title: Small intestine, Hypoxia+Nitrate3

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature 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 readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: Small intestine

extract_protocol:
The isolated small intestine are quickly put into RNA later(Invitrogen, Waltham, Massachusetts, USA)and stored at low temperature. TRIzol(Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from islets according to the manufacturer's protocol. The amount of total RNA was measured with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA), and the quality was evaluated by 1% agarose gel electrophoresis, and stained with 4S Red Plus nucleic acid stain (Sango, Shanghai, China).
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit.

value: Small intestine

value: Hypoxia+Nitrate


title: batch4_H12e

status: Public on Jan 02 2024

type: SRA

city: Stockholm

first: Jinxin

middle: Phaedo

last: Chen

address: Tomtebodavägen 23

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Single-nucleus/mild lysis/nick repair

library_source: genomic

data_processing:
Reads were trimmed for quality and Nextera adapter sequences, and the reads whose R1 sequence overlapped with the R2 sequence were removed
Then, filtered reads were mapped to GRCh38.p13, circular spike-in DNA reference, and linear spike-in DNA reference using Burrows–Wheeler Aligner MEM 0.7.17-r1188 (https:// github.com/lh3/bwa) with -p flag; duplicates were removed with Picard MarkDuplicates 2.25.5-2 (https:// broadinstitute.github.io/picard/). The mapping rate over GRCh38.p13 was calculated with samtools 1.13-5 (www.htslib.org) flagstat. The enrichment of circular spike-in DNA over linear spike-in DNA was calculated by dividing the reads mapped to the circular spike-in reference by the total reads mapped to all spike-in DNA (circular and linear references). If the mapping rate of a sample was low (below 90%) and the enrichment of circular spike-in DNA over linear spike-in DNA was low (less than 80%), the sample would not be used for downstream analysis.
Circle regions were identified with the deduplicated bam file according to methods that were previously described 7. Firstly, genomic regions enriched in raw reads were called with Homer (homer.ucsd.edu/homer/) findPeaks to get the raw circle bed file. Then, the regions in the raw circle bed file were merged to get the merged circle bed file. Next, the borders of the circle regions were refined by bedtools v2.30.0 (https://bedtools.readthedocs.io/en/latest/) closet with the coverage calculated from the bam file to get the final circle bed file. We extracted circle-supporting reads (discordant reads and split reads) from the called circle regions and filtered them with a threshold of mapQ>20, while we removed R2R1 reads. Next, chimeric junctions were identified by extracting both ends of split reads and those chimeric junctions with at least 2 recurrent reads within 500 bp of each end were kept for visualization and downstream analysis. Meanwhile, circle-supporting reads overlapping the edge of circle regions were recorded. The circle read enrichment was calculated by dividing the reads inside circle regions by the total reads.
Assembly: GRCh38
Supplementary files format and content: Bam files
Supplementary files format and content: Bed files
Supplementary files format and content: Bedpe files

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa, batch4, scCircle-seq

growth_protocol: All cell lines used in the study were bought from ATCC and verified by STR genotyping. Colo320DM and PC3 cells were cultured in RPMI-1640 medium (Gibco, C11875500BT) supplemented with 15% fetal bovine serum (Gibco, 10091148) and 1% penicillin–streptomycin (Gibco, 15140122). HeLa and 293T cells were cultured in DMEM medium (Gibco, C11995500BT) supplemented with 10% fetal bovine serum (Gibco, 10091148). K562 cells were cultured in IMDM medium (Gibco, C12440500BT) supplemented with 15% fetal bovine serum (Gibco, 10091148). Colo320DM and K562 cells were cultured at 37 °C with 10% CO2 while PC3, HeLa and HEK293T cells were cultured at 37 °C with 5% CO2.

extract_protocol:
Single cells were mouth-pipetted into PCR tubes that contained 6.75 µl nucleus isolation buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, IGEPAL CA-630 0.3%, 0.1% Bovine serum albumin, 2 mM dithiothreitol) and 0.25 µl Dynabeads™ MyOne™ Silane beads. After incubation on ice for 30 min, sample tubes were gently vortexed for 1 min. Sample tubes were then centrifuged at 500 r.c.f. for 5 min at 4 °C. Afterwards, 5.4 µl supernatant containing cytoplasmic RNA was transferred into a new tube for scRNA sequencing using Smart-seq2 library preparation (see further below), leaving the bead pellet containing the nuclei undisturbed.
After the nucleus isolation, 0.4 µl nick repair mix (0.25 ng/ml linear spike-in DNA, 0.25 ng/ml circular spike-in DNA, 5X NEBNext FFPE DNA Repair Buffer, 0.1225X NEBNext FFPE DNA Repair Mix) was added into each tube containing the bead pellets. Sample tubes were incubated at 20 °C for 1 h after gentle vortexing.
After nick repair, 1.54 µl nuclear lysis mix (40 mM Tris-HCl, 40 mM NaCl, 0.2% TritonX-100, 30 mM dithiothreitol, 2 mM EDTA, 1.6 µg/µl QIAGEN Protease) was added into each sample tube containing repaired product. After gently vortexing, the sample tubes were incubated at 50 °C for 30 min and held at 4 °C. Next, 0.5 µl diluted inhibition mix (10X Protease Inhibitor cocktail (Sigma-Aldrich)) was added to each tube, and tubes were incubated at 37 °C for 1 h.
The lysed products were then subjected to linear DNA digestion. 1.2 µl digestion mix (8.3 mM ATP, 4.16X Plasmid-Safe Reaction Buffer (Lucigen), 0.83-2.49 U/µl Plasmid-Safe ATP-Dependent DNase (Lucigen), 2.08 mM dithiothreitol) was added into each tube, and samples were incubated at 37 °C for 20 h, 70 °C for 10 min and held at 4 °C. Next, 5 µl amplification mix (2X Phi29 buffer (NEB), 2 mM dNTP, 100 µM Exo-Resistant Random Primer (Invitrogen), 0.002 U/µl Pyrophosphatase inorganic (Invitrogen), 1.6 U/µl Phi29 DNA Polymerase (NEB)) was added into each tube, and the sample tubes were incubated at 30 °C for 2-4 h, 65 °C for 10 min and held at 4 °C.
The amplified DNA was purified with DNA Clean & Concentrator-5 (Zymo), after which 10 ng of the purified DNA was subjected to the Nextera XT DNA Library Preparation Kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: HeLa cells were passaged to several 6-well plates, after which the cells were treated with 100 nM methotrexate and the medium containing 100 nM methotrexate was renewed every 2 days. Drug-treated cells were collected at day 7 and at day 17 and subjected to subsequent operation.

tag: tissue

value: Cervical carcinoma

tag: cell line

value: HeLa

tag: cell type

value: Cervical carcinoma cells (epithelial)

tag: treatment


title: H3K27ac hiChIP from hASCs of pear shaped Subject 6 gluteofemoral depot

city: St Petersburg

first: Edina

last: Erdős

address: 501 6th Ave S

country: USA

institute: Johns Hopkins University

data_processing:
HiChIP data were analyzed using the default parameters of nf-core/hic (doi: 10.5281/zenodo.2669513).
In summary, the following steps were followed: 1) mapping to hg19 reference genome using a two steps strategy to rescue reads spanning the ligation sites (bowtie2). 2) Detection for valid interaction products 3) Duplicates removal 4) generate raw and normalized contact maps (iced) 4) Generate raw and normalized contact maps 5) Create genome-wide contact maps at various resolutions using cooler.
Valid interactions were detected by hiCPro.
Assembly: hg19
Supplementary files format and content: validpairs
Library strategy: hiChIP

source_name: subcutaneous gluteofemoral fat

growth_protocol: Adipose–derived stem cells were cultured in aMEM medium (Gibco) supplemented with 2.5% FBS, EGF and FGF.

extract_protocol:
Briefly, approximately 5x106 cells were crosslinked in 1% (methanol-free, dissolved in phosphate buffered saline - PBS) formaldehyde for 10 minutes at room temperature in 10ml final volume. Formaldehyde was quenched with the additional of 1.5ml 1M Glycine for 5 minutes at room temperature. Cells were scraped and lysed in lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0). Cells were rotated in a cold room in lysis buffer for 1 hour to isolate nuclei. Nuclei were pelleted by centrifugation and resuspended in 100ul 0.5% SDS and incubated for 10 minutes at 65C. SDS was quenched by the addition of Triton-X and incubated for 15 minutes at 37°C. Nuclei were incubated overnight at 37C in a vigorous shaker (speed – 850rpm) in the presence of MboI (375U). Mbo I was heat inactivated at 65 for 20 minutes and samples were incubated at room temperature for 20 minutes to cool. Biotin fill-in of sticky ends were performed for 1 hour at 37C in a vigorous shaker (speed – 850rpm) followed by ligation of blunt ends at room temperature for 6 hours while rotating. Nuclei were spun and resuspended in lysis buffer in the presence of 5ug H3K27ac antibody (abcam cat), and incubated overnight on a rotator at 4C. Next day, antibody chromatin complexes were pulled down with protein A paramagnetic beads and were washed once in Wash Buffer 1 (1% Triton, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in Wash Buffer 2 (1% Triton, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), once in Wash Buffer 3 (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC), and finally, in TE-buffer. After the removal of TE-buffer, DNA was eluted from the beads in elution buffer. DNA was quantified with Qubit dsDNA HS kit. Approximately, 40-50ng DNA was used for biotin pull-down with streptavidin paramagnetic beads.
Sequencing libraries were constructed with Nugen Ovation Ultralow V2 kit according to the manufacturer’s recommendations. Libraries were quantified with Quibt dsDNA HS kit and subjected to bioanalyzer fragment analysis before paired-end sequencing

value: subcutaneous gluteofemoral fat

value: adipose derived stem cells (ASC)

value: stem cells

tag: chip antibody


title: batch4_H13e

description: Single-nucleus/mild lysis/nick repair


title: batch4_H10e

description: Single-nucleus/mild lysis/nick repair


title: batch4_H11e

description: Single-nucleus/mild lysis/nick repair


title: Small intestine, Hypoxia+Nitrate2

city: Beijing

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

value: WT


title: H3K27ac hiChIP from hASCs of pear shaped Subject 5 gluteofemoral depot


title: H3K27ac hiChIP from hASCs of pear shaped Subject 3 gluteofemoral depot


title: Small intestine, Hypoxia+Nitrate1


title: batch4_H8e

description: Single-nucleus/mild lysis/nick repair


title: Small intestine, Hypoxia+Nitrate4


title: batch4_H9e

description: Single-nucleus/mild lysis/nick repair


title: Small intestine, Hypoxia2

value: Hypoxia


title: Small intestine, Hypoxia3


title: Small intestine, Hypoxia1


title: H3K27ac hiChIP from hASCs of pear shaped Subject 1 gluteofemoral depot


title: H3K27ac hiChIP from hASCs of pear shaped Subject 10 gluteofemoral depot


title: batch4_H6e

description: Single-nucleus/mild lysis/nick repair


title: Normal Aminocytes, blank, rep2

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

data_processing:
The clean reads were mapped to the Homo sapiens (GRCh38) reference genome using HISAT2/Bowtie2
Differentially expressed genes (DEGs) were identified by setting padj (Q value) <0.05 and |log2 (fold change)| ≥0.59 using DESeq2
Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA) were performed on the online Dr. Tom software (https://biosys.bgi.com) with padj (Qvalue) <0.05 as the threshold.
Assembly: GRCh38
Supplementary files format and content: TPM_FPKM.xlsx

source_name: amniotic fluid

growth_protocol: DS and Euploid/Normal aminocytes derived from pregnant women in the second trimester were diagnosed through karyotyping from the Prenatal Diagnosis Center of Henan Provincial People's Hospital (Zhengzhou, China). Amniocytes were cultured in BIO-AMF™-3 Medium (Biological Industries, Beit Haemek, Israel) and maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
Total RNA of male aminocytes from different group was extracted using TRIzol (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s instructions.
total RNA was quantified using an Agilent 2100 bioanalyzer (Thermo Fisher Scientific, USA) and purified using oligo(dT)-attached magnetic beads. The library was constructed, and single-end 50-base reads were generated on the BGIseq500 platform (BGI-Shenzhen, China). Raw data were filtered with SOAPnuke to remove adaptor sequences, unknown reads containing polyN sequences, and low-quality reads, thus obtaining clean reads and stored in FASTQ format.

