title: week-10_H3K9me3_rep1

description:
10weeks-1-H3K9me3_combined
processed data file: 10weeks-H3K9me3_Input_peaks.broadPeak


title: Primary human CD34 sgRBM12 rep3

status: Public on Jun 14 2022

type: SRA

city: Philadelphia

first: Aoi

last: Wakabayashi

state: Pennsylvania

address: 3615 Civic Center Blvd, Abramson Research Center Rm 315A

department: Hematology/Oncology

country: USA

institute: Children's Hospital of Philadelphia

library_source: transcriptomic

data_processing:
Sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/)
Gene set Gencode v29 was used for mapping the reads to the human genome (hg38 assembly) using STAR
Gene quantification was done via RSEM workflow
Assembly: hg38
Supplementary files format and content: .tsv

molecule: total RNA

organism: Homo sapiens

source_name: Hematopoietic Stem and Progenitor Cells

growth_protocol: Primary human CD34+ HSPCs were cultured in vitro using a 3 phase erythroid differentiation system.

extract_protocol:
Cells were lysed in buffer RLT plus BME and RNA was column-purified using the Qiagen RNEasy kit.
Libraries were prepared following Illumina's TruSeq Stranded mRNA kit protocol.

treatment_protocol: HSPCs were electroporated with either an RBM12 targeting or non-targeting sgRNA that is in complex with Cas9 protein at day 0 of differentiation.

tag: cell type

value: human CD34+ HSPCs

tag: day of differentiation

value: day 7 of erythroid differentiation

tag: treatment

value: targeted with RBM12 sgRNA


title: Primary human CD34 sgRBM12 rep2


title: week-10_Input_rep1

city: Wuhan

first: Min

last: Wu

state: Hubei

address: Room 5005, Life Science College, Wuhan University

department: College of Life Science and Technology of Huazhong Agricultural University

country: China

institute: Wuhan universioty

library_source: genomic

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
ChIP-seq clean data were obtained by removing adaptor from raw fastq with Cutadapt (version 1.16, http://cutadapt.readthedocs.io/en/stable/guide.html, parameters were “-u 4 -u 35 -U 4 -U 35 -m 30”)
Cleaned reads were aligned in paired-end mode to mouse reference genome mm10 with BWA mem (version 0.7.15, http://bio-bwa.sourceforge.net )
Duplicate reads were removed by Picard MarkDuplicate (http://picard.sourceforge.net/). Only unique mapped reads were used in following work.
Peaks were called by MACS2 (version 2.1.1, https://github.com/taoliu/MACS, with parameters “--nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147” ) at false discovery rate (FDR) < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

organism: Mus musculus

growth_protocol: The 8-week-old Wild-type C57BL/6J mice were purchased from Beijing HFK Bioscience Co. Ltd.

extract_protocol:
DNA were clarified from nuclei treated with micrococcal nuclease and histone-DNA complexes were isolated with antibody. Briefly, around 30 milligrams of each tissue were cut into 1 mm3 pieces in PBS with protease inhibitor. Tissue pieces were cross-linked for 10min at room temperature with 1% formaldehyde and then quenched with 0.125 M of glycine for 5 min. Cross-linked tissues were triturated in tissue grinding instrument for 60s at 60 Hz, and then centrifuged at 12000 rpm, 4 °C for 10 min. Supernatant with massive oil was discarded and the precipitates were lysed with 1 mL lysis buffer (50 mM Tris-HCl pH 8.0, 0.1% SDS, 5 mM EDTA) for 4 min with gentle rotation. After centrifugation at 12000 rpm, 4 °C for 2 min, the pellet was washed once with digestion buffer (50 mM Tris-HCl pH8.0, 1 mM CaCl2, 0.2% Triton X-100), incubated in 630-μL digestion buffer with 1 μL MNase (NEB, M0247S) at 37°C for 20min and quenched with 8 μL 0.5M EDTA. The resulted mixture was sonicated and the pellet was discarded after centrifugation. 30 μL supernatant was taken for checking the efficiency of digestion. Immunoprecipitation was performed with 150 μL sheared chromatin, 2 μg antibody, 50 μL Protein G beads and 800 μL dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) overnight at 4 °C. Next day, the beads were washed once with Wash buffer I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with Wash buffer II (20mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with Wash buffer III (10mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Na-deoxycholate, 1% NP-40) and twice with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The beads were eluted twice with 100 μL elution buffer (1% SDS, 0.1M NaHCO3, 20mg/mL Proteinase K) at room temperature. The elution was incubated at 65 °C for 6 h and then purified with DNA purification kit (TIANGEN DP214-03).
ChIP-seq libraries were constructed with ChIP and input DNA using VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606). Briefly, 10 ng DNA was end-repaired for dA tailing, followed by adaptor ligation. Each adaptor was marked with a barcode of 8 bp DNA. Adaptor-ligated DNA was purified by AMPure XP beads (1:1) and then amplified by PCR of 10 cycles with the primer matching with adaptor universal part. Amplified DNA was purified again using AMPure XP beads (1:1) in 35 μL EB elution buffer. For multiplexing, libraries with different barcode were mixed with equal molar quantities (30-50 million reads per library). Libraries were sequenced by Illumina Nova-seq platform with pair-end reads of 150 bp.

treatment_protocol: The mice were randomly divided into four experimental groups (2 weeks, 4 weeks, 7 weeks, 10 weeks) and one control group (n = 5 per group). The mice in the experimental groups were given a single intraperitoneal injection of AOM (10 mg/kg body weight). Seven days after the AOM injection, the mice were given 2.5% DSS (w/v) in their drinking water for 7 days. The 2weeks group mice were sacrificed. The other three experimental group mice fed with distilled water for 14 days and then 4 weeks group mice were sacrificed. After that, the remained two experimental group mice were given 2.5% DSS (w/v) in their drinking water for 7 days and next distilled water for 14 days. The 7 weeks group mice were sacrificed. Afterwards the last 10 weeks group mice were given 2.5% DSS (w/v) in their drinking water for 7 days and then distilled water for 14 days and sacrificed. The control group (0 week) mice were fed with distilled water for 70 days and sacrificed. The colorectum of all mice were collected for RNA-seq and ChIP-seq.

tag: strain

tag: time point

tag: tissue

value: Colon


title: Tet TKO chimera plate 44

city: Rehovot

first: Markus

last: Mittnenzweig

state: Shfela

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
1106TKO29_03

library_source: transcriptomic single cell

data_processing:
MARS-seq data was processed as detailed in the MARS-seq2.0 protocol (Keren-Shaul et al. 2019):
1. bcl2fastq/2.15.0.4
2. Pool_barcode (4 bps) and well_barcode (7 bps) plus UMI barcode (8 bps) were removed from Read 1 and Read 2 (respectively) and concatenated to the fastq header.
3. Read 1 sequences were mapped to the mm9 genome using bowtie2.
4. Demultiplexing and construction of mRNA count matrix were based on 4bp plate barcode, 7bp well barcode and 8bp UMI barcode
5. Header structure of labeled Read 1 fastq files: "ORIGINALHEADER_barcode=similar_oligo-pool_barcode_quality-well_barcode_quality-UMI_quality-pool_barcode-well_barcode-UMI". Concatenated entries are separated by "-"
6. well_barcode (7bp), pool_barcode (4bp) and external_barcode (8bp) of each single cell can be found in metadata.
PBAT data was processed as detailed (Meir et al., 2020): PE 150bp or 300bp reads were aligned to the mm9 reference genome using an in-house script based on Bowtie2. In cases where the two reads ends were not aligned in a concordant manner, the reads were discarded. Reads that were mapped to the same genome coordinates where marked as duplicates and were used only once. We subsample methylation of single-cells to have only one methylation call per CpG.
Assembly: mm9
Supplementary files format and content: Tab-separated text file for each 384-well plate containing UMI counts per gene per single cell. metadata_cells_scrna_sequencing.txt file contains metadata for each processed single cell.
Supplementary files format and content: Tab-separated text file for each sample, containing a row per genomic CpG with the following columns: 'chrom','start','end' - coordinates in 0-based form, 'cov' - # of times the CpG was covered, 'meth' # of times the CpG was methylated.

source_name: E7.5 chimera embryo

growth_protocol: Control and mutant mESCs were cultured on irradiated mouse embryonic fibroblasts (MEFs) with standard serum medium for 2-3 days and replaced with 2i+LIF medium containing an additional 1 mM PD0325901 and 3 mM CHIR99021 for another growth of 10-12 hours.

extract_protocol:
Whole-embryo chimera, mixed chimera, and AAV-Cre treated embryos were dissected in ice-cold 1×PBS, followed by imaging in a drop of DMEM medium supplemented with 10% foetal bovine serum (FBS) under a Nikon Eclipse Ti2 inverted microscope. Embryos were then rinsed in ice-cold 1×PBS, transferred into an Eppendorf tube containing 35 µl 0.25% Trypsin/0.02% EDTA Solution A, and incubated at 37 °C for 5 min with 2-3 times pipetting. Trypsinization was stopped by adding 10% FBS/DMEM medium. Cell suspensions were filtered through a 35 µm strainer before sorting.
For MARS-seq analysis, single cells were index-sorted into a pre-barcoded 384-well capture plate that contains 2 µl of lysis solution and barcoded poly (T) reverse-transcription (RT) primers. In each plate, 12 wells at positions C1, C2, D1, D2, J6, J7, K6, K7, O23, O24, P23, and P24 were kept as non-cell controls. Immediately after sorting, each plate was sealed, spun down, snap-frozen on dry ice, and stored at -80 °C until library preparation.
For bisulfite sequencing, Tet-TKO1, Tet-TKO2, Ctrl1, and Ctrl2 cells were sorted from E8.5 chimera embryos respectively. Cell pellets were kept at -80 °C until library preparation. Genomic DNA was extract using commercial kit.
Single-cell cDNA libraries were prepared using the MARS-Seq method as described (Keren-Shaul et al., 2019). Briefly, reverse transcription was performed in individual wells of the sorted 384-well plate to get complementary DNA (cDNA). Subsequently, all liquid from each 384-well plate was pooled and converted to double-stranded DNA, transcribed using T7 RNA polymerase, and fragmented. A unique plate adaptor was added to each library to be sequenced together, and RNA::ssDNA (plate adaptor) ligation was performed. The purified ligates were applied to a second RT step with a primer complementary to the ligated adaptor, and the library is completed by cDNA enrichment through PCR amplification. Library concentration and profile were evaluated before sequencing.  Bulk PBAT library was performed as previously described (Meir et al., 2020). Briefly, genomic DNA was converted with bisulfate, and applied to the first and second strand synthesis. The product was treated by Klenow fragment and purified. A final PCR was performed using a universal primer and indexed primers. The final product was clean and sequenced.

treatment_protocol:
(1) To obtain whole-embryo and mixed chimeric embryos, mESCs were injected into diploid or tetraploid B6D2F x B6D2F1 E3.5 blastocysts and surgically implanted into E2.5 postcoitum pseudo-pregnant Hsd:ICR (CD-1) females following standard procedures. Females were sacrificed at embryonic day 7.5-9.5 based on the design of the experiment.
(2) To obtain AAV-Cre treated Tet knockout embryos, zygotes from Tet triple floxed mice were collected in M2 medium. Following acidic Tryode’s solution treatment, zygotes were rinsed in M2 medium and transferred to KSOM for incubation in a tissue culture incubator. Drops containing 35 µl KSOM medium were placed in 35 mm plates under mineral oil. 6e9 vg AAV1-Cre-GFP viral were added to each drop, followed by a 15 min incubation at 37 °C in the same tissue culture incubator. Subsequently, zygotes were transferred into the viral drop and cultured for 24 hrs. Qualified 2-cell embryos were rinsed in M2 medium and transferred into the oviduct of E0.5 pseudo-pregnant ICR females. Recipient females were allowed to carry the embryos and sacrificed at E7.5.

value: E7.5 chimera embryo

tag: genotype

value: Host cells and injected mESC-derived Tet TKO cells

value: Chimera assay

tag: developmental stage


title: week-10_Input_rep2


title: week-10_Input_rep3


title: Tet TKO chimera plate 16

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190325_P02

value: Host cells and injected mESC-derived Control and Tet TKO cells


title: week-10_H3K27me3_rep3

description:
10weeks-3-H3K27me3_combined
processed data file: 10weeks-H3K27me3_Input_peaks.broadPeak

tag: chip antibody


title: 72 hpf miR-34a-/- replicate 2

city: Ottawa

first: Sergey

last: Prykhozhij

state: ON

address: Room 318/319 | CAREG, 20 Marie-Curie Private

country: Canada

institute: CHEO Research Institute/University of Ottawa

data_processing:
Read trimming: the raw reads had the adapters removed and filtered by the quality of 20 with the Trim Galore (v0.4.4).
Read mapping: The RNA-Seq data were mapped with STAR (v2.7.8) using the Genome Reference Consortium Zebrafish Build 11 (danRer11).
Read counting: The counts were obtained by STAR as part of read alignment.
Assembly: danRer11
Supplementary files format and content: The processed .csv file contains read counts for all genes.

