 weeks old, male ROSA26-eYFP+/+ Cdh5-CreERT2+ mice were fed a tamoxifen diet (Envigo TD 130856) for 2 weeks to induce YFP expression in endothelial cells. Wet food was provided 3 times a week to ensure adequate consumption. At 8 weeks, the mice were fed either normal chow (NC; 5.8 % fat; Envigo TD 7012) or high fat diet (HFD; 60% fat; Bio-Serve F3282) for 12-13 weeks.

value: Epididymal Adipose

value: Endothelial Cells

value: ROSA26-eYFP+/+ Cdh5-CreERT2+

value: High Fat Diet (60% fat)


title: JWK-09-Ps-209_LS

value: skin


title: JWK-09-Ps-210_LS


title: Control mouse, Tomato+, irradiated,  Day 3, rep3

value: LepR Tomato+ cells

value: Facs sorted Tomato+ Bone marrow stromal cells


title: Control mouse, Tomato+, irradiated,  Day 3, rep2


title: JWK-09-Ps-210_NL

value: NL

value: Pretreatment


title: Control mouse, Tomato+, irradiated,  Day 3, rep4

value: LeprTomato+ WT


title: HFD Mes B

source_name: Mesentery

value: Mesentery


title: NC Mes B

value: Normal Chow


title: NC Epi B


title: P24

value: partially response


title: HFD Epi A


title: Control mouse, Tomato+, irradiated,  Day 3, rep1

value: B6 mice, Bone marrow

value: Irradiated


title: JWK-09-Ps-207_LS

value: Psoriasis

value: LS


title: P21

value: nasopharyngeal carcinoma

value: paclitaxel


title: P22


title: Control mouse, Tomato+, no irradiation, Day 3, rep4


title: LNCaP, RNASeq, 6hr, EPI-001, 25 µM, Rep 2

value: LNCaP

value: human prostate adenocarcinoma

value: 6 hours


title: JWK-09-Ps-209_NL

value: skin


title: NC Epi A

value: Epididymal Adipose

value: Endothelial Cells

value: ROSA26-eYFP+/+ Cdh5-CreERT2+


title: HFD Mes A

value: High Fat Diet (60% fat)


title: JWK-09-Ps-207_NL

value: NL

value: Pretreatment


title: P25

value: partially response


title: Control mouse, Tomato+, no irradiation, Day 3, rep3

value: B6 mice, Bone marrow

value: LepR Tomato+ cells

value: Facs sorted Tomato+ Bone marrow stromal cells

value: LeprTomato+ WT

value: NO irradiation


title: P15

value: nasopharyngeal carcinoma

value: complete response

value: paclitaxel


title: Control mouse, Tomato+, no irradiation, Day 3, rep1


title: Control mouse, Tomato+, no irradiation, Day 3, rep2


title: P14


title: JWK-09-Ps-205_LS

value: Psoriasis

value: LS


title: NC Mes A

value: Mesentery

value: Normal Chow


title: P13


title: HFD Epi C

data_processing:
Adapters were trimmed by with the BBDuk function of BBMap (v38.57). The paired-end reads were mapped to the mm39 reference genome using STAR (v2.7.9a). Gene counts were generated with FeatureCounts in the Subread package. DESeq2 (v. 1.34.0) was used to identify differentially expressed genes (Padj < 0.05). Ensemble IDs were converted to gene symbols using the org.Mm.eg.db package.
Assembly: mm39
Supplementary files format and content: csv file is normalized counts using DESeq2

extract_protocol:
Mesentery, epididymal fat pads, and lungs were dissected and placed in ice cold FACS buffer (1% BSA, 3% FBS, 96% Ca2+ and Mg2+ free PBS) with 1 g/ml Actinomycin D (ThermoFisher BP606-5). After isolation, samples were moved to a digestion solution (0.2 mg/mlg Liberase TM in PBS (ThermoFisher 50-100-3280), 1 g/ml Actinomycin D). Samples were minced and incubated at 37 C for 1 hour or until adequately digested. The samples were further homogenized by passing through a 1 ml pipette tip and 19 G needle. The samples were incubated for 30 min at 37 C after which they were diluted to 14 ml with cold FACS buffer and placed on ice. The samples were centrifuged at 400 x g for 10 min. The supernatant was collected and centrifuged for 1000 x g for 10 min. Both pellets were recombined and resuspended in RBC lysis buffer (ThermoFisher 00-4333-57) and incubated for a maximum of 5 min. RBC lysis was stopped by addition of 10 ml FACS buffer. The cells were centrifuged at 800 x g for 8 min. The pellets were resuspended and filtered through 70 m filters. Tissues from 6 mice were combined in a single sample. The single cell suspensions were centrifuged at 800 x g for 8 min and resuspended in a solution of 3% non-acetylated BSA in PBS. Cell viability was determined with Sytox blue (1 l/ml; ThermoFisher S34857).  Cells were sorted on the Becton Dickinson Influx Cell Sorter with the assistance of UVA Flow Cytometry Core staff. Cells were gated as shown in Supplementary Figure 1. Lung from a Cre+ mouse and mesentery from a Cre- mouse were used as positive (YFP only) and negative (no color) controls respectively. This experiment was repeated twice to provide two independent replicates.
PE150 reads were generated with the Illumina NovoSeq platform.

value: Epididymal Adipose

value: Endothelial Cells

value: ROSA26-eYFP+/+ Cdh5-CreERT2+


title: HFD Mes C

value: High Fat Diet (60% fat)


title: P12


title: JWK-09-Ps-213_LS

value: skin

value: Pretreatment


title: NC Epi C


title: P11

value: partially response


title: DKO, 12h, RPF

first: Xuerui

last: Yang

state: Beijing

address: Tsinghua University

department: School of Life Sciences

institute: Tsinghua University

description: Ribosome protected fragments

data_processing:
Adaptor sequence (CTGTAGGCACCATCAAT) was trimmed from both the mRNA and ribosome profiling sequencing data, and low-quality reads were discarded by fastx quality filter.  Contaminants of ribosomal RNA were identified by aligning reads to the human rRNA sequences using Bowtie and then mapped reads were eliminated from subsequent analysis. Reads of length between 25-35 nt were remained for ribosome profiling analysis.  The remaining reads were mapped to the human reference genome assembly (GRCh38) with the annotation file (Homo_sapiens.GRCh38.88.gtf) (downloaded from Ensembl genome browser) using STAR(https://doi.org/10.1093/bioinformatics/bts635) with following parameters: (--alignEndsType EndToEnd --outFilterMismatchNmax 1 --outFilterMultimapNmax 5 --quantMode TranscriptomeSAM GeneCounts)
Assembly: hg38 (GRCh38)
Supplementary files format and content: tab-delimited text files include raw reads count for each sample