treatment_protocol: The Normal aminocytes were infected with MX1-OE lentivirus and backbone lentivirus, followed by 2 μg/ml puromycin (Solarbio, Beijing, China) selection to obtain stable express cells

value: amniotic fluid

value: aminocytes

value: backbone lentivirus


title: batch4_H5e

description: Single-nucleus/mild lysis/nick repair


title: D2.0R cells, Culture, 3

city: Seattle

first: Cyrus

last: Ghajar

state: WA

address: 1100 Fairview Ave. N. P.O. Box 19024

institute: Fred Hutch

data_processing:
Sequenced reads were trimmed for adapter sequences/ low quality sequences using Trim Galore! 0.6.7 (stringency = 3)
Trimmed reads were aligned to GRCm39 using STAR 2.7.10 with parameters - mismatch max = 10, mismatch-to-mapped length ratio ≤ 0.3, mismatch-to-read length ratio ≤ 1.0, deletion open penalty = -2, deletion extension penalty = -2, insertion open penalty = -2, insertion extension penalty = -2, and splice junction stitching mismatch max = 0 (canonical motifs), -1 (non-canonical motifs).
Counts were assembled using HTSeq-count
Raw counts were log base 10 (CPM) normalized
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts
Supplementary files format and content: comma-delimited file includes log CPM counts

source_name: In Vitro

extract_protocol:
RNA was isolated from lung samples and 2-D culture samples using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher). Cells were snap-frozen at -80 C before RNA extraction.
cDNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech), followed by sequencing library preparation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then analyzed on an Illumina NovaSeq 6000.

value: In Vitro

value: mammary carcinoma

tag: strain


title: H3K27ac hiChIP from hASCs of apple shaped Subject 9 gluteofemoral depot


title: H3K27ac hiChIP from hASCs of apple shaped Subject 7 gluteofemoral depot


title: H3K27ac hiChIP from hASCs of apple shaped Subject 8 gluteofemoral depot


title: D2.0R cells, Culture, 2


title: batch4_H4e

description: Single-nucleus/mild lysis/nick repair


title: batch4_H7e

description: Single-nucleus/mild lysis/nick repair


title: Small intestine, Hypoxia4


title: H3K27ac hiChIP from hASCs of pear shaped Subject 4 gluteofemoral depot


title: batch4_H3e

description: Single-nucleus/mild lysis/nick repair


title: D2.0R cells, Culture, 1


title: H3K27ac hiChIP from hASCs of pear shaped Subject 2 gluteofemoral depot


title: H3K27ac hiChIP from hASCs of apple shaped Subject 6 gluteofemoral depot


title: batch4_H2e

description: Single-nucleus/mild lysis/nick repair


title: H3K27ac hiChIP from hASCs of apple shaped Subject 5 gluteofemoral depot


title: batch4_H1e

description: Single-nucleus/mild lysis/nick repair


title: D2.A1 cells, Culture, 1


title: H3K27ac hiChIP from hASCs of apple shaped Subject 4 gluteofemoral depot


title: D2.0R cells, Athymic nude mouse, 2

source_name: Lung

value: Lung

value: Athymic Nude


title: batch4_C39e

description: Single-nucleus/mild lysis/nick repair

source_name: Colo320DM, batch4, scCircle-seq

value: Colon adenocarcinoma

value: Colon adenocarcinoma cells (epithelial)

value: NO


title: batch4_C40e

description: Single-nucleus/mild lysis/nick repair


title: batch4_C38e

description: Single-nucleus/mild lysis/nick repair


title: H3K27ac hiChIP from hASCs of apple shaped Subject 3 gluteofemoral depot


title: H3K27ac hiChIP from hASCs of apple shaped Subject 2 gluteofemoral depot


title: batch4_C37e

description: Single-nucleus/mild lysis/nick repair


title: D2.0R cells, Athymic nude mouse, 1


title: H3K27ac hiChIP from hASCs of apple shaped Subject 1 gluteofemoral depot


title: H3K27ac hiChIP from hASCs of apple shaped Subject 10 gluteofemoral depot


title: batch4_C36e

description: Single-nucleus/mild lysis/nick repair


title: batch4_C35e

description: Single-nucleus/mild lysis/nick repair


title: H3K27ac hiChIP from hASCs of pear shaped Subject 8 abdominal depot

source_name: subcutaneous abdominal fat

value: subcutaneous abdominal fat


title: D2.A1 cells, Athymic nude mouse, 2


title: D2.A1 cells, Athymic nude mouse, 1


title: D2.0R cells, BALB/C mouse, 3

value: BALB/C


title: H3K27ac hiChIP from hASCs of pear shaped Subject 7 abdominal depot


title: batch4_C33e

description: Single-nucleus/mild lysis/nick repair


title: H3K27ac hiChIP from hASCs of pear shaped Subject 6 abdominal depot


title: batch4_C34e

description: Single-nucleus/mild lysis/nick repair


title: batch4_C32e

description: Single-nucleus/mild lysis/nick repair


title: H3K27ac hiChIP from hASCs of pear shaped Subject 5 abdominal depot


title: D2.0R cells, BALB/C mouse, 1


title: D2.A1 cells, Athymic nude mouse, 3


title: batch4_C29e

description: Single-nucleus/mild lysis/nick repair


title: H3K27ac hiChIP from hASCs of pear shaped Subject 3 abdominal depot


title: D2.A1 cells, BALB/C mouse, 3


title: H3K27ac hiChIP from hASCs of pear shaped Subject 9 abdominal depot


title: H3K27ac hiChIP from hASCs of pear shaped Subject 4 abdominal depot


title: D2.A1 cells, BALB/C mouse, 2


title: metafemale, rep3 [XXX3]

first: Lin

last: Sun

address: Xinjiekouwai Street

institute: Beijing Normal University

description: metafemale

data_processing:
Basecalls performed using CASAVA.
Trimmomatic was used to filter the raw data.
Reads were mapped to the genome by HISAT2.
Transcripts were assembled and quantitated using StringTie.
Assembly: Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa
Supplementary files format and content: Matrix table of normalized data

organism: Drosophila melanogaster

source_name: metafemale

growth_protocol: All the stocks are incubated at 25 degree

extract_protocol:
The sequencing library was constructed by removing ribosomal RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: third-instar larvae

value: AA;XXX

tag: Sex

value: female


title: D2.A1 cells, Culture, 2

value: WT


title: batch4_C31e

description: Single-nucleus/mild lysis/nick repair


title: batch4_C28e

description: Single-nucleus/mild lysis/nick repair


title: D2.A1 cells, BALB/C mouse, 1


title: metafemale, rep2 [XXX2]

description: metafemale


title: H3K27ac hiChIP from hASCs of pear shaped Subject 2 abdominal depot

value: adipose derived stem cells (ASC)

value: stem cells


title: batch4_C27e

description: Single-nucleus/mild lysis/nick repair


title: H3K27ac hiChIP from hASCs of pear shaped Subject 1 abdominal depot


title: mCCD Tmprss2 KO 2 - rep 3

city: Lausanne

first: Muriel

last: Auberson

address: Bugnon 27

department: Department of Biomedical Sciences

country: Switzerland

institute: Université de Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 2.5, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus_musculus.GRCm38 genome using STAR (v. 2.5.3a, Dobin et al. 2013).  Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using gene annotation. The htseq-generated counts data was used for the analysis.
Assembly: GRCm38
Supplementary files format and content: One single raw counts matrix with one sample per column and one gene per row provided as supplementary file

source_name: cell line

growth_protocol: mCCDcl1 cells were maintained at 37°C and 5% CO2 in full growth medium: DMEM/F-12 GlutaMAX medium; supplemented with 5g/mL insulin; 50nM dexamethasone; 60nM selenium; 5μg/mL transferrin; 1nM triiodothyronine; 5ng/mL mouse EGF; 50U/ml penicillin and 50μg/mL streptomycin; 2% (v/v) decomplemented fetal bovine serum.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen). RNA quality was determined by fragment analyzer and all samples were considered good quality with an RNA quality number >8.3.
RNA quality was assessed on a Fragment Analyzer (Agilent Technologies). The RNAs had RQNs between 7.8 and 10. RNA-seq libraries were prepared from 108 ng of total RNA with the Illumina Stranded mRNA Prep reagents (Illumina). Libraries were quantified by a fluorometric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies). Sequencing was performed on an Illumina NovaSeq 6000 for 100 cycles single read. Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina

treatment_protocol: 500,000 cells were seeded per well of a 6-well plate

value: cell line

value: spontaneously transformed mouse CCD primary cultures

value: CRISPR KO of Tmprss2


title: mCCD Tmprss2 KO 2 - rep 2


title: D2.0R cells, BALB/C mouse, 2

value: mammary carcinoma


title: trisomy 2L male, rep3 [2LM3]

source_name: trisomy 2L male

value: male


title: H3K27ac hiChIP from hASCs of pear shaped Subject 10 abdominal depot


title: batch4_C25e

description: Single-nucleus/mild lysis/nick repair


title: mCCD Tmprss2 KO 2 - rep 1


title: trisomy 2L male, rep2 [2LM2]


title: H3K27ac hiChIP from hASCs of apple shaped Subject 9 abdominal depot


title: trisomy 2L male, rep1 [2LM1]


title: mCCD Tmprss2 KO 1 - rep 3


title: mCCD Tmprss2 KO 1 - rep 2


title: H3K27ac hiChIP from hASCs of apple shaped Subject 8 abdominal depot


title: H3K27ac hiChIP from hASCs of apple shaped Subject 7 abdominal depot


title: batch4_C24e

description: Single-nucleus/mild lysis/nick repair


title: batch4_C23e

description: Single-nucleus/mild lysis/nick repair


title: trisomy 2L female, rep3 [2LF3]

source_name: trisomy 2L female


title: mCCD Tmprss2 KO 1 - rep 1


title: H3K27ac hiChIP from hASCs of apple shaped Subject 6 abdominal depot


title: metafemale, rep1 [XXX1]

description: metafemale


title: trisomy 2L female, rep2 [2LF2]


title: batch4_C26e

description: Single-nucleus/mild lysis/nick repair


title: batch4_C21e

description: Single-nucleus/mild lysis/nick repair


title: batch4_C22e

description: Single-nucleus/mild lysis/nick repair


title: H3K27ac hiChIP from hASCs of apple shaped Subject 5 abdominal depot


title: trisomy 2L female, rep1 [2LF1]


title: batch4_C20e

description: Single-nucleus/mild lysis/nick repair


title: Control male, rep3 [CM3]

source_name: Control male

value: AA;XY


title: mCCD control 2 – rep 2


title: mCCD control 2 – rep 3


title: H3K27ac hiChIP from hASCs of apple shaped Subject 4 abdominal depot


title: batch4_C19e

description: Single-nucleus/mild lysis/nick repair

value: Colon adenocarcinoma


title: mCCD control 2 – rep 1


title: Control male, rep2 [CM2]


