title: DZZ

status: Public on May 04 2025

city: Kunming

first: Lirong

state: Yunnan

address: No.88 Xuefu Road

department: Xishuangbanna Tropical Botanical Garden

institute: Chinese Academy of Sciences

data_processing:
NRF>0.9、PBC1>0.9和PBC2>3
The raw sequencing reads were subjected to quality filtering using Trimmomatic (version 0.36) and aligned to the rice reference genome (rice.uga.edu, version 7.0) using bwa (0.7.12-r1039) with default parameters. The peak analysis was conducted using MACS2 (2.2.7.1) with the parameters “-B -f BAMPE -q 0.05”.
Assembly: Oryza sativa genome (rice.uga.edu, version 7.0)
Library strategy: DAP-seq

organism: Oryza sativa

source_name: Shoot

extract_protocol:
A total of 2 g of seedling shoots from transgenic pUbi:OsWRKY11-Myc plants were harvested and fixed in a crosslinking solution containing 1% (w/v) formaldehyde under vacuum for 30 min on ice. crosslinking was terminated by treating with 0.125 mM glycine under vacuum for 5 min.
A genomic DNA library (200~800 bp) prepared from Nipponbare

treatment_protocol: The OsWRKY11-Halo protein and GFP-Halo were synthesized in vitro, and a genomic DNA library (200~800 bp) was derived from of Oryza sativa seedling. The SYZ samples were obtained by performing the DAP reaction of the OsWRKY11-Halo protein with the DNA library, while DDZ was obtained by DAP reaction of the GFP-Halo protein with the DNA library. GFP-Halo was used as a control.

value: Shoot


title: SYZ2

type: SRA

last: Zhao

country: China

library_source: genomic

molecule: genomic DNA

tag: tissue


title: WT_BLM_1

status: Public on May 05 2025

city: Hangzhou

first: Jun

last: Luo

state: State...

address: College of Pharmaceutical Sciences, Zhejiang University， Hangzhou, Zhejiang P. R. China 31005

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Illumina HiSeq X Ten platform
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.
Raw data (raw reads) were processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