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish experiments and husbandry follows standard protocols in accordance with the standards of the University of Ottawa Animal Care Committee (approval number: CHEOe-3168-A1). Zebrafish embryos were maintained at 28.5 °C during development and as adults. Embryos were grown in egg water (1x E3 prepared from 60x E3 stock).

extract_protocol:
Each total RNA sample was extracted from 30-50 zebrafish embryos by homogenizing them in 500 µL Trizol reagent (Thermo Fisher Scientific, 15596026) using 1 mL syringe and 22G needle. Lysates were centrifuged at 12,000 g at 4ºC for 5 minutes and the supernatant was transferred to Phasemaker Tubes (Thermo Fisher Scientific, A33248) and RNA was purified according to the Phasemaker Tubes protocol manual.
Total RNA samples were measured and analyzed for integrity on Agilent Tape Station. Samples with RNA integration number ≥8 were selected for library preparation. Poly-A enrichment was performed from 20 µg of total RNA to enrich for mRNA (Dyna beads mRNA direct micro Kit). 100ng of poly-A enriched RNA was fragmented using RNase III and purified using magnetic bead clean up module (RNA Seq V2 kit, Life Technologies). The size distribution of the fragmented RNA was assessed on Agilent Tape Station using RNA HS screen tape assay and 50 ng of fragmented polyA-enriched RNA was used to prepare whole transcriptome library (RNA seq V2). Yield and size distribution of the library was analyzed on Agilent Tape Station using D1000 screen tape. The library was sequenced on the NextSeq 550 instrument (Illumina).

value: whole embryo

tag: Stage

value: 72 hpf


title: 72 hpf miR-34a-/- replicate 3


title: week-10_H3K27me3_rep2

description:
10weeks-2-H3K27me3_combined
processed data file: 10weeks-H3K27me3_Input_peaks.broadPeak


title: TRPV1 K823R rep 1

city: Shanghai

first: Yong

last: Li

address: 280 South Chongqing Road

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
fastp v 0.19.5
Then clean reads were separately aligned to a reference genome with orientation mode using the HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.The criteria for mapping were that sequencing reads should be uniquely matched to the genome with less than 3 mismatches, without insertions or deletions.
The gene regions were expanded following depths of sites and the operon was obtained. In addition, the whole genome was segmented into multiple 15 kb fragments that share the same 5 kb fragments. If more than 2 consecutive fragments were without overlapped region and at least 2 reads mapped per fragment in the same orientation, we consider it to be a newly transcribed region of gene.
Each transcript expression level was calculated according to the fragments per kb of transcript per million mapped reads (FPKM) method. The gene abundances were quantified using the RSEM software, while the EdgeR software was used for differential expression analysis and quantified transcript read counts.
Assembly: GRCm38.p6
Supplementary files format and content: matrix.txt represents FPKMs (the result of abundance measurement)

source_name: Trigeminal ganglion

extract_protocol:
Two pairs of trigeminal ganglia were isolated on ice from 8-week-old TRPV1K823R KI and their littermate control mice and quickly frozen in liquid nitrogen. The samples were delivered to the company (Majorbio Bio-pharm Technology) to prepare RNA samples and conduct high-throughput RNA-seq. Total RNA was extracted from TG using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (Takara). The RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using ND-2000 (NanoDrop Technologies). Only high-quality RNA samples (OD 260/280 = 1.8~2.2, OD 260/230 ≥ 2.0, RIN ≥ 6.5, 28S:18S ≥ 1.0, > 1 μg) were used to construct sequencing library. The RNA integrity was also confirmed with agarose gel electrophoresis.
1 μg RNA samples were used to construct sequencing library. Briefly,  messenger RNA (mRNA) was first isolated from total RNA samples and then fragmented in a fragmentation buffer. Second, double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA, USA) with random hexamer primers (Illumina, CA, USA). Third, the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Then, 200-300 bp cDNA target fragments were isolated using 2% agarose followed by PCR amplification. The isolated cDNA fragments were selected to construct the sequencing library. Libraries were quantified by TBS380 and sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length) (Illumina).

value: Trigeminal ganglion

tag: Sex

value: male

value: TRPV1 K823R transgenic

tag: age

value: 8 weeks old


title: 72 hpf wild-type replicate 3

value: wild-type


title: WT rep 1

value: WT


title: WT rep 2


title: 72 hpf wild-type replicate 2


title: 72 hpf wild-type replicate 1


title: 8 hpf miR-34a-/- replicate 4

value: 8 hpf


title: 8 hpf miR-34a-/- replicate 1


title: week-10_H3K27me3_rep1

description:
10weeks-1-H3K27me3_combined
processed data file: 10weeks-H3K27me3_Input_peaks.broadPeak


title: 8 hpf miR-34a-/- replicate 3


title: week-10_H3K4me3_rep3

description:
10weeks-3-H3K4me3_combined
processed data file: 10weeks-H3K4me3_Input_peaks.broadPeak


title: 8 hpf wild-type replicate 3


title: 72 hpf miR-34a-/- replicate 1


title: Grp8b db/db+renin+ACEI+JNJ39933673 Kidney rep3

city: St. Louis

first: Haojia

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

description:
V3107
whole kidney bulk RNA-seq

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a maximum of one mismatch in the indexing read for sample demultiplexing. RNA-seq reads were then aligned to the mm10 (for mouse) or GRCh38 (for human) with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Raw counts and RPKM were output for downstream analysis.
Assembly: mm10 (GRCm38) and GRCh38
Supplementary files format and content: *csv: Processed files are the raw read counts and RPKM for each gene/sample in comma-separated text format.

growth_protocol: Mouse diabetic nephropathy protocol: To establish the model, female db/db mice (BKS.Cg-Dock7m +/+ Leprdb/J from Jackson, BKS background, Lot 642) were subject to left nephrectomy at 5 weeks of age, and at 12 weeks, infected with a renin expressing adeno-associated virus (ReninAAV, 109 genomic copies) to induce hypertension and accelerate disease progression. In addition to the ReninAAV Unx db/db mice, db/m and Unx db/db mice infected with an empty viral vector (LacZ AAV) were included as healthy and diabetic non-hypertensive controls, respectively.

extract_protocol:
Total mRNA were isolated from mouse kidney and human RPTECs using a RNA kit from Qiagen (RNeasy Mini prep kit, Cat# 74104).
Total RNA integrity was determined using Agilent 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol:
Drug treatment protocol: Drug treatments were given to mice as follows:  1. Vehicle (drinking water);   2. Lisinopril (An ACE inhibitor, 10 mg/kg/d in the drinking water);    3. Rosiglitazone (A PPARꙋ activator, 0.007% w/w via admix diet, p.o. ~10 mg/kg/d);   4. JNJ-39933673 (A SGLT2 inhibitor, 0.0075% w/w via admix diet, p.o. 1 ~ mg/kg/d);   5. ACEi plus SGLT2i (dosed as before);   6. ACEi plus rosiglitazone (dosed as before). Terminal samples were collected 48 hours and 2 weeks after treatment inception.
In vitro experiment was performed on human primary tubular epithelial cells (RPTEC) purchased from Lonza (cat# CC-2553, lot 0000635750). RPTECs were treated with SRSF7 siRNA (siGenome, cat# M-015909-01-0020) at concentrations of 100 uM and 200 uM. Scrambled siRNA was used as negative control.

value: Kidney

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

value: female

value: renin AAV + ACEI + JNJ39933673

tag: treatment timepoint

value: 2 weeks


title: Grp8b db/db+renin+ACEI+JNJ39933673 Kidney rep5

description:
P3109
whole kidney bulk RNA-seq


title: 8 hpf miR-34a-/- replicate 2


title: 8 hpf wild-type replicate 4


title: 8 hpf wild-type replicate 1


title: 8 hpf wild-type replicate 2


title: TRPV1 K823R rep 2


title: week-10_H3K4me1_rep2

description:
10weeks-2-H3K4me1_combined
processed data file: 10weeks-H3K4me1_Input_peaks.broadPeak

value: Colon


title: week-10_H3K4me3_rep1

description:
10weeks-1-H3K4me3_combined
processed data file: 10weeks-H3K4me3_Input_peaks.broadPeak


title: Grp8b db/db+renin+ACEI+JNJ39933673 Kidney rep2

description:
U3106
whole kidney bulk RNA-seq


title: Hi-C, MCF7-DR, 1

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

data_processing:
The raw sequenced Hi-C reads were first mapped to the human genome hg19 with BWA.
The normalization of valid mapped Hi-C reads was carried out using the HiCExplorer suite of tools (v3.6) according to the documentation provided with the software
The valid reads were used to generate raw Hi-C matrices at different resolution using hicBuildMatrix for each sample.
The application hicPlotMatrix in HiCExplorer was used to generate the heatmaps to visualize interaction frequencies.
Assembly: hg19
Supplementary files format and content: Hi-C_library_sequencing_statistics.xlsx, Identified_chromatin_loops.xlsx, Identified_topologically_associating_domains.xlsx

source_name: Breast cancer cell line

growth_protocol: The MCF7 and doxorubicin-resistant MCF7 (MCF7-DR) cell lines originally obtained from the Cell Bank of the Type Culture Collection of the Chinese Academy of Sciences Committee (Shanghai, China), were kindly provided by the key laboratory of breast cancer in Shanghai, Fudan University. All cells were cultured in DMEM medium (KEL Biotech, China), supplemented with 2 mM L-Glutamine (Gibco, USA), 10% fetal bovine serum (KEL Biotech, China), 0.1 M sodium pyruvate (Gibco, USA), 50 units/mL penicillin and 50 µg/mL streptomycin (Sigma-Aldrich, USA). The MCF7 and MCF7-DR cells were grown in 10-cm culture dishes at 37 °C in a humidified 5% CO2 atmosphere, and the medium was renewed every 2-3 days.

