title: WL_pil1hfr1


title: G1_1st trimester female gonad

status: Public on Jan 02 2024

type: SRA

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 two donors

library_source: transcriptomic

data_processing:
For all samples Cell Ranger Single Cell Software Suite 2.1.1 was used to perform sample demultiplexing, barcode processing, read aligning and single cell 3’ gene counting using the Illumina BCL files as input.
Genome_build: GRCh38 (refdata-cellranger-GRCh38-1.2.0)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

organism: Homo sapiens

source_name: Fetal ovary 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.

tag: Sex

value: Female

tag: trimester

tag: number of donors

tag: age of donors (week of gestation)

tag: tissue

value: Fetal ovary tissue

tag: sequencing run


title: hs_Sub9_pear_glut_RNAPII

city: St Petersburg

first: Edina

last: Erdős

address: 501 6th Ave S

country: USA

institute: Johns Hopkins University

library_source: genomic

data_processing:
Burrows-Wheeler Alignment (BWA) tool (v07.10)
BAM files were generated with SAMtools (v0.1.19)
To remove the artifacts from the predicted peaks, we used the blacklisted genomic regions of the Encyclopedia of DNA Elements (ENCODE)
“Peaks” were predicted and broadPeak were created using the Model-based Analysis of ChIP-Seq (MACS2) tool (v2.0.10)
Coverage (bigwig) files were created by bamCoverage in the deepTools program
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

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:
Fat biospsies were collected and SVF were isolated by centrifugation. For ATAC-seq, nuclei were used for tagmentation using Nextera DNA Library Preparation Kit (Illumina).DNA was purified with MinElute PCR Purification Kit (Qiagen). For ChIP-seq, lysates were clarified from sonicated nuclei and histone/CTCF or RNAPII-DNA complexes were isolated with antibody.
ATAC-seq and ChIP-seq libraries were prepared and sequenced using standard Illumina protocols for HiSeq 2500 instrument.

value: subcutaneous gluteofemoral fat

tag: cell line

value: adipose derived stem cells (ASC)

tag: cell type

value: stem cells

tag: chip antibody

value: RNAPII


title: hs_Sub9_pear_glut_H3K4me3


title: G2_2nd trimester female gonad

description: one donor


title: GPNMB+ GAL-3+MT Immu cells

city: Shanghai

first: qiudong

last: zhao

address: 225 Changhai Road

department: Tumor Immunology and Gene Therapy Center

country: China

institute: Shanghai Eastern Hepatobiliary Surgery Hospital

description: DP

data_processing:
The sequencing reads were automatically uploaded and evaluated for quality using Illumina BaseSpace Onsite Computing platform.
Fastq sequence files were generated and analysis was performed using applications available on BaseSpace Onsite Computing platform
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Clustering and correlation analysis were carried out using Metaboanalyst 3.0 software analysis package (http://www.metaboanalyst.ca).
Assembly: Rnor6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.Matrix table with raw gene counts for every gene and every sample.

organism: Rattus norvegicus

source_name: liver

extract_protocol:
The total RNA  was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-2501) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: time

value: DEN up to 16 weeks


title: G3 _1st trimester male gonad

description: pool of two donors

source_name: Fetal testis tissue

value: Male

value: Fetal testis tissue


title: hs_Sub9_pear_glut_H3K27me3


title: hs_Sub9_pear_glut_CTCF

value: CTCF


title: hs_Sub9_pear_glut_ATAC_rep2


title: hs_Sub9_pear_glut_H3K4me2


title: hs_Sub9_pear_abd_RNAPII

source_name: subcutaneous abdominal fat

value: subcutaneous abdominal fat


title: hs_Sub9_pear_glut_H3K27ac


title: hs_Sub9_pear_abd_H3K4me3


title: hs_Sub9_pear_glut_ATAC_rep1


title: hs_Sub9_pear_abd_H3K4me2


title: hs_Sub9_pear_abd_ATAC_rep1


title: G4_2nd trimester male gonad

description: one donor


title: hs_Sub8_apple_glut_RNAPII


title: Fscn2-/- mouse_8 weeks of age 3

type: RNA

city: Yantai

first: Wenjing

last: Shang

state: Shandong

address: NO.346 Guanhai Road

institute: Binzhou Medical University

description: Gene expression of inner ears from Fscn2-/- mouse_8 weeks of age 3

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0  pmol Cy3/μg cRNA) was fragmented at 60°C for 30  minutes in a reaction volume of 22.5μl containing 1x  Agilent fragmentation buffer and 2x Agilent blocking  agent following the manufacturers' instructions. On  completion of the fragmentation reaction, 22.5μl of  2x Agilent hybridization buffer was added to the  fragmentation mixture and hybridized to Agilent Mouse lncRNA V3 (4*180K) for 17 hours at 65°C  in a rotating Agilent hybridization oven. After  hybridization, microarrays were washed 1 minute at  room temperature with GE Wash Buffer 1 (Agilent)  and 1 minute with 37°C GE Wash buffer 2 (Agilent),  then dried immediately by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on  the Agilent DNA Microarray Scanner (G2505C) using  one color scan setting for 4x180k array slides (Scan  Area 61x21.6 mm, Scan resolution 3um, Dye channel  is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature  Extraction Software 10.7.1.1 (Agilent) using default  parameters to obtain background subtracted and  spatially detrended Processed Signal intensities as  the raw data. Raw data were normalized in quantile  algorithm with Genespring 13.0(Agilent). Probe that  at least 1 out of 2 samples flagged as Detected were  maintained.

molecule: total RNA

organism: Mus musculus

source_name: inner ears, NO. 6 mouse (No gender limitation)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2  μg RNA using the One-Color Low RNA Input Linear  Amplification PLUS kit (Agilent) according to the  manufacturer's instructions, followed by RNAeasy  column purification (QIAGEN, Valencia, CA). Dye  incorporation and cRNA yield were checked with the  NanoDrop ND-1000 Spectrophotometer

growth_protocol: Experimental mice were bred in a specific pathogen-free animal facility at Binzhou Medical University. The animal studies were conducted in accordance with the principles set forth in the Guide for the Care and Use of Laboratory Animals of Binzhou Medical University and were approved by that university’s Institutional Animal Use and Care Committee (protocol 14-0514)

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The Fscn2 knockout mice were generated on the C57BL/6J background from Cyagen Biosciences (Guangzhou, China). The Fscn2 null mutation was made using the TALEN technique, with two vectors targeting the first exon of Fscn2 The wild-type mice (Fscn2+/+), heterozygous mice (Fscn2+/-), and homozygous mice (Fscn2-/-) were genotyped using a polymerase chain reaction (PCR).

value: inner ear

tag: genotype


title: hs_Sub9_pear_abd_H3K27me3


title: hs_Sub8_apple_glut_H3K9me3


title: hs_Sub9_pear_abd_H3K27ac


title: Fscn2-/- mouse_8 weeks of age 2

description: Gene expression of inner ears from Fscn2-/- mouse_8 weeks of age 2

source_name: inner ears, NO. 5 mouse (No gender limitation)


title: hs_Sub8_apple_glut_H3K27ac


title: hs_Sub9_pear_abd_ATAC_rep2


title: hs_Sub8_apple_glut_H3K4me3


title: hs_Sub8_apple_glut_H3K4me2


title: hs_Sub8_apple_glut_ATAC_rep2


title: hs_Sub8_apple_glut_H3K27me3


title: hs_Sub8_apple_abd_H3K4me3


title: Fscn2-/- mouse_8 weeks of age 1

description: Gene expression of inner ears from Fscn2-/- mouse_8 weeks of age 1

source_name: inner ears, NO. 4 mouse (No gender limitation)


title: Fscn2+/+ mouse_8 weeks of age 2

description: Gene expression of inner ears from Fscn2+/+ mouse_8 weeks of age 2

source_name: inner ears, NO. 2 mouse (No gender limitation)


title: Fscn2+/+ mouse_8 weeks of age 3

description: Gene expression of inner ears from Fscn2+/+ mouse_8 weeks of age 3

source_name: inner ears, NO. 3 mouse (No gender limitation)


title: hs_Sub8_apple_glut_ATAC_rep1


title: hs_Sub9_pear_abd_CTCF


title: hs_Sub8_apple_abd_RNAPII


title: hs_Sub8_apple_abd_H3K27me3


title: hs_Sub8_apple_abd_H3K9me3


title: Fscn2+/+ mouse_8 weeks of age 1

description: Gene expression of inner ears from Fscn2+/+ mouse_8 weeks of age 1

source_name: inner ears, NO. 1 mouse (No gender limitation)