title: H3K27ac hiChIP from hASCs of apple shaped Subject 3 abdominal depot


title: HASMC_Media_2

city: Toronto

first: Sneha

last: Raju

state: ON

address: 101 College Street, PMCRT 3-309

country: Canada

institute: University of Toronto

data_processing:
Raw reads were processed to generate clean reads by removing reads containing adaptor, reads containing poly-N, and low quality reads.
Paired-end clean reads were aligned to reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count read numbers mapped to each gene
FPKM of each gene was calculated based on length of gene and read counts
Differential expression analysis was completed using DESeq2
Assembly: Genes with adjusted p-value ≤ 0.05 (Benjamini and Hochberg) were used in downstream analysis
Supplementary files format and content: Excel file with gene counts

source_name: primary cells

growth_protocol: Complete media

extract_protocol:
TRIzol RNA extraction
Constructed by Novogene

treatment_protocol: Endothelial extracellular vesicles from quiescent and activated states (IL-1𝜷)

value: primary cells

value: Human Aortic Smooth Muscle Cells (HASMCs)

value: media


title: Control male, rep1 [CM1]


title: mCCD control 1 – rep 2


title: batch4_C17e

description: Single-nucleus/mild lysis/nick repair

value: Colon adenocarcinoma cells (epithelial)

value: NO


title: Control female, rep3 [CF3]

source_name: Control female

value: third-instar larvae

value: AA;XX


title: H3K27ac hiChIP from hASCs of apple shaped Subject 1 abdominal depot

value: subcutaneous abdominal fat


title: H3K27ac hiChIP from hASCs of apple shaped Subject 10 abdominal depot

value: adipose derived stem cells (ASC)


title: batch4_C16e

description: Single-nucleus/mild lysis/nick repair


title: Control female, rep2 [CF2]

value: female


title: batch4_C15e

description: Single-nucleus/mild lysis/nick repair


title: OT1_set_II_WT_3

city: Cleveland

first: Lily

last: Wang

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

description: Day 8

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10

source_name: T lymphocytes

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 100 ng and 200ng for polyTIL  and OT1 samples respectively of total RNA was used for the construction of sequencing libraries.
For RNA-seq PolyTIL RNA libraries for RNA-seq were prepared using Takara SMART-Seq v4 Ultra low Input RNA kit following manufacturer's protocols. And for RNA-seq OT1 RNA libraries for RNA-seq were prepared using illumina TruSeq mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: T lymphocytes

value: WT


title: SCC25_M_EPZ_Input_ChIPseq

city: Maiami

first: Yuichiro

last: Nakata

address: 1501 NW 10th Ave

institute: University of Miami

data_processing:
ChIP-seq: Single-end ChIP-seq fastq files were processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2).
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq).
Assembly: hg19
Supplementary files format and content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

growth_protocol: Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F-12) with 10% fetal bovine serum, GlutaMAX, Penicillin-Streptomycin and hydrocortisone

extract_protocol:
Cells were initially cross-linked with ChIP Cross-link Gold (Diagenode, # C01019027) to be formed reversible DNA-protein links in PBS with 1 mM of MgCl2. After incubation at RT for 30min, the cells were fixed with 11% solution containing formaldehyde (Thermo Fisher #28908), 50mM HEPES-KOH (pH 7.5), 100mM NaCl, 0.5M EDTA, 0.5M EGTA for 10 min. Then, to stop the fixation, 2.5M of Glycine was added and incubated for 5 min. The cells were washed twice with PBS and harvested on ice using cell scrapers. The harvested cells were resuspended in Lysis Buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), allowed to rotate for 10 min at 4°C. After centrifuging, the cells were resuspended in Lysis Buffer 2 (10 mM Tris-HCL pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), allowed to rotate for 10 min at room temperature. After centrifuging, the cells were resuspended in Lysis Buffer 3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated on a Bioruptor Pico at 4°C for 20 min with sonication beads. The sonicated cells were centrifuged, and the supernatant was transferred to new tubes.  5 μg of antibodies were used along with 2 μg of Spike-in antibodies (Active Motif, #61686) were bound to 50 μl of Dynabeads Protein G (Thermo Fisher, #10004D), previously washed with 0.5% BSA in PBS and rotated end-to-end overnight at 4°C. 30 μg of shared chromatin and 20 ng of spike-in chromatin from Drosophila (Active Motif, #53083) were incubated with antibodies/beads mixture overnight at 4°C. The beads were washed 6 times with Wash Buffer (50 mM Hepes-KOH, pH 7.6; 500 mM LiCl, 1 mM EDTA, 1% NP-40; 0.5% Na-Deoxycholate) and once with TE containing 50 mM NaCl. After elution of immunocomplexes from beads with Elution Buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA, 1% SDS) by incubation at 65°C for 15 min, the supernatant was reverse crosslinked at 65°C for 3hrs, treated sequentially with RNAse A (Sigma, #R5503) at 37°C for 2hrs and then treated with Proteinase K (NEB, #P8107S) at 55°C for 2 hrs. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen, # 28106).
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.

value: Head and neck squamous cell carcinomas

tag: cell source

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah

tag: modifications

value: Lentiviraly expressed with histone H3.3K36 mutation


title: Control female, rep1 [CF1]


title: hASCs, case3, on COL3+Fmod modified PLCL nanoyarns, mirna

city: Shanghai

first: Tian

last: Tu

address: 639 Zhi Zao Ju Road

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

description: All.miRNA.mature.Counts.exp.txt

data_processing:
(rRNA-free RNA)We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
(rRNA-free RNA)Hisat2 2.0.4 mapping to reference genome
(rRNA-free RNA)count counting
(circRNA)Circular RNA was predicted based on the sequencing data with ACFS circRNA prediction pipeline. Unmapped Reads was collected utilizing BWA-mem (bwa mem -t 1 -k 16 -T 20) for circRNA identification: head-to-tail junction was identified and highest splicing strength score was calculated by MaxEntScan33 with a filtering criterion greater than or equal to 10. Base on the re-alignment of the unmapped reads on the circular RNA candidates, Reads that mapped to the circular RNA back splicing junction (with an overhang of at least 6 nt) were counted for each circRNA.
(circRNA)count counting
(miRNA)We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) a)10% base quality <15 b) 13% base quality <20 c) 15bp < read length < 30bp.
(miRNA)Utilizing the BWA software, we mapped the clean data to miRBase 22.0 Homo Sapiens miRNA database and GRCH38 genome.
(miRNA)count counting
Assembly: GRCh38 / miRBase 22.0
Supplementary files format and content: TXT file contain counts for each sample

source_name: human adipose derived stem cells

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

extract_protocol:
(rRNA-free RNA)Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
(miRNA)Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
(rRNA-free RNA)RNA libraries were prepared for sequencing using standard Illumina protocols
(miRNA)RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The hASCs were seeded on scaffolds with  different surface interfaces, including pure PLCL and COL1+Fmod dual modified PLCL.

value: human adipose derived stem cells

value: MSCs

value: COL3+Fmod modified PLCL nanoyarns


title: batch4_C14e

description: Single-nucleus/mild lysis/nick repair

value: Colon adenocarcinoma


title: OT1_set_II_WT_2

description: Day 8


title: SCC25_M_DMSO_Input_ChIPseq


title: hASCs, case2, on COL2+Fmod modified PLCL nanoyarns, mirna

description: All.miRNA.mature.Counts.exp.txt

value: COL2+Fmod modified PLCL nanoyarns


title: OT1_set_II_WT_1

description: Day 8


title: batch4_C13e

description: Single-nucleus/mild lysis/nick repair

value: Colon adenocarcinoma cells (epithelial)


title: FaDU_M_EPZ_Input_ChIPseq

growth_protocol: Eagle's minimal essential medium (EMEM) with 10% fetal bovine serum, GlutaMAX and Penicillin-Streptomycin

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah


title: batch4_C12e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: OT1_set_II_LRIG1_KO_3

description: Day 8

value: LRIG1 KO


title: batch4_C18e

description: Single-nucleus/mild lysis/nick repair


title: H3K27ac hiChIP from hASCs of apple shaped Subject 2 abdominal depot

value: subcutaneous abdominal fat

value: stem cells


title: mCCD control 1 – rep 3

value: cell line

value: spontaneously transformed mouse CCD primary cultures


title: hASCs, case1, on COL1+Fmod modified PLCL nanoyarns, mirna

description: All.miRNA.mature.Counts.exp.txt

value: WT

value: COL1+Fmod modified PLCL nanoyarns


title: mCCD control 1 – rep 1


title: batch4_C11e

description: Single-nucleus/mild lysis/nick repair


title: OT1_set_II_LRIG1_KO_2

description: Day 8

value: T lymphocytes


title: hASCs, control3, on PLCL nanoyarns, mirna

description: All.miRNA.mature.Counts.exp.txt

value: PLCL nanoyarns


title: SCC25_M_Input_ChIPseq

value: Head and neck squamous cell carcinomas

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah

value: Lentiviraly expressed with histone H3.3K36 mutation


title: OT1_set_II_LRIG1_KO_1

description: Day 8


title: hASCs, control2, on PLCL nanoyarns, mirna

description: All.miRNA.mature.Counts.exp.txt

value: human adipose derived stem cells

value: MSCs


title: Poly_Female_WT_3

description: Day 18


title: hASCs, control1, on PLCL nanoyarns, mirna

description: All.miRNA.mature.Counts.exp.txt


title: SCC25_WT_Input_ChIPseq

value: Lentiviraly expressed with histone H3.3


title: hASCs, case3, on COL3+Fmod modified PLCL nanoyarns

description:
All.counts.exp.txt
all.counts.CircRNA.txt

value: COL3+Fmod modified PLCL nanoyarns


title: Poly_Female_WT_2

description: Day 18


title: batch4_C10e

description: Single-nucleus/mild lysis/nick repair

value: Colon adenocarcinoma

value: Colon adenocarcinoma cells (epithelial)

value: NO


title: batch4_C9e

description: Single-nucleus/mild lysis/nick repair


title: batch4_C8e

description: Single-nucleus/mild lysis/nick repair


title: Gingival_M_IgG_Cut/Run

data_processing:
library strategy: Cut/Run-seq
ChIP-seq: Single-end ChIP-seq fastq files were processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2).
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq).
Assembly: hg19
Supplementary files format and content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

growth_protocol: Dermal cell basal medium supplemented with keratinocyte grow kit

extract_protocol:
Cut&Run assays were performed with CUTANATM ChIC/CUT&RUN kit according to the manufacturer’s protocol (EpiCypher, #14-1048). Briefly, fresh 500,000 cells collected carefully with a cell lifter (Corning, #3008) were dissolved in wash buffer (Pre-wash buffer (EpiCypher, #21-1002), protease inhibitor, and 0.5 mM spermidine) and bound to activated Concanavalin A beads. The cells bound to the beads were dissolved in Antibody buffer (Cell permeabilization buffer and 2 mM EDTA) and incubated with antibodies at 4°C overnight. After extensive washing with Cell permeabilization buffer (Wash buffer and 0.01% digitonin), the cells were incubated with pAG-MNase (EpiCypher, #15-1016) for 10 min at room temperature, and then chromatin digestion was performed with calcium chloride for 2 h, at 4°C. After chromatin digestion, the stop buffer and E. coli spike-in DNA (EpiCypher, #18-1401) were added and incubated for 10 min at 37°C. After discarding beads, chromatin fragments were purified with DNA cleanup columns.
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.