extract_protocol: Three million cells were fixed with freshly made 1% formaldehyde for 10 min at room temperature for each sample. The reaction was quenched by adding 2 M glycine to a final concentration of 0.2 M for 5 min at room temperature. Fixed cells were lysed in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl and 0.2% IGEPAL CA-630 with proteinase inhibitor) for 1h at 4 °C with rotation. The supernatant was discarded and the pellet was gently resuspended in 1 × CutSmart Buffer (NEB, B7204) containing 0.1% SDS and incubated at 65°C for 10 min. Permeabilization was quenched by adding 10% Triton X-100 and incubated at 37°C for 1h. Chromatin was digested overnight at 37 °C with rotation by adding the DpnII restriction enzyme (NEB, R0543M). Digested chromatin ends were filled and marked with biotin-14-dATP (Thermo Fisher, 19524016) using a large Klenow fragment of DNA polymerase I (NEB, M0210) for 1h at 37 °C. Samples were then diluted and ligated using T4 DNA ligase (Thermo Fisher, EL0013) at 16 °C overnight. Chromatin was de-cross-linked, and proteins were removed by proteinase K, followed by phenol/chloroform extraction coupled with isopropanol precipitation using glycogen as a carrier. Biotin-14-dATP from unligated DNA ends was removed by T4 DNA polymerase (NEB, M0203) at 12 °C for 2 h. DNA was purified by phenol/chloroform and sonicated using a Covaris S220 (Covaris, USA) to approximately 300-600 bp. Biotinylated DNA fragments were then pulled down using Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher, 65001). The DNA ends were subsequently repaired and phosphorylated using T4 DNA polymerase (NEB, M0203), Klenow fragment of DNA polymerase I (NEB, M0210), and T4 Polynucleotide Kinase NK (NEB, M0201). The DNA was further prepared for sequencing using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme Biotech, ND607) and barcoded adaptors were ligated using TruePrep Index Kit V2 for Illumina (Vazyme Biotech, TD202). Each Hi-C library was indexed uniquely and amplified by 12 cycles of PCR for all samples. PCR purification and size selection was carried out using the VAHTS DNA Clean Beads (Vazyme Biotech, N411). Library quantity was assessed using a Qubit 3.0 Fluorometer (Invitrogen, USA). For each individual, the library was sequenced with 150 bp paired-end reads on the Illumina HiSeq X Ten platform.

treatment_protocol: The parental MCF7 cells were grown in a drug-free medium, resistant-derived cells were maintained in doxorubicin hydrochloride (MedChem Express, USA) at a concentration of 1 μM.

tag: cell line

value: MCF7 cell line

value: treated with 1 μM doxorubicin hydrochloride

tag: phenotype

value: doxorubicin-resistant


title: week-10_H3K4me1_rep1

description:
10weeks-1-H3K4me1_combined
processed data file: 10weeks-H3K4me1_Input_peaks.broadPeak


title: week-10_H3K27ac_rep3

description:
10weeks-3-H3K27ac_combined
processed data file: 10weeks-H3K27ac_Input_peaks.broadPeak


title: Grp8b db/db+renin+ACEI+JNJ39933673 Kidney rep4

description:
O3108
whole kidney bulk RNA-seq


title: week-10_H3K4me1_rep3

description:
10weeks-3-H3K4me1_combined
processed data file: 10weeks-H3K4me1_Input_peaks.broadPeak


title: week-10_H3K4me3_rep2

description:
10weeks-2-H3K4me3_combined
processed data file: 10weeks-H3K4me3_Input_peaks.broadPeak


title: Hi-C, MCF7, 2

value: untreated

value: parental


title: Grp8b db/db+renin+ACEI+JNJ39933673 Kidney rep1

description:
J3105
whole kidney bulk RNA-seq


title: Hi-C, MCF7, 1


title: week-10_H3K27ac_rep2

description:
10weeks-2-H3K27ac_combined
processed data file: 10weeks-H3K27ac_Input_peaks.broadPeak


title: Grp8a db/db+renin+ACEI+JNJ39933673 Kidney rep5

description:
P3104
whole kidney bulk RNA-seq

value: 2 days


title: control06_ATAC_C010-V-ctrl2

city: Heidelberg

first: Dieter

last: Weichenhan

address: Im Neuenheimer Feld

department: Cancer Epigenomics

country: Germany

institute: Deutsches Krebsforschungszentrum

description: control

data_processing:
Peak calling of processed ATAC-seq data was done using MACS2 callpeak v. 2.1.0.20140616 with q<0.05 and default parameters.
Assembly: mm10
Supplementary files format and content: tab-delimited text files

source_name: Fetal liver cells

growth_protocol: Fetal liver hematopietic cells were obtained at embryonic days 14.5 (E14.5) and maintained in liquid culture (Dulbecco's modified Eagle's medium supplemented with 18% fetal bovine serum, 10 ng/mL human interleukin [IL]-6, 6 ng/mL murine IL-3, and 100 ng/mL murine stem cell factor). All culture media and growth factors were obtained from StemCell Technologies Inc..

extract_protocol:
Cell permeabilization of native cells and tagmentation reaction with pA-Tn5 transposome-antibody complex for "Antibody-guided chromatin tagmentation (ACT-seq)" according to Carter et al (PMID: 31431618) and with a Tn5 transposome for "Assay for transposase-accessible chromatin by sequencing (ATAC-seq)" according to Corces et al. (PMID: 28846090). Tagmented DNA was either purified with MinElute (Qiagen) columns (ACTseq) according to the provider's instruction or with HighPrep beads (Biozym) after guanidinium-mediated inactivation of the transposome according to Weichenhan et al. (PMID: 29224141).
Libraries were prepared according to Weichenhan et al. PMID: 29224141). Briefly, tagmented DNA was amplified by PCR under real-time conditions using a universal Illumina forward and a barcoded reverse primer and the NEBNext High Fidelity 2x PCR Master-Mix (NEB), and amplfication was monitored by inspecting real time the amplification curves. DNA was HighPrep bead-purified, Qubit (Invitrogen) quantitated and sized by TapeStation (Agilent) profiling.

value: Fetal liver hematopietic cells E 14.5

value: Embryonic day 14.5

value: MNX1 overexpression

value: Fetal liver from C57BL/6


title: Hi-C, MCF7-DR, 2


title: tumor06_ATAC_C010-LK4-B

description: tumor

source_name: Bone marrow from mice after transplantation with fetal liver cells

value: Fetal liver from C57BL/6 transplanted to NOD.Cg-KitW-41J Tyr + Prkdcscid Il2rgtm1Wjl/ThomJ (NBSGW) mice


title: SiRNA2_PTBP1

city: Hangzhou

first: Yixuan

last: Cen

state: Zhejiang

address: No.1 Xue Shi Road, Hangzhou City, Zhejiang Province, China

institute: Women's Hospital School Of Medicine Zhejiang University

data_processing:
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Then these libraries were sequenced on the Illumina sequencing platform ( Illumina HiSeq X Ten) and 150bp paired-end reads were generated.
Raw data(raw reads)were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
Genome_build: hg19
Supplementary_files_format_and_content: differentially expressed genes of two RNA-Seqs

source_name: cervical cancer cell line (SiHa)

growth_protocol: SiHa cells were seeded in 6-well plates for further treatment.

extract_protocol:
total RNA was extracted by TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SiHa cells were transfected with si-oligo/siRNA-PTBP1 respectively. Cells were collected at 72h after transfecteion.

value: SiHa

tag: sirna

value: transfected with siRNA-PTBP1


title: control06_ATAC_C010-V-ctrl3

description: control


title: SiRNA3_PTBP1


title: week-7_Input_rep3


title: tumor06_ATAC_C010-LK2-B

description: tumor


title: tumor06_ATAC_C010-LK3-B

description: tumor


title: SiRNA1_PTBP1


title: Grp8a db/db+renin+ACEI+JNJ39933673 Kidney rep4

description:
O3103
whole kidney bulk RNA-seq

value: Kidney

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

value: female


title: siRNA3_oligo

value: transfected with siRNA-oligo


title: week-7_Input_rep2

value: Colon


title: Grp8a db/db+renin+ACEI+JNJ39933673 Kidney rep3

description:
H3102
whole kidney bulk RNA-seq

value: renin AAV + ACEI + JNJ39933673


title: Grp8a db/db+renin+ACEI+JNJ39933673 Kidney rep2

description:
G3101
whole kidney bulk RNA-seq


title: tumor06_ATAC_C010-LK1-B

description: tumor


title: week-7_Input_rep1


title: control06_ATAC_C010-Ctrl1

description: control


title: week-7_H3K9me3_rep3

description:
7weeks-3-H3K9me3_combined
processed data file: 7weeks-H3K9me3_Input_peaks.broadPeak


title: siRNA2_oligo


title: week-10_H3K27ac_rep1

description:
10weeks-1-H3K27ac_combined
processed data file: 10weeks-H3K27ac_Input_peaks.broadPeak


title: week-7_H3K9me3_rep2

description:
7weeks-2-H3K9me3_combined
processed data file: 7weeks-H3K9me3_Input_peaks.broadPeak


title: Tet2/3 DKO chimera plate 9

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23_8

value: E7.5 chimera embryo

value: mESC-derived Tet2/3 DKO cells

value: Chimera assay


title: Grp8a db/db+renin+ACEI+JNJ39933673 Kidney rep1

description:
A3100
whole kidney bulk RNA-seq

value: 2 days


title: control05_ACT_C010-V-ctrl3

description:
control
V-ctrl3_2_filt_tn5correct_peaks.broadPeak

data_processing:
Peak calling of processed H3K27me3 ACT-seq data was done using processed IgG ACT-seq data as background, MACS2 with q<0.05 and default parameters.
Assembly: mm10
Supplementary files format and content: tab-delimited text files
Library strategy: Antibody-guided chromatin tagmentation (ACT-seq)

value: Fetal liver hematopietic cells E 14.5

value: IgG

tag: antibody manufacturer

value: Millipore

tag: antibody catalog_number

value: Empty vector


title: Grp7b db/db+renin+JNJ39933673 Kidney rep4

description:
M3098
whole kidney bulk RNA-seq

value: renin AAV + JNJ39933673

value: 2 weeks


title: control05_ACT_C010-V-ctrl2

description:
control
V-ctrl2_2_filt_tn5correct_peaks.broadPeak

value: Embryonic day 14.5

value: Fetal liver from C57BL/6


title: Grp7b db/db+renin+JNJ39933673 Kidney rep2

description:
M3096
whole kidney bulk RNA-seq

value: Kidney

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous


title: tumor05_ACT_C010-LK4-B

description:
tumor
LK4-B2_filt_tn5correct_peaks.broadPeak

value: MNX1 overexpression

value: Fetal liver from C57BL/6 transplanted to NOD.Cg-KitW-41J Tyr + Prkdcscid Il2rgtm1Wjl/ThomJ (NBSGW) mice


title: siRNA1_oligo

value: SiHa

value: transfected with siRNA-oligo


title: week-7_H3K27me3_rep2

description:
7weeks-2-H3K27me3_combined
processed data file: 7weeks-H3K27me3_Input_peaks.broadPeak

value: Colon


title: control02_ACT_C010-V-ctrl2

value: Cell Signaling


title: Grp7b db/db+renin+JNJ39933673 Kidney rep1

description:
I3095
whole kidney bulk RNA-seq

value: female


title: week-7_H3K4me3_rep3

description:
7weeks-3-H3K4me3_combined
processed data file: 7weeks-H3K4me3_Input_peaks.broadPeak


title: week-7_H3K9me3_rep1

description:
7weeks-1-H3K9me3_combined
processed data file: 7weeks-H3K9me3_Input_peaks.broadPeak


title: tumor02_ACT_C010-LK3-B

description:
tumor
LK3-B2_filt_tn5correct_peaks.broadPeak

value: Fetal liver hematopietic cells E 14.5


title: tumor02_ACT_C010-LK4-B


title: Grp7b db/db+renin+JNJ39933673 Kidney rep3

description:
T3097
whole kidney bulk RNA-seq


title: Tet2/3 DKO chimera plate 5

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23_2

value: E7.5 chimera embryo

value: mESC-derived Tet2/3 DKO cells

value: Chimera assay


title: week-7_H3K27me3_rep3

description:
7weeks-3-H3K27me3_combined
processed data file: 7weeks-H3K27me3_Input_peaks.broadPeak


title: Tet2/3 DKO chimera plate 7

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23_5


title: Grp7a db/db+renin+JNJ39933673 Kidney rep4

description:
M3093
whole kidney bulk RNA-seq

value: renin AAV + JNJ39933673

value: 2 days


title: Tet2/3 DKO chimera plate 3

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23_0303_P03


title: Grp7b db/db+renin+JNJ39933673 Kidney rep5

description:
N3099
whole kidney bulk RNA-seq

value: 2 weeks


title: Grp7a db/db+renin+JNJ39933673 Kidney rep5

description:
N3094
whole kidney bulk RNA-seq


title: Tet2/3 DKO chimera plate 6

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23_4


title: tumor05_ACT_C010-LK3-B

value: Embryonic day 14.5

value: IgG

value: Millipore


title: week-7_H3K4me3_rep1

description:
7weeks-1-H3K4me3_combined
processed data file: 7weeks-H3K4me3_Input_peaks.broadPeak