title: hs_Sub8_apple_abd_H3K4me2


title: hs_Sub8_apple_abd_H3K27ac


title: hs_Sub7_apple_glut_H3K4me3


title: hs_Sub8_apple_abd_CTCF


title: hs_Sub7_apple_glut_H3K27ac


title: hs_Sub7_apple_glut_CTCF


title: hs_Sub7_apple_glut_ATAC_rep2


title: hs_Sub7_apple_abd_RNAPII


title: hs_Sub8_apple_abd_ATAC_rep1


title: hs_Sub7_apple_abd_H3K4me3


title: hs_Sub7_apple_glut_RNAPII


title: hs_Sub8_apple_glut_CTCF


title: hs_Sub7_apple_glut_H3K4me2


title: hs_Sub7_apple_abd_H3K4me2


title: hs_Sub7_apple_abd_H3K27me3


title: hs_Sub7_apple_abd_H3K27ac


title: hs_Sub7_apple_abd_CTCF


title: hs_Sub8_apple_abd_ATAC_rep2


title: hs_Sub7_apple_abd_ATAC_rep2


title: hs_Sub7_apple_abd_ATAC_rep1


title: hs_Sub7_apple_glut_H3K27me3


title: hs_Sub6_pear_glut_H3K9me3


title: hs_Sub6_pear_glut_ATAC_rep1


title: hs_Sub6_pear_glut_H3K4me2


title: hs_Sub7_apple_glut_ATAC_rep1


title: hs_Sub6_pear_glut_H3K27me3


title: hs_Sub6_pear_glut_CTCF


title: hs_Sub6_pear_glut_H3K4me3


title: hs_Sub6_pear_abd_RNAPII


title: hs_Sub6_pear_abd_H3K9me3


title: hs_Sub6_pear_glut_H3K27ac


title: hs_Sub6_pear_abd_H3K4me2


title: hs_Sub6_pear_abd_H3K27ac


title: hs_Sub6_pear_abd_ATAC_rep2


title: hs_Sub5_apple_glut_H3K4me3


title: hs_Sub5_apple_glut_H3K27me3


title: hs_Sub6_pear_glut_ATAC_rep2


title: hs_Sub5_apple_glut_H3K9me3


title: hs_Sub5_apple_glut_H3K27ac


title: hs_Sub6_pear_abd_ATAC_rep1


title: hs_Sub5_apple_glut_H3K4me2


title: hs_Sub5_apple_glut_CTCF


title: hs_Sub6_pear_glut_RNAPII


title: hs_Sub5_apple_glut_ATAC_rep1


title: hs_Sub5_apple_abd_RNAPII


title: hs_Sub5_apple_glut_ATAC_rep2


title: hs_Sub6_pear_abd_H3K4me3


title: hs_Sub6_pear_abd_H3K27me3


title: hs_Sub5_apple_abd_H3K9me3


title: hs_Sub5_apple_abd_H3K27me3


title: hs_Sub5_apple_abd_H3K4me2


title: hs_Sub6_pear_abd_CTCF


title: hs_Sub5_apple_abd_H3K4me3


title: hs_Sub5_apple_abd_ATAC_rep2


title: hs_Sub5_apple_abd_CTCF


title: hs_Sub4_apple_glut_RNAPII


title: hs_Sub4_apple_glut_H3K9me3


title: hs_Sub5_apple_abd_ATAC_rep1


title: hs_Sub5_apple_abd_H3K27ac


title: hs_Sub4_apple_glut_H3K27me3


title: hs_Sub4_apple_glut_CTCF


title: hs_Sub5_apple_glut_RNAPII


title: hs_Sub4_apple_abd_RNAPII


title: hs_Sub4_apple_glut_ATAC_rep2


title: hs_Sub4_apple_glut_ATAC_rep1


title: hs_Sub4_apple_glut_H3K27ac


title: hs_Sub4_apple_abd_H3K4me3


title: hs_Sub4_apple_abd_H3K4me2


title: hs_Sub4_apple_abd_H3K27me3


title: hs_Sub4_apple_glut_H3K4me2


title: hs_Sub4_apple_abd_CTCF


title: hs_Sub4_apple_abd_ATAC_rep2


title: hs_Sub4_apple_abd_ATAC_rep1


title: hs_Sub4_apple_abd_H3K9me3


title: hs_Sub4_apple_abd_H3K27ac


title: hs_Sub3_apple_glut_H3K4me3


title: hs_Sub3_apple_glut_H3K4me2


title: hs_Sub3_apple_glut_RNAPII


title: hs_Sub3_apple_glut_H3K27me3


title: hs_Sub4_apple_glut_H3K4me3


title: hs_Sub3_apple_glut_H3K27ac


title: hs_Sub3_apple_glut_ATAC_rep2


title: hs_Sub3_apple_glut_CTCF


title: hs_Sub3_apple_abd_H3K4me2


title: hs_Sub3_apple_abd_H3K4me3


title: hs_Sub3_apple_abd_H3K27me3


title: hs_Sub3_apple_abd_RNAPII


title: hs_Sub3_apple_abd_H3K27ac


title: hs_Sub3_apple_abd_CTCF


title: hs_Sub3_apple_abd_ATAC_rep1


title: hs_Sub2_pear_glut_RNAPII


title: hs_Sub3_apple_abd_ATAC_rep2


title: hs_Sub2_pear_glut_H3K4me3


title: hs_Sub2_pear_glut_H3K4me2


title: hs_Sub2_pear_glut_H3K27me3


title: hs_Sub2_pear_glut_H3K27ac


title: human pluripotent stem cell-derived aggregates, Day3

status: Public on Jan 03 2024

city: Sakyo-ku

first: Yusuke

last: Seto

state: Kyoto

address: 53 Shogoin Kawara-cho

country: Japan

institute: Kyoto University

data_processing:
Cellranger mkfastq v5.0.1 to generate FASTQ
Cellranger count v5.0.1 to generate count matrix
Seurat v4.1.0 for downstream analyses
Assembly: human NCBI genomme build 38
Supplementary files format and content: Cellranger output files including tab-separated value files (barcodes.tsv, features.tsv), and Matrix Market file (matrix.mtx)
Supplementary files format and content: Rds files which contain single cell data processed with Seurat

growth_protocol: Aggregates of human pluripotent stem cells were cultured in NCC inductino medium (DMEM/F-12 with GlutaMAX supplemented with 1x B-27 minus vitamin A and 5 mg/ml bovine serum albumin.

extract_protocol:
Aggregates were dissociated using TrypLE Express. Dissociated single cells were used in library construction using v3 Chromium Single Cell 3′ Reagent Kit (10X Genomics)
10x Genomics Chromium 3’ v3 Single Cell Gene Expression Kit

value: differentiation day3


title: hs_Sub2_pear_glut_CTCF


title: hs_Sub2_pear_glut_ATAC_rep1


title: hs_Sub2_pear_glut_ATAC_rep2


title: hs_Sub2_pear_abd_H3K9me3


title: hs_Sub2_pear_abd_RNAPII


title: hs_Sub2_pear_abd_H3K4me3


title: hs_Sub3_apple_glut_ATAC_rep1


title: hs_Sub2_pear_abd_H3K27me3


title: hs_Sub2_pear_abd_H3K27ac


title: hs_Sub2_pear_abd_CTCF


title: hs_Sub2_pear_abd_ATAC_rep2


title: hs_Sub2_pear_abd_ATAC_rep1


title: hs_Sub1_pear_glut_RNAPII


title: hs_Sub1_pear_glut_H3K9me3


title: hs_Sub1_pear_glut_H3K27ac


title: hs_Sub1_pear_glut_H3K4me2


title: hs_Sub2_pear_glut_H3K9me3


title: hs_Sub1_pear_glut_ATAC_rep2


title: hs_Sub1_pear_glut_ATAC_rep1


title: hs_Sub1_pear_abd_RNAPII


title: hs_Sub1_pear_abd_H3K4me3


title: hs_Sub1_pear_abd_H3K9me3


title: hs_Sub1_pear_abd_H3K27me3


title: hs_Sub1_pear_abd_H3K27ac


title: hs_Sub1_pear_abd_CTCF


title: hs_Sub1_pear_abd_ATAC_rep2


title: hs_Sub1_pear_abd_H3K4me2


title: hs_Sub1_pear_abd_ATAC_rep1


title: hs_Sub10_pear_glut_RNAPII


title: hs_Sub2_pear_abd_H3K4me2


title: hs_Sub10_pear_glut_H3K27ac


title: hs_Sub10_pear_glut_CTCF


title: hs_Sub10_pear_glut_H3K27me3


title: hs_Sub1_pear_glut_H3K4me3


title: hs_Sub10_pear_glut_ATAC_rep2


title: hs_Sub10_pear_abd_H3K4me3


title: hs_Sub10_pear_glut_H3K4me2


title: hs_Sub1_pear_glut_H3K27me4


title: hs_Sub10_pear_abd_H3K4me2


title: hs_Sub10_pear_glut_H3K4me3


title: hs_Sub10_pear_abd_RNAPII


title: hs_Sub10_pear_abd_H3K27ac


title: hs_Sub10_pear_abd_CTCF


title: hs_Sub10_pear_abd_ATAC_rep2


title: hs_Sub10_pear_abd_H3K27me3


title: hs_Sub1_pear_glut_CTCF


title: S35_R1

city: Changsha

first: Jie

last: Tang

address: No. 932, Lushan South Road, Yuelu District, Changsha City, Hunan Province

institute: Hunan Cancer Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
GRCh38
xls file contain counts for each sample
Supplementary files format and content: Excel table files include counts for each Sample

source_name: Plasma

extract_protocol:
sEVs were purified from 2 mL plasma of AOC patients by differential ultracentrifugation.
Small RNA of the sample was extracted or purified sRNA fragments, successively ligated with the 3 ′ end and 5 ′ adaptors, reverse transcribed into cDNA and then subjected to PCR amplification. Subsequently, the target fragments were recovered, and the qualified libraries were sequenced by machine.

value: Plasma

tag: sample type

value: small extracellular vesicles

tag: disease state

value: AOC

tag: residual disease


title: S37_R1


title: S36_R1


title: S33_R1


title: S34_R1


title: S32_R1


title: S31_R1


title: hs_Sub10_pear_glut_ATAC_rep1


title: S29_R1


title: S28_R1


title: S30_R1


title: S26_R1


title: S25_R1


title: S27_R1


title: S24_R1


title: S23_R1


title: S21_R1


title: S20_R1


title: S17_R0


title: S18_R1


title: S19_R1


title: S22_R1


title: S15_R0


title: S13_R0


title: S16_R0


title: S12_R0


title: S11_R0


title: hs_Sub10_pear_abd_ATAC_rep1


title: S10_R0


title: S9_R0


title: S8_R0


title: S5_R0


title: S6_R0


title: S4_R0


title: S2_R0


title: S3_R0


title: S1_R0


title: batch4_C38c

city: Stockholm

first: Jinxin

middle: Phaedo

last: Chen

address: Tomtebodavägen 23

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Paired scRNA-seq data

library_source: transcriptomic single cell

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

source_name: Colo320DM, batch4, Smart-seq2

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.