value: Primary gingival keratinocytes were purchased from American Type Culture Collection (ATCC)

value: Rabbit IgG CUT&RUN Negative Control Antibody (EpiCypher 13-0042K)


title: FaDU_M_DMSO_Input_ChIPseq

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah


title: hASCs, case2, on COL2+Fmod modified PLCL nanoyarns

value: WT

value: COL2+Fmod modified PLCL nanoyarns


title: Poly_Female_WT_1

description: Day 18

value: T lymphocytes


title: FaDU_M_Input_ChIPseq


title: FaDU_WT_Input_ChIPseq


title: Gingival_WT_IgG_Cut/Run


title: hASCs, case1, on COL1+Fmod modified PLCL nanoyarns

value: COL1+Fmod modified PLCL nanoyarns


title: batch4_C5e

description: Single-nucleus/mild lysis/nick repair


title: Poly_Female_LRIG1_KO_1

description: Day 18

value: LRIG1 KO


title: Detroit_M_IgG_Cut/Run

value: Head and neck squamous cell carcinomas

value: Detroit562 parental cells were purchased from American Type Culture Collection (ATCC)


title: WT_gex_S9

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Separate feature barcoding libraries sequenced targeting 5,000 reads per cell at 10,000 cells per sample and were mapped to cells using cellranger software. Antibody counts were compiled with gene expression data in Seurat V4.0 software and normalized via CLR normalization methods for plotting.
Assembly: mm10
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: polyA RNA

source_name: T cells

extract_protocol:
T  10 WT and 10 LRIG1 KO tumors were pooled and digested to obtain single cell suspensions. Tumor infiltrating T cells were stained using  anti-CD3 antibody as well as antibody Derived Tag directed against surface markers CD4, CD8, PD1, SLAMF6, CX3CR1, and TIM3. Each antibody is barcoded with a unique Oligonucleotide Hash Tag.   10e4 sorted viable cells  were loaded into a Chromium Controller (10X Genomics).
Viable sorted CD3+ cells were washed three times before being processed using 10X genomics Feature barcoding protocol and workflow with v3.1 3’ technology. The single-cell RNAseq libraries are prepared by the Genomics Core facility at Lerner Research Institute. The single-cell RNAseq libraries are prepared according to the manufacturer’s Chromium Single Cell 3ʹ v3.1 with Feature Barcode technology for Cell Surface Protein (CSP) protocol. Briefly,cDNA for the 3’ gene expression library was initially synthesized from poly-adenylated mRNA, and DNA for the CSP library was synthesized from the cell surface protein feature Barcode. A minimum of 1 nanogram of cDNA was used to beginfragmentation, followed by end-repair, adapter ligation, and sample indexing. Each sequencing library including the CSP library was tagged with a dual index (10-nucleotide long each) sample barcode that identifies from which sample a sequence was derived. In addition, a 12-base unique molecular indexes (UMIs) were introduced to reduce duplicate reads.Constructed libraries are pooled and quantified using a Quantabio Q cycler.NovaSeq 6000RapidRun flow cells are used to sequence a minimum of 20,000 read pairs per cell for the Gene expression library and a minimum of 5,000 read pairs per cell for the Cell surface protein library using specifications recommended by the manufacturer (10X Genomics, document # CG000317).

value: T cells

value: tumor infiltrating lymphocytes


title: hASCs, control3, on PLCL nanoyarns

value: human adipose derived stem cells

value: MSCs

value: PLCL nanoyarns


title: hASCs, control2, on PLCL nanoyarns


title: Detroit_WT_IgG_Cut/Run

value: Lentiviraly expressed with histone H3.3


title: hASCs, control1, on PLCL nanoyarns


title: batch4_C7e

description: Single-nucleus/mild lysis/nick repair

value: Colon adenocarcinoma

value: Colon adenocarcinoma cells (epithelial)

value: NO


title: KO_gex_S10


title: batch4_C3e

description: Single-nucleus/mild lysis/nick repair


title: batch4_C2e

description: Single-nucleus/mild lysis/nick repair


title: Poly_Female_LRIG1_KO_3

description: Day 18


title: Pf3d7_CX_3

city: Cambridge

first: Holly

last: Craven

address: 208 Molteno Building, Tennis Court Road

department: Pathology

country: United Kingdom

institute: University of Cambrdige

data_processing:
FastQ reads were trimmed using trimmomatic (v 0.39)
Unique reads were aligned against PlasmoDB v57 P.  falciparum genome with HISAT2 (2.1.0)
Counts were generated using featureCounts (v1.6.0) package
Differential gene expression analysis performed using DESeq2 (v1.36.0)
Assembly: PlasmoDB v57 P. falciparum genome
Supplementary files format and content: all counts (.txt)
Supplementary files format and content: “Geneid” “Chr” “Start” “End” “Strand” “Length” “CX_1.sorted.bam” “CX_2.sorted.bam” “CX_3.sorted.bam” “med_1.sorted.bam” “med_2.sorted.bam” “med_3.sorted.bam” “QF_1.sorted.bam” “QF_2.sorted.bam” “QF_3.sorted.bam”

organism: Plasmodium falciparum

source_name: 3D7 WT

growth_protocol: Custom made RPMI 1640 (with 2.3 g/L sodium bicarbonate, 4 g/L dextrose, 5.957 g/L HEPES, 0.05 g/L hypoxanthine, 5 g/L Albumax II, Invitrogen), 5% pooled human serum, 4% haematocrit O+ human red blood cells, 3% oxygen, 5% CO2 and 92% nitrogen gas mixture at 37C.

extract_protocol:
Parasites were saponin extracted and stored in trizol. Total RNA was extracted by phenol-chloroform and treated with Dnase, then polyA mRNA was extracted using NEBNext® Poly(A) mRNA Magnetic Isolation Module.
First strand cDNA synthesis was performed using Sensiscript Vand Ampure bead cleanup. Second strand synthesis using NEBNext® Ultra™ II Non-Directional RNA Second Strand Synthesis Module was performed and another ampure bead cleanup. Samples were covaris sheared and libraries prepared using Kapa Hyper prep kit

treatment_protocol: Synchronised 30-32 hpi parasites were incubated with 2X EC50 QF, CX or no drug for 4 hours.

value: 3D7 WT


title: batch4_C1e

description: Single-nucleus/mild lysis/nick repair


title: KO_ab_S8

description: Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

library_source: other

molecule: protein


title: FaDU_M_IgG_Cut/Run

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah

value: Lentiviraly expressed with histone H3.3K36 mutation

value: Rabbit IgG CUT&RUN Negative Control Antibody (EpiCypher 13-0042K)


title: SCC25_WT_IgG_Cut/Run

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah


title: WT_ab_S7


title: D2.A1 cells, Culture, 3

value: In Vitro

value: mammary carcinoma

value: WT


title: batch4_C6e

description: Single-nucleus/mild lysis/nick repair


title: Pf3d7_CX_2


title: Pf3d7_CX_1


title: H24e

description: Single-nucleus/mild lysis/nick repair

source_name: HeLa, batch2, scCircle-seq

value: Cervical carcinoma

value: HeLa

value: Cervical carcinoma cells (epithelial)


title: H23e

description: Single-nucleus/mild lysis/nick repair


title: FaDU_WT_IgG_Cut/Run

value: Head and neck squamous cell carcinomas


title: SingleCell Vista KO antibody [KO_ab]

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

data_processing:
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
Separate feature barcoding libraries sequenced targeting 5,000 reads per cell at 10,000 cells per sample and were mapped to cells using cellranger software. Antibody counts were compiled with gene expression data in Seurat V4.0 software and normalized via CLR normalization methods for plotting.
Assembly: mouse_mm10-2020-A
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy:

source_name: tumor tissue

extract_protocol:
MC38 tumors were pooled and digested to obtain single cell suspensions. Tumor infiltrating MDSCs were stained using antibodies CD45.1 vs CD45.2 to distinguish WT vs KO cells. Cells were also stained with antibody Derived Tag directed against surface markers CD11C, Ly6c, Ly6G . Each antibody is barcoded with a unique Oligonucleotide Hash Tag.   10e4 sorted viable cells  were loaded into a Chromium Controller (10X Genomics).
Viable sorted CD11b+ cells were washed three times before being processed using 10X genomics Feature barcoding protocol and workflow with v3.1 3’ technology. The single-cell RNAseq libraries are prepared by the Genomics Core facility at Lerner Research Institute. The single-cell RNAseq libraries are prepared according to the manufacturer’s Chromium Single Cell 3ʹ v3.1 with Feature Barcode technology for Cell Surface Protein (CSP) protocol. Briefly,cDNA for the 3’ gene expression library was initially synthesized from poly-adenylated mRNA, and DNA for the CSP library was synthesized from the cell surface protein feature Barcode. A minimum of 1 nanogram of cDNA was used to beginfragmentation, followed by end-repair, adapter ligation, and sample indexing. Each sequencing library including the CSP library was tagged with a dual index (10-nucleotide long each) sample barcode that identifies from which sample a sequence was derived. In addition, a 12-base unique molecular indexes (UMIs) were introduced to reduce duplicate reads.Constructed libraries are pooled and quantified using a Quantabio Q cycler.NovaSeq 6000RapidRun flow cells are used to sequence a minimum of 20,000 read pairs per cell for the Gene expression library and a minimum of 5,000 read pairs per cell for the Cell surface protein library using specifications recommended by the manufacturer (10X Genomics, document # CG000317).

value: tumor tissue

value: tumor infiltrating myeloid suppressor cells

tag: library type

value: PROTEIN

tag: antibodies/tags


title: batch4_C4e

description: Single-nucleus/mild lysis/nick repair

value: Colon adenocarcinoma

value: Colon adenocarcinoma cells (epithelial)


title: SingleCell Vista KO gene expression [KO_gex]

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: RNA


title: Pf3d7_QF_3

value: 3D7 WT

value: 2X Ec50 quarfloxin (220 nM)


title: H22e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: SCC25_M_EPZ_RING1B_Rep2_ChIPseq

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah

value: Lentiviraly expressed with histone H3.3K36 mutation and treated with EPZ

value: Mouse moniclonal Anti-RING1B antibody (MBL D139-3)


title: Pf3d7_QF_2


title: SingleCell WT antibody [WT_ab]


title: SCC25_M_IgG_Cut/Run

value: Lentiviraly expressed with histone H3.3K36 mutation

value: Rabbit IgG CUT&RUN Negative Control Antibody (EpiCypher 13-0042K)


title: SCC25_M_EPZ_RING1B_Rep1_ChIPseq


title: H21e

description: Single-nucleus/mild lysis/nick repair

value: Cervical carcinoma

value: HeLa


title: Pf3d7_QF_1


title: H20e

description: Single-nucleus/mild lysis/nick repair

value: Cervical carcinoma cells (epithelial)


title: SCC25_M_DMSO_RING1B_Rep2_ChIPseq

value: Head and neck squamous cell carcinomas

value: Lentiviraly expressed with histone H3.3K36 mutation and treated with DMSO


title: SingleCell WT gene expression [WT_gex]

value: tumor tissue

value: tumor infiltrating myeloid suppressor cells


title: MC38_WT3

data_processing:
Fastq Files were aligned using genecode GRCm38
Counts were extracted using subread featurecounts
Differential expression was performed using Deseq2
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Takara SMART-Seq  RNA kit following manufacturer's protocols.