title: Grp7a db/db+renin+JNJ39933673 Kidney rep3

description:
P3092
whole kidney bulk RNA-seq

value: Kidney

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous


title: Grp7a db/db+renin+JNJ39933673 Kidney rep2

description:
O3091
whole kidney bulk RNA-seq


title: tumor02_ACT_C010-LK2-B

description:
tumor
LK2-B2_filt_tn5correct_peaks.broadPeak

value: MNX1 overexpression

value: Fetal liver from C57BL/6 transplanted to NOD.Cg-KitW-41J Tyr + Prkdcscid Il2rgtm1Wjl/ThomJ (NBSGW) mice


title: Grp4b db/db+renin+ACEI Kidney rep5

description:
H3069
whole kidney bulk RNA-seq

source_name: db/db+renin+ACEI

value: renin AAV + ACEI


title: week-7_H3K4me1_rep3

description:
7weeks-3-H3K4me1_combined
processed data file: 7weeks-H3K4me1_Input_peaks.broadPeak

value: Colon


title: Grp4b db/db+renin+ACEI Kidney rep4

description:
G3068
whole kidney bulk RNA-seq

value: female


title: week-7_H3K4me1_rep1

description:
7weeks-1-H3K4me1_combined
processed data file: 7weeks-H3K4me1_Input_peaks.broadPeak


title: tumor02_ACT_C010-LK1-B

description:
tumor
LK1-B2_filt_tn5correct_peaks.broadPeak

value: Fetal liver hematopietic cells E 14.5

value: Cell Signaling


title: Tet1/3 DKO chimera plate 6

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
Tet13_0309_P03

value: E7.5 chimera embryo

value: mESC-derived Tet1/3 DKO cells


title: tumor05_ACT_C010-LK1-B


title: Tet2/3 DKO chimera plate 2

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23_0303_P02

value: mESC-derived Tet2/3 DKO cells

value: Chimera assay


title: Tet2/3 DKO chimera plate 4

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23_1


title: control02_ACT_C010-V-ctrl3

description:
control
V-ctrl3_2_filt_tn5correct_peaks.broadPeak

value: Empty vector

value: Fetal liver from C57BL/6


title: control02_ACT_C010-Ctrl1

description:
control
Ctrl1_2_filt_tn5correct_peaks.broadPeak

value: Embryonic day 14.5


title: week-7_H3K4me3_rep2

description:
7weeks-2-H3K4me3_combined
processed data file: 7weeks-H3K4me3_Input_peaks.broadPeak


title: Tet2/3 DKO chimera plate 1

description:
MARS-seq of chimera embryos injected with Tet2/3 double KO cells
Tet23_0303_P01


title: tumor05_ACT_C010-LK2-B

value: IgG

value: Millipore


title: week-7_H3K27ac_rep2

description:
7weeks-2-H3K27ac_combined
processed data file: 7weeks-H3K27ac_Input_peaks.broadPeak


title: control05_ACT_C010-Ctrl1


title: week-7_H3K27me3_rep1

description:
7weeks-1-H3K27me3_combined
processed data file: 7weeks-H3K27me3_Input_peaks.broadPeak


title: Grp7a db/db+renin+JNJ39933673 Kidney rep1

description:
G3090
whole kidney bulk RNA-seq

value: Kidney

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

value: renin AAV + JNJ39933673

value: 2 days


title: Grp4b db/db+renin+ACEI Kidney rep1

description:
I3065
whole kidney bulk RNA-seq

value: renin AAV + ACEI

value: 2 weeks


title: week-7_H3K4me1_rep2

description:
7weeks-2-H3K4me1_combined
processed data file: 7weeks-H3K4me1_Input_peaks.broadPeak

value: Colon


title: Tet1/3 DKO chimera plate 8

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
Tet13_0309_P05


title: Grp4b db/db+renin+ACEI Kidney rep3

description:
Q3067
whole kidney bulk RNA-seq

value: female


title: Tet1/3 DKO chimera plate 7

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
Tet13_0309_P04

value: E7.5 chimera embryo


title: Grp4a db/db+renin+ACEI Kidney rep4

description:
G3063
whole kidney bulk RNA-seq


title: High fat - high sugar diet_rep 1

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
Reads were preprocessed using Illumina BaseSpace.
Reads were aligned using STAR (Aligner) version 2.6.1a. Gene counts were quantified for each sample based on the number of aligned reads that match each annotated gene using RnaReadCounter tool within the BaseSpace RNA-Seq Alignment app v2.0.2 to generate Counts Per Million (CPM).
Genome_build: mm10

molecule: polyA RNA

source_name: Liver

extract_protocol:
Livers were flash frozen in liquid nitrogen, homogenized in Trizol (Invitrogen), and total RNA was isolated with the RNeasy mini kit (Qiagen). 1 µg of total RNA was used to isolate polyA RNA with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) and polyA RNA was enriched with the SMARTer Apollo NGS library prep system (Takara Bio USA, Mountain View, CA).
The library was prepared with the dUTP-based stranded library NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs).

value: Male

value: Liver

tag: diet

value: High fat + high sugar diet


title: High fat - high sugar diet_rep 2


title: week-7_H3K27ac_rep3

description:
7weeks-3-H3K27ac_combined
processed data file: 7weeks-H3K27ac_Input_peaks.broadPeak


title: Grp4b db/db+renin+ACEI Kidney rep2

description:
P3066
whole kidney bulk RNA-seq

tag: treatment


title: Grp4a db/db+renin+ACEI Kidney rep1

description:
D3060
whole kidney bulk RNA-seq


title: Tet1/2 DKO chimera plate 9

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0228_P09

value: mESC-derived Tet1/2 DKO cells

value: Chimera assay


title: Tet1/2 DKO chimera plate 14

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0303_P04


title: Tet1/3 DKO chimera plate 5

description:
MARS-seq of chimera embryos injected with Tet1/3 double KO cells
Tet13_0309_P02

value: mESC-derived Tet1/3 DKO cells


title: Grp4a db/db+renin+ACEI Kidney rep5

description:
H3064
whole kidney bulk RNA-seq


title: High fat - high sugar diet_rep 3

tag: strain


title: week-7_H3K27ac_rep1

description:
7weeks-1-H3K27ac_combined
processed data file: 7weeks-H3K27ac_Input_peaks.broadPeak

tag: time point


title: week-4_Input_rep2

tag: tissue


title: week-4_Input_rep3


title: week-4_H3K9me3_rep1

description:
4weeks-1-H3K9me3_combined
processed data file: 4weeks-H3K9me3_Input_peaks.broadPeak


title: Tet1/2 DKO chimera plate 13

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0303_P03

tag: genotype


title: Tet1/2 DKO chimera plate 12

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0303_P02

tag: developmental stage


title: week-4_Input_rep1


title: Grp4a db/db+renin+ACEI Kidney rep3

description:
J3062
whole kidney bulk RNA-seq


title: Tet1/2 DKO chimera plate 11

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0303_P01


title: Grp4a db/db+renin+ACEI Kidney rep2

description:
I3061
whole kidney bulk RNA-seq


title: Chow diet_rep 3

value: Chow diet


title: Tet1/2 DKO chimera plate 10

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0228_P10


title: week-4_H3K9me3_rep3

description:
4weeks-3-H3K9me3_combined
processed data file: 4weeks-H3K9me3_Input_peaks.broadPeak

tag: chip antibody


title: Chow diet_rep 2


title: Tet1/2 DKO chimera plate 8

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0228_P08


title: WT_2 dpf_RNAseq

city: Higashi-Hiroshima

first: Yutaka

last: Kikuchi

state: Hiroshima

address: 1-3-1, Kagamiyama

country: Japan

institute: Hiroshima University

data_processing:
The FASTQ-format sequence reads were trimmed of adaptors and low-quality bases were filtered using Trim Galore (version 0.6.4) with Cutadapt (version 1.18 or 2.10) and FastQC (version 0.11.8 or 0.11.9). After trimming, the reads were aligned to the zebrafish genome (danRer10) using HISAT2 (version 2.1.0). Alignment of datasets was performed using the strand-specific option. Aligned files (.bam) were sorted and indexed using Samtools (version 1.9). In addition, the strand-specific aligned files were generated using Samtools (version 1.9). Read coverage was normalized with 1 bin size by counts per million mapped reads (CPM) using the bamCoverage tool from the DeepTools (version 3.3.2) and visualized using the IGV (version 2.7.2).
Genome_build: danRer10
Supplementary_files_format_and_content: bigWig

source_name: 2 dpf larvae

extract_protocol:
Tissue lysates were prepared from 30 pooled 2 dpf WT and MZdnmt3aa-/- mutant larvae by homogenization using TissueLyser LT (QIAGEN) with zirconia beads for 10 s at 50 Hz. RNA was extracted from the lysate using the PureLink® RNA Mini Kit (Thermo Fisher Scientific). RNA quality of all samples was RNA Integrity Number (RIN) > 9.0, using the 4150 TapeStation System (Agilent). Total RNA was treated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) for mRNA isolation.
Strand-specific RNA-seq libraries were constructed using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (New England Biolabs). The libraries with adapters were sequenced on the Novaseq 6000 (Illumina) with 2 × 150 bp paired-end reads. RNA extraction, mRNA isolation, library preparation, and sequencing were performed by Rhelixa Inc. (Tokyo, Japan).

value: whole-body

value: 2 days post-fertilization

value: wild type


title: week-4_H3K9me3_rep2

description:
4weeks-2-H3K9me3_combined
processed data file: 4weeks-H3K9me3_Input_peaks.broadPeak


title: Grp3b db/db+renin Kidney rep4

description:
A3038
whole kidney bulk RNA-seq

source_name: db/db+renin

value: Kidney

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

value: renin AAV


title: week-4_H3K27me3_rep3

description:
4weeks-3-H3K27me3_combined
processed data file: 4weeks-H3K27me3_Input_peaks.broadPeak


title: Tet1/2 DKO chimera plate 7

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0228_P07


title: Grp3b db/db+renin Kidney rep5

description:
B3039
whole kidney bulk RNA-seq

value: 2 weeks


title: Chow diet_rep 1


title: Grp3b db/db+renin Kidney rep2

description:
J3036
whole kidney bulk RNA-seq


title: ATAC-seq, 16hr, R2

city: Brookline

first: Sylvan

middle: C

last: Baca

state: MA

address: 450 Brookline Ave

institute: Dana–Farber Cancer Institute, Dana-704

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA for ATAC-seq and ChIP-seq data, and STAR for RNAseq data
bigwig files represent normalized read counts in treatment conditions
Assembly: hg19
Supplementary files format and content: bigwig (normalized read pileup)

source_name: LNCaP

growth_protocol: LNCaP cells (ATCC CRL-1740) were cultured in phenol red free RPMI (#11835030, Gibco) with 10% charcoal stripped FBS (#100-119, Gembio) for 3 days

extract_protocol: ATAC seq libraries were prepared using Omni-ATAC protocol

treatment_protocol: After 3 days, cells were stimulated with either 10 nM DHT (5α-Androstan-17β-ol-3-one, Dihydrotestosterone, A8380, Sigma) or EtOH (Vehicle) for 16 hours.