value: Colon adenocarcinoma

value: Colon adenocarcinoma cells (epithelial)

tag: treatment

value: NO


title: batch4_C37c

description: Paired scRNA-seq data


title: batch4_C34c

description: Paired scRNA-seq data


title: batch4_C33c

description: Paired scRNA-seq data


title: batch4_C27c

description: Paired scRNA-seq data


title: batch4_C32c

description: Paired scRNA-seq data


title: batch4_C36c

description: Paired scRNA-seq data


title: batch4_C29c

description: Paired scRNA-seq data


title: S14_R0


title: batch4_C35c

description: Paired scRNA-seq data


title: batch4_C24c

description: Paired scRNA-seq data


title: batch4_C25c

description: Paired scRNA-seq data


title: batch4_C26c

description: Paired scRNA-seq data


title: batch4_C23c

description: Paired scRNA-seq data


title: batch4_C31c

description: Paired scRNA-seq data


title: S7_R0


title: batch4_C19c

description: Paired scRNA-seq data


title: batch4_C18c

description: Paired scRNA-seq data


title: batch4_C22c

description: Paired scRNA-seq data


title: batch4_C21c

description: Paired scRNA-seq data


title: batch4_C16c

description: Paired scRNA-seq data


title: batch4_C15c

description: Paired scRNA-seq data


title: batch4_C39c

description: Paired scRNA-seq data


title: batch4_C13c

description: Paired scRNA-seq data


title: batch4_C14c

description: Paired scRNA-seq data


title: batch4_C12c

description: Paired scRNA-seq data


title: batch4_C11c

description: Paired scRNA-seq data


title: batch4_C10c

description: Paired scRNA-seq data


title: batch4_C7c

description: Paired scRNA-seq data


title: batch4_C5c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KPU 4 (Biol replicate 1)

city: Washington

first: Juntae

last: Kwon

state: Dristrict of Colombia

address: 3970 Reservoir Rd NW

institute: Georgetown University

description:
KPU63162r1
raw_counts.txt

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

source_name: Lung

extract_protocol:
RNA was extracted using Rnease mini plus kit. 1ug of total RNA was used for the construction of sequencing libraries
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA.

value: Lung

value: KPU


title: batch4_C6c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KPU 3 (Biol replicate 3)

description:
KPU63114r3
raw_counts.txt


title: batch4_C3c

description: Paired scRNA-seq data


title: batch4_C2c

description: Paired scRNA-seq data


title: batch4_C20c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KPU 3 (Biol replicate 2)

description:
KPU63114r2
raw_counts.txt


title: Bulk_RNA-seq_KPU 4 (Biol replicate 2)

description:
KPU63162r2
raw_counts.txt


title: batch4_C4c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KPU 3 (Biol replicate 1)

description:
KPU63114r1
raw_counts.txt


title: P11c

description: Paired scRNA-seq data

source_name: PC3, batch2, Smart-seq2

value: Prostate cancer

value: Prostate cancer cells (epithelial)

value: No


title: P10c

description: Paired scRNA-seq data


title: P12c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KPU 2 (Biol replicate 3)

description:
KPU63110r3
raw_counts.txt


title: P9c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KPU 2 (Biol replicate 2)

description:
KPU63110r2
raw_counts.txt


title: Bulk_RNA-seq_KPU 1 (Biol replicate 2)

description:
KPU63107r2
raw_counts.txt


title: Bulk_RNA-seq_KPU 2 (Biol replicate 1)

description:
KPU63110r1
raw_counts.txt


title: P6c

description: Paired scRNA-seq data


title: batch4_C9c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KPU 1 (Biol replicate 1)

description:
KPU63107r1
raw_counts.txt


title: P5c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KP 4 (Biol replicate 3)

description:
KP63169r3
raw_counts.txt

value: KP


title: Bulk_RNA-seq_KPU 4 (Biol replicate 3)

description:
KPU63162r3
raw_counts.txt


title: P3c

description: Paired scRNA-seq data


title: batch4_C8c

description: Paired scRNA-seq data


title: P2c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KP 4 (Biol replicate 2)

description:
KP63169r2
raw_counts.txt


title: Bulk_RNA-seq_KP 3 (Biol replicate 2)

description:
KP63150r2
raw_counts.txt


title: Bulk_RNA-seq_KP 3 (Biol replicate 3)

description:
KP63150r3
raw_counts.txt


title: H24c

description: Paired scRNA-seq data

source_name: HeLa, batch2, Smart-seq2

value: Cervical carcinoma

value: HeLa

value: Cervical carcinoma cells (epithelial)


title: Bulk_RNA-seq_KP 4 (Biol replicate 1)

description:
KP63169r1
raw_counts.txt


title: H23c

description: Paired scRNA-seq data


title: H21c

description: Paired scRNA-seq data


title: P1c

description: Paired scRNA-seq data


title: H20c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KP 2 (Biol replicate 2)

description:
KP63128r2
raw_counts.txt


title: H22c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KP 3 (Biol replicate 1)

description:
KP63150r1
raw_counts.txt


title: H19c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KPU 1 (Biol replicate 3)

description:
KPU63107r3
raw_counts.txt


title: P8c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KP 2 (Biol replicate 1)

description:
KP63128r1
raw_counts.txt


title: H18c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KP 1 (Biol replicate 3)

description:
KP63126r3
raw_counts.txt


title: Bulk_RNA-seq_KP 1 (Biol replicate 2)

description:
KP63126r2
raw_counts.txt


title: H17c

description: Paired scRNA-seq data


title: H16c

description: Paired scRNA-seq data


title: H14c

description: Paired scRNA-seq data


title: H15c

description: Paired scRNA-seq data


title: H10c

description: Paired scRNA-seq data


title: H11c

description: Paired scRNA-seq data


title: Bulk_RNA-seq_KP 1 (Biol replicate 1)

description:
KP63126r1
raw_counts.txt


title: Bulk_RNA-seq_KP 2 (Biol replicate 3)

description:
KP63128r3
raw_counts.txt


title: H9c

description: Paired scRNA-seq data


title: H12c

description: Paired scRNA-seq data


title: H8c

description: Paired scRNA-seq data


title: H7c

description: Paired scRNA-seq data


title: H6c

description: Paired scRNA-seq data


title: H5c

description: Paired scRNA-seq data


title: H3c

description: Paired scRNA-seq data


title: H4c

description: Paired scRNA-seq data


title: C10c

description: Paired scRNA-seq data

source_name: Colo320DM, batch2, Smart-seq2


title: C9c

description: Paired scRNA-seq data


title: H1c

description: Paired scRNA-seq data


title: H2c

description: Paired scRNA-seq data


title: C6c

description: Paired scRNA-seq data


title: C5c

description: Paired scRNA-seq data


title: C3c

description: Paired scRNA-seq data


title: C4c

description: Paired scRNA-seq data


title: C7c

description: Paired scRNA-seq data


title: C2c

description: Paired scRNA-seq data


title: Human Treg cells P9 from THI-2

city: Krakow

first: Magdalena

last: Rutkowska-Zapala

address: Wielicka 265

country: Poland

institute: Jagiellonian University Medical College

description: Gene expression data of Treg cells isolated during resolution phase of hypogammaglobulinemia

hyb_protocol: Samples for array hybridization were processed with GeneChip WT PLUS Reagent Kit and GeneChip 3000 instrument system (Affymetrix) in line of protocol.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The Transcriptome Analysis Console (TAC) Software (Affymetrix) was used to analyze raw data for quality, expression patterns of genes, exons, lncRNA and pathways

label: biotin

source_name: patient 9 from THI-2 group

extract_protocol: the total RNA was extracted from Treg cells samples using RNeasy Micro Kit (Qiagen, Germany) according to the manufacturer’s protocol.

value: Treg cells

value: female


title: Human Treg cells P7 from THI-2

source_name: patient 7 from THI-2 group

label_protocol: Samples for array hybridization were processed with GeneChip WT PLUS Reagent Kit and GeneChip 3000 instrument system (Affymetrix) in line of protocol.

value: male


title: T23e

description: Single-nucleus/mild lysis/nick repair

source_name: HEK293T, batch11, scCircle-seq

value: Kidney

value: Kidney (epithelial)


title: Human Treg cells P8 from THI-2

source_name: patient 8 from THI-2 group


title: T24e

description: Single-nucleus/mild lysis/nick repair


title: C1c

description: Paired scRNA-seq data

value: Colon adenocarcinoma


title: H13c

description: Paired scRNA-seq data


title: Human Treg cells P5 from THI-2

source_name: patient 5 from THI-2 group


title: Human Treg cells P6 from THI-2

source_name: patient 6 from THI-2 group


title: T22e

description: Single-nucleus/mild lysis/nick repair


title: MDAMB231_Api_2

city: East Lansing

first: Andrea

last: Doseff

state: Michigan

address: 4153 BPS, 567 Wilson Rd

department: BPS

institute: Michigan State University

data_processing:
Reads were demultiplexed using Illumina CASAVA pipeline version 1.8.2. Quality and duplication levels were evaluated by FASTQC, and aligned to the human genome assembly 19 (hg19) using TopHat v1.4.1 with default parameters
Uniquely aligned reads were kept for further analysis. Raw read counts were obtained using HTseq (v 0.11.0), loaded into R and normalized for library sizes using DESeq2 (R version 3.6)
To detect differential slternative splicing events, MISO (version 0.5.4) was used with default parameters
Assembly: hg19

growth_protocol: MDA-MB-231 cells  were maintained in DMEM supplemented with 5% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37ᵒC

extract_protocol: Total RNA was isolated by the Trizol method according to the manufacturer’s suggestions (ThermoFisher Scientific, Cat. #: 15596026), followed by 1U DNAse-I treatment (ThermoFisher Scientific, Cat. #: 18047019). RNA quality was evaluated by the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) obtaining a (RIN) higher than 8.

treatment_protocol: MDA-MB-231 cells were treated with diluent DMSO or 50 μM  apigenin for 48 h

value: triple negative breast cancer cell line

value: wildtype

value: apigenin 50 microM

value: 48 hours


title: MDAMB231_Api_1


title: MDAMB231_DMSO_3

value: DMSO


title: MDAMB231_Api_3


title: Human Treg cells P4 from THI-2

source_name: patient 4 from THI-2 group


title: Human Treg cells P3 from THI-2

source_name: patient 3 from THI-2 group


title: Human Treg cells P2 from THI-2

source_name: patient 2 from THI-2 group


title: MDAMB231_DMSO_1


title: T20e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: Human Treg cells P1 from THI-2

source_name: patient 1 from THI-2 group


title: T18e

description: Single-nucleus/mild lysis/nick repair


title: T19e

description: Single-nucleus/mild lysis/nick repair


title: T21e

description: Single-nucleus/mild lysis/nick repair


title: Human Treg cells P9 from THI-1

description: Gene expression data of Treg cells isolated during hypogammaglobulinemia

source_name: patient 9 from THI-1 group


title: CDi-on-chip no immune cells, WT, control, rep 3, CTC side

city: Manila

first: Ryan

last: Lintao

address: 547 Pedro Gil Street

department: College of Medicine

country: Philippines

institute: University of the Philippines Manila

description: Sample 48A

data_processing:
CLC Genomics Workbench v23.0.3
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomics Workbench (quality threshold 0.05)
Trimmed sequence reads were mapped to GRCh38.p9 using CLC Genomics Workbench.
Read count extraction and normalization were performed using CLC Genomics Workbench
Assembly: GRCh38.p9
Supplementary files format and content: Spreadsheet files includes raw and normalized counts per sample

source_name: Immortalized chorion trophoblast cells from term not in labor placenta

extract_protocol:
RNA was extracted using RNeasy Mini Plus kit (Qiagen). 30 ng of total RNA was used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using QIAseq Targeted RNA Human Inflammation & Immunity Transcriptome Panel (RHS-005Z-96, Qiagen) according to manufacturer’s instructions.