tag: strain background

value: WT

tag: time point

value: Day 7


title: Pf3d7_Media_3

value: 3D7 WT

value: no drug control


title: MC38_WT2


title: SCC25_M_DMSO_RING1B_Rep1_ChIPseq


title: H19e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: MC38_WT1


title: H18e

description: Single-nucleus/mild lysis/nick repair


title: Pf3d7_Media_1


title: FaDU_M_EPZ_RING1B_Rep1_ChIPseq

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah


title: MC38_KO3

value: VISTA KO


title: FaDU_M_EPZ_RING1B_Rep2_ChIPseq

value: Lentiviraly expressed with histone H3.3K36 mutation and treated with EPZ

value: Mouse moniclonal Anti-RING1B antibody (MBL D139-3)


title: 1876-A041717_S12

data_processing:
Adaptors trimmed
Reads were mapped to the genome using Bowtie with the hg38 assembly
Aligned reads were quantified and normalized using median ratio

source_name: extracellular vesicles

growth_protocol: EV-free media

extract_protocol:
Ultracentrifugation
Constructed by HTG Molecular Diagnostics

value: extracellular vesicles

value: HAEC

value: human aortic endothelial cells

value: IL-1Beta treated


title: H17e

description: Single-nucleus/mild lysis/nick repair

value: Cervical carcinoma

value: HeLa

value: Cervical carcinoma cells (epithelial)


title: FaDU_M_DMSO_RING1B_Rep2_ChIPseq

value: Head and neck squamous cell carcinomas

value: Lentiviraly expressed with histone H3.3K36 mutation and treated with DMSO


title: H16e

description: Single-nucleus/mild lysis/nick repair


title: MC38_KO2

value: tumor tissue

value: Day 7


title: H15e

description: Single-nucleus/mild lysis/nick repair


title: MC38_KO1


title: SCC25_M_EPZ_H3K36M_Rep2_Cut/Run

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah

value: Rabbit monoclonal Anti-H3K36M antibody (Cayman 31547)


title: H14e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: 1876-A041714_S3


title: 1876-A041715_S13


title: MYOX_MUT_5

city: Memphis

first: Yong-Dong

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: MYOX MUT replicate 5

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm39/mm39 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include TPM values for all 17 samples

source_name: C57BL/6J mice embryos

extract_protocol:
Pregnant dams were harvested, embryos were dissected, and each embryo was placed in a 1.5 mL Eppendorf tube and flash frozen in liquid nitrogen, then stored at -80C while genotyping was performed. Once embryos were generated, all samples were purified at the same time.  Each whole embryo was homogenized, and RNA was extracted by using RNeasy Micro Kit (Qiagen) using the manufacturer’s protocol.
RNA sequencing libraries for each sample were prepared with 1 mg total RNA by using the TruSeq RNA Sample Prep v2 Kit (Illumina) per the manufacturer’s instructions, and sequencing was completed on the Illumina NovaSeq 6000.

value: embryos

tag: age

value: MYOX MUT


title: 1876-A041712_S1


title: MYOX_MUT_4

description: MYOX MUT replicate 4


title: H13e

description: Single-nucleus/mild lysis/nick repair

data_processing:
Reads were trimmed for quality and Nextera adapter sequences, and the reads whose R1 sequence overlapped with the R2 sequence were removed
Then, filtered reads were mapped to GRCh38.p13, circular spike-in DNA reference, and linear spike-in DNA reference using Burrows–Wheeler Aligner MEM 0.7.17-r1188 (https:// github.com/lh3/bwa) with -p flag; duplicates were removed with Picard MarkDuplicates 2.25.5-2 (https:// broadinstitute.github.io/picard/). The mapping rate over GRCh38.p13 was calculated with samtools 1.13-5 (www.htslib.org) flagstat. The enrichment of circular spike-in DNA over linear spike-in DNA was calculated by dividing the reads mapped to the circular spike-in reference by the total reads mapped to all spike-in DNA (circular and linear references). If the mapping rate of a sample was low (below 90%) and the enrichment of circular spike-in DNA over linear spike-in DNA was low (less than 80%), the sample would not be used for downstream analysis.
Circle regions were identified with the deduplicated bam file according to methods that were previously described 7. Firstly, genomic regions enriched in raw reads were called with Homer (homer.ucsd.edu/homer/) findPeaks to get the raw circle bed file. Then, the regions in the raw circle bed file were merged to get the merged circle bed file. Next, the borders of the circle regions were refined by bedtools v2.30.0 (https://bedtools.readthedocs.io/en/latest/) closet with the coverage calculated from the bam file to get the final circle bed file. We extracted circle-supporting reads (discordant reads and split reads) from the called circle regions and filtered them with a threshold of mapQ>20, while we removed R2R1 reads. Next, chimeric junctions were identified by extracting both ends of split reads and those chimeric junctions with at least 2 recurrent reads within 500 bp of each end were kept for visualization and downstream analysis. Meanwhile, circle-supporting reads overlapping the edge of circle regions were recorded. The circle read enrichment was calculated by dividing the reads inside circle regions by the total reads.
Assembly: GRCh38
Supplementary files format and content: Bam files
Supplementary files format and content: Bed files
Supplementary files format and content: Bedpe files

extract_protocol:
Single cells were mouth-pipetted into PCR tubes that contained 6.75 µl nucleus isolation buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, IGEPAL CA-630 0.3%, 0.1% Bovine serum albumin, 2 mM dithiothreitol) and 0.25 µl Dynabeads™ MyOne™ Silane beads. After incubation on ice for 30 min, sample tubes were gently vortexed for 1 min. Sample tubes were then centrifuged at 500 r.c.f. for 5 min at 4 °C. Afterwards, 5.4 µl supernatant containing cytoplasmic RNA was transferred into a new tube for scRNA sequencing using Smart-seq2 library preparation (see further below), leaving the bead pellet containing the nuclei undisturbed.
After the nucleus isolation, 0.4 µl nick repair mix (0.25 ng/ml linear spike-in DNA, 0.25 ng/ml circular spike-in DNA, 5X NEBNext FFPE DNA Repair Buffer, 0.1225X NEBNext FFPE DNA Repair Mix) was added into each tube containing the bead pellets. Sample tubes were incubated at 20 °C for 1 h after gentle vortexing.
After nick repair, 1.54 µl nuclear lysis mix (40 mM Tris-HCl, 40 mM NaCl, 0.2% TritonX-100, 30 mM dithiothreitol, 2 mM EDTA, 1.6 µg/µl QIAGEN Protease) was added into each sample tube containing repaired product. After gently vortexing, the sample tubes were incubated at 50 °C for 30 min and held at 4 °C. Next, 0.5 µl diluted inhibition mix (10X Protease Inhibitor cocktail (Sigma-Aldrich)) was added to each tube, and tubes were incubated at 37 °C for 1 h.
The lysed products were then subjected to linear DNA digestion. 1.2 µl digestion mix (8.3 mM ATP, 4.16X Plasmid-Safe Reaction Buffer (Lucigen), 0.83-2.49 U/µl Plasmid-Safe ATP-Dependent DNase (Lucigen), 2.08 mM dithiothreitol) was added into each tube, and samples were incubated at 37 °C for 20 h, 70 °C for 10 min and held at 4 °C. Next, 5 µl amplification mix (2X Phi29 buffer (NEB), 2 mM dNTP, 100 µM Exo-Resistant Random Primer (Invitrogen), 0.002 U/µl Pyrophosphatase inorganic (Invitrogen), 1.6 U/µl Phi29 DNA Polymerase (NEB)) was added into each tube, and the sample tubes were incubated at 30 °C for 2-4 h, 65 °C for 10 min and held at 4 °C.
The amplified DNA was purified with DNA Clean & Concentrator-5 (Zymo), after which 10 ng of the purified DNA was subjected to the Nextera XT DNA Library Preparation Kit (Illumina) following the manufacturer’s instructions.


title: Pf3d7_Media_2

value: 3D7 WT

value: no drug control


title: 1876-A041711_S11

value: extracellular vesicles

value: HAEC


title: SCC25_M_DMSO_H3K36M_Rep2_Cut/Run


title: MYOX_MUT_3

description: MYOX MUT replicate 3


title: H12e

description: Single-nucleus/mild lysis/nick repair


title: SCC25_M_DMSO_H3K36M_Rep1_Cut/Run


title: MYOX_MUT_2

description: MYOX MUT replicate 2


title: 1876-A041709_S14

value: human aortic endothelial cells

value: quiescent


title: 1876-A041710_S7

value: IL-1Beta treated


title: MYOX_MUT_1

description: MYOX MUT replicate 1


title: H10e

description: Single-nucleus/mild lysis/nick repair

value: Cervical carcinoma

value: HeLa

value: Cervical carcinoma cells (epithelial)


title: 1876-A041708_S16


title: FaDU_M_EPZ_H3K36M_Rep2_Cut/Run

value: Head and neck squamous cell carcinomas

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah

value: Lentiviraly expressed with histone H3.3K36 mutation and treated with EPZ


title: FaDU_M_DMSO_RING1B_Rep1_ChIPseq

value: Lentiviraly expressed with histone H3.3K36 mutation and treated with DMSO

value: Mouse moniclonal Anti-RING1B antibody (MBL D139-3)


title: H11e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: MYOX_WT_4

description: MYOX WT replicate 4

value: embryos

value: MYOX WT


title: H9e

description: Single-nucleus/mild lysis/nick repair


title: 1876-A041706_S18


title: H8e

description: Single-nucleus/mild lysis/nick repair


title: MYOX_WT_3

description: MYOX WT replicate 3


title: FaDU_M_DMSO_H3K36M_Rep2_Cut/Run

value: Rabbit monoclonal Anti-H3K36M antibody (Cayman 31547)


title: SCC25_M_EPZ_H3K36M_Rep1_Cut/Run

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah


title: 1876-A041704_S4

value: extracellular vesicles

value: HAEC


title: FaDU_M_DMSO_H3K36M_Rep1_Cut/Run


title: 1876-A041703_S6

value: human aortic endothelial cells

value: quiescent


title: 1876-A041702_S8


title: SCC25_M_RING1B_Rep2_ChIPseq

value: Lentiviraly expressed with histone H3.3K36 mutation


title: H6e

description: Single-nucleus/mild lysis/nick repair

value: Cervical carcinoma

value: HeLa


title: Disp1CSINDEL_4

description: Disp1 MUT replicate 4

value: Disp1 MUT


title: H7e

description: Single-nucleus/mild lysis/nick repair

value: Cervical carcinoma cells (epithelial)


title: MYOX_WT_1

description: MYOX WT replicate 1


title: MYOX_WT_2

description: MYOX WT replicate 2


title: SCC25_M_RING1B_Rep1_ChIPseq

value: Head and neck squamous cell carcinomas


title: 213-A035739_S3

value: IL-1Beta treated


title: H5e

description: Single-nucleus/mild lysis/nick repair


title: Disp1CSINDEL_2

description: Disp1 MUT replicate 2


title: Disp1CSINDEL_3

description: Disp1 MUT replicate 3


title: H3e

description: Single-nucleus/mild lysis/nick repair


title: 213-A035741_S12


title: FaDU_M_EPZ_H3K36M_Rep1_Cut/Run

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah

value: Lentiviraly expressed with histone H3.3K36 mutation and treated with EPZ


title: 213-A035735_S24


title: SCC25_WT_RING1B_Rep2_ChIPseq

value: Lentiviraly expressed with histone H3.3

value: Mouse moniclonal Anti-RING1B antibody (MBL D139-3)


title: FaDU_M_RING1B_Rep2_ChIPseq


title: H2e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: 213-A035742_S15


title: Disp1WT_4

description: Disp1 WT replicate 4

value: embryos

value: Disp1 WT


title: FaDU_M_RING1B_Rep1_ChIPseq


title: 213-A035740_S14

value: extracellular vesicles

value: HAEC


title: H1e

description: Single-nucleus/mild lysis/nick repair


title: FaDU_WT_RING1B_Rep2_ChIPseq


title: Disp1WT_3

description: Disp1 WT replicate 3


title: FaDU_WT_RING1B_Rep1_ChIPseq


title: SCC25_WT_RING1B_Rep1_ChIPseq

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah


title: H4e

description: Single-nucleus/mild lysis/nick repair


title: C11e

description: Single-nucleus/mild lysis/nick repair

source_name: Colo320DM, batch2, scCircle-seq

value: Colon adenocarcinoma

value: Colon adenocarcinoma cells (epithelial)


title: C7e

description: Single-nucleus/mild lysis/nick repair


title: SCC25_M_H3K4me2_Rep2_Cut/Run

value: Lentiviraly expressed with histone H3.3K36 mutation

value: Rabbit polyconal Histone H3K4me2 antibody (Active Motif  39141)


title: Disp1WT_2

description: Disp1 WT replicate 2


title: C9e

description: Single-nucleus/mild lysis/nick repair


title: C5e

description: Single-nucleus/mild lysis/nick repair


title: SCC25_WT_H3K4me2_Rep2_Cut/Run


title: C6e

description: Single-nucleus/mild lysis/nick repair


title: KO-2CD326

city: tianjin

first: huachen

last: wang

address: pingjiang road 23

institute: the second hospital of tianjin medical university

description:
Murine cecal ligation and puncture (CLP)-induced acute lung injury (ALI) model.
Sepsis-induced ALI.