growth_protocol: WT cell, Ataxin2 KO, Ataxin2L KO, Ataxin2/2L KO cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
The Ribosome protected fragment (RPF) was isolated by 34% sucrose cushion and UREA-TBE gel size selection. Total RNA and RPF were then extracted using TRIzol regent.
Both fragmented total RNA and ribosome-protected RNA fragment were subjected to library preparation following standard procedure of ARTseq™ Ribosome Profiling Kit with minor modification. In brief, RNA samples were end repaired with T4 PNK and ligated with 3' adaptor, followed by cDNA synthesis and cDNA purification. The cDNA was then subjected to circularization and PCR amplification.

treatment_protocol: Cells were synchronized with 200 nM of DXMS for 4 hours and 12 hours.

value: Human bone osteosarcoma epithelial cells

value: Ataxin2/2L double knockout

value: 12 hours after synchronization with DXMS


title: DKO, 4h, RPF

description: Ribosome protected fragments

value: 4 hours after synchronization with DXMS


title: P10

value: nasopharyngeal carcinoma

value: complete response


title: NC Mes C


title: P09

value: paclitaxel


title: ORX/PPE

city: Fukuoka

first: Aono

last: Kentaro

state: Fukuoka

address: Jyonan-ku, Nanakuma, 8-19-1

department: Faculty of pharmacy

institute: Fukuoka university

description: Gene expression after 3 weeks PPE administration

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: ORX + PPE inhalation

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: strain

value: lung

value: ORX

value: PPE


title: HFD Epi B

value: Epididymal Adipose


title: JWK-09-Th2-015_NL

value: Mixed

value: NL


title: Ataxin2L KO, 12h, RPF

description: Ribosome protected fragments

value: Ataxin2L knockout


title: HFD Mes B

value: Mesentery

value: Endothelial Cells

value: ROSA26-eYFP+/+ Cdh5-CreERT2+

value: High Fat Diet (60% fat)


title: JWK-09-Th2-014_LS

value: skin

value: LS

value: Pretreatment


title: JWK-09-AD-313_LS


title: JWK-09-Ps-204_NL

value: Psoriasis


title: P18

value: nasopharyngeal carcinoma

value: complete response


title: P05

value: partially response

value: paclitaxel


title: JWK-09-Ps-203_LS


title: sham/PBS

description: Gene expression after 3 weeks PBS administration

source_name: sham + PBS inhalation

value: lung

value: sham

value: PBS


title: JWK-09-Ps-205_NL

value: NL


title: ORX/PBS

source_name: ORX + PBS inhalation

value: ORX


title: Ataxin2L KO, 4h, RPF

description: Ribosome protected fragments

value: Human bone osteosarcoma epithelial cells

value: Ataxin2L knockout

value: 4 hours after synchronization with DXMS


title: JWK-09-AD-313_NL


title: Ataxin2 KO, 12h, RPF

description: Ribosome protected fragments

value: Ataxin2 knockout

value: 12 hours after synchronization with DXMS


title: P04


title: NC Mes B

value: Mesentery

value: Endothelial Cells

value: ROSA26-eYFP+/+ Cdh5-CreERT2+

value: Normal Chow


title: sham/PPE

source_name: sham + PPE inhalation

value: PPE


title: JWK-09-AD-312_LS

value: skin

value: LS

value: Pretreatment


title: NC Epi B

value: Epididymal Adipose


title: JWK-09-AD-312_NL


title: HFD Epi A

value: High Fat Diet (60% fat)


title: P03

value: nasopharyngeal carcinoma

value: partially response

value: paclitaxel


title: Ataxin2 KO, 4h, RPF

description: Ribosome protected fragments

value: Human bone osteosarcoma epithelial cells


title: P02


title: WT, 12h, RPF

description: Ribosome protected fragments

value: WT


title: R2_P

source_name: S26 R+Pac

value: pacritinib


title: JWK-09-AD-311_LS


title: HFD Mes A


title: WT, 4h, RPF

description: Ribosome protected fragments

value: 4 hours after synchronization with DXMS


title: NC Epi A


title: R1_P


title: NC Mes A

value: Mesentery


title: DKO, 4h, RNA

description: total RNA

value: Ataxin2/2L double knockout


title: R2

source_name: S26 R

value: S26 resistant cells


title: JWK-09-AD-309_NL

value: NL


title: JWK-09-Th2-015_LS

value: Mixed


title: R1


title: Ataxin2L KO, 12h, RNA

description: total RNA

value: Ataxin2L knockout

value: 12 hours after synchronization with DXMS


title: In-vivo lung cells, infected + DDP treatment, replicate 3

city: Milan

first: Luca

last: Mazzarella

state: M

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: IEO European Institute of Oncology IRCCS

data_processing:
For each sample fastq.gz were aligned on reference genome (mm10) using STAR aligner (version 2.7.3a)
Each resulting SAM was sorted with samtools sort function
raw counts have been obtained by the mean of htseq-count using the following parameters: -f sam, -m intersection-strict, -s reverse, -t exon, -i gene_id, -r pos
Normalized count matrix was obtained from raw counts using DESeq2 R package
Assembly: mm10
Supplementary files format and content: tab-delimited text file matrix with variance stabilized DESeq2 normalized counts for each Sample
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

growth_protocol: B6.Cg-Tg(K18-ACE2)2Prlmn/J mice were purchased from The Jackson Laboratory. Mice were housed under specific pathogen–free conditions, and heterozygous mice of both sexes were used at 8 to 10 weeks of age.

extract_protocol:
RNA extraction was performed by combining phenol/guanidine-based lysis with silica membrane-based purification.
mRNA-seq libraries were prepared according to the TruSeq low sample protocol (Illumina, San Diego, CA, USA), starting with 1 µg of total RNA per sample.