tag: ctc genotype

value: wild-type

value: control

tag: immune cells_in_decidua

value: absent


title: CDi-on-chip no immune cells, WT, control, rep 2, DEC side

description: Sample 47B

source_name: Primary decidual cells from term not in labor placenta


title: CDi-on-chip no immune cells, WT, control, rep 2, CTC side

description: Sample 47A

value: Immortalized chorion trophoblast cells from term not in labor placenta


title: CDi-on-chip no immune cells, WT, control, rep 1, DEC side

description: Sample 46B

value: Primary decidual cells from term not in labor placenta


title: CDi-on-chip no immune cells, WT, control, rep 1, CTC side

description: Sample 46A


title: T16e

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, HLAG KO, mOS, rep 3, DEC side

description: Sample 45B

value: HLAG KO

value: CSE - DEC side

value: present


title: MDAMB231_DMSO_2


title: Human Treg cells P7 from THI-1

source_name: patient 7 from THI-1 group

value: Treg cells

tag: Sex

value: male


title: CDi-on-chip, HLAG KO, mOS, rep 3, CTC side

description: Sample 45A


title: CDi-on-chip, HLAG KO, mOS, rep 2, DEC side

description: Sample 44B


title: Human Treg cells P6 from THI-1

source_name: patient 6 from THI-1 group


title: T15e

description: Single-nucleus/mild lysis/nick repair

value: Kidney

value: Kidney (epithelial)


title: CDi-on-chip no immune cells, WT, control, rep 3, DEC side

description: Sample 48B


title: T14e

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, HLAG KO, mOS, rep 2, CTC side

description: Sample 44A


title: Human Treg cells P5 from THI-1

source_name: patient 5 from THI-1 group

value: female


title: CDi-on-chip, HLAG KO, mOS, rep 1, DEC side

description: Sample 43B


title: CDi-on-chip, HLAG KO, mOS, rep 1, CTC side

description: Sample 43A


title: T13e

description: Single-nucleus/mild lysis/nick repair


title: Human Treg cells P4 from THI-1

source_name: patient 4 from THI-1 group


title: T17e

description: Single-nucleus/mild lysis/nick repair


title: T12e

description: Single-nucleus/mild lysis/nick repair


title: Human Treg cells P8 from THI-1

source_name: patient 8 from THI-1 group


title: CDi-on-chip, HLAG KO, fOS, rep 2, CTC side

description: Sample 41A

value: CSE - CTC side


title: T11e

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, HLAG KO, fOS, rep 2, DEC side

description: Sample 41B


title: CDi-on-chip, HLAG KO, fOS, rep 1, CTC side

description: Sample 40A


title: Human Treg cells P2 from THI-1

source_name: patient 2 from THI-1 group


title: Human Treg cells P3 from THI-1

source_name: patient 3 from THI-1 group


title: Human Treg cells P1 from THI-1

source_name: patient 1 from THI-1 group


title: CDi-on-chip, HLAG KO, fOS, rep 1, DEC side

description: Sample 40B


title: CDi-on-chip, HLAG KO, pIC, rep 2, DEC side

description: Sample 38B

value: polyIC - DEC side


title: T9e

description: Single-nucleus/mild lysis/nick repair

source_name: HEK293T, batch11, scCircle-seq


title: 219_TA_control

city: Huddinge

first: HONG

last: QIAN

state: Stockholms Lan

address: Neo, HERM, Floor 7, Hälsovägen 7,

department: Department of Medicine

institute: Karolinska Institute

data_processing:
The data were geenerated on the Illumina Nextseq 2000 P3 100 cycle sequencing run, generating 58 base paired end reads with dual index
Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.7). Reads were aligned to a reference built from Ensembl GRCh38 genome sequences using STAR (v2.6.1d).
All mapped counts to each gene were further calculated by FeatureCounts function from Subread package installed in R. Genes with Reads Per Kilobase of transcript per Million mapped reads (RPKM) values more than 0.1 were considered as being actively transcribed and proceeded to the analysis of Differential Gene Expression (DGE).6
The normalized read counts assigned to each sample were generated by Deseq2 and used for unsupervised clustering.
The differentially expressed genes between the MSC subsets were identified by adjusted P value (padj < 0.05) using Benjamini-Hochberg correction for multiple testing, together with thresholds at log2fold changes >1 (up-regulated) or <-1 (down-regulated).
Assembly: GRCh38
Supplementary files format and content: excel file; Matrix table with raw and normarized gene counts for every gene and every sample, together with multiple testing results with Benjamini-Hochberg correction

source_name: bone marrow

growth_protocol: BM MSCs at passage 2-3 were plated and subjected to either triamcinolone acetonide 10nM in complete DMEM or in complete DMEM only as control for 24 h.

extract_protocol:
RNA extraction was done with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
To construct libraries suitable for Illumina sequencing, the Illumina stranded mRNA prep ligation sample preparation protocol was used with starting concentration between 25-1000 ng total RNA.
The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries. The yield and quality of the amplified libraries was analyzed using Qubit by Thermo Fisher and quality was checked by using Agilent Tapestation. The indexed cDNA libraries were normalized and combined

treatment_protocol: The cells were then collected and lysed in RLT buffer (Qiagen, Germantown, MD, USA) and kept at -80°C.

value: bone marrow

value: mesenchymal stem cell


title: T10e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: CDi-on-chip, HLAG KO, pIC, rep 3, CTC side

description: Sample 39A


title: CDi-on-chip, HLAG KO, pIC, rep 1, DEC side

description: Sample 37B


title: T8e

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, HLAG KO, fOS, rep 3, DEC side

description: Sample 42B


title: 219_TA_10nM


title: CDi-on-chip, HLAG KO, pIC, rep 1, CTC side

description: Sample 37A


title: CDi-on-chip, HLAG KO, LPS, rep 3, DEC side

description: Sample 36B

value: LPS - DEC side


title: 217_TA_control


title: CDi-on-chip, HLAG KO, LPS, rep 3, CTC side

description: Sample 36A


title: CDi-on-chip, HLAG KO, fOS, rep 3, CTC side

description: Sample 42A


title: T7e

description: Single-nucleus/mild lysis/nick repair


title: T6e

description: Single-nucleus/mild lysis/nick repair


title: 217_TA_10nM


title: T5e

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, HLAG KO, LPS, rep 2, CTC side

description: Sample 35A


title: T4e

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, HLAG KO, pIC, rep 2, CTC side

description: Sample 38A


title: CDi-on-chip, HLAG KO, LPS, rep 1, DEC side

description: Sample 34B


title: CDi-on-chip, HLAG KO, control, rep 3, CTC side

description: Sample 33A

value: control


title: CDi-on-chip, HLAG KO, pIC, rep 3, DEC side

description: Sample 39B


title: 166_TA_control


title: 166_TA_10nM


title: 137_TA_control


title: CDi-on-chip, HLAG KO, control, rep 3, DEC side

description: Sample 33B


title: CDi-on-chip, HLAG KO, control, rep 2, CTC side

description: Sample 32A

value: Immortalized chorion trophoblast cells from term not in labor placenta


title: CDi-on-chip, HLAG KO, control, rep 2, DEC side

description: Sample 32B

value: Primary decidual cells from term not in labor placenta


title: CDi-on-chip, HLAG KO, control, rep 1, DEC side

description: Sample 31B

value: HLAG KO


title: T2e

description: Single-nucleus/mild lysis/nick repair


title: 137_TA_10nM


title: T1e

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, PGRMC2 KO, mOS, rep 3, DEC side

description: Sample 30B

value: PGRMC2 KO

value: CSE - DEC side


title: CDi-on-chip, PGRMC2 KO, mOS, rep 3, CTC side

description: Sample 30A

value: present


title: CDi-on-chip, HLAG KO, control, rep 1, CTC side

description: Sample 31A


title: CDi-on-chip, HLAG KO, LPS, rep 2, DEC side

description: Sample 35B


title: CDi-on-chip, HLAG KO, LPS, rep 1, CTC side

description: Sample 34A


title: C9P5 HET(WT)x

city: San Francisco

first: Claire

last: Clelland

institute: UCSF

description: Single molecule sequencing 5mC methylation around C9orf72 gene locus

data_processing:
SMRT Link v13.0 generated HiFi reads with 5mC methylation tags using CCS (BAM)
pb-CpG-tools v2.3.2 generated combined methylation proportions using "--pileup-mode count" (BED and BW)
Assembly: hg38
Supplementary files format and content: BED containing combined methylation proportions
Supplementary files format and content: BW containing combined methylation proportions
Library strategy: single molecule sequencing of C9orf72

source_name: iPSCs

growth_protocol: iPSC culture

extract_protocol:
Genomic tip
No-Amp (PacBio)

value: iPSCs

value: C9orf72 patient derived iPSC line

value: iPSC

value: C9orf72 repeat expansion carrier


title: CDi-on-chip, PGRMC2 KO, mOS, rep 2, DEC side

description: Sample 29B


title: C9P5 1Ax


title: CDi-on-chip, PGRMC2 KO, mOS, rep 2, CTC side

description: Sample 29A


title: D7-H48

description: Single-nucleus/mild lysis/nick repair

source_name: HeLa, batch7, scCircle-seq

value: Cervical carcinoma

value: HeLa

value: Cervical carcinoma cells (epithelial)