data_processing:
CLC Genomics Workbench v 11.0.1.
Sequence reads were trimmed for adaptor sequence using CLC Genomics Workbench.
Trimmed sequence reads were mapped to GRCm38 using CLC Genomics Workbench.
Read count extraction and normalization were performed using CLC Genomics Workbench.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Excel file includes raw counts for each sample.
Supplementary files format and content: Excel file includes FPKM values for each sample.

source_name: Lung epithelial cells

extract_protocol:
Total RNA of epithelial cell isolated from lung tissue was extracted using RNeasy mini kit (Qiagen, Hilden, Germany).
SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Lung epithelial cells

value: IL-36R KO

value: CLP


title: KO-3CD326


title: KO-1CD326


title: SCC25_M_H3K4me2_Rep1_Cut/Run

value: Head and neck squamous cell carcinomas


title: SCC25_WT_H3K4me2_Rep1_Cut/Run


title: C4e

description: Single-nucleus/mild lysis/nick repair


title: C10e

description: Single-nucleus/mild lysis/nick repair


title: Disp1WT_1

description: Disp1 WT replicate 1


title: FaDU_M_H3K4me2_Rep2_Cut/Run

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah


title: WT-3CD326

value: WT


title: Disp1CSINDEL_1

description: Disp1 MUT replicate 1

value: Disp1 MUT


title: FaDU_M_H3K4me2_Rep1_Cut/Run


title: C3e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: WT-2CD326


title: FaDU_WT_H3K4me2_Rep2_Cut/Run

value: Lentiviraly expressed with histone H3.3


title: 213-A035734_S18

value: human aortic endothelial cells

value: quiescent


title: WT-1CD326


title: FaDU_WT_H3K4me2_Rep1_Cut/Run


title: C1e

description: Single-nucleus/mild lysis/nick repair


title: heart, PAMH-male, rep5

city: shanghai

first: Ling

last: Gao

address: 419 Fangxie Rd

institute: Fudan University

data_processing:
Quality control of raw sequencing data was performed using FastQC (v0.11.9)
Raw reads were processed using Trimmomatic (v0.38) according to the quality control report of each sample.
Clean reads were mapped to the genome using hisat2 (v2.2.1) with default parameters.
The number of aligned reads for each gene was counted with the htseq-count (v0.13.5) program.
Differential expression analysis was performed in R (v3.4.1) using DESeq2 (v1.18.1).
Assembly: Assembly: mm10
Supplementary files format and content: Comma separated value files include FPKM values for each sample

source_name: heart

growth_protocol: Pregnant mice were treated with prenatal Anti-mullerian hormone (PAMH) treatment or PBS, and male offspring from each group were used for experiment.

extract_protocol:
Total RNA was extracted using the Trizol method following the manufacturer’s protocol
RNA libararies for RNA-seq were prepared using VAHTSUniversalRNA-seqLibraryPrepKitforIllumina following the manufacturer’s protocol

value: heart

value: prenatal AMH


title: FaDU_M_SETD2_Rep2_ChIPseq

value: Mouse moniclonal Anti-SETD2 antibody (CST #23486)


title: FaDU_WT_SETD2_Rep2_ChIPseq

value: Rabbit monoclonal Anti-LSD2 antibody (Abcam  ab193080)


title: heart, PAMH-male, rep3


title: heart, PAMH-male, rep4


title: FaDU_WT_SETD2_Rep1_ChIPseq


title: P11e

description: Single-nucleus/mild lysis/nick repair

source_name: PC3, batch2, scCircle-seq

value: Prostate cancer

value: Prostate cancer cells (epithelial)


title: P9e

description: Single-nucleus/mild lysis/nick repair


title: heart, PAMH-male, rep2


title: heart, control-male, rep5

value: prenatal vehicle


title: P10e

description: Single-nucleus/mild lysis/nick repair


title: P8e

description: Single-nucleus/mild lysis/nick repair


title: P7e

description: Single-nucleus/mild lysis/nick repair


title: SCC25_H3.3_Rep2_ChIPseq

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah

value: Parental

value: Rabbit polyconal Anti-Histone H3.3 antibody (Millipore 09-838)


title: D2.0R cells, Athymic nude mouse, 3

data_processing:
Sequenced reads were trimmed for adapter sequences/ low quality sequences using Trim Galore! 0.6.7 (stringency = 3)
Trimmed reads were aligned to GRCm39 using STAR 2.7.10 with parameters - mismatch max = 10, mismatch-to-mapped length ratio ≤ 0.3, mismatch-to-read length ratio ≤ 1.0, deletion open penalty = -2, deletion extension penalty = -2, insertion open penalty = -2, insertion extension penalty = -2, and splice junction stitching mismatch max = 0 (canonical motifs), -1 (non-canonical motifs).
Counts were assembled using HTSeq-count
Raw counts were log base 10 (CPM) normalized
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts
Supplementary files format and content: comma-delimited file includes log CPM counts

source_name: Lung

extract_protocol:
RNA was isolated from lung samples and 2-D culture samples using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher). Cells were snap-frozen at -80 C before RNA extraction.
cDNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech), followed by sequencing library preparation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then analyzed on an Illumina NovaSeq 6000.

value: Lung

value: mammary carcinoma

value: Athymic Nude


title: FaDU_H3.3_Rep2_ChIPseq

source_name: FaDU

value: Head and neck squamous cell carcinomas

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah


title: heart, control-male, rep3

value: WT


title: C2e

description: Single-nucleus/mild lysis/nick repair

value: Colon adenocarcinoma

value: Colon adenocarcinoma cells (epithelial)

value: NO


title: FaDU_H3.3_Rep1_ChIPseq


title: AAA_7, scRNAseq

city: Hangzhou

first: Zhejun

last: Cai

state: Zhejiang

address: 88 Jiefang Road

department: Department of Cardiology, The Second Affiliated Hospital

institute: Zhejiang University School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The 10X Genomics Cell Ranger workflow was used to demultiplex raw data and map them to the reference genome using default settings. Except as otherwise noted, all downstream single-cell analyses were carried out using CellRanger and Seurat(16, 17). In order to create digital expression matrices, specific molecular identifiers were counted for each gene and each cell barcode (filtered by CellRanger). Seurat used a secondary filtration method in which a gene had to be expressed in at least 200 cells and in more than 3 cells to be regarded to be expressed. Additionally, we removed some of the foreignDNA from mitochondria.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Infrarenal segment of the aorta

extract_protocol:
Before taking infrarenal abdominal aorta samples, animals were euthanized by cervical dislocation and injected with 5 ml PBS at the left ventricular apex to perfuse the blood vessels. The infrarenal aorta was removed and crushed. Aortic samples were incubated in hank solution (450 units/ml collagenase I, 125 units/ml XI, 60 units/ml hyaluronidase, and 60 units/ml DNase I dissolved in PBS) at 37 °C for 1 hour. The cell solution was filtered with 70 μm cell mesh and centrifuged to remove lumpy tissues. To isolate CD45-positive immune cells, the cell pellet was resuspended in buffer with CD45 and viability microbeads and magnetically separated. Each group (n=20 AAA, n=50 control) mixes all aortic sample cells.
A 10× Chromium Controller (10X Genomics) barcoded the cell solution in Chromium microfluidic chips with 3' chemistry. RNA from barcoded cells was reverse-transcribed and sequencing libraries were created using reagents from a Chromium Single Cell 3’ v2 reagent kit (10X Genomics). Illumina's instructions guided sequencing.

value: Infrarenal segment of the aorta

value: CD45+ cells

value: Immune cells

value: Wild type

value: Induced with PBS


title: P6e

description: Single-nucleus/mild lysis/nick repair

value: Prostate cancer

value: Prostate cancer cells (epithelial)


title: heart, control-male, rep4

value: heart

value: prenatal vehicle


title: P5e

description: Single-nucleus/mild lysis/nick repair


title: heart, control-male, rep2


title: FaDU_M_SETD2_Rep1_ChIPseq

value: Lentiviraly expressed with histone H3.3K36 mutation

value: Mouse moniclonal Anti-SETD2 antibody (CST #23486)


title: SCC25_M_H3K27me3_Rep2_Cut/Run

value: Head and neck squamous cell carcinomas

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah

value: Rabbit polyconal Histone H3K27me3 antibody (Active Motif  39155)


title: P12e

description: Single-nucleus/mild lysis/nick repair


title: heart, PAMH-male, rep1

value: WT

value: prenatal AMH


title: P4e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: KO_LPS_biol_rep_3

city: Charlottesville

first: Dina

last: Bai

state: VA

address: McCormick Rd.

department: Chemistry

institute: University of Virginia

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads
Alternative splicing analysis was performed by the software rMATS
Assembly: NCBI/UCSC/Ensembl
Supplementary files format and content: gzip text file, read counts
Supplementary files format and content: gzip text file, fpkm

source_name: Bone Marrow Derived Macrophages (BMDMs)

growth_protocol: The bone marrow was cultured with RPMI media supplemented with 10% FBS (Omega Scientific), 5% HEPES (Gibco), 1% antibiotic-antimitotic (penicillin-streptomycin, Gibco), and 10% L929-conditioned media (L929 cells purchased from ATCC)in a 37°C incubator with 5% CO2.

extract_protocol:
Invitrogen™ PureLink™ RNA Mini Kit
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: on day 6, cells were traeted with LPS (PBS as vehicle) for 16 h

value: Bone Marrow Derived Macrophages (BMDMs)

value: DAGLB KO

value: Lipopolysaccharide (LPS)


title: heart, control-male, rep1


title: P3e

description: Single-nucleus/mild lysis/nick repair


title: SCC25_H3.3_Rep1_ChIPseq

value: Parental

value: Rabbit polyconal Anti-Histone H3.3 antibody (Millipore 09-838)


title: SCC25_M_H3K27me3_Rep1_Cut/Run


title: KO_LPS_biol_rep_1


title: KO_LPS_biol_rep_2


title: KO_PBS_biol_rep_3


title: SCC25_WT_H3K27me3_Rep2_Cut/Run

value: Lentiviraly expressed with histone H3.3


title: P2e

description: Single-nucleus/mild lysis/nick repair

value: Prostate cancer

value: Prostate cancer cells (epithelial)


title: SCC25_WT_H3K27me3_Rep1_Cut/Run


title: P1e

description: Single-nucleus/mild lysis/nick repair


title: PC3-Bulk

description: Bulk Circle-seq

source_name: PC3, batch1, Bulk Circle-seq


title: FaDU_M_H3K27me3_Rep1_Cut/Run

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah


title: KO_PBS_biol_rep_1


title: KO_PBS_biol_rep_2


title: FaDU_M_H3K27me3_Rep2_Cut/Run

value: Lentiviraly expressed with histone H3.3K36 mutation


title: WT_LPS_biol_rep_3

value: DAGLB WT


title: WT_LPS_biol_rep_2


title: T2

description: Single-nucleus/mild lysis/nick repair

source_name: HEK293T, batch1, scCircle-seq

value: Kidney

value: Kidney (epithelial)