treatment_protocol: Unanesthetized K18-hACE2 mice were placed in a nose-only Allay restrainer on the inhalation chamber (DSI Buxco respiratory solutions, DSI). To reach a target accumulated inhaled aerosol (also known as delivered dose) of 2 × 105 TCID50, mice were exposed to aerosolized SARS-CoV2 for 20 to 30 min (depending on the total volume of diluted virus and on the number of mice simultaneously exposed). Primary inflows and pressure were controlled and set to 0.5 liter/min per port and −0.5 cmH2O, respectively. As control, K18-hACE2 mice received the same volume of aerosolized PBS (125 μl per mouse).

value: Lung

value: Infected + DDP


title: Ataxin2L KO, 4h, RNA

description: total RNA


title: P1

source_name: S26 P

value: S26 patental


title: JWK-09-AD-308_NL

value: skin

value: Pretreatment


title: In-vivo lung cells, infected + DDP treatment, replicate 1


title: In-vivo lung cells, infected + DDP treatment, replicate 2


title: JWK-09-AD-310_LS

value: LS


title: DKO, 12h, RNA

description: total RNA

value: Human bone osteosarcoma epithelial cells


title: Ataxin2 KO, 4h, RNA

description: total RNA

value: Ataxin2 knockout


title: In-vivo lung cells, infected, replicate 3

value: Infected


title: In-vivo lung cells, infected + DDP treatment, replicate 4


title: JWK-09-Ps-213_NL

value: Psoriasis


title: WT, 12h, RNA

description: total RNA

value: WT


title: JWK-09-AD-307_LS


title: JWK-09-AD-306_LS


title: In-vivo lung cells, infected, replicate 2


title: Nlk KO biol rep 2

city: New Haven

first: Leon

middle: L

last: Tejwani

state: CT

address: 295 Congress Ave, BCMM139

department: Neuroscience

institute: Yale University

data_processing:
TopHat2 v2.1.0 was utilized to align reads to the mouse reference genome (mm10).
The iGenomes mm10 gtf file was used for annotation.
Cuffquant from Cufflinks v2.2.1 was used for gene expression quantification.
Differential expression analysis was carried out using Cuffdiff from Cufflinks v2.2.1.
Cuffnorm was utilized for generating normalized expression values.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files contain normalized FPKMs for each biological sample, as well as Cuffdiff output for each comparison.

extract_protocol:
RNA was extracted using a Qiagen RNeasy Mini Kit, following the manufacturer's protocol. RNA was sent to the Yale Center for Genome Analysis for library prepration and sequencing.
The RNA libraries for all experiments were conducted using standard Illumina protocols.

value: neuroblastoma

value: Nlk KO


title: WT, 4h, RNA

description: total RNA

value: 4 hours after synchronization with DXMS


title: Nlk KO biol rep 1


title: JWK-09-AD-305_LS


title: JWK-09-AD-305_NL

value: NL


title: JWK-09-AD-307_NL


title: Ataxin2 KO, 12h, RNA

description: total RNA


title: JWK-09-AD-304_LS


title: In-vivo lung cells, infected, replicate 1


title: Nlk KO biol rep 3


title: WT biol rep 3

value: wild-type


title: In-vivo lung cells, not infected, replicate 2

value: Not infected


title: RNA-Seq PC3 Scrambled Peptide treat. repl3

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

data_processing:
RNA-Seq data were aligned to mouse transcriptome GenCode.v39 using RNA Star. Counts per gene were determined using FeatureCounts. Differentially expressed genes and normalized reads were determined using DeSeq2.
Assembly: hg38

growth_protocol: PC3 cells were grown in RPMI, 10% FCS and Pen/Strep.

extract_protocol:
Total RNA was extracted by using the RNeasy Mini system (Qiagen) including an on-column DNaseI digestion.
RNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina).

treatment_protocol: Knockdown was performed using lentiviral vectors bearing the respective shRNA. Peptide treatment was pefomed for 24h with 12,5 µM in cells cultured with 2,5% FCS.

value: prostate cancer cell line

value: Scrambled peptide


title: WT biol rep 2


title: RNA-Seq PC3 Scrambled Peptide treat. repl1


title: RNA-Seq PC3 Scrambled Peptide treat. repl2


title: DM48h_siBoth_A

city: Worcester

first: Tapan

last: Sharma

state: MA

address: 368 Plantation Street

department: Gene Therapy Centre

institute: University of Massachusetts Medical School

data_processing:
Libraries were sequenced using the DNBseq platform, averagely generating about 4.52 Gb bases per sample. Reads were filtered to remove adaptor-polluted, low quality and high content of unknown base reads.
About 97% of the raw reads were identified as clean reads. Of these, about 94% reads were mapped to genome with approximately 70% reads uniquely mapped to mouse reference genome mm10 using HISAT2.
Transcripts were reconstructed using StringTie, and novel transcripts were identified using Cuffcompare. All transcripts were then combined together and mapped to the mm10 reference transcriptome using Bowtie.
Gene expression levels were calculated using RSEM. DEseq2 algorithm was used to detect differentially expressed genes (DEG).
Genome_build: mm10
Supplementary_files_format_and_content: Spreadsheet files in xls format containing FPKM values for each Sample.

source_name: Immortalized myoblast cell line

growth_protocol: C2C12 cells were grown at 37℃ in 5% CO2 and maintained at a confluency of 70% or less in Dulbecco's Modified Eagle's Medium with high glucose (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin solution (Gibco). For induction of differentiation, cells were allowed to become 90% confluent and media was changed to Dulbecco's Modified Eagle's Medium with high glucose (Gibco) supplemented with 2% horse serum (Gibco) and 1% penicillin-streptomycin solution (Gibco). Insulin was added freshly to a final concentration of (2ug/ml).

extract_protocol:
Cells were harvested after the required treatments at specified timepoints. RNA was extracted by Trizol-chloroform phase separation followed by iso-propanol precipitaion. RNA pellet was resuspended in nuclease-free water.
RNA libraries were prepared by BGI Americas according to their standard protocol.