title: D7-H47

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, PGRMC2 KO, mOS, rep 1, DEC side

description: Sample 28B


title: D7-H46

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, PGRMC2 KO, mOS, rep 1, CTC side

description: Sample 28A


title: CDi-on-chip, PGRMC2 KO, fOS, rep 3, DEC side

description: Sample 27B

value: CSE - CTC side


title: CDi-on-chip, PGRMC2 KO, fOS, rep 3, CTC side

description: Sample 27A


title: CDi-on-chip, PGRMC2 KO, fOS, rep 2, DEC side

description: Sample 26B


title: C9P5 HET(Mut)x


title: C9P5 unedited


title: CDi-on-chip, PGRMC2 KO, fOS, rep 1, DEC side

description: Sample 25B


title: T3e

description: Single-nucleus/mild lysis/nick repair

value: Kidney

value: Kidney (epithelial)

value: NO


title: C9P5 Rex


title: Liver, DIO-NASH-HCC, Rep 10

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

data_processing:
Reads were aligned to the GRCm38 Ensembl Mus musculus genome and counted using STAR v.2.7.0f with default settings.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file contaning raw counts from each sample

source_name: Liver tumor

extract_protocol:
Liver tissue (Chow mice, GAN DIO-NASH-HCC mice) and liver tumour samples (GAN DIO-NASH-HCC mice) were collected and snap-frozen in liquid nitrogen. RNA was isolated using the NucleoSpin® kit (MACHEREY-NAGEL).
RNA sequence libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on NextSeq 500 (Illumina, San Diego, CA) with NextSeq 500/550 High Output Kit V2 (#75 CYS, Illumina)

value: Liver tumor

value: DIO-NASH-HCC


title: D7-H44

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, PGRMC2 KO, fOS, rep 1, CTC side

description: Sample 25A

value: Immortalized chorion trophoblast cells from term not in labor placenta


title: CDi-on-chip, PGRMC2 KO, pIC, rep 3, DEC side

description: Sample 24B

value: Primary decidual cells from term not in labor placenta

value: PGRMC2 KO

value: polyIC - DEC side


title: D7-H45

description: Single-nucleus/mild lysis/nick repair


title: Liver, Parenchyme, Rep 10

source_name: Liver

value: Liver

value: Parenchyme


title: CDi-on-chip, PGRMC2 KO, pIC, rep 3, CTC side

description: Sample 24A

value: present


title: CDi-on-chip, PGRMC2 KO, pIC, rep 2, DEC side

description: Sample 23B


title: D7-H42

description: Single-nucleus/mild lysis/nick repair


title: Liver, DIO-NASH-HCC, Rep 9


title: D7-H43

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, PGRMC2 KO, pIC, rep 1, DEC side

description: Sample 22B


title: Liver, Parenchyme, Rep 9


title: CDi-on-chip, PGRMC2 KO, pIC, rep 2, CTC side

description: Sample 23A


title: D7-H40

description: Single-nucleus/mild lysis/nick repair


title: D7-H41

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, PGRMC2 KO, pIC, rep 1, CTC side

description: Sample 22A


title: CDi-on-chip, PGRMC2 KO, fOS, rep 2, CTC side

description: Sample 26A


title: Liver, DIO-NASH-HCC, Rep 8


title: CDi-on-chip, PGRMC2 KO, LPS, rep 2, DEC side

description: Sample 20B

value: LPS - DEC side


title: CDi-on-chip, PGRMC2 KO, LPS, rep 2, CTC side

description: Sample 20A


title: Liver, Parenchyme, Rep 8


title: CDi-on-chip, PGRMC2 KO, LPS, rep 3, DEC side

description: Sample 21B


title: CDi-on-chip, PGRMC2 KO, LPS, rep 1, DEC side

description: Sample 19B


title: CDi-on-chip, PGRMC2 KO, LPS, rep 1, CTC side

description: Sample 19A


title: Liver, Parenchyme, Rep 7


title: D7-H37

description: Single-nucleus/mild lysis/nick repair

value: Cervical carcinoma


title: CDi-on-chip, PGRMC2 KO, control, rep 3, CTC side

description: Sample 18A

value: control


title: Liver, DIO-NASH-HCC, Rep 6


title: CDi-on-chip, PGRMC2 KO, LPS, rep 3, CTC side

description: Sample 21A


title: CDi-on-chip, PGRMC2 KO, control, rep 2, DEC side

description: Sample 17B


title: D7-H36

description: Single-nucleus/mild lysis/nick repair

value: HeLa

value: Cervical carcinoma cells (epithelial)


title: CDi-on-chip, PGRMC2 KO, control, rep 2, CTC side

description: Sample 17A


title: D7-H35

description: Single-nucleus/mild lysis/nick repair


title: Liver, Parenchyme, Rep 6


title: CDi-on-chip, PGRMC2 KO, control, rep 1, DEC side

description: Sample 16B


title: D7-H38

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, PGRMC2 KO, control, rep 1, CTC side

description: Sample 16A


title: D7-H34

description: Single-nucleus/mild lysis/nick repair


title: D7-H39

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, WT, mOS, rep 3, CTC side

description: Sample 15A

value: wild-type

value: CSE - DEC side


title: CDi-on-chip, WT, mOS, rep 3, DEC side

description: Sample 15B


title: Liver, DIO-NASH-HCC, Rep 7


title: Liver, Parenchyme, Rep 5


title: CDi-on-chip, WT, mOS, rep 2, CTC side

description: Sample 14A


title: Liver, DIO-NASH-HCC, Rep 5


title: CDi-on-chip, WT, mOS, rep 1, DEC side

description: Sample 13B


title: CDi-on-chip, PGRMC2 KO, control, rep 3, DEC side

description: Sample 18B


title: D7-H32

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, WT, mOS, rep 1, CTC side

description: Sample 13A


title: CDi-on-chip, WT, fOS, rep 3, DEC side

description: Sample 12B

value: CSE - CTC side


title: D7-H31

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, WT, fOS, rep 3, CTC side

description: Sample 12A


title: D7-H30

description: Single-nucleus/mild lysis/nick repair


title: Liver, Parenchyme, Rep 4


title: CDi-on-chip, WT, fOS, rep 2, CTC side

description: Sample 11A


title: CDi-on-chip, WT, fOS, rep 1, DEC side

description: Sample 10B


title: CDi-on-chip, WT, fOS, rep 2, DEC side

description: Sample 11B


title: D7-H29

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, WT, pIC, rep 3, DEC side

description: Sample 9B


title: CDi-on-chip, WT, fOS, rep 1, CTC side

description: Sample 10A


title: Liver, DIO-NASH-HCC, Rep 2

value: Liver tumor


title: D7-H28

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, WT, pIC, rep 3, CTC side

description: Sample 9A


title: D7-H33

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, WT, pIC, rep 2, DEC side

description: Sample 8B


title: Liver, Parenchyme, Rep 2


title: CDi-on-chip, WT, pIC, rep 2, CTC side

description: Sample 8A


title: D7-H27

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, WT, pIC, rep 1, DEC side

description: Sample 7B


title: D7-H26

description: Single-nucleus/mild lysis/nick repair


title: Liver, DIO-NASH-HCC, Rep 4

value: DIO-NASH-HCC


title: Liver, Chow, Rep 5

value: Chow


title: CDi-on-chip, WT, pIC, rep 1, CTC side

description: Sample 7A

value: Immortalized chorion trophoblast cells from term not in labor placenta


title: CDi-on-chip, WT, LPS, rep 3, DEC side

description: Sample 6B

value: Primary decidual cells from term not in labor placenta


title: D7-H25

description: Single-nucleus/mild lysis/nick repair


title: Liver, Chow, Rep 4


title: CDi-on-chip, WT, LPS, rep 3, CTC side

description: Sample 6A


title: Liver, DIO-NASH-HCC, Rep 3


title: CDi-on-chip, WT, LPS, rep 2, DEC side

description: Sample 5B


title: Liver, Parenchyme, Rep 3


title: Liver, Chow, Rep 3


title: D7-H23

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, WT, LPS, rep 2, CTC side

description: Sample 5A


title: CDi-on-chip, WT, LPS, rep 1, DEC side

description: Sample 4B


title: Liver, Chow, Rep 2


title: CDi-on-chip, WT, LPS, rep 1, CTC side

description: Sample 4A


title: CDi-on-chip, WT, control, rep 3, DEC side

description: Sample 3B


title: Liver, Chow, Rep 1


title: D7-H22

description: Single-nucleus/mild lysis/nick repair


title: D7-H21

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, WT, control, rep 3, CTC side

description: Sample 3A


title: CDi-on-chip, WT, control, rep 2, CTC side

description: Sample 2A


title: CDi-on-chip, WT, control, rep 2, DEC side

description: Sample 2B


title: 33_RORA CTRL_ZT20

city: Basel

first: Shivani

last: Mansingh

address: Spitalstrasse 41

country: Switzerland

institute: Biozentrum, University of Basel

description: RORalpha_KO_vs_WT.T20.filter_10reads_3samples.replicate.genotype_type.all.txt

data_processing:
Samples were sequenced Single-reads 76 bases using the NextSeq 500 High Output Kit 75-cycles (Illumina, Cat# FC-404-1005), and primary data analysis was performed with the Illumina RTA version 2.4.11 and Basecalling Version bcl2fastq-2.20.0.422.
After an initial QC assessment [multiqc], sequenced reads where mapped onto GRCm39 mouse genomes ENSEMBL version 104 using the STAR software [STAR]. Both raw and trimmed (trimmomatic [trimmomatic] with option LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15) where aligned; the raw reads yielded more uniquely mapped reads and were thus kept for the rest of the analysis.
Gene expression levels were assessed using STAR the "--quantMode GeneCounts" option. Differential analysis was performed using the R software (version 4.1) with the DESeq2 library [DESeq2].
Only genes with at least 10 reads in at least a number of 3 samples (equivalent to the number of replicates) were kept. Each biological replicate was used to produced two technical replicates which were sequenced in separate lanes, this information was integrated to the DESeq2 model in order to account for potential a batch effect. An FDR threshold of 0.01 was used to declare genes as differentially expressed (DE).
Assembly: mm9

source_name: muscle

extract_protocol:
Total RNA from muscle tissues was extracted using a hybrid method combining TRI-Reagent (Sigma-Aldrich T9424) and RNeasy Mini Kit (QIAGEN 74104). RNA quality was determined on the Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Nano Chip (Agilent, Cat# 5067-1511) and quantified by Spectrophotometry using the NanoDrop ND-1000 Instrument (NanoDrop Technologies, Wilmington, DE, USA).
Library preparation was performed with 1μg total RNA using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Cat# RS-122-2103, Illumina, San Diego, CA, USA). Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical, Ames, IA, USA) using the Standard Sensitivity NGS Fragment Analysis Kit (Cat# DNF-473, Advanced Analytical) revealing excellent quality of libraries (average concentration was 152±9 nmol/L and average library size was 374±4 base pairs). Samples were pooled to equal molarity. Each pool was quantified by PicoGreen Fluorometric measurement in order to be adjusted to 1.8pM and used for clustering on the NextSeq 500 instrument (Illumina).