title: T1

description: Single-nucleus/mild lysis/nick repair


title: FaDU_WT_H3K27me3_Rep1_Cut/Run

value: Head and neck squamous cell carcinomas

value: Rabbit polyconal Histone H3K27me3 antibody (Active Motif  39155)


title: T3

description: Single-nucleus/mild lysis/nick repair


title: WT_PBS_biol_rep_3


title: WT_LPS_biol_rep_1


title: Primary_Gingival_Cell_WT_H3K36me3_Rep1_Cut/Run

value: Primary gingival cell

value: Primary gingival keratinocytes were purchased from American Type Culture Collection (ATCC)

value: Rabbit polyclonal Anti-H3K36me3 antibody (Active motif 61101)


title: P6-2

description: Single-nucleus/mild lysis/nick repair

source_name: PC3, batch1, scCircle-seq

value: NO


title: BRAF organoid, D31, cAMP+4OHT+PD+LY, rep2

city: Brussels

first: Mirian

last: Romitti

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

data_processing:
the public sever  https://usegalaxy.eu was used for mapping and counting analysis
mapping used HISAT2 sofware, allowing soft clipping.
read counts extraction used HTseq count software with unstranded option.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts

source_name: organoid

growth_protocol: TRE-Nkx2-1-Pax8_bTg-NES-BrafV637E-ERT2 mouse embryonic stem cells were differentiated into thyroid follicles with 5 days of 1µg/ml doxycycline and 2 weeks of 0.3 nmol 8-Br-cAMP

extract_protocol:
Total RNA was extracted from thyroid organoids by addition of lysis RLT Lysis buffer (Qiagen) + 1% 2-mercaptoethanol. RNA was isolated using RNeasy micro kit (Qiagen) according to the manufacturer’s instructions.
Indexed cDNA libraries were obtained using the TruSeq Stranded mRNA Sample Prep kit (Illumina) using a S2 flow cell and sequences were produced using a 200 cycles reagent kit

treatment_protocol:
Cells were incubated with 1 µM of 4-Hydroxytamoxifen and 8-Br-cAMP for 5 days
Cells were incubated with 250nM of PD0325901, 5µM of LY204002, 1 µM of 4-Hydroxytamoxifen and 8-Br-cAMP for 3 days

value: organoid

value: Embryonic stem cells


title: Detroit562_WT_H3K36me3_Rep1_Cut/Run

value: Detroit562 parental cells were purchased from American Type Culture Collection (ATCC)


title: Detroit562_M_H3K36me3_Rep1_Cut/Run


title: BRAF organoid, D31, cAMP+4OHT+PD+LY, rep1


title: P5-5

city: Stockholm

first: Jinxin

address: Tomtebodavägen 23

institute: Karolinska Institutet

description: Single-nucleus/mild lysis/nick repair


title: P6-3

description: Single-nucleus/mild lysis/nick repair


title: WT_PBS_biol_rep_1

value: Bone Marrow Derived Macrophages (BMDMs)


title: P6-1

description: Single-nucleus/mild lysis/nick repair

value: Prostate cancer


title: Primary_Gingival_Cell_M_H3K36me3_Rep1_Cut/Run


title: FaDU_WT_H3K27me3_Rep2_Cut/Run

value: Lentiviraly expressed with histone H3.3


title: SCC25_M_H3K36me3_Rep2_Cut/Run

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah


title: BRAF organoid, D31, cAMP+4OHT, rep1


title: P5-4

description: Single-nucleus/mild lysis/nick repair

value: Prostate cancer cells (epithelial)


title: SCC25_M_H3K36me3_Rep1_Cut/Run

value: Lentiviraly expressed with histone H3.3K36 mutation


title: P5-3

description: Single-nucleus/mild lysis/nick repair


title: BRAF organoid, D31, cAMP+4OHT, rep2


title: BRAF organoid, D31, cAMP, rep2


title: SCC25_WT_H3K36me3_Rep2_Cut/Run


title: BRAF organoid, D31, cAMP, rep1


title: P5-2

description: Single-nucleus/mild lysis/nick repair


title: WT_PBS_biol_rep_2

value: DAGLB WT


title: heart, HFD, rep3

growth_protocol: Mice were fed with HFD or normal chow from 4-week age to 12-week age.

extract_protocol:
Total RNA was extracted using the Trizol method following the manufacturer’s protocol
RNA libararies for RNA-seq were prepared using VAHTS mRNA-seq Library Prep Kit for Illumina following the manufacturer’s protocol

value: heart

value: WT

value: HFD from 4-week age to 12-week age.


title: P5-1

description: Single-nucleus/mild lysis/nick repair


title: P4-3

description: Single-nucleus/mild lysis/nick repair


title: FaDU_M_H3K36me3_Rep2_Cut/Run

value: Head and neck squamous cell carcinomas

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah


title: heart, HFD, rep2


title: P4-2

description: Single-nucleus/mild lysis/nick repair


title: heart, HFD, rep1


title: heart, NC, rep2

value: normal chow from 4-week age to 12-week age.


title: FaDU_WT_H3K36me3_Rep2_Cut/Run

value: Rabbit polyclonal Anti-H3K36me3 antibody (Active motif 61101)


title: P3-5

description: Single-nucleus/mild lysis/nick repair

value: NO


title: P4-1

description: Single-nucleus/mild lysis/nick repair


title: SCC25_WT_H3K36me3_Rep1_Cut/Run


title: heart, NC, rep3


title: heart, NC, rep1


title: P3-4

description: Single-nucleus/mild lysis/nick repair


title: P3-3

description: Single-nucleus/mild lysis/nick repair


title: FaDU_WT_H3K36me3_Rep1_Cut/Run


title: Primary_Gingival_Cell_WT_H3K36me2_Rep1_Cut/Run

value: Primary gingival cell

value: Primary gingival keratinocytes were purchased from American Type Culture Collection (ATCC)

value: Rabbit polyclonal Anti-H3K36me2 antibody (Millipore 07-369-I)


title: mouse mammary tumor [mid174]

type: RNA

city: Berkeley

first: Jian-Hua

last: Mao

state: CA

address: One Cyclotron Road

institute: Lawrence Berkeley National Laboratory

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with by Robust Multi-array Analysis (RMA).
probe group file: MoEx-2_0-st-v1.r2.pgf
meta-probeset file: MoEx-2_0-st-v1.r2.dt1.mm8.mps

label: biotin

source_name: biospy of mammary tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2016, Affymetrix).

growth_protocol: spontaneous mammary tumors from genetically diverse MMTV-ErbB2 mice

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

treatment_protocol: Biopsy before docetaxel treatment

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2)

value: female

value: biospy of mammary tumor


title: mouse mammary tumor [mid194]


title: heart, PCOS, rep5

growth_protocol: Polycystic ovary syndrome (PCOS) in female mice was induced by prenatal Anti-mullerian hormone (PAMH) treatment; control mice were prenatally treated with PBS.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol
RNA libararies for RNA-seq were prepared using TruSeq Stranded mRNA LTSample Prep Kit following the manufacturer’s protocol

value: prenatal AMH


title: FaDU_M_H3K36me3_Rep1_Cut/Run

extract_protocol:
Cut&Run assays were performed with CUTANATM ChIC/CUT&RUN kit according to the manufacturer’s protocol (EpiCypher, #14-1048). Briefly, fresh 500,000 cells collected carefully with a cell lifter (Corning, #3008) were dissolved in wash buffer (Pre-wash buffer (EpiCypher, #21-1002), protease inhibitor, and 0.5 mM spermidine) and bound to activated Concanavalin A beads. The cells bound to the beads were dissolved in Antibody buffer (Cell permeabilization buffer and 2 mM EDTA) and incubated with antibodies at 4°C overnight. After extensive washing with Cell permeabilization buffer (Wash buffer and 0.01% digitonin), the cells were incubated with pAG-MNase (EpiCypher, #15-1016) for 10 min at room temperature, and then chromatin digestion was performed with calcium chloride for 2 h, at 4°C. After chromatin digestion, the stop buffer and E. coli spike-in DNA (EpiCypher, #18-1401) were added and incubated for 10 min at 37°C. After discarding beads, chromatin fragments were purified with DNA cleanup columns.
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.

value: Lentiviraly expressed with histone H3.3K36 mutation


title: Detroit562_M_H3K36me2_Rep1_Cut/Run

value: Detroit562 parental cells were purchased from American Type Culture Collection (ATCC)


title: mouse mammary tumor [mid303]


title: mouse mammary tumor [mid220]


title: mouse mammary tumor [mid319]


title: P3-2

last: Chen

description: Single-nucleus/mild lysis/nick repair

growth_protocol: All cell lines used in the study were bought from ATCC and verified by STR genotyping. Colo320DM and PC3 cells were cultured in RPMI-1640 medium (Gibco, C11875500BT) supplemented with 15% fetal bovine serum (Gibco, 10091148) and 1% penicillin–streptomycin (Gibco, 15140122). HeLa and 293T cells were cultured in DMEM medium (Gibco, C11995500BT) supplemented with 10% fetal bovine serum (Gibco, 10091148). K562 cells were cultured in IMDM medium (Gibco, C12440500BT) supplemented with 15% fetal bovine serum (Gibco, 10091148). Colo320DM and K562 cells were cultured at 37 °C with 10% CO2 while PC3, HeLa and HEK293T cells were cultured at 37 °C with 5% CO2.

value: Prostate cancer

value: Prostate cancer cells (epithelial)


title: Primary_Gingival_Cell_M_H3K36me2_Rep1_Cut/Run


title: mouse mammary tumor [mid166]


title: Detroit562_WT_H3K36me2_Rep1_Cut/Run

value: Lentiviraly expressed with histone H3.3


title: mouse mammary tumor [mid256]


title: heart, PCOS, rep3

value: heart

value: WT


title: mouse mammary tumor [mid265]


title: SCC25_M_H3K36me2_Rep2_Cut/Run

value: Head and neck squamous cell carcinomas

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah


title: P2-5

description: Single-nucleus/mild lysis/nick repair

value: NO


title: heart, PCOS, rep2


title: heart, PCOS, rep1


title: mouse mammary tumor [mid295]


title: P2-4

description: Single-nucleus/mild lysis/nick repair


title: heart, control, rep6

value: prenatal vehicle


title: mouse mammary tumor [mid257]


title: P2-3

description: Single-nucleus/mild lysis/nick repair


title: SCC25_WT_H3K36me2_Rep2_Cut/Run


title: heart, control, rep5


title: SCC25_WT_H3K36me2_Rep1_Cut/Run


title: heart, PCOS, rep4


title: mouse mammary tumor [mid162]


title: FaDU_M_H3K36me2_Rep2_Cut/Run

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah


title: P2-2

description: Single-nucleus/mild lysis/nick repair


title: mouse mammary tumor [mid250]


title: P2-1

description: Single-nucleus/mild lysis/nick repair


title: heart, control, rep4


title: FaDU_M_H3K36me2_Rep1_Cut/Run

value: Rabbit polyclonal Anti-H3K36me2 antibody (Millipore 07-369-I)


title: P3-1

description: Single-nucleus/mild lysis/nick repair


title: P1-5

description: Whole-cel/harsh lysisl/no nick repair


title: SCC25_M_H3K36me2_Rep1_Cut/Run


title: P1-4

description: Whole-cel/harsh lysisl/no nick repair


title: FaDU_WT_H3K36me2_Rep2_Cut/Run


title: mouse mammary tumor [mid226]