treatment_protocol: C2C12 cells were plated on culture plates in DMEM medium 12h before transfection. Cells were transfected at 50% confluence using the Lipofectamine (Invitrogen) reagent with 25 nM siRNA oligos relevant to sample description. 36h post-transfection, the cells were induced for differentiation and samples were harvested at indicated times for further analysis.

value: Myoblasts

value: Cells from 48h differentiated stage, treated with siRNA targeting BRG1 and BRM


title: DM48h_siBoth_B


title: In-vivo lung cells, not infected, replicate 1

source_name: Lung

value: Lung


title: WT biol rep 1


title: RNA-Seq PC3 Mut Peptide treat. repl3

value: Mutant peptide


title: RNA-Seq PC3 Mut Peptide treat. repl2


title: Sample_S30350_NoMHV_DDP10_M_trep2

data_processing:
STAR aligner version 2.7.3a used for reads alignment.
samtools version 1.7 used for sam/bam sorting.
htseq-count version 0.13.5 used for read count table generation for each sample with the parameters -f sam -m intersection-strict -s reverse -t exon -i gene_id -r pos, using the reference GFF.
normalized read counts were obtained using DESeq2 (Galaxy Version 2.11.40.6+galaxy1) hosted on Galaxy website (https://usegalaxy.org/) truning off outliers filtering.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with DESeq2 normalized counts for every gene and every sample based on factor comparison (i.e. treated vs untreated)
Supplementary_files_format_and_content: tab-delimited with differentally expressed genes based on factor comparison (i.e. treated vs untreated)

source_name: MACS_DDP 10 µM for 24 hrs_not infected

growth_protocol: BMDM were obtained from bone marrow of 6-10 week old female C57Bl6 mice (Charles River). 1*10^6 cells were plated in 10 cm untreated cell culture dishes, resuspended in 8ml of Alpha MEM containing 20% FBS, 2 mM of L-glutamine, antibiotics, 40ng/ml of rm M-CSF (R&D System) and allowed to differentiate for 7 days.

extract_protocol:
Total RNA was purified using the RNeasy kit (Qiagen).
mRNA-seq libraries were prepared according to the TruSeq low sample protocol (Illumina, San Diego, CA, USA), starting with 1 µg of total RNA per sample.

treatment_protocol: infected and non-infected BMDM treated with DDP 2.5/10µM for 24 hours.

value: bone marrow-derived macrophages

value: treated with DDP 10 uM for 24 hours

value: not infected


title: JWK-09-AD-304_NL

value: skin

value: Pretreatment


title: Sample_S30349_NoMHV_DDP10_M_trep1


title: Sample_S30348_NoMHV_DDP2_5_M_trep2

source_name: MACS_DDP 2.5 µM for 24 hrs_not infected

value: treated with DDP 2.5 uM for 24 hours


title: DM48h_siBRM_A

value: Cells from 48h differentiated stage, treated with siRNA targeting BRM


title: ATAC_HID_2weeks_1

city: Rehovot

first: Ido

last: Goldstein

address: POB 12

department: Institute of Biochemistry, Food Science and Nutrition

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Binary Base Call (BCL) output files from a Nextseq 500 machine were converted to FASTQ format, using BCL to FASTQ (bcl2fastq v2.20.0.422 Copyright (c) 2007-2017 Illumina, Inc.).
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: liver tissue

extract_protocol:
Total RNA was isolated from liver pieces (30 mg) using NucleoSpin kit (Macherey-Nagel cat# 740955.25) according to the manufacturer’s protocol. ATAC: To isolate nuclei, liver samples (10 mg) were homogenized in hypotonic sucrose buffer (250 mM sucrose, 10 mM Tris-Hcl pH 7.8, 0.1% Igepal, 3mM MgCl2, 10mM KCl, 0.2 mM Dithiothreitol, 0.5 mM spermidine, protease inhibitor cocktail) in a dounce homogenizer. Homogenate was filtered through a 20 µM filter, spun and washed (10 mM Tris-Hcl pH 7.5, 3 mM MgCl2, 10 mM NaCl, 0.1% tween-20). 50,000 nuclei were included for next steps as described (Corces et al., 2017). Each sample was sequenced at a depth of at least 50X10^6 reads (paired-end).
For quality control of RNA yield and library synthesis products, the RNA ScreenTape and D1000 ScreenTape kits (both from Agilent Technologies), Qubit® RNA HS Assay kit, and Qubit® DNA HS Assay kit (both from Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (KAPA biosystems, cat# KK8421).

treatment_protocol: Males, 8 weeks-old mice (C57BL/6JOlaHsd) were randomly assigned to either the chow or HID groups (3 mice per group). The experiment started after 1 week of acclimation. all groups had ad libitum access to chow diet (Teklad TD2018) or 2% carbonyl iron diet (TD 09521-2% carbonyl iron diet, Teklad) and water for 2 weeks or 2 days.