value: muscle

value: WT


title: CDi-on-chip, WT, control, rep 1, DEC side

description: Sample 1B


title: 30_RORA MKO_ZT16

description: RORalpha_KO_vs_WT.T16.filter_10reads_3samples.replicate.genotype_type.all.txt

value: RORA MKO


title: D7-H20

description: Single-nucleus/mild lysis/nick repair


title: D7-H19

description: Single-nucleus/mild lysis/nick repair


title: CDi-on-chip, WT, control, rep 1, CTC side

description: Sample 1A

source_name: Immortalized chorion trophoblast cells from term not in labor placenta

value: present


title: U2-3

city: Boston

first: Yu-Xin

last: Xu

state: United States

address: 185 Cambridge Street Simches Research Building, CPZN 5.500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
Base calling:  RTA-1.18.64.0
FASTQ generation:  bcl2fastq-1.8.4
Read trimming:  trimmomatic-0.35
Read QC:  fastQC-0.10.1
Alignment:  STAR-2.4.2
Mapping statistics:  bamtools-2.3.0
Differential expression:  cufflinks-2.2.1
Assembly: Rattus_norvegicus.Rnor_6.0.85.chr.gtf
Supplementary files format and content: tab-delimited gene-level differential expression output from Cuffdiff

source_name: Heterologous SmarcAL1 KO McA cell clone transfected with lentivirus containing CRISPR/cas9 and SmarcAL1 sgRNA

growth_protocol: Standard culture with DMEM medium suppplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s procedures
Ilumina TruSeq Stranded Total RNA with Ribo-Zero Globin

treatment_protocol: The cells were infected with lentiviruses containing CRISPR/cas9 with control and EDEM3 sgRNAs

value: Rat hepatoma cells

value: Heterologous SmarcAL1 KO Cells


title: U2-1


title: D7-H18

description: Single-nucleus/mild lysis/nick repair

value: Cervical carcinoma


title: 27_RORA CTRL_ZT16


title: CDi-on-chip, WT, mOS, rep 2, DEC side

description: Sample 14B

source_name: Primary decidual cells from term not in labor placenta


title: D7-H24

description: Single-nucleus/mild lysis/nick repair

value: HeLa


title: U2-2


title: D7-H17

description: Single-nucleus/mild lysis/nick repair

value: Cervical carcinoma cells (epithelial)


title: WT4

source_name: SmarcAL1 WT McA cell clone transfected with lentivirus containing CRISPR/cas9 and control sgRNA

value: WT SmarcAL1 Cells


title: D17-H26

description: Single-nucleus/mild lysis/nick repair


title: lung epithelial cell, KP infected, 48h, rep 3

city: Pittsburgh

first: Giraldina

last: Trevejo-Nunez

email: gtrevejomd@gmail.com, gjt9@pitt.edu

state: Pennsylvania

address: 200 Lothrop St. BST-E1056

institute: University of Pittsburgh

description: 10X genomics

data_processing:
Murine lung epithelial cells were processed  and sorted by flow cytometry. The sequenced single- cell RNA sequence library was processed and aligned to the mm10 mouse reference genome using Cell Ranger software (version 3.1.0) from 10x Genomics, with unique molecular identifier (UMI) counts summarized for each barcode. To distinguish cells from the background, cell calling was performed on the full raw UMI count matrix, with the filtered UMI count matrix generated.
Single cell RNA-seq raw data were processed by Cell Ranger version 3.0.1 (10X Genomics) and aligned to the GRCm38 (mm10) mouse reference genome
Seurat V2.3.4 was used for the downstream analysis, including tSNE, heatmap, and violin plots
Assembly: mm10
Supplementary files format and content: Tab separate values and matrix files

source_name: Lung

extract_protocol: Lungs were perfused with 10 ml PBS, followed by adminitration of collagenase and DNase. Single cell suspensions were prepared for flow cytometry. Single cells were incubated with biotynilated Ly6G, CD11c, CD11b, CD31 and Siglec F for 30 minutes on ice at 4 ℃ in the dark and passed through LS colum for negative selection which was stained for CD45, CD31 and Epcam at 4oC for 20 min. The negative selection fraction (CD45-CD31-Epcam+) was sorted by FACSAriaTM (BD Bioscience).

value: Lung

value: Epithelial

value: Klebsiella pneumoniae


title: 18_RORA MKO_ZT8

description: RORalpha_KO_vs_WT.T8.filter_10reads_3samples.replicate.genotype_type.all.txt


title: WT3


title: lung epithelial cell, KP infected, 48h, rep 1

description: 10X genomics


title: WT2


title: 21_RORA CTRL_ZT12

description: RORalpha_KO_vs_WT.T12.filter_10reads_3samples.replicate.genotype_type.all.txt


title: D17-H24

description: Single-nucleus/mild lysis/nick repair


title: lung epithelial cell, KP infected, 48h, rep 4

description: 10X genomics


title: LX2 DMSO treatment 48h sample3

city: Beijing

first: Dian

last: Jiao

state: Beijing

address: Tsinghua University Beijing China

institute: Tsinghua University

data_processing:
The clean reads were mapped to the reference genome using HISAT2，
FPKM was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: hg19
Supplementary files format and content: fpkm.xls:FPKM of each gene in different groups
Supplementary files format and content: counts.xls: counts data of different groups

growth_protocol: 12 well plates

extract_protocol:
TRIzol reagent
VAHTS Universal V6 RNA-seq Library Prep Kit

treatment_protocol: 30μM compounds 48h

value: DMSO


title: 15_RORA CTRL_ZT8


title: 36_RORA MKO_ZT20


title: D17-H25

description: Single-nucleus/mild lysis/nick repair


title: LX2 aristolactam AII (AL) treatment 48h sample3

value: aristolactam AII


title: 24_RORA MKO_ZT12


title: D17-H22

description: Single-nucleus/mild lysis/nick repair


title: LX2 aristolactam AII (AL) treatment 48h sample2


title: D17-H21

description: Single-nucleus/mild lysis/nick repair


title: 12_RORA MKO_ZT4

description: RORalpha_KO_vs_WT.T4.filter_10reads_3samples.replicate.genotype_type.all.txt


title: LX2 aristolochic acid I (AA) treatment 48h sample2

value: aristolochic acid I


title: lung epithelial cell, KP infected, 48h, rep 2

description: 10X genomics


title: LX2 DMSO treatment 48h sample2


title: 3_RORA CTRL_ZT0

description: RORalpha_KO_vs_WT.T0.filter_10reads_3samples.replicate.genotype_type.all.txt


title: 6_RORA MKO_ZT0


title: LX2 DMSO treatment 48h sample1


title: LX2 aristolactam AII (AL) treatment 48h sample1


title: D17-H23

description: Single-nucleus/mild lysis/nick repair


title: LX2 aristolochic acid I (AA) treatment 48h sample1


title: D17-H20

description: Single-nucleus/mild lysis/nick repair


title: LX2 aristolochic acid I (AA) treatment 48h sample3


title: HepG2 DMSO treatment 48h sample1


title: D17-H19

description: Single-nucleus/mild lysis/nick repair


title: HepG2 DMSO treatment 48h sample2


title: D17-H18

description: Single-nucleus/mild lysis/nick repair


title: 35_RORA MKO_ZT20


title: HepG2 aristolactam AII (AL) treatment 48h sample1


title: 32_RORA CTRL_ZT20


title: HepG2 aristolactam AII (AL) treatment 48h sample2


title: D17-H17

description: Single-nucleus/mild lysis/nick repair


title: 9_RORA CTRL_ZT4


title: 29_RORA MKO_ZT16


title: HepG2 aristolochic acid I (AA) treatment 48h sample3


title: D17-H16

description: Single-nucleus/mild lysis/nick repair


title: HepG2 aristolochic acid I (AA) treatment 48h sample2


title: HepG2 DMSO treatment 48h sample3


title: HepG2 aristolochic acid I (AA) treatment 48h sample1


title: 26_RORA CTRL_ZT16


title: 23_RORA MKO_ZT12


title: D17-H15

description: Single-nucleus/mild lysis/nick repair


title: LEAT_P20

city: Tokyo

first: Satoshi

last: Miyashita

address: 4-1-1, Ogawahigashimachi, Kodaira

department: Institute of Neuroscience

institute: National Center of Neurology and Psychiatry

data_processing:
Quality of fastq data was measured and low quality read were removed by fastp with default settings. Filtered reads were then aligned to the human genome reference(hg38) with STAR.
The numbers of reads were counted per gene per sample using  HTSeq.Differentially expressed genes (DEGs) were identified by DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files for raw count matrix containing all samples used in this study.

source_name: Surgical specimen of tumor region in BRAF V600E-LEAT

extract_protocol:
RNA was extracted from surgical specimen using Qiagen Allprep DNA/RNA kit (Cat#80204) according to the manufacturer's protocols
The SMART-seqR v4 UltraR Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit (Illumina) were used for library preparation.