value: LNCaP

value: DHT


title: week-4_H3K27me3_rep1

description:
4weeks-1-H3K27me3_combined
processed data file: 4weeks-H3K27me3_Input_peaks.broadPeak

value: Colon


title: Tet1/2 DKO chimera plate 5

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0228_P05

value: E7.5 chimera embryo


title: Grp3b db/db+renin Kidney rep3

description:
K3037
whole kidney bulk RNA-seq

value: female


title: Tet1/2 DKO chimera plate 4

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0228_P04


title: MZdnmt3aa_2 dpf_RNAseq

value: maternal-zygotic dnmt3aa-/-


title: week-4_H3K27me3_rep2

description:
4weeks-2-H3K27me3_combined
processed data file: 4weeks-H3K27me3_Input_peaks.broadPeak


title: ATAC-seq, veh, R2

value: control


title: week-4_H3K4me3_rep3

description:
4weeks-3-H3K4me3_combined
processed data file: 4weeks-H3K4me3_Input_peaks.broadPeak


title: ATAC-seq, 16hr, R1


title: week-4_H3K4me3_rep2

description:
4weeks-2-H3K4me3_combined
processed data file: 4weeks-H3K4me3_Input_peaks.broadPeak


title: Tet1/2 DKO chimera plate 3

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0228_P03

value: mESC-derived Tet1/2 DKO cells

value: Chimera assay


title: Tet1/2 DKO chimera plate 6

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0228_P06


title: week-4_H3K4me3_rep1

description:
4weeks-1-H3K4me3_combined
processed data file: 4weeks-H3K4me3_Input_peaks.broadPeak


title: week-4_H3K4me1_rep3

description:
4weeks-3-H3K4me1_combined
processed data file: 4weeks-H3K4me1_Input_peaks.broadPeak


title: Grp3a db/db+renin Kidney rep3

description:
D3032
whole kidney bulk RNA-seq

value: 2 days


title: Tet1/2 DKO chimera plate 1

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0228_P01


title: Grp3a db/db+renin Kidney rep5

description:
B3034
whole kidney bulk RNA-seq


title: week-4_H3K4me1_rep2

description:
4weeks-2-H3K4me1_combined
processed data file: 4weeks-H3K4me1_Input_peaks.broadPeak


title: H3K27ac ChIP-seq, veh, R3

extract_protocol: Ten million cells were fixed with 1 % formaldehyde at room temperature for 10 minutes and quenched with 0.25M glycine, Harvested cells in lysis buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS and protease inhibitor (#11873580001, Roche) in PBS) were sheared to 300–800 bp chromatin using a Covaris E220 sonicator (140 watt peak incident power, 5% duty cycle, 200 cycleburtst). Sonicated chromatin was subjected to H3K27ac antibody (C15410196, Diagenode) coupled with Dynabeads protein A/G (Life Technology  # 10001D, 10003D) overnight at 4 °C. Chromatin was washed in LiCl wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) 6 times for 10 minutes sequentially. Immuno-precipitated chromatin and input were treated with RNase A at 37 °C for 30 minutes and decrosslinked in elution buffer (1% SDS, 0.1 M NaHCO3) with proteinase K for 6–12 hours at 65 °C with gentle rocking. DNA was purified using Qiagen Qiaquick columns (#28104). Libraries were prepared using SMARTer ThruPLEX DNA-Seq Kit (Takara Bio # R400675)

value: H3K27ac (C15410196, Diagenode)


title: Grp3b db/db+renin Kidney rep1

description:
B3035
whole kidney bulk RNA-seq


title: Grp3a db/db+renin Kidney rep4

description:
A3033
whole kidney bulk RNA-seq


title: H3K27ac ChIP-seq, 16hr, R3


title: Grp2 db/db+PBS Kidney rep4

description:
B3027
whole kidney bulk RNA-seq

source_name: db/db+PBS

value: PBS


title: SA1556_TUMOR_custom_NA

city: Sacramento

first: Robert

middle: J

last: Canter

state: CA

address: 4645 2nd Ave, Research III, Room 2200D

department: Surgery

institute: University of California, Davis

data_processing:
Read Count with DGEList (Edge R)
Preprocessing and normalization factors in EdgeR/limma
Log transformed normalized expression with CPM function
Voom transformation and calculation of variance weights, filtering linear models in limma
Assembly: GRCh 38
Supplementary files format and content: Excel file

source_name: UPS, tumor

extract_protocol:
The collection of matched whole blood and tumor specimens was approved by the IRB at the University of California, Davis. Human peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using a density gradient centrifugation, followed by red blood cell lysis. Tumor tissue from patients undergoing STS resection was collected in sterile RPMI-1640, diluted with PBS and passed through a 70 µm filter, and then subjected to red blood cell lysis. Human cells were washed with PBS and staining buffer, and then incubated with Fc receptor blocking solution for 15 minutes. Cells were stained with the following fluorochrome-conjugated monoclonal antibodies: CD3-FITC, CD56-PE, CD45-BV510 and CD8-BV785. Live/dead staining was performed using Fixable Viability Dye 780. Data were acquired using a BD LSRFortessa flow cytometer and analyzed using FlowJo Software. Fluorescence-associated cell sorting (FACS) was performed using a BD inFlux cell sorter. Cells were sorted for blood and intra-tumoral NK cells (live CD45+CD3-CD56+), blood and intra-tumoral T cells (live CD45+CD3+CD56-), and tumor cells (live CD45-). Following FACS isolation, cells were cryopreserved and stored in liquid nitrogen for subsequent RNA extraction and sequencing. Cells were processed for RNA isolation using the Total RNA Purification Plus Micro Kit.
RNAseq libraries were prepared by the University of California, Davis, Bioinformatics Core. Gene expression profiling was carried out using a 3'-Tag-RNA-Seq protocol. Up to forty-eight libraries were sequenced per lane on an Illumina HiSeq 4000 sequencer with single-end 100 base pair reads. Differential gene expression analysis was performed with the DESeq2 package for R. The Benjamini-Hochberg procedure was used to adjust for False Discovery Rate (FDR).

value: tumor

value: tissue

tag: cell type

value: Tumor

tag: disease state

value: UPS


title: Tet1/2 DKO chimera plate 2

description:
MARS-seq of chimera embryos injected with Tet1/2 double KO cells
Tet12_0228_P02


title: Whole-embryo control plate 10

description:
MARS-seq of tetraploid complemented embryos injected with control cells
0217_P04

source_name: E7.5 whole embryo

value: E7.5 whole embryo

value: mESC-derived Control cells

value: Tetraploid complementation assay


title: Grp3a db/db+renin Kidney rep1

description:
I3030
whole kidney bulk RNA-seq

value: Kidney

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

tag: Sex

value: renin AAV


title: H3K27ac ChIP-seq, 16hr, R2

value: LNCaP

value: DHT


title: week-4_H3K27ac_rep2

description:
4weeks-2-H3K27ac_combined
processed data file: 4weeks-H3K27ac_Input_peaks.broadPeak

value: Colon


title: Grp3a db/db+renin Kidney rep2

description:
C3031
whole kidney bulk RNA-seq

value: female

tag: treatment timepoint


title: Whole-embryo control plate 14

description:
MARS-seq of tetraploid complemented embryos injected with control cells
191125_P07


title: SA1556_TUMOR_NK_custom_NA

source_name: UPS, tumor NK

tag: cell line

value: NK cells


title: SA1556_TUMOR_T_custom_NA

source_name: UPS, tumor T

value: T cells


title: ATAC-seq, veh, R1

value: control


title: Whole-embryo control plate 11

description:
MARS-seq of tetraploid complemented embryos injected with control cells
0217_P05


title: Grp2 db/db+PBS Kidney rep5

description:
C3028
whole kidney bulk RNA-seq

value: PBS

value: 2 days


title: SA1556_BLOOD_T_custom_NA

source_name: UPS, peripheral T

value: peripheral blood

value: tissue


title: Whole-embryo control plate 7

description:
MARS-seq of tetraploid complemented embryos injected with control cells
0217_P01

value: E7.5 whole embryo


title: Whole-embryo control plate 9

description:
MARS-seq of tetraploid complemented embryos injected with control cells
0217_P03

value: mESC-derived Control cells


title: week-4_H3K27ac_rep1

description:
4weeks-1-H3K27ac_combined
processed data file: 4weeks-H3K27ac_Input_peaks.broadPeak


title: Whole-embryo control plate 12

description:
MARS-seq of tetraploid complemented embryos injected with control cells
191125_P05

value: Tetraploid complementation assay


title: week-4_H3K4me1_rep1

description:
4weeks-1-H3K4me1_combined
processed data file: 4weeks-H3K4me1_Input_peaks.broadPeak


title: Grp2 db/db+PBS Kidney rep2

description:
B3025
whole kidney bulk RNA-seq

value: Kidney


title: week-2_Input_rep2


title: SA1556_BLOOD_NK_custom_NA

source_name: UPS, peripheral NK

value: UPS


title: week-4_H3K27ac_rep3

description:
4weeks-3-H3K27ac_combined
processed data file: 4weeks-H3K27ac_Input_peaks.broadPeak


title: Grp1 db/m+PBS Kidney rep4

description:
G3022
whole kidney bulk RNA-seq

source_name: db/m+PBS

value: BKS.Cg-Dock7m +/- Leprdb/J Leprdb- heterozygous


title: Whole-embryo control plate 6

description:
MARS-seq of tetraploid complemented embryos injected with control cells
190916_P06


title: Grp2 db/db+PBS Kidney rep1

description:
N3024
whole kidney bulk RNA-seq

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous


title: H3K27ac ChIP-seq, veh, R2

value: LNCaP

value: H3K27ac (C15410196, Diagenode)


title: X011_TUMOR_custom_NA

source_name: Myxofibrosarcoma, tumor

value: tumor

value: Tumor

value: Myxofibrosarcoma


title: week-2_Input_rep3

value: Colon


title: week-2_Input_rep1


title: Grp1 db/m+PBS Kidney rep5

description:
H3023
whole kidney bulk RNA-seq

value: female

value: PBS


title: Grp1 db/m+PBS Kidney rep3

description:
F3021
whole kidney bulk RNA-seq

value: 2 days


title: Grp2 db/db+PBS Kidney rep3

description:
A3026
whole kidney bulk RNA-seq


title: Whole-embryo control plate 4

description:
MARS-seq of tetraploid complemented embryos injected with control cells
190916_P04


title: Grp1 db/m+PBS Kidney rep2

description:
A3020
whole kidney bulk RNA-seq


title: Whole-embryo control plate 8

description:
MARS-seq of tetraploid complemented embryos injected with control cells
0217_P02


title: X011_TUMOR_NK_custom_NA

source_name: Myxofibrosarcoma, tumor NK

value: tissue

value: NK cells


title: Whole-embryo control plate 3

description:
MARS-seq of tetraploid complemented embryos injected with control cells
190916_P03

value: E7.5 whole embryo

value: mESC-derived Control cells


title: Whole-embryo control plate 2

description:
MARS-seq of tetraploid complemented embryos injected with control cells
190916_P02

value: Tetraploid complementation assay


title: Whole-embryo control plate 5

description:
MARS-seq of tetraploid complemented embryos injected with control cells
190916_P05


title: LLC1.1.5Days.EP2iEP4i3

city: Kyoto

first: Shuh

last: Narumiya

state: Kyoto

address: Yoshidahonmachi

department: Department of Drug Discovery Medicine

institute: Kyoto University

data_processing:
Illumina Novaseq6000 used for basecalling
CellRanger software package used for alignment, filtering, barcode reading.
Remove ambient mRNA using decontx in celda package (S Yang, 2020)
Data integration and normalization using Seurat package (Stuart, Butler, et al., Cell, 2019)
Genome_build: mm10
Supplementary_files_format_and_content: ExpressionMatrix.csv files are generated from normalized count of RNA assays in seurat object class.
Supplementary_files_format_and_content: Metadata files indicate cell identity from downstream analysis

source_name: CD45+ tumor-infiltrating immune cells

growth_protocol: Mice were shaved on their right flank and injected with 3x10^5 cells/100 ul of the Lewis Lung Carcinoma line 1 (LLC1) tumor cells.