value: liver


title: ATAC_HID_2weeks_2


title: RNA-Seq PC3 Mut Peptide treat. repl1


title: JWK-09-Ps-212_LS

source_name: human skin biopsy

value: Psoriasis

value: LS


title: ATAC_HID_2weeks_3


title: RNA-Seq PC3 WT Peptide treat. repl3

value: WT peptide


title: DM48h_siBRG1_B

value: Cells from 48h differentiated stage, treated with siRNA targeting BRG1


title: DM48h_siBRG1_A


title: DM48h_siBRM_B


title: ATAC_chow_2weeks_2


title: Sample_S30346_NoMHV_DMSO_trep2

source_name: MACS_untreated_not infected

value: untreated


title: Sample_S30345_NoMHV_DMSO_trep1


title: RNA-Seq PC3 WT Peptide treat. repl2

value: prostate cancer cell line


title: DM48h_siScr_B

value: Myoblasts

value: Cells from 48h differentiated stage, treated with non-targeting siRNA


title: RNA-Seq PC3 WT Peptide treat. repl1


title: Sample_S30344_MHV_DDP10_M_rep3

source_name: MACS_DDP 10 µM for 24 hrs_MHV

value: infected with Murine hepatitis virus strain A59


title: RNAseq_HID_2days_3


title: Sample_S30342_MHV_DDP10_M_rep1

value: bone marrow-derived macrophages


title: Sample_S30343_MHV_DDP10_M_rep2

value: treated with DDP 10 uM for 24 hours


title: ATAC_chow_2weeks_1


title: RNA-Seq PC3 EloC KD repl3

value: EloC KD


title: JWK-09-AD-306_NL

value: skin

value: NL


title: GM_siBoth_B

value: Cells from proliferative stage, treated with siRNA targeting BRG1 and BRM


title: DM48h_siScr_A


title: Sample_S30341_MHV_DDP2_5_M_rep3

source_name: MACS_DDP 2.5 µM for 24 hrs_MHV

value: treated with DDP 2.5 uM for 24 hours


title: Sample_S30347_NoMHV_DDP2_5_M_trep1

value: not infected


title: ATAC_chow_2weeks_3

value: liver


title: GM_siBRM_B

value: Cells from proliferative stage, treated with siRNA targeting BRM


title: RNA-Seq PC3 EloC KD repl1


title: GM_siBoth_A


title: RNA-seq_HID_2weeks_3


title: RNA-Seq PC3 EloB KD repl3

value: EloB KD


title: Sample_S30340_MHV_DDP2_5_M_rep2


title: GM_siBRM_A


title: RNA-Seq PC3 EloB KD repl2


title: Sample_S30339_MHV_DDP2_5_M_rep1


title: RNA-seq_HID_2weeks_2


title: GM_siBRG1_B

value: Cells from proliferative stage, treated with siRNA targeting BRG1


title: RNA-Seq PC3 EloB KD repl1


title: RNA-seq_chow_2weeks_3


title: GM_siBRG1_A


title: RNA-seq_HID_2weeks_1


title: Sample_S30338_MHV_DMSO_rep3

value: untreated


title: RNAseq_HID_2days_2


title: RNA-Seq PC3 EloC KD repl2

value: prostate cancer cell line


title: RNAseq_HID_2days_1


title: Sample_S30336_MHV_DMSO_rep1


title: GM_siScr_B

value: Myoblasts

value: Cells from proliferative stage, treated with non-targeting siRNA


title: RNA-Seq PC3 Control KD repl2

value: Control KD


title: RNA-Seq PC3 Control KD repl1


title: GM_siScr_A


title: Sample_S30337_MHV_DMSO_rep2

value: bone marrow-derived macrophages

value: infected with Murine hepatitis virus strain A59


title: RNA-seq_chow_2weeks_2


title: RNA-seq_chow_2weeks_1


title: Extracellular vesicles (EVs)-E370K-dCO_1

status: Public on Jun 23 2023

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

data_processing:
RNA-seq reads were mapped to the mouse genome (mm10) using STAR (Dobin et al., 2013). Expression of genes in TPM was calculated with RSEM (Li et al., 2011).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Neural progenitor cells

growth_protocol: NPCs were cultured in NPM medium according to Boyer et al., 2012. DMEM/F12 , 1× N2 supplement, 1× B27 supplement, Laminin (1 µg/ml), 1x Antibiotic mixture Anti-Anti

extract_protocol:
Trizol and RNA clean and concentrator kit (Zymo research)
Smarter ultra low input-v4 (Clontech 634888) and Microplex-v2 (Diagenode C05010012)

treatment_protocol: Acute treatment (12 hours) with dEVs or vEVs isolated from conditioned media of dorsally or ventrally patterned human spheroids originated from control iPSCs or EPM1 patients-iPSCs. Experiments were performed in biological triplicates.

value: iPScs-derived neural progenitor cells

value: NPCs acutely treated (12 hours) with Extracellular vesicles (EVs) purified by the conditioned medium of dorsally patterned human spheroids originated from E370K mutant-iPSCs cells.


title: Extracellular vesicles (EVs)-E370K-dCO_3


title: Extracellular vesicles (EVs)-E370K-vCO_3

value: NPCs acutely treated (12 hours) with Extracellular vesicles (EVs) purified by the conditioned medium of ventrally patterned human spheroids originated from E370K mutant-iPSCs cells.


title: Extracellular vesicles (EVs)-E370K-vCO_1


title: Extracellular vesicles (EVs)-E370K-vCO_2


title: RNA-Seq PC3 Control KD repl3


title: Extracellular vesicles (EVs)-vCO_3

value: NPCs acutely treated (12 hours) with Extracellular vesicles (EVs) purified by the conditioned medium of ventrally patterned human cerebral organoids originated from control-iPSCs cells.


title: Extracellular vesicles (EVs)-dCO_3

value: NPCs acutely treated (12 hours) with Extracellular vesicles (EVs) purified by the conditioned medium of dorsally patterned human cerebral organoids originated from control-iPSCs cells.


title: Extracellular vesicles (EVs)-dCO_2


title: Extracellular vesicles (EVs)-dCO_1


title: WT_Wh_R3

city: MERCED

first: Ruihao

last: Li

address: 5200 NORTH LAKE ROAD

department: QSB/MCB

institute: University of California, Merced

description: Wildtype, White planktonic cell, Replicate3

data_processing:
STAR (Spliced Transcripts Alignment to a Reference) v 2.7.6a
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuk with normal parameter settings (k=13; ktrim=r; useshortkmers=t; mink=5; qtrim=r; trimq=10; minlength=20)
rimmed sequence reads were mapped to C_albicans_SC5314_A21 using STAR (parameters: max number of multiple alignments allowed for a read=25; minimum overhang for unannotated junctions=8; minimum overhang for annotated junctions=1; max number of mismatches per pair relative to read length=0.3; minimum intron length=20)
Read count extraction was done using STAR --quantMode. The read counts were normalized by TMM (edgeR)
Assembly: C_albicans_SC5314_A21
Supplementary files format and content: tab-delimited text files include read numbers per gene

organism: Candida albicans

source_name: White planktonic cell

growth_protocol: Synthetic Defined with amino acids and Uridine (SD+aa+Uri) was used to grow strains and maintain the white and opaque states at 25⁰C. Stains were streaked out on SD+aa+Uri and grown for 5-10 days. A single colony isolate was then picked and used to inoculate a 5mL overnight liquid culture that was incubated for 12-16 hours. The OD600 was measured and used to make new 45mL back dilute cultures at a calculated OD600 of 0.1. Back diluted cultures were grown to and then collected at an OD600 of 0.7-0.9.