value: Human surgical brain


title: LEAT_P19


title: LEAT_P21


title: LEAT_P17


title: HepG2 aristolactam AII (AL) treatment 48h sample3


title: LEAT_P16


title: D17-H13

description: Single-nucleus/mild lysis/nick repair


title: 14_RORA CTRL_ZT8

value: muscle


title: D17-H12

description: Single-nucleus/mild lysis/nick repair


title: LEAT_P15


title: LEAT_P18


title: LEAT_P14


title: LEAT_P13


title: 11_RORA MKO_ZT4


title: LEAT_P12


title: D17-H10

description: Single-nucleus/mild lysis/nick repair


title: LEAT_P10


title: LEAT_P11


title: 8_RORA CTRL_ZT4

value: WT


title: D17-H9

description: Single-nucleus/mild lysis/nick repair


title: D17-H14

description: Single-nucleus/mild lysis/nick repair


title: 20_RORA CTRL_ZT12


title: LEAT_P07


title: 5_RORA MKO_ZT0

value: RORA MKO


title: LEAT_P08


title: LEAT_P09


title: D17-H8

description: Single-nucleus/mild lysis/nick repair


title: 2_RORA CTRL_ZT0


title: LEAT_P06


title: 17_RORA MKO_ZT8


title: 31_RORA CTRL_ZT20


title: LEAT_P03


title: LEAT_P05


title: LEAT_P04


title: D17-H7

description: Single-nucleus/mild lysis/nick repair


title: LEAT_P01


title: 34_RORA MKO_ZT20


title: 28_RORA MKO_ZT16


title: D17-H6

description: Single-nucleus/mild lysis/nick repair


title: LEAT_P02


title: D17-H11

description: Single-nucleus/mild lysis/nick repair


title: Control_C03

source_name: Temporal tip of hippocampal sclerosis (Control)


title: 25_RORA CTRL_ZT16


title: Control_C02


title: D17-H5

description: Single-nucleus/mild lysis/nick repair


title: D17-H3

description: Single-nucleus/mild lysis/nick repair


title: Control_C01


title: Glioma, ID_016

city: Wuhan

first: Haoyu

address: 169 Donghu Rd

institute: Wuhan University

data_processing:
RNAseq fastq files were pre-processed with fastp (V0.23.2)
Gene count for each patient was obtained by using STAR (V2.7.11a) quantMode set with the ‘GeneCounts’ parameter.
Assembly: GRCh38.109
Supplementary files format and content: RNA_seq_raw_count.txt

source_name: glioma specimen

extract_protocol:
Separating one part of human GBM tissue, the RNA isolation was performed using the RNAiso Plus (TAKARA, 9109) according to the manufacturer’s instructions. 1.5ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, no.E7775)

value: glioma specimen

tag: tissue type

value: IDH wild-type grade IV


title: Glioma, ID_019


title: Glioma, ID_007


title: 19_RORA CTRL_ZT12


title: D17-H1

description: Single-nucleus/mild lysis/nick repair


title: Control_C04


title: rep2_HSC_2_WT_H3K36me3

city: Maiami

first: Yuichiro

last: Nakata

address: 1501 NW 10th Ave

institute: University of Miami

data_processing:
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq).
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).
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.
Library strategy: cut&run

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

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) weredissolved 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 incubatedfor 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.

tag: cell source

value: HSC_2 parental cells were kindly gifted from Dr. Alissa Weaver

value: Head and neck squamous cell carcinomas

value: Lentiviraly expressed with histone H3.3

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

tag: genetic modification


title: rep2_HSC_2_WT_H3K36M

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


title: 13_RORA CTRL_ZT8

tag: tissue


title: C4-1

description: Single-nucleus/mild lysis/nick repair

source_name: Colo320DM, batch6, scCircle-seq, Paired-cell

value: Colon adenocarcinoma

value: Colon adenocarcinoma cells (epithelial)

value: NO


title: rep2_HSC_2_M_H3K36me3

value: Lentiviraly expressed with histone H3.3K36 mutation


title: D17-H2

description: Single-nucleus/mild lysis/nick repair

value: Cervical carcinoma

value: HeLa

value: Cervical carcinoma cells (epithelial)


title: rep2_HSC_2_WT_H3K36me2

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


title: D17-H4

description: Single-nucleus/mild lysis/nick repair


title: C4-2

description: Single-nucleus/mild lysis/nick repair


title: rep2_HSC_2_M_H3K36me2


title: 10_RORA MKO_ZT4

value: muscle


title: rep2_HSC_2_M_H3K36M


title: C3-2

description: Single-nucleus/mild lysis/nick repair


title: 7_RORA CTRL_ZT4

value: WT


title: rep2_HSC_2_WT_H3K27me3

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


title: C3-1

description: Single-nucleus/mild lysis/nick repair


title: rep1_HSC_2_WT_H3K36me3


title: rep2_HSC_2_M_H3K27me3


title: 4_RORA MKO_ZT0

value: RORA MKO


title: rep1_HSC_2_WT_H3K36me2

value: HSC_2 parental cells were kindly gifted from Dr. Alissa Weaver


title: C2-2

description: Single-nucleus/mild lysis/nick repair


title: rep1_HSC_2_WT_H3K36M

value: Head and neck squamous cell carcinomas


title: 16_RORA MKO_ZT8


title: 1_RORA CTRL_ZT0


title: rep1_HSC_2_WT_H3K27me3

value: Lentiviraly expressed with histone H3.3


title: C2-1

description: Single-nucleus/mild lysis/nick repair


title: 43_PER2 MKO_ZT20

value: PER2 MKO


title: rep1_HSC_2_M_H3K36me3

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


title: rep1_HSC_2_M_H3K27me3


title: rep1_HSC_2_M_H3K36me2


title: 39_PER2 CTRL_ZT20


title: HSC-2_Fix_Input

data_processing:
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq).
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).
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:
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.


title: K40e

description: Single-nucleus/mild lysis/nick repair

source_name: K562, batch6, scCircle-seq

value: Chronic myelogenous leukemia

value: Chronic myelogenous leukemia cells


title: K39e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: Colo320DM-Bulk

description: Bulk Circle-seq

source_name: Colo320DM, batch6, Bulk Circle-seq

value: Colon adenocarcinoma

value: Colon adenocarcinoma cells (epithelial)


title: rep1_HSC_2_M_H3K36M

value: Lentiviraly expressed with histone H3.3K36 mutation

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


title: 34_PER2 MKO_ZT16


title: Detroit_Fix_FLAG

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

value: Rabbit monoclonal Anti-FLAG tag antibody (CST 14793S)


title: rep4_SCC25_M_NSD3

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

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

value: Rabbit monoclonal Anti-NSD3 antibody (CST #92056)


title: HSC-2_Fix_FLAG


title: 31_PER2 CTRL_ZT16

value: muscle

value: WT


title: K37e

description: Single-nucleus/mild lysis/nick repair


title: 28_PER2 MKO_ZT12


title: rep4_SCC25_M_Input_L2_S3

value: Head and neck squamous cell carcinomas


title: rep3_SCC25_M_LSD2

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


title: K36e

description: Single-nucleus/mild lysis/nick repair


title: 27_PER2 MKO_ZT12

value: PER2 MKO


title: rep3_SCC25_M_Input_L2_S3


title: rep2_SCC25_WT_shNSD3_IgG_no

value: Lentiviraly expressed with histone H3.3

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


title: 24_PER2 CTRL_ZT12


title: K35e

description: Single-nucleus/mild lysis/nick repair

value: Chronic myelogenous leukemia

value: Chronic myelogenous leukemia cells


title: rep2_SCC25_WT_shNSD3_IgG_dox


title: 35_PER2 MKO_ZT16


title: Detroit_Fix_Input


title: 21_PER2 MKO_ZT8


title: K34e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: rep2_SCC25_WT_shNSD3_H3K36me3_no

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


title: K38e

description: Single-nucleus/mild lysis/nick repair


title: 20_PER2 MKO_ZT8


title: rep2_SCC25_WT_shNSD3_H3K36me2_dox

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


title: K33e

description: Single-nucleus/mild lysis/nick repair


title: rep2_SCC25_WT_shNSD3_H3K36me3_dox


title: rep4_SCC25_M_LSD2

value: Lentiviraly expressed with histone H3.3K36 mutation


title: rep2_SCC25_WT_shNSD3_H3K36me2_no


title: rep2_SCC25_WT_shNSD3_H3K27me3_no

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


title: K32e

description: Single-nucleus/mild lysis/nick repair


title: rep3_SCC25_M_NSD3


title: 13_PER2 MKO_ZT4


title: rep2_SCC25_WT_shNSD3_H3K27me3_dox


title: 14_PER2 MKO_ZT4


title: rep2_Detroit_WT_H3K36me2

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


title: rep2_Detroit_WT_H3K36M

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


title: rep2_Detroit_WT_H3K27me3


title: rep2_Detroit_WT_H3K36me3


title: rep2_Detroit_M_H3K36me2


title: 10_PER2 CTRL_ZT4


title: K28e

description: Single-nucleus/mild lysis/nick repair


title: rep2_Detroit_M_H3K36M


title: 7_PER2 MKO_ZT0


title: rep2_Detroit_M_H3K27me3


title: rep1_SCC25_WT_shNSD3_IgG_no

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

value: Lentiviraly expressed with histone H3.3 and inducible shRNA of NSD3, non-treated with Dox


title: 17_PER2 CTRL_ZT8

value: muscle

value: WT


title: K27e

description: Single-nucleus/mild lysis/nick repair


title: 3_PER2 CTRL_ZT0


title: K26e

description: Single-nucleus/mild lysis/nick repair


title: rep1_SCC25_WT_shNSD3_IgG_dox

value: Head and neck squamous cell carcinomas

value: Lentiviraly expressed with histone H3.3 and inducible shRNA of NSD3, treated with Dox


title: rep1_SCC25_WT_shNSD3_H3K36me3_dox


title: rep1_SCC25_WT_shNSD3_H3K36me2_no


title: K25e

description: Single-nucleus/mild lysis/nick repair


title: rep1_SCC25_WT_shNSD3_H3K36me3_no


title: K31e

description: Single-nucleus/mild lysis/nick repair


title: rep1_SCC25_WT_shNSD3_H3K36me2_dox


title: rep1_SCC25_WT_shNSD3_H3K27me3_no


title: rep1_SCC25_WT_shNSD3_H3K27me3_dox


title: rep1_SCC25_Fix_FLAG

value: Lentiviraly expressed with histone H3.3

value: Rabbit monoclonal Anti-FLAG tag antibody (CST 14793S)


title: K23e

description: Single-nucleus/mild lysis/nick repair

value: Chronic myelogenous leukemia


title: 42_PER2 MKO_ZT20

value: PER2 MKO


title: 38_PER2 CTRL_ZT20


title: K29e

description: Single-nucleus/mild lysis/nick repair

value: Chronic myelogenous leukemia cells

value: NO


title: K24e

description: Single-nucleus/mild lysis/nick repair


title: K30e

description: Single-nucleus/mild lysis/nick repair


title: 41_PER2 MKO_ZT20


title: rep1_SCC25_Fix_Input


title: 37_PER2 CTRL_ZT20


title: 6_PER2 MKO_ZT0


title: K22e

description: Single-nucleus/mild lysis/nick repair


title: K21e

description: Single-nucleus/mild lysis/nick repair


title: rep1_FaDU_Fix_Input

source_name: FaDU

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

value: FaDU


title: rep1_FaDU_Fix_FLAG


title: 33_PER2 MKO_ZT16


title: rep1_Detroit_WT_H3K27me3

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


title: rep1_Detroit_M_H3K27me3

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

value: Lentiviraly expressed with histone H3.3K36 mutation


title: SCC25_M_LSD2_Rep2_ChIPseq

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

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


title: K20e

description: Single-nucleus/mild lysis/nick repair


title: 30_PER2 CTRL_ZT16

value: muscle


title: 26_PER2 MKO_ZT12


title: SCC25_WT_LSD2_Rep2_ChIPseq


title: K19e

description: Single-nucleus/mild lysis/nick repair


title: SCC25_M_LSD2_Rep1_ChIPseq


title: rep2_Detroit_M_H3K36me3

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


title: SCC25_WT_LSD2_Rep1_ChIPseq

value: Head and neck squamous cell carcinomas


title: K18e

description: Single-nucleus/mild lysis/nick repair


title: FaDU_M_LSD2_Rep2_ChIPseq


title: FaDU_M_LSD2_Rep1_ChIPseq


title: K17e

description: Single-nucleus/mild lysis/nick repair


title: FaDU_WT_LSD2_Rep2_ChIPseq


title: FaDU_WT_LSD2_Rep1_ChIPseq


title: SCC25_M_NSD3_Rep2_ChIPseq

value: Rabbit monoclonal Anti-NSD3 antibody (CST #92056)


title: 19_PER2 MKO_ZT8


title: SCC25_WT_NSD3_Rep2_ChIPseq

value: Lentiviraly expressed with histone H3.3


title: K15e

description: Single-nucleus/mild lysis/nick repair


title: K16e

description: Single-nucleus/mild lysis/nick repair


title: 16_PER2 CTRL_ZT8

value: WT


title: SCC25_WT_NSD3_Rep1_ChIPseq


title: FaDU_M_NSD3_Rep2_ChIPseq


title: K14e

description: Single-nucleus/mild lysis/nick repair

value: Chronic myelogenous leukemia


title: 12_PER2 MKO_ZT4

value: PER2 MKO


title: K13e

description: Single-nucleus/mild lysis/nick repair

value: Chronic myelogenous leukemia cells


title: FaDU_M_NSD3_Rep1_ChIPseq


title: 9_PER2 CTRL_ZT4


title: FaDU_WT_NSD3_Rep2_ChIPseq


title: 5_PER2 MKO_ZT0


title: FaDU_WT_NSD3_Rep1_ChIPseq


title: K12e

description: Single-nucleus/mild lysis/nick repair

value: NO


title: RNA-WT-Rep2-21R068

city: Memphis

first: Beisi

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Paired-end 100-cycle sequencing Reads were first trimmed for adapters using trim_galore (parameters: "--paired --retain_unpaired").
Then alignment to the reference genome hg38 (GRCh38.p6) by STAR (version 2.7.1a, parameters: " --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS nM XS --outSAMunmapped Within KeepPairs --twopassMode Basic –outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66")
For differential gene expression analysis, HTSeq (version 0.6.1p1) were used to estimate the counts based on GENCODE (hg38 version 31). After normalization by TMM, Voom was used to identify differential expressed genes.
For splicing analysis, rMATS (Docker version v4.1.1, parameters: " --readLength 100 --variable-read-length --novelSS --allow-clipping ") were used to call alternative splicing events. We performed three analyses as KO#1 (2 replicates) versus WT (2 replicates), KO#2 (2 replicates) versus WT and KO (4 replicates) versus WT. To assure the confidence, we take the results of four KO samples versus two WT samples and require they also significant in results for KO#1 vs WT and KO#2 vs WT, then we further required at least 10 reads and 0.5 counts per million.
rmats2sashimiplot (https://github.com/Xinglab/rmats2sashimiplot v2.0.4 "--exon_s 1 --intron_s 5 --no-text-background") were used to make sashimi plots.
Assembly: hg38 (GRCh38.p6)
Supplementary files format and content: Tab-separated raw counts file
Supplementary files format and content: Tab-separated DEG results and FPKM from Voom/Limma

extract_protocol:
Total RNAs  were extracted using TRNzol according to the manufacturer's instructions. NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RF/fr-firststrand

value: kidney


title: K11e

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: 40_PER2 MKO_ZT20


title: RNA-KO2-Rep1-21R071

value: THUMPD2 KO#2


title: K10e

description: Single-nucleus/mild lysis/nick repair


title: 23_PER2 CTRL_ZT12


title: K9e

description: Single-nucleus/mild lysis/nick repair


title: SCC25_M_NSD3_Rep1_ChIPseq


title: 36_PER2 CTRL_ZT20


title: RNA-KO1-Rep2-21R070

value: THUMPD2 KO#1


title: RNA-KO1-Rep1-21R069


title: HASMC_ActivatedEVs_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: Activated endothelial EVs


title: 32_PER2 MKO_ZT16


title: HASMC_ActivatedEVs_1


title: HASMC_ActivatedEVs_3


title: HASMC_QuiescentEVs_3

value: Quiescent endothelial EVs


title: 29_PER2 CTRL_ZT16

value: muscle


title: K8e

city: Stockholm

first: Jinxin

institute: Karolinska Institutet

description: Single-nucleus/mild lysis/nick repair


title: K7e

description: Single-nucleus/mild lysis/nick repair


title: 25_PER2 MKO_ZT12


title: HASMC_QuiescentEVs_1


title: K6e

description: Single-nucleus/mild lysis/nick repair


title: 2_PER2 CTRL_ZT0


title: RNA-WT-Rep1-21R067


title: DS Aminocytes, T-5224 treated, rep3

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: To explore the role of inhibiting AP-1 activity on DS, DSACs were treated with 40 μM T-5224 (M9373, Abmole, Houston, USA) for 48 hours, and dimethyl sulfoxide (DMSO) treated DSACs were used as NC group.

value: amniotic fluid

value: aminocytes

value: Down syndrome


title: 22_PER2 CTRL_ZT12


title: HASMC_Media_3

value: media


title: RNA-KO2-Rep2-21R072


title: K5e

address: Tomtebodavägen 23

description: Single-nucleus/mild lysis/nick repair


title: DS Aminocytes, T-5224 treated, rep2


title: 22_RORA MKO_ZT12

value: RORA MKO


title: 18_PER2 MKO_ZT8


title: HASMC_Media_1


title: K4e

description: Single-nucleus/mild lysis/nick repair

value: Chronic myelogenous leukemia


title: DS Aminocytes, NC-DMSO, rep3

value: DMSO


title: 11_PER2 MKO_ZT4

value: PER2 MKO


title: 15_PER2 CTRL_ZT8

value: WT


title: K2e

description: Single-nucleus/mild lysis/nick repair

value: Chronic myelogenous leukemia cells

value: NO


title: 8_PER2 CTRL_ZT4


title: CD14_ActivatedEVs_2

value: CD14+ monocytes


title: CD14_ActivatedEVs_3

value: primary cells


title: HASMC_QuiescentEVs_2

value: Human Aortic Smooth Muscle Cells (HASMCs)


title: DS Aminocytes, NC-DMSO, rep2


title: 4_PER2 MKO_ZT0


title: CD14_ActivatedEVs_1

value: Activated endothelial EVs


title: 1_PER2 CTRL_ZT0


title: K1e

description: Single-nucleus/mild lysis/nick repair


title: CD14_QuiescentEVs_2

value: Quiescent endothelial EVs


title: malbac_p7e

description: Single-nucleus/mild lysis/nick repair

source_name: PC3, batch5, malbac_amplification

value: Prostate cancer

value: Prostate cancer cells (epithelial)


title: DS Aminocytes, NC-DMSO, rep1

value: amniotic fluid

value: aminocytes


title: malbac_p4e

description: Single-nucleus/mild lysis/nick repair


title: CD14_QuiescentEVs_1


title: malbac_p5e

description: Single-nucleus/mild lysis/nick repair


title: K3e

description: Single-nucleus/mild lysis/nick repair


title: malbac_p3e

description: Single-nucleus/mild lysis/nick repair


title: Normal Aminocytes, MX1_OE, rep3

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: MX1-OE lentivirus


title: Normal Aminocytes, MX1_OE, rep1


title: CD14_QuiescentEVs_3


title: CD14_Media_2

value: media


title: Normal Aminocytes, MX1_OE, rep4


title: batch4_H16e

description: Single-nucleus/mild lysis/nick repair

source_name: HeLa, batch4, scCircle-seq

value: Cervical carcinoma

value: HeLa

value: Cervical carcinoma cells (epithelial)


title: DS Aminocytes, T-5224 treated, rep1

value: Down syndrome


title: batch4_H15e

description: Single-nucleus/mild lysis/nick repair


title: CD14_Media_1


title: malbac_p2e

description: Single-nucleus/mild lysis/nick repair


title: Normal Aminocytes, blank, rep1

value: WT

value: backbone lentivirus


title: CD14_Media_3

value: CD14+ monocytes


title: batch4_H14e

description: Single-nucleus/mild lysis/nick repair


title: Normal Aminocytes, blank, rep3


title: Normal Aminocytes, MX1_OE, rep2


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

city: St Petersburg

first: Edina

last: Erdős

address: 501 6th Ave S

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

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


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


title: malbac_p1e

last: Chen

description: Single-nucleus/mild lysis/nick repair

value: NO


title: Normal Aminocytes, blank, rep4


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