extract_protocol:
Tumor tissues were harvested and enzymatically digested with the mouse tumor dissociation kit (Miltenyi) and the subjected to agitation and rotation at 37℃ according the manufacturer’s protocol. Cell suspensions were then filtered through a 70 μm filter (Falcon) and wash with FACS buffer containing 1% BSA (Sigma). For scRNAseq experiment of EP2/4 antagonists treated mice, live CD45+ cells were sorted from the dissected LLC1 tumor using BD FACS Aria3. Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet.
library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kits v3.1 User Guide Rev C

treatment_protocol: Mice were orally administered EP2 and EP4 antagonists treatment for 1.5 days when tumor size reached 20~30 mm3 (day 10 or 11 after transplanted with LLC1 tumor cells)

tag: age

value: post natal 6week

value: wild type

value: treated with EP2/EP4 antagonists for 1.5 days


title: week-2_H3K9me3_rep1

description:
2weeks-1-H3K9me3_combined
processed data file: 2weeks-H3K9me3_Input_peaks.broadPeak


title: CCS24011_BLOOD_NK_custom_NA

source_name: Myxofibrosarcoma, peripheral NK

value: peripheral blood


title: week-2_H3K9me3_rep2

description:
2weeks-2-H3K9me3_combined
processed data file: 2weeks-H3K9me3_Input_peaks.broadPeak


title: Grp1 db/m+PBS Kidney rep1

description:
E3019
whole kidney bulk RNA-seq

value: Kidney

value: BKS.Cg-Dock7m +/- Leprdb/J Leprdb- heterozygous


title: week-2_H3K27me3_rep3

description:
2weeks-3-H3K27me3_combined
processed data file: 2weeks-H3K27me3_Input_peaks.broadPeak


title: week-2_H3K9me3_rep3

description:
2weeks-3-H3K9me3_combined
processed data file: 2weeks-H3K9me3_Input_peaks.broadPeak


title: X003_TUMOR_custom_NA

source_name: Liposarcoma, tumor

value: tumor

value: Tumor

value: Liposarcoma


title: X011_TUMOR_T_custom_NA

source_name: Myxofibrosarcoma, tumor T

value: T cells

value: Myxofibrosarcoma


title: Whole-embryo control plate 1

description:
MARS-seq of tetraploid complemented embryos injected with control cells
190916_P01


title: week-2_H3K27me3_rep1

description:
2weeks-1-H3K27me3_combined
processed data file: 2weeks-H3K27me3_Input_peaks.broadPeak

value: Colon


title: Whole-embryo Tet TKO and control plate 3

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells or control cells
190916_P09

source_name: E7.5 - E9.5 whole embryo

value: E7.5 - E9.5 whole embryo

value: mESC-derived Tet TKO cells and mESC-derived Control cells


title: X003_TUMOR_T_custom_NA

source_name: Liposarcoma, tumor T

value: tissue


title: LLC1.1.5Days.EP2iEP4i2


title: week-2_H3K27me3_rep2

description:
2weeks-2-H3K27me3_combined
processed data file: 2weeks-H3K27me3_Input_peaks.broadPeak


title: LLC1.1.5Days.Control3

value: untreated


title: week-2_H3K4me3_rep3

description:
2weeks-3-H3K4me3_combined
processed data file: 2weeks-H3K4me3_Input_peaks.broadPeak


title: Whole-embryo Tet TKO plate 25

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
190916_P08

value: mESC-derived Tet TKO cells

value: Tetraploid complementation assay


title: LLC1.1.5Days.EP2iEP4i1

value: post natal 6week

value: wild type


title: CCS24011_BLOOD_T_custom_NA

source_name: Myxofibrosarcoma, peripheral T

value: peripheral blood


title: X003_TUMOR_NK_custom_NA

source_name: Liposarcoma, tumor NK

value: NK cells


title: LLC1.1.5Days.Control2


title: week-2_H3K4me3_rep2

description:
2weeks-2-H3K4me3_combined
processed data file: 2weeks-H3K4me3_Input_peaks.broadPeak


title: Whole-embryo Tet TKO and control plate 2

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells or control cells
190916_P07


title: Whole-embryo Tet TKO plate 23

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
190819_P04


title: CCS24003_BLOOD_NK_custom_NA

source_name: Liposarcoma, peripheral NK


title: CCS24003_BLOOD_T_custom_NA

source_name: Liposarcoma, peripheral T


title: LLC1.1.5Days.Control1


title: week-2_H3K4me3_rep1

description:
2weeks-1-H3K4me3_combined
processed data file: 2weeks-H3K4me3_Input_peaks.broadPeak


title: week-2_H3K4me1_rep3

description:
2weeks-3-H3K4me1_combined
processed data file: 2weeks-H3K4me1_Input_peaks.broadPeak


title: X002_TUMOR_custom_NA


title: Whole-embryo Tet TKO plate 22

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
190819_P03


title: Whole-embryo Tet TKO plate 21

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
190819_P02


title: X002_TUMOR_T_custom_NA


title: week-2_H3K4me1_rep2

description:
2weeks-2-H3K4me1_combined
processed data file: 2weeks-H3K4me1_Input_peaks.broadPeak


title: Grp8b db/db+renin+ACEI+JNJ39933673 rep4

description:
snRNA-seq using 10X Chromium
O3108

data_processing:
Illumina data were demultiplexed and the resulting fastq files were processed by the 10X Genomics cellranger pipeline (version 6.0.1). Reads were mapped to mouse genome mm10. Both exonic and intronic reads were incorporated in the final molecule counts.
We used CellBender to remove the ambient RNA contamination. In brief, the unfiltered count matrices sampleID.h5 from cellranger were input into CellBender. CellBender remove-background was run (on cuda mode) with parameters “expected-cells” and “total-droplets-included” were chosen for each dataset based on the total UMI per cell vs. cell barcode curve in accordance with CellBender documentation. Other parameters were left at their default values. The CellBender corrected count matrices were then input to DoubletFinder to remove the potential doublets. We used default parameters to run DoubletFinder except for the nExp, which is estimated based on the total cell number of the sample (nNuc) and a linear regression equation derived from the Demuxlet study, i.e. nExp = nNuc * (0.018+8.4e-06* nNuc).
Genome_build: mm10
Supplementary_files_format_and_content: The hdf5 files contain the count matrix generated by CellRanger for each sample. The count_matrix_combined_after_cellbender.tar.gz file contains the gene-by-cell count matrix for all cells combined after data QC. The metadata.csv file is the meta data (e.g. cell type annotation, mouseID, group ID and the UMAP coordinates) for all high-quality cells included in the analysis.

extract_protocol:
Single nucleus were isolated using a protocol developed from our lab (dx.doi.org/10.17504/protocols.io.nahdab6).
Single nucleus suspensions at a concentration of 1000 nuclei/ul were loaded into the Chromium Controller as per manufacturer instructions, which target 10,000 nuclei per sample. 12 PCR cycles were used for cDNA synthesis. Each library was sequenced using an Illumina NovaSeq instrument, 8 samples per S4 lane, with one 150 bp read located near the 3′ end of the mRNA.
10x chromium 3' kit version 3 chemistry

treatment_protocol:
To establish the model, female db/db mice (BKS.Cg-Dock7m +/+ Leprdb/J from Jackson, BKS background, Lot 642) were subject to left nephrectomy at 5 weeks of age and, at 12 weeks, infected with a renin expressing adeno-associated virus (ReninAAV, 109 genomic copies) to induce hypertension and accelerate disease progression. In addition to the ReninAAV Unx db/db mice, db/m and Unx db/db mice infected with an empty viral vector (LacZ AAV) were included as healthy and diabetic non-hypertensive controls, respectively.
Drug treatments were given to mice as follows:   1. Vehicle (drinking water)  2. Lisinopril (An ACE inhibitor, 10 mg/kg/d in the drinking water),    3. Rosiglitazone (A PPARꙋ activator, 0.007% w/w via admix diet, p.o. ~10 mg/kg/d)  4. JNJ-39933673 (A SGLT2 inhibitor, 0.0075% w/w via admix diet, p.o. 1 ~ mg/kg/d)  5. ACEi plus SGLT2i (dosed as before).   6. ACEi plus rosiglitazone (dosed as before). Terminal samples were collected 48 hours and 2 weeks after treatment inception

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

value: female

value: renin AAV + ACEI + JNJ39933673

value: 2 weeks


title: week-2_H3K4me1_rep1

description:
2weeks-1-H3K4me1_combined
processed data file: 2weeks-H3K4me1_Input_peaks.broadPeak


title: Whole-embryo Tet TKO and control plate 1

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells or control cells
190819_P01


title: Grp8b db/db+renin+ACEI+JNJ39933673 rep5

description:
snRNA-seq using 10X Chromium
P3109


title: CCS24002_BLOOD_T_custom_NA

value: T cells


title: X002_TUMOR_NK_custom_NA

value: tumor

value: Myxofibrosarcoma


title: Grp8b db/db+renin+ACEI+JNJ39933673 rep3

description:
snRNA-seq using 10X Chromium
V3107


title: Whole-embryo Tet TKO plate 7

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
191125_P03

value: E7.5 - E9.5 whole embryo


title: week-2_H3K27ac_rep3

description:
2weeks-3-H3K27ac_combined
processed data file: 2weeks-H3K27ac_Input_peaks.broadPeak

value: Colon


title: CCS24002_BLOOD_NK_custom_NA

value: tissue


title: week-2_H3K27ac_rep2

description:
2weeks-2-H3K27ac_combined
processed data file: 2weeks-H3K27ac_Input_peaks.broadPeak


title: Grp8a db/db+renin+ACEI+JNJ39933673 rep5

description:
snRNA-seq using 10X Chromium
P3104

value: 2 days


title: transplanted cells derived from CLSTN2 sorted progenitors, 4 months, scRNAseq

first: Yuejun

last: Chen

state: Shanghai

address: 320 Yueyang Road

institute: Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences

description: 10x Genomics

data_processing:
scRNA-seq data were aligned with the human reference genome, GRCh38-3.0.0, and demultiplexed using the default parameters of Cellranger software (10x Genomics, v3.0.2 or v4.0.0). Obtained filtered count matrix was used for downstream analysis.The filtered count matrix was analyzed and processed using Seurat (v3.1.4) and Scanpy (v3.0.46), including data filtering, normalization, highly variable genes selection, scaling, dimension reduction, and clustering.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For in vitro differentiated samples, attached colonies (day 8-stage I) or neurospheres (day 14-stage II, day 21- stage III, day 28-stage IV, day 35-stage V) were digested using TrypLE Express Enzyme for 10 minutes at 37°C and washed twice with neural induction medium. Cells were then passed through a 35-μm cell sieve (BD) to obtain a single-cell suspension.   For graft sampels, scRNA-seq of graft samples using the 10x genomics chromium platform. 3-month-old PD mice received striatal injections of mDA progenitors derived from surface marker- tdT/AAVS1-CAG-EGFPnls-WPRE-polyA or AAVS1-CAG-EGFPnls-WPRE-polyA cell lines. Four months after transplantation, mice were deeply anesthetized, followed by transcardial perfusion with ice-cold oxygenated artificial cerebrospinal fluid (aCSF, in mM: 124 NaCl, 2.5 KCl, 1 NaH2PO4, 25 NaHCO3, 37 glucose, 2 CaCl2, 2 MgSO4). The brain was removed, 200 μm vibratome sections were collected, and the graft (most in the striatum) was microdissected under a stereo fluorescence microscope with a cooled platform. The graft pieces were dissociated using a self-made ice-cold oxygenated dissection medium (DM, in mM: 81.76 Na2SO4, 120 K2SO4, 5.8 MgCl2, 25.2 CaCl2, 1 HEPES, 20 glucose, 20 NaOH) that contained 20 units/ml papain (Worthington), 1.1 mM EDTA, 0.067 mM 2-mercaptoethanol, 5.5 mM cysteine-HCl (Sigma), and 100 units/ml DNase I (Thermo Scientific), with 30-40 minutes enzymatic digestion, followed by manual trituration using fire-polished Pasteur pipettes and filtering through a 35 μm DM-equilibrated cell strainer. Cells were then pelleted at 400g for 5 minutes. The supernatant was carefully removed. Cells were resuspended in 1-2 ml DM containing 2.5% Certified Fetal Bovine Serum (FBS, Biological Industries). Then, the debris was removed from the cell suspension using Debris Removal Solution (MiltenyiBiotec). Cell pellets were then resuspended in 200-400 μl DM containing 2.5% FBS for cell sorting, with the goal of enriching for EGFPnls-positive human cells for grafting.
For in vitro differentiated samples, Chromium Single Cell 3' Reagent Kits (v2) were used for library preparation (10X Genomics).   For graft samples, Chromium Single Cell 3' Reagent Kits (v3) were used for library preparation (10X Genomics). Libraries were sequenced on an Illumina Novaseq 6000.