extract_protocol:
RNA was isolated using RiboPure™ RNA Purification Kit.
500 ng of total RNA was subjected to library synthesis using Lexogen’s QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina kit; 3' Tag Seq

tag: aaron hernday_yeast_number

value: White planktonic cell

value: Wildtype


title: WOR4_Wh_R3

description: WOR4 knockout, White planktonic cell, Replicate3

value: WOR4 homozygous knockout


title: WOR4_Wh_R2

description: WOR4 knockout, White planktonic cell, Replicate2


title: WOR4_Wh_R1

description: WOR4 knockout, White planktonic cell, Replicate1


title: WOR1_Wh_R3

description: WOR1 knockout, White planktonic cell, Replicate3

value: WOR1 homozygous knockout


title: Extracellular vesicles (EVs)-E370K-dCO_2


title: WOR1_Wh_R1

description: WOR1 knockout, White planktonic cell, Replicate1


title: WT_Wh_R2

description: Wildtype, White planktonic cell, Replicate2


title: WT_Op_R2

description: Wildtype, Opaque planktonic cell, Replicate2

source_name: Opaque planktonic cell

value: Opaque planktonic cell


title: WOR3_Op_R2

description: WOR3 knockout, Opaque planktonic cell, Replicate2

value: WOR3 homozygous knockout


title: WOR3_Op_R1

description: WOR3 knockout, Opaque planktonic cell, Replicate1


title: WOR3_Wh_R2

description: WOR3 knockout, White planktonic cell, Replicate2


title: WOR3_Wh_R1

description: WOR3 knockout, White planktonic cell, Replicate1


title: EFG1_Op_R3

description: EFG1 knockout, Opaque planktonic cell, Replicate3

value: EFG1 homozygous knockout


title: WOR1_Wh_R2

description: WOR1 knockout, White planktonic cell, Replicate2


title: EFG1_Op_R1

description: EFG1 knockout, Opaque planktonic cell, Replicate1


title: Extracellular vesicles (EVs)-vCO_1


title: Extracellular vesicles (EVs)-vCO_2


title: WT_Op_R3

description: Wildtype, Opaque planktonic cell, Replicate3


title: EFG1_Wh_R2

description: EFG1 knockout, White planktonic cell, Replicate2


title: EFG1_Wh_R3

description: EFG1 knockout, White planktonic cell, Replicate3


title: EFG1_Wh_R1

description: EFG1 knockout, White planktonic cell, Replicate1


title: WT_Wh_R1

description: Wildtype, White planktonic cell, Replicate1


title: WT_Op_R1

description: Wildtype, Opaque planktonic cell, Replicate1


title: AHR1_Op_R2

description: AHR1 knockout, Opaque planktonic cell, Replicate2

value: AHR1 homozygous knockout


title: AHR1_Op_R3

description: AHR1 knockout, Opaque planktonic cell, Replicate3


title: AHR1_Wh_R2

description: AHR1 knockout, White planktonic cell, Replicate2


title: AHR1_Wh_R3

description: AHR1 knockout, White planktonic cell, Replicate3


title: AHR1_Op_R1

description: AHR1 knockout, Opaque planktonic cell, Replicate1


title: WOR3_Wh_R3

description: WOR3 knockout, White planktonic cell, Replicate3


title: AHR1_Wh_R1

description: AHR1 knockout, White planktonic cell, Replicate1


title: SSN6_Op_R2

description: SSN6 knockout, Opaque planktonic cell, Replicate2

value: SSN6 homozygous knockout


title: SSN6&WOR1_Wh_R2

description: SSN6&WOR1 knockout, White planktonic cell, Replicate2

value: SSN6&WOR1 homozygous knockout


title: SSN6&WOR1_Wh_R1

description: SSN6&WOR1 knockout, White planktonic cell, Replicate1


title: SSN6&WOR1_Wh_R3

description: SSN6&WOR1 knockout, White planktonic cell, Replicate3


title: EFG1_Op_R2

description: EFG1 knockout, Opaque planktonic cell, Replicate2


title: SSN6_Op_R1

description: SSN6 knockout, Opaque planktonic cell, Replicate1


title: RBF1_Op_R2

description: RBF1 knockout, Opaque planktonic cell, Replicate2

value: RBF1 homozygous knockout


title: RBF1_Op_R3

description: RBF1 knockout, Opaque planktonic cell, Replicate3


title: RBF1&WOR1_Wh_R1

description: RBF1&WOR1 knockout, White planktonic cell, Replicate1

value: RBF1&WOR1 homozygous knockout


title: CZF1_Op_R3

description: CZF1 knockout, Opaque planktonic cell, Replicate3

value: CZF1 homozygous knockout


title: WOR3_Op_R3

description: WOR3 knockout, Opaque planktonic cell, Replicate3


title: SSN6_Op_R3

description: SSN6 knockout, Opaque planktonic cell, Replicate3


title: RBF1&WOR1_Wh_R3

description: RBF1&WOR1 knockout, White planktonic cell, Replicate3


title: RBF1&WOR1_Wh_R2

description: RBF1&WOR1 knockout, White planktonic cell, Replicate2


title: CZF1_Wh_R3

description: CZF1 knockout, White planktonic cell, Replicate3


title: CZF1_Wh_R1

description: CZF1 knockout, White planktonic cell, Replicate1


title: CZF1_Op_R1

description: CZF1 knockout, Opaque planktonic cell, Replicate1


title: RBF1_Op_R1

description: RBF1 knockout, Opaque planktonic cell, Replicate1


title: CZF1_Op_R2

description: CZF1 knockout, Opaque planktonic cell, Replicate2


title: WOR2_Wh_R2

description: WOR2 knockout, White planktonic cell, Replicate2

value: WOR2 homozygous knockout


title: WOR2_Wh_R1

description: WOR2 knockout, White planktonic cell, Replicate1


title: CZF1_Wh_R2

description: CZF1 knockout, White planktonic cell, Replicate2


title: P2

value: nasopharyngeal carcinoma

value: S26 patental


title: input_wildtype_opaque_bio_rep_1

data_processing:
sequence reads were trimmed for adaptor sequences using homerTools trim function with the following parameters: "-3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20"
trimmed reads were aligned to Candida albicans genome assembly 21 using the Star aligner with the following parameters: STAR --genomeDir GenomeIndexForhg38/ --runThreadN 24 --readFilesIn exp1.csRNA.fastq.gz.trimmed --outFileNamePrefix exp1.csRNA.fastq.gz.trimmed. --outSAMstrandField intronMotif --outMultimapperOrder Random --outSAMmultNmax 1 --outFilterMultimapNmax 10000 --limitOutSAMoneReadBytes 10000000
tag directories were created using HOMER's "makeTagDirectory " function. These tag directories were subsequently used as input to create bigwig files using HOMER's "makeUCSCfile" function (default parameters).
Assembly: Candida albicans Assembly21
Supplementary files format and content: bigwig visualization files