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2)


title: heart, control, rep2


title: mouse mammary tumor [mid133]

value: female


title: heart, control, rep1


title: FaDU_WT_H3K36me2_Rep1_Cut/Run


title: Primary_Gingival_Cell_M_H3K36M_Rep1_Cut/Run

value: Primary gingival cell

value: Primary gingival keratinocytes were purchased from American Type Culture Collection (ATCC)

value: Rabbit monoclonal Anti-H3K36M antibody (Cayman 31547)


title: P1-1

description: Whole-cel/harsh lysisl/no nick repair


title: BPH1-CRAF THYMUS R075

city: Los Angeles

first: Owen

last: Witte

state: California

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

description: BPH1-CRAF_merged_rsem_genes_expected_counts.txt

data_processing:
TOIL pipeline v 3.12.0 (https://github.com/BD2KGenomics/toil-rnaseq)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt and FastQC TOIL pipeline
Trimmed sequence reads were mapped to hg38 using STAR from TOIL pipeline
Transcript read counts were quantified using RSEM from TOIL pipeline
Assembly: hg38 human genome
Supplementary files format and content: tab-delimited text files include raw count values for each sample

growth_protocol: BPH-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1 mM glutamine and in humidified atmosphere with 5% CO2 at 37C, RWPE were cultured in keratinocyte serum-free medium (K-SFM) (Gibco) supplemented with 0.05 mg/mL bovine pituitary extract (Gibco), 5 ng/mL EGF (Gibco), penicillin (100 U/mL), and streptomycin (100 μg/mL)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using ILMN mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: prostate epithelial

value: C-Raf overexpression bone met


title: BPH1-CRAF BONE R075

value: C-Raf overexpression thymus met


title: P1-2

description: Whole-cel/harsh lysisl/no nick repair

value: Prostate cancer

value: Prostate cancer cells (epithelial)


title: mouse mammary tumor [mid232]

value: biospy of mammary tumor


title: heart, control, rep3

value: heart

value: WT


title: mouse mammary tumor [mid236]


title: Detroit562_M_H3K36M_Rep1_Cut/Run

value: Head and neck squamous cell carcinomas

value: Detroit562 parental cells were purchased from American Type Culture Collection (ATCC)

value: Lentiviraly expressed with histone H3.3K36 mutation


title: mouse mammary tumor [mid224]


title: mouse mammary tumor [mid287]


title: mouse mammary tumor [mid258]


title: Detroit562_WT_H3K36M_Rep1_Cut/Run

value: Lentiviraly expressed with histone H3.3


title: Primary_Gingival_Cell_WT_H3K36M_Rep1_Cut/Run


title: Hypoxia_WT4

source_name: BM myeloid cells

value: BM myeloid cells

value: hypoxia


title: BPH1-CRAF BONE R074


title: Hypoxia_WT3


title: BPH1-CRAF BONE R072


title: P1-3

description: Whole-cel/harsh lysisl/no nick repair

value: NO


title: SCC25_M_H3K36M_Rep2_Cut/Run

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah


title: mouse mammary tumor [mid284]

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2)

value: female


title: Hypoxia_WT2


title: mouse mammary tumor [mid291]


title: mouse mammary tumor [mid231]


title: SCC25_M_H3K36M_Rep1_Cut/Run

value: Rabbit monoclonal Anti-H3K36M antibody (Cayman 31547)


title: BPH1-CRAF BONE R071

value: prostate epithelial

value: C-Raf overexpression bone met


title: Hypoxia_WT1


title: mouse mammary tumor [mid271]


title: Hypoxia_KO4

value: VISTA KO


title: mouse mammary tumor [mid285]

value: biospy of mammary tumor


title: BPH1-C-Raf-sGluc_3

description: BPH1-CRAF-SGLUC_merged_rsem_genes_expected_counts.txt

value: C-Raf overexpression


title: BPH1-CRAF BONE R069


title: BPH1-C-Raf-sGluc_1


title: mouse mammary tumor [mid276]


title: mouse mammary tumor [mid211]


title: SCC25_WT_H3K36M_Rep2_Cut/Run


title: Normoxia_WT4

value: WT

value: normoxia

value: Day 4


title: BPH1-C-Raf-sGluc_2


title: BPH1-ILYW-sGLuc_2

value: Vector control


title: FaDU_WT_H3K36M_Rep1_Cut/Run

value: Head and neck squamous cell carcinomas

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah

value: Lentiviraly expressed with histone H3.3


title: Hypoxia_KO3

value: BM myeloid cells

value: hypoxia


title: Hypoxia_KO1


title: BPH1-ILYW-sGLuc_3


title: SCC25_WT_H3K36M_Rep1_Cut/Run

value: SCC25 parental cells were kindly gifted from Dr. Aznar-Benitah


title: Normoxia_WT3


title: FaDU_M_H3K36M_Rep2_Cut/Run

value: Lentiviraly expressed with histone H3.3K36 mutation


title: FaDU_WT_H3K36M_Rep2_Cut/Run

value: Rabbit monoclonal Anti-H3K36M antibody (Cayman 31547)


title: BPH1-ILYW-sGluc_1

value: prostate epithelial


title: FaDU_M_H3K36M_Rep1_Cut/Run


title: SCC25_M_Rep2_RNAseq

data_processing:
ChIP-seq: Single-end ChIP-seq fastq files were processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2).
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq).
Assembly: hg19
Supplementary files format and content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

extract_protocol:
DNase-treated RNA was isolated with RNeasy micro kit (Qiagen, #74004) according to manufacturer's instructions.
Library preparation was perfromed on Dnase-treated RNA using the Illumina TruSeq Stranded Total RNA Library Prep Gold (Illumina 20020598). TruSeq RNA UD Indexes (Illumina 20022371) were used for the adapter ligation step. Samples were normalized to a concentration of ranging from 100-250ng for input, and 1 ul of ERCC spike-in Mix 1 (Thermo Fisher 4456740) diluted 1:200 was added to the samples.


title: mouse mammary tumor [mid263]

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2)

value: female


title: mouse mammary tumor [mid275]

value: biospy of mammary tumor


title: mouse mammary tumor [mid195]


title: Normoxia_WT2


title: mouse mammary tumor [mid165]


title: RWPE-CRAF-Bone6

description: RWPE-CRAF_merged_rsem_genes_expected_counts.txt

value: C-Raf overexpression bone met


title: SCC25_M_Rep1_RNAseq


title: mouse mammary tumor [mid245]


title: Hypoxia_KO2

value: VISTA KO


title: Normoxia_KO3

value: normoxia


title: Normoxia_KO2

value: Day 4


title: Normoxia_KO4


title: RWPE-CRAF-4

value: C-Raf overexpression


title: RWPE-CRAF-Bone4


title: mouse mammary tumor [mid234]


title: RWPE-CRAF-Spine2

value: C-Raf overexpression spine met


title: mouse mammary tumor [mid175]


title: SCC25_WT_Rep2_RNAseq

value: Head and neck squamous cell carcinomas


title: mouse mammary tumor [mid260]


title: mouse mammary tumor [mid251]


title: SCC25_WT_Rep1_RNAseq

value: Lentiviraly expressed with histone H3.3


title: FaDU_M_Rep2_RNAseq

value: FaDU parental cells were kindly gifted from Dr. Aznar-Benitah


title: mouse mammary tumor [mid290]


title: RWPE-CRAF-3


title: FaDU_M_Rep1_RNAseq


title: RWPE-CRAF-2


title: Normoxia_KO1

value: BM myeloid cells


title: Normoxia_WT1

value: WT


title: mouse mammary tumor [mid296]


title: RAW264.7 cells, high glucose+emetine [EM3]

city: Guangzhou

first: Jiaqiong

last: Lin

address: Guangzhou dadaobei 1838

institute: South medical university

data_processing:
Base Calling by CASAVA
Filtering low-quality sequence
Clean Reads mapped to GRCm39 using Hisat2
Read count extraction by StringTie
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: RAW 264.7 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), which were maintained under controlled conditions of 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated from the study samples using Trizol reagent. 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS® mRNA Isolation Master Kit

treatment_protocol: high glucose group (40 mM), and high glucose group with pre-treatment of emetine (5 nM)

value: macrophages

value: high glucose+emetine


title: FaDU_WT_Rep1_RNAseq


title: RAW264.7 cells, high glucose+emetine [EM2]


title: RWPE-CRAF-Spine

description: RWPE-CRAF-B1_merged_rsem_genes_expected_counts.txt

value: prostate epithelial


title: mouse mammary tumor [mid280]

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2)


title: RAW264.7 cells, high glucose+emetine [EM1]


title: mouse mammary tumor [mid235]

value: female


title: RAW264.7 cells, high glucose [HG3]

value: high glucose


title: KW737, HTO-derived cDNA

city: Boston

first: Kai

middle: W

last: Wucherpfennig

state: MA

address: One Jimmy Fund Way

institute: Dana-Farber Cancer Institute

description:
Hashtag-derived oligonucleotide (HTO)
KW737_barcodes.tsv.gz
KW737_features.tsv.gz
KW737_matrix.mtx.gz

data_processing:
Raw fastq files were processed by cellranger v7.0.0. Briefly, ‘cellranger count’ was used to quantify both transcript and HTO counts from the same cell, using GRCh38 and TotalSeqB references and default settings.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Sorted human CD3+ T cells isolated from bone marrow of NSG mice engrafted with human Raji leukemia cells followed by adoptive transfer of CD161+ T cells

extract_protocol:
10X Genomics
10X Genomics

treatment_protocol: NSG mice were injected I.V. with NY-ESO-1+ Raji cells, followed by I.V. injection of NY-ESO-1 TCR+ CD161+ cells. Mice were treated with either isotype control or CD161 blocking antibody (n=5 per treatment group). On day 13, cells were isolated from both hind limbs and FACS sorted to isolate live CD3+ T cells (human CD45+ human CD19neg, ZsGreenneg, mouse CD45neg).  Cells were analyzed by scRNA-seq using the 10X Genomics platform.

value: Primary T cells

value: T cell

value: antibody-treated


title: RWPE-CRAF-LN1B

value: C-Raf overexpression lymph node met


title: mouse mammary tumor [mid229]

value: biospy of mammary tumor


title: KW737, mRNA-derived cDNA

description:
poly A RNA
KW737_barcodes.tsv.gz
KW737_features.tsv.gz
KW737_matrix.mtx.gz

value: Sorted human CD3+ T cells isolated from bone marrow of NSG mice engrafted with human Raji leukemia cells followed by adoptive transfer of CD161+ T cells


title: isotype, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
isotype_barcodes.tsv.gz
isotype_features.tsv.gz
isotype_matrix.mtx.gz

value: control-antibody


title: RWPE-CRAF-LN1A


title: isotype, mRNA-derived cDNA

description:
poly A RNA
isotype_barcodes.tsv.gz
isotype_features.tsv.gz
isotype_matrix.mtx.gz


title: FaDU_WT_Rep2_RNAseq

value: Head and neck squamous cell carcinomas

value: Lentiviraly expressed with histone H3.3


title: mouse mammary tumor [mid193]


title: 1st and 2nd trimester male and female gonads and mesonephros B

city: Leiden

first: Susana

last: Chuva de Sousa Lopes

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

description: pool of ten donors

data_processing:
For all samples Cell Ranger Single Cell Software Suite 6.1.1 was used to perform sample demultiplexing, barcode processing, read aligning and single cell 3’ gene counting using the Illumina BCL files as input.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Fetal tests, ovary and mesonephros tissue

extract_protocol:
Tissue was cut in small pieces and treated overnight in 1mg/ml colII in 0.25% Trypsin/EDTA at 4C. Next day, it was incubated 1h at 37C in DMEM/F12 with DNAseI (27 IU/ml), filtered through a 100um strainer and single cells were cryopreserved. Before library preparation, cells were thawed, ressuspended in 1% BSA/DPBS and FACS-sorted for live cells (7AAD-negative cells).
Sequencing libraries were prepared according to the user guide of the 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v2, Product Code 120237.

value: Female and male

tag: trimester

tag: number of donors

tag: age of donors (week of gestation)

tag: sequencing run