value: transplanted cells derived from neural progenitors

value: 4plus1 months


title: Whole-embryo Tet TKO plate 4

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
TKO26_tetra_191111_P04

value: mESC-derived Tet TKO cells

value: Tetraploid complementation assay


title: Grp8b db/db+renin+ACEI+JNJ39933673 rep2

description:
snRNA-seq using 10X Chromium
U3106


title: week-2_H3K27ac_rep1

description:
2weeks-1-H3K27ac_combined
processed data file: 2weeks-H3K27ac_Input_peaks.broadPeak


title: Whole-embryo Tet TKO plate 6

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
191125_P02


title: Grp8b db/db+renin+ACEI+JNJ39933673 rep1

description:
snRNA-seq using 10X Chromium
J3105


title: week-0_Input_rep3


title: Grp8a db/db+renin+ACEI+JNJ39933673 rep4

description:
snRNA-seq using 10X Chromium
O3103


title: week-0_Input_rep2


title: Whole-embryo Tet TKO plate 3

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
TKO26_tetra_191111_P03


title: transplanted cells derived from PTPRO sorted progenitors, 4 months, scRNAseq

description: 10x Genomics


title: Whole-embryo Tet TKO and control plate 4

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells or control cells
191125_P04

value: mESC-derived Tet TKO cells and mESC-derived Control cells


title: Whole-embryo Tet TKO plate 2

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
TKO26_tetra_191111_P02


title: transplanted cells derived from unsorted progenitors, batch 2, 4 months, scRNAseq

description: 10x Genomics


title: transplanted cells derived from unsorted progenitors, batch 1, 4 months, scRNAseq

description: 10x Genomics


title: Whole-embryo Tet TKO plate 1

description:
MARS-seq of tetraploid complemented embryos injected with Tet1/2/3 triple KO cells
TKO26_tetra_191111_P01_NOVAseq


title: Grp8a db/db+renin+ACEI+JNJ39933673 rep3

description:
snRNA-seq using 10X Chromium
H3102


title: week-0_Input_rep1


title: Grp8a db/db+renin+ACEI+JNJ39933673 rep2

description:
snRNA-seq using 10X Chromium
G3101


title: stage V, day 35, scRNAseq

description: 10x Genomics

value: H9-derive neural progenitors

value: WT

value: day 35


title: Grp8a db/db+renin+ACEI+JNJ39933673 rep1

description:
snRNA-seq using 10X Chromium
A3100

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

value: female

value: renin AAV + ACEI + JNJ39933673


title: week-0_H3K9me3_rep3

description:
ctrl-3-H3K9me3_combined
processed data file: ctrl-H3K9me3_Input_peaks.broadPeak


title: week-0_H3K9me3_rep2

description:
ctrl-2-H3K9me3_combined
processed data file: ctrl-H3K9me3_Input_peaks.broadPeak


title: Tet TKO chimera plate 64

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
191108_P08

source_name: E7.5 chimera embryo

value: E7.5 chimera embryo

value: Host cells and injected mESC-derived Control and Tet TKO cells

value: Chimera assay


title: stage IV, day 28, scRNAseq

description: 10x Genomics

value: day 28


title: Tet TKO chimera plate 63

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
191108_P07


title: Grp7b db/db+renin+JNJ39933673 rep5

description:
snRNA-seq using 10X Chromium
N3099

value: renin AAV + JNJ39933673

value: 2 weeks


title: stage III, day 21, scRNAseq

description: 10x Genomics

value: day 21


title: Grp7b db/db+renin+JNJ39933673 rep4

description:
snRNA-seq using 10X Chromium
M3098


title: week-0_H3K27me3_rep3

description:
ctrl-3-H3K27me3_combined
processed data file: ctrl-H3K27me3_Input_peaks.broadPeak

value: Colon


title: Tet TKO chimera plate 62

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
191108_P06


title: Grp7b db/db+renin+JNJ39933673 rep3

description:
snRNA-seq using 10X Chromium
T3097


title: stage II, day 14, scRNAseq

description: 10x Genomics

value: day 14


title: Tet TKO chimera plate 61

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
191108_P05


title: week-0_H3K27me3_rep1

description:
ctrl-1-H3K27me3_combined
processed data file: ctrl-H3K27me3_Input_peaks.broadPeak


title: stage I, day 8, scRNAseq

description: 10x Genomics

value: day 8


title: Grp7b db/db+renin+JNJ39933673 rep2

description:
snRNA-seq using 10X Chromium
M3096


title: week-0_H3K27me3_rep2

description:
ctrl-2-H3K27me3_combined
processed data file: ctrl-H3K27me3_Input_peaks.broadPeak


title: Tet TKO chimera plate 60

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
191108_P04


title: Tet TKO chimera plate 59

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
191108_P03


title: LMX1A-EN1-double-positive cells, batch3, Day27

data_processing:
Clean sequencing reads were mapped to the UCSC human GRCh38 genome with HISAT2 software (v2.1.0).
Bam files were generated using Samtools (v1.7).
Reads were counted by the ‘summarizeOverlaps’ function in the GenomicFeatures R package (v1.38.2) and a RangedSummarizedExperiment object was obtained.
RangedSummarizedExperiment object was processed by DeSeq2 (v1.26.0).
Differential expression analysis was performed using the ‘glmTreat’ function in edgeR R package (v3.28.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Cells were pelleted at 400 g for 5 min and lysed with TRIzol (Thermo Scientific).
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) and index codes were added to attribute sequences to each sample.

value: midbrain dopamine neuron-directed differentiation

tag: time

value: Day 27


title: Grp7a db/db+renin+JNJ39933673 rep5

description:
snRNA-seq using 10X Chromium
N3094

value: 2 days


title: Tet TKO chimera plate 58

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
191108_P02


title: LMX1A-EN1-double-positive cells, batch2, Day27

value: H9-derive neural progenitors


title: Grp7b db/db+renin+JNJ39933673 rep1

description:
snRNA-seq using 10X Chromium
I3095

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous


title: week-0_H3K4me3_rep2

description:
ctrl-2-H3K4me3_combined
processed data file: ctrl-H3K4me3_Input_peaks.broadPeak

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
ChIP-seq clean data were obtained by removing adaptor from raw fastq with Cutadapt (version 1.16, http://cutadapt.readthedocs.io/en/stable/guide.html, parameters were “-u 4 -u 35 -U 4 -U 35 -m 30”)
Cleaned reads were aligned in paired-end mode to mouse reference genome mm10 with BWA mem (version 0.7.15, http://bio-bwa.sourceforge.net )
Duplicate reads were removed by Picard MarkDuplicate (http://picard.sourceforge.net/). Only unique mapped reads were used in following work.
Peaks were called by MACS2 (version 2.1.1, https://github.com/taoliu/MACS, with parameters “--nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147” ) at false discovery rate (FDR) < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

extract_protocol:
DNA were clarified from nuclei treated with micrococcal nuclease and histone-DNA complexes were isolated with antibody. Briefly, around 30 milligrams of each tissue were cut into 1 mm3 pieces in PBS with protease inhibitor. Tissue pieces were cross-linked for 10min at room temperature with 1% formaldehyde and then quenched with 0.125 M of glycine for 5 min. Cross-linked tissues were triturated in tissue grinding instrument for 60s at 60 Hz, and then centrifuged at 12000 rpm, 4 °C for 10 min. Supernatant with massive oil was discarded and the precipitates were lysed with 1 mL lysis buffer (50 mM Tris-HCl pH 8.0, 0.1% SDS, 5 mM EDTA) for 4 min with gentle rotation. After centrifugation at 12000 rpm, 4 °C for 2 min, the pellet was washed once with digestion buffer (50 mM Tris-HCl pH8.0, 1 mM CaCl2, 0.2% Triton X-100), incubated in 630-μL digestion buffer with 1 μL MNase (NEB, M0247S) at 37°C for 20min and quenched with 8 μL 0.5M EDTA. The resulted mixture was sonicated and the pellet was discarded after centrifugation. 30 μL supernatant was taken for checking the efficiency of digestion. Immunoprecipitation was performed with 150 μL sheared chromatin, 2 μg antibody, 50 μL Protein G beads and 800 μL dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) overnight at 4 °C. Next day, the beads were washed once with Wash buffer I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with Wash buffer II (20mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with Wash buffer III (10mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Na-deoxycholate, 1% NP-40) and twice with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The beads were eluted twice with 100 μL elution buffer (1% SDS, 0.1M NaHCO3, 20mg/mL Proteinase K) at room temperature. The elution was incubated at 65 °C for 6 h and then purified with DNA purification kit (TIANGEN DP214-03).
ChIP-seq libraries were constructed with ChIP and input DNA using VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606). Briefly, 10 ng DNA was end-repaired for dA tailing, followed by adaptor ligation. Each adaptor was marked with a barcode of 8 bp DNA. Adaptor-ligated DNA was purified by AMPure XP beads (1:1) and then amplified by PCR of 10 cycles with the primer matching with adaptor universal part. Amplified DNA was purified again using AMPure XP beads (1:1) in 35 μL EB elution buffer. For multiplexing, libraries with different barcode were mixed with equal molar quantities (30-50 million reads per library). Libraries were sequenced by Illumina Nova-seq platform with pair-end reads of 150 bp.


title: week-0_H3K4me3_rep3

description:
ctrl-3-H3K4me3_combined
processed data file: ctrl-H3K4me3_Input_peaks.broadPeak


title: LMX1A-EN1-double-positive cells, batch1, Day27


title: Grp7a db/db+renin+JNJ39933673 rep4

description:
snRNA-seq using 10X Chromium
M3093

value: female


title: week-0_H3K9me3_rep1

description:
ctrl-1-H3K9me3_combined
processed data file: ctrl-H3K9me3_Input_peaks.broadPeak


title: week-0_H3K4me3_rep1

description:
ctrl-1-H3K4me3_combined
processed data file: ctrl-H3K4me3_Input_peaks.broadPeak


title: Tet TKO chimera plate 57

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
191108_P01

data_processing:
MARS-seq data was processed as detailed in the MARS-seq2.0 protocol (Keren-Shaul et al. 2019):
1. bcl2fastq/2.15.0.4
2. Pool_barcode (4 bps) and well_barcode (7 bps) plus UMI barcode (8 bps) were removed from Read 1 and Read 2 (respectively) and concatenated to the fastq header.
3. Read 1 sequences were mapped to the mm9 genome using bowtie2.
4. Demultiplexing and construction of mRNA count matrix were based on 4bp plate barcode, 7bp well barcode and 8bp UMI barcode
5. Header structure of labeled Read 1 fastq files: "ORIGINALHEADER_barcode=similar_oligo-pool_barcode_quality-well_barcode_quality-UMI_quality-pool_barcode-well_barcode-UMI". Concatenated entries are separated by "-"
6. well_barcode (7bp), pool_barcode (4bp) and external_barcode (8bp) of each single cell can be found in metadata.
PBAT data was processed as detailed (Meir et al., 2020): PE 150bp or 300bp reads were aligned to the mm9 reference genome using an in-house script based on Bowtie2. In cases where the two reads ends were not aligned in a concordant manner, the reads were discarded. Reads that were mapped to the same genome coordinates where marked as duplicates and were used only once. We subsample methylation of single-cells to have only one methylation call per CpG.
Assembly: mm9
Supplementary files format and content: Tab-separated text file for each 384-well plate containing UMI counts per gene per single cell. metadata_cells_scrna_sequencing.txt file contains metadata for each processed single cell.
Supplementary files format and content: Tab-separated text file for each sample, containing a row per genomic CpG with the following columns: 'chrom','start','end' - coordinates in 0-based form, 'cov' - # of times the CpG was covered, 'meth' # of times the CpG was methylated.