source_name: input small RNA, wildtype opaque cells

growth_protocol: Candida albicans cultures were grown overnight in 5 mL synthetic dextrose (+complete amino acid mix) (SDAA) liquid media inside a shaking incubator (25 deg C, 210 RPM shaking). Overnight cultures were subsequently backdiluted to 0.1 optical density in 50 mL SDAA liquid media and incubated inside a shaking incubator (25 deg C, 210 RPM shaking). When O.D of cultures reached 0.6 - 0.8 O.D, cells were imediately pelleted using a centrifuge and liquid supernatant removed.

extract_protocol:
RNA from cell pellets were extracted using mirVana miRNA isolation kit from thermofisher per manufactureres instructions.
Sequencing ready libraries were prepared using using NEB’s small RNA library preparation kit.

treatment_protocol: no treatment

value: planktonic cells

value: wildtype

value: no treatment


title: input_wildtype_opaque_bio_rep_2


title: capped_wildtype_opaque_bio_rep_1

source_name: capped small RNA, wildtype opaque cells


title: input_wildtype_opaque_bio_rep_3


title: capped_wildtype_opaque_bio_rep_3


title: capped_wildtype_opaque_bio_rep_2


title: input_wildtype_white_bio_rep_3

source_name: input small RNA, wildtype white cells


title: capped_wildtype_white_bio_rep_3

source_name: capped small RNA, wildtype white cells


title: input_wildtype_white_bio_rep_2


title: capped_wildtype_white_bio_rep_1


title: capped_wildtype_white_bio_rep_2


title: E17.5 (embryonic day 17.5) skin, Tie1 knockout [skin_Tie1ECDKO_2]

city: Suzhou

first: Yulong

last: He

address: 199 Ren-Ai Road

institute: Soochow University

data_processing:
Single end 50 bases reads were generated with a target depth of 20 million reads on BGIseq500 platform (BGI-Shenzhen, China).
The sequencing data was filtered with SOAPnuke (v1.5.2), and clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set.
Gene expression level was calculated by RSEM (v1.2.12)
Assembly: Mus_musculus：GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files including read count for each sample

extract_protocol:
Skin tissues were harvested from Tie1 knockout and control mice (E17.5) and kept frozen in liquid nitrogen. Total RNA was extracted from the tissues using Trizol (Invitrogen) according to the manufacturer’s instruction
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented, converted into cDNA and amplified by PCR, and finally made into RNAseq libraries.

value: skin

tag: developmental stage

value: E17.5 (embryonic day 17.5)

value: knockout

tag: strain background


title: E17.5 (embryonic day 17.5) skin, Tie1 control [skin_Tie1ECDWT_2]

tag: tissue

value: control


title: E17.5 (embryonic day 17.5) skin, Tie1 knockout [skin_Tie1ECDKO_1]


title: E17.5 (embryonic day 17.5) skin, Tie1 knockout [skin_Tie1ECDKO_3]


title: E17.5 (embryonic day 17.5) skin, Tie1 control [skin_Tie1ECDWT_3]


title: E17.5 (embryonic day 17.5) skin, Tie1 control [skin_Tie1ECDWT_1]


title: NEB, TotalH3, Set2, 10ng

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
All ChIP-Seq reads were trimmed to 36 bp and mapped to the human genome (hg19). Mapping was performed using Bowtie (version 1.1.2), allowing for no more than two mismatches and retaining only reads that were mapped to unique positions. To avoid PCR bias, when multiple reads were mapped to the same genomic position, only one read was retained for analysis.
H3K4me3 and CTCF peaks were detected using MACS (version 1.4.2, p-value cutoff 1e-5 and window size 300 bp). Peaks that overlapped ENCODE blacklisted regions were removed. H3K4me3 peak calling was performed without a control library reference. CTCF peaks in each library were called by taking the corresponding total input library as a control.
The H3K27me3 enriched domains were initially identified using the enriched domain detector (EDD version 1.1.16), without any significance threshold (i.e. the FDR cutoff for EDD was set to be larger than 1). The EDD gap penalty and bin size were set to 10 and 20 kb, respectively. After peak calling with EDD, for each 20 kb bin, the z-score was calculated as: (p0-p)/σ, where p0=Number of ChIP reads/(Number of ChIP reads+Number of total H3 reads), p=0.5 and σ=sqrt(p×(1-p)/Number of ChIP reads+Number of total H3 reads).   The p-value for each candidate domain was calculated using Stouffer's Z-score method by combining all the bins within the putative domain. The p-values were corrected using the method of Benjamini & Hochberg (BH). The domains with FDR ≤ 0.05 were called as significantly enriched with H3K27me3. To minimize the effect of total H3 library quality, a combined total H3 was used as a control for the detection of H3K27me3 enriched domains with 15M reads from the total H3 library prepared by each protocol at the 10 ng level.
Genome_build: hg19
Supplementary_files_format_and_content: Peak locations in bed format. The peak file name contains how many reads were used for peak calling for that sample.

source_name: androgen-sensitive human prostate adenocarcinoma cell line LNCaP

growth_protocol: LNCaP cells were cultured in RPMI 1640 (+) L-Glutamine medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin-streptomycin, and 1 mM sodium pyruvate. Cells were maintained in 5% CO2 at 37°C and cultured in 10 cm plates to a confluency of 70-80% before fixation.

extract_protocol:
Lysates were prepared from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Bioo ChIP libraries were prepared using the NEXTflex ChIP-Seq Kit (Bioo Scientific, now PerkinElmer) following the manufacturer’s protocol. "Diagenode" ChIP libraries were prepared using the Diagenode MicroPlex Library Preparation Kit v2 (Diagenode) following the manufacturer’s protocol. "KAPA" ChIP libraries were prepared using the KAPA HyperPrep Kit (Roche) following the manufacturer’s protocol. "NEB" ChIP-Seq libraries were prepared using the NEBNext® Ultra II™ DNA Library Prep Kit for Illumina® (New England BioLabs, Inc., Ipswich, MA) following the manufacturer’s protocol.

treatment_protocol: Not applicable

tag: cell line

tag: chip antibody

value: total H3

tag: input dna level

tag: library preparation protocol

value: NEB NEBNext Ultra II


title: NEB, TotalH3, Set1, 10ng

value: androgen-sensitive human prostate adenocarcinoma cell line LNCaP


title: NEB, Input, Set3


title: NEB, Input, Set2


title: NEB, Input, Set1


title: NEB, H3K4me3, Set2, 5ng


title: input_wildtype_white_bio_rep_1

tag: cell type

tag: treatment


title: NEB, H3K4me3, Set2, 500pg


title: NEB, H3K4me3, Set2, 1ng


title: NEB, H3K4me3, Set2, 10ng


title: NEB, H3K4me3, Set2, 250pg


title: NEB, H3K4me3, Set2, 100pg


title: NEB, H3K4me3, Set1, 250pg


title: NEB, H3K4me3, Set1, 500pg


title: NEB, H3K4me3, Set1, 5ng


title: CML patient, biological replicate 4

city: Aachen

first: Mirle

last: Schemionek

state: NRW

address: Pauwelsstr. 30

department: Hematology, Oncology, Hemostaseology and SCT

institute: University Hospital RWTH Aachen

description: primary human MSCs isolated by plastic adherence stemming from a patient with CML at the timepoint of diagnosis (patient received no treatment)

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45°C on GeneChip Human Genome Array. GeneChips were washed and stained with the Affymetrix Fluidic station 450 (Thermo Fisher Scientific Inc, MA. USA), with the protocol FS450_0001.

scan_protocol: Arrays were scanned on a GeneChip 3000 7G Scanner (Thermo Fisher Scientific Inc, MA. USA)

data_processing: To generate the summarized data, first raw .CEL files were read with into R (v4.3.0) with  the oligo package (v1.62.2) function read.celfiles.  Then RMA was run (background correction + normalization) with the rma function from oligo setting the target parameter to “core”.

label: Biotin

source_name: human MSCs isolated by plastic adherence and used for analysis at passage 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: disease state

value: chronic myeloid leukemia (CML)

value: MSCs from bone marrow

tag: gender

value: Male

tag: age

tag: timepoint

value: yes


title: NEB, H3K4me3, Set1, 1ng


title: CML patient, biological replicate 2

description: primary human MSCs isolated by plastic adherence stemming from a patient with CML 12 months after diagnosis (patient received Imatinib treatment for 12 months)

value: Imatinib treatment for 12 months before isolation of MSCs

value: no


title: NEB, H3K27me3, Set2, 250pg


title: CML patient, biological replicate 1


title: CML patient, biological replicate 3


title: NEB, H3K27me3, Set2, 5ng


title: NEB, H3K27me3, Set2, 500pg


title: NEB, H3K27me3, Set2, 10ng


title: Healthy Donor, biological replicate 1

description: primary human MSCs isolated by plastic adherence stemming from a healthy donor

value: healthy

value: not applicable


title: Healthy Donor, biological replicate 4


title: NEB, H3K27me3, Set1, 250pg


title: NEB, H3K27me3, Set1, 10ng


title: NEB, H3K27me3, Set1, 5ng


title: NEB, H3K27me3, Set1, 1ng


title: NEB, H3K27me3, Set1, 100pg


title: NEB, CTCF, Set3

value: CTCF


title: NEB, H3K4me3, Set1, 100pg


title: NEB, H3K27me3, Set2, 100pg


title: NEB, H3K27me3, Set1, 500pg


title: NEB, H3K4me3, Set1, 10ng


title: KAPA, TotalH3, Set2, 10ng

value: Roche KAPA HyperPrep


title: KAPA, TotalH3, Set1, 10ng


title: Healthy Donor, biological replicate 3


title: NEB, CTCF, Set2


title: Healthy Donor, biological replicate 2


title: KAPA, Input, Set3


title: NEB, CTCF, Set1


title: NEB, H3K27me3, Set2, 1ng


title: KAPA, Input, Set2


title: KAPA, Input, Set1


title: KAPA, H3K4me3, Set2, 5ng


title: KAPA, H3K4me3, Set2, 500pg


title: KAPA, H3K4me3, Set2, 250pg


title: KAPA, H3K4me3, Set1, 250pg


title: KAPA, H3K4me3, Set2, 100pg


title: KAPA, H3K4me3, Set1, 5ng


title: KAPA, H3K4me3, Set2, 10ng


title: KAPA, H3K4me3, Set2, 1ng


title: KAPA, H3K4me3, Set1, 500pg


title: KAPA, H3K27me3, Set2, 5ng


title: KAPA, H3K4me3, Set1, 100pg


title: KAPA, H3K27me3, Set2, 500pg


title: KAPA, H3K27me3, Set2, 100pg


title: KAPA, H3K4me3, Set1, 10ng


title: KAPA, H3K27me3, Set1, 5ng


title: KAPA, H3K27me3, Set1, 500pg


title: KAPA, H3K27me3, Set2, 10ng


title: KAPA, CTCF, Set3


title: KAPA, H3K27me3, Set1, 100pg


title: KAPA, H3K27me3, Set1, 1ng


title: KAPA, H3K27me3, Set1, 10ng


title: KAPA, H3K27me3, Set2, 1ng


title: WOR2_Wh_R3

description: WOR2 knockout, White planktonic cell, Replicate3

value: White planktonic cell

tag: genotype

value: WOR2 homozygous knockout


title: KAPA, H3K27me3, Set1, 250pg


title: Diagenode, TotalH3, Set2, 10ng

value: Diagenode MicroPlex


title: KAPA, CTCF, Set2


title: KAPA, H3K27me3, Set2, 250pg


title: KAPA, CTCF, Set1


title: Diagenode, TotalH3, Set1, 10ng