extract_protocol:
Whole-embryo chimera, mixed chimera, and AAV-Cre treated embryos were dissected in ice-cold 1×PBS, followed by imaging in a drop of DMEM medium supplemented with 10% foetal bovine serum (FBS) under a Nikon Eclipse Ti2 inverted microscope. Embryos were then rinsed in ice-cold 1×PBS, transferred into an Eppendorf tube containing 35 µl 0.25% Trypsin/0.02% EDTA Solution A, and incubated at 37 °C for 5 min with 2-3 times pipetting. Trypsinization was stopped by adding 10% FBS/DMEM medium. Cell suspensions were filtered through a 35 µm strainer before sorting.
For MARS-seq analysis, single cells were index-sorted into a pre-barcoded 384-well capture plate that contains 2 µl of lysis solution and barcoded poly (T) reverse-transcription (RT) primers. In each plate, 12 wells at positions C1, C2, D1, D2, J6, J7, K6, K7, O23, O24, P23, and P24 were kept as non-cell controls. Immediately after sorting, each plate was sealed, spun down, snap-frozen on dry ice, and stored at -80 °C until library preparation.
For bisulfite sequencing, Tet-TKO1, Tet-TKO2, Ctrl1, and Ctrl2 cells were sorted from E8.5 chimera embryos respectively. Cell pellets were kept at -80 °C until library preparation. Genomic DNA was extract using commercial kit.
Single-cell cDNA libraries were prepared using the MARS-Seq method as described (Keren-Shaul et al., 2019). Briefly, reverse transcription was performed in individual wells of the sorted 384-well plate to get complementary DNA (cDNA). Subsequently, all liquid from each 384-well plate was pooled and converted to double-stranded DNA, transcribed using T7 RNA polymerase, and fragmented. A unique plate adaptor was added to each library to be sequenced together, and RNA::ssDNA (plate adaptor) ligation was performed. The purified ligates were applied to a second RT step with a primer complementary to the ligated adaptor, and the library is completed by cDNA enrichment through PCR amplification. Library concentration and profile were evaluated before sequencing.  Bulk PBAT library was performed as previously described (Meir et al., 2020). Briefly, genomic DNA was converted with bisulfate, and applied to the first and second strand synthesis. The product was treated by Klenow fragment and purified. A final PCR was performed using a universal primer and indexed primers. The final product was clean and sequenced.


title: Grp7a db/db+renin+JNJ39933673 rep3

description:
snRNA-seq using 10X Chromium
P3092


title: LMX1A-EN1-double-positive cells, batch2, Day20

value: Day 20


title: Tet TKO chimera plate 41

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
20190806_P09

value: E7.5 chimera embryo


title: Grp7a db/db+renin+JNJ39933673 rep2

description:
snRNA-seq using 10X Chromium
O3091


title: week-0_H3K4me1_rep3

description:
ctrl-3-H3K4me1_combined
processed data file: ctrl-H3K4me1_Input_peaks.broadPeak


title: week-0_H3K4me1_rep2

description:
ctrl-2-H3K4me1_combined
processed data file: ctrl-H3K4me1_Input_peaks.broadPeak


title: week-0_H3K4me1_rep1

description:
ctrl-1-H3K4me1_combined
processed data file: ctrl-H3K4me1_Input_peaks.broadPeak


title: Tet TKO chimera plate 39

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
20190806_P07

value: Host cells and injected mESC-derived Control and Tet TKO cells


title: Tet TKO chimera plate 40

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
20190806_P08

value: Chimera assay


title: control-cells, batch2, Day27


title: Tet TKO chimera plate 38

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
20190806_P03

value: Host cells and injected mESC-derived Tet TKO cells


title: week-0_H3K27ac_rep3

description:
ctrl-3-H3K27ac_combined
processed data file: ctrl-H3K27ac_Input_peaks.broadPeak


title: Grp6b db/db+renin+ACEI+Rosiglitazone rep3

description:
snRNA-seq using 10X Chromium
K3087

source_name: db/db+renin+ACEI+Rosiglitazone

value: renin AAV + ACEI + Rosiglitazone


title: LMX1A-EN1-double-positive cells, batch1, Day20


title: week-0_H3K27ac_rep2

description:
ctrl-2-H3K27ac_combined
processed data file: ctrl-H3K27ac_Input_peaks.broadPeak


title: Grp7a db/db+renin+JNJ39933673 rep1

description:
snRNA-seq using 10X Chromium
G3090

value: renin AAV + JNJ39933673


title: control-cells, batch3, Day27


title: LMX1A-EN1-double-positive cells, batch3, Day20


title: control-cells, batch1, Day27


title: week-0_H3K27ac_rep1

description:
ctrl-1-H3K27ac_combined
processed data file: ctrl-H3K27ac_Input_peaks.broadPeak


title: Grp6b db/db+renin+ACEI+Rosiglitazone rep4

description:
snRNA-seq using 10X Chromium
L3089

value: 2 weeks


title: Grp6b db/db+renin+ACEI+Rosiglitazone rep2

description:
snRNA-seq using 10X Chromium
L3086


title: Tet TKO chimera plate 36

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
20190806_P01


title: control-cells, batch2, Day20


title: Tet TKO chimera plate 35

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190806_P06


title: Grp6b db/db+renin+ACEI+Rosiglitazone rep1

description:
snRNA-seq using 10X Chromium
F3085


title: Grp6a db/db+renin+ACEI+Rosiglitazone rep5

description:
snRNA-seq using 10X Chromium
K3084


title: Tet TKO chimera plate 34

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190806_P05


title: control-cells, batch1, Day20


title: Tet TKO chimera plate 37

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
20190806_P02


title: Grp6a db/db+renin+ACEI+Rosiglitazone rep4

description:
snRNA-seq using 10X Chromium
L3083


title: Tet TKO chimera plate 33

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190806_P04


title: control-cells, batch3, Day20


title: Grp6a db/db+renin+ACEI+Rosiglitazone rep3

description:
snRNA-seq using 10X Chromium
N3082


title: Tet TKO chimera plate 32

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
190730_P11


title: O_SiHa2

data_processing:
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Then these libraries were sequenced on the Illumina sequencing platform ( Illumina HiSeq 4000) and 150bp paired-end reads were generated.
Raw data(raw reads)were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cervical cancer cell line (SiHa)

treatment_protocol: SiHa cells were transfected with vector/hsa_circ_000538 plasmid  respectively. Cells were collected at 72h after transfecteion.

value: SiHa

value: transfected with hsa_circ_0005358 plasmid


title: WT cDC2_activated (LPS)_rep3

type: RNA

city: Perugia

first: Marco

last: Gargaro

state: Perugia

address: Polo Unico Sant'Andrea delle Fratte, P.le Gambuli, Bldg C, 4th Floor

department: Medicine and Surgery

country: Italy

institute: University of Perugia

description: WT cDC2_activated (LPS)_rep3

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Gene 1.0 ST arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G 3000 Scanner.

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

label: biotin

source_name: cDC2 isolated from WT Flt3-BMDCs

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico reagent kit from 100pg-2ng total RNA.

extract_protocol: Column extraction of total RNA was performed acording to the manufacturer's instructions.

treatment_protocol: WT Bone marrow derived  cDC1, cDC2 and pDCs sort-purifed were left untreated or treated with E. coli LPS (0.250 μg/ml) for 24 h.

value: Bone marrow derived DCs

value: WT


title: O_SiHa1


title: Tet TKO chimera plate 31

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
190730_P10


title: Grp6a db/db+renin+ACEI+Rosiglitazone rep2

description:
snRNA-seq using 10X Chromium
M3081


title: N_SiHa3

value: transfected with vector plasmid


title: Tet TKO chimera plate 30

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190730_P09


title: WT cDC2_activated (LPS)_rep2

description: WT cDC2_activated (LPS)_rep2


title: Grp5b db/db+renin+Rosiglitazone rep5

description:
snRNA-seq using 10X Chromium
J3079

source_name: db/db+renin+Rosiglitazone

value: renin AAV + Rosiglitazone


title: O_SiHa3


title: Tet TKO chimera plate 28

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190730_P07


title: Grp6a db/db+renin+ACEI+Rosiglitazone rep1

description:
snRNA-seq using 10X Chromium
F3080

value: 2 days


title: N_SiHa2


title: WT cDC2_activated (LPS)_rep1

description: WT cDC2_activated (LPS)_rep1


title: Tet TKO chimera plate 29

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190730_P08


title: Grp5b db/db+renin+Rosiglitazone rep4

description:
snRNA-seq using 10X Chromium
I3078

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous


title: N_SiHa1


title: Grp5b db/db+renin+Rosiglitazone rep3

description:
snRNA-seq using 10X Chromium
R3077

value: female


title: Tet TKO chimera plate 27

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190730_P06


title: Grp5b db/db+renin+Rosiglitazone rep2

description:
snRNA-seq using 10X Chromium
K3076


title: WT cDC2_untreated_rep2

description: WT cDC2_untreated_rep2


title: WT cDC2_untreated_rep1

description: WT cDC2_untreated_rep1


title: WT cDC1_activated (LPS)_rep3

description: WT cDC1_activated (LPS)_rep3

source_name: cDC1 isolated from WT Flt3-BMDCs


title: Tet TKO chimera plate 25

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells
190730_P04


title: WT cDC2_untreated_rep3

description: WT cDC2_untreated_rep3


title: Grp5b db/db+renin+Rosiglitazone rep1

description:
snRNA-seq using 10X Chromium
E3075


title: WT cDC1_activated (LPS)_rep2

description: WT cDC1_activated (LPS)_rep2


title: Tet TKO chimera plate 24

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190730_P03


title: Grp5a db/db+renin+Rosiglitazone rep5

description:
snRNA-seq using 10X Chromium
J3074


title: Grp5a db/db+renin+Rosiglitazone rep3

description:
snRNA-seq using 10X Chromium
L3072


title: Tet TKO chimera plate 23

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190730_P02


title: C57, IMQ, Dermis

first: Fangzhou

last: Lou

department: Shanghai Institute of Immunology

description: 10x Genomics

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were processed using Cell Ranger software provided by 10x Genomics.
Assembly: mm10
Supplementary files format and content: tsv files with barcodes and genes
Supplementary files format and content: mtx files with gene counts for every gene and every cell with a unique barcode

source_name: dermis

extract_protocol:
Single cell suspensions were generated through enzyme digestion and dead cells were removed using FACS.
Libraries were generated using Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.

treatment_protocol: C57BL/6 mice were treated with imiquimod for 5 consecutive days on the ear.

value: wild type

value: dermis

value: 10 week

value: imiquimod


title: C57, IMQ, Epidermis

description: 10x Genomics

source_name: epidermis

value: epidermis


title: WT cDC1_activated (LPS)_rep1

description: WT cDC1_activated (LPS)_rep1


title: MSC_A5_1

city: Mainz

first: Pablo

last: Llavona

state: Rhineland-Palatinate

address: Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4

institute: IMB

data_processing:
Adapter sequences were trimmed from paired end RNA-seq reads using TrimGalore (https://github.com/FelixKrueger/TrimGalore).
Quality filtered reads were mapped using STAR against the mouse genome (GRCm39).
Read counts were quantified with HTSeq and differential expression analysis was carried out with these counts using Bioconductor package DESeq2.
Assembly: GRCm39
Supplementary files format and content: RPKM values for each Sample and the comparison of the reads between WT and KO

source_name: bone marrow

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 8.7ng of total RNA was used for the construction of sequencing libraries.
Library preparation was performed using NEBNext End Repair module, dA-Tailing module and Quick Ligation module (New England BioLabs).

value: bone marrow

value: primary

value: mesenchymal stromal cells

value: ANXA5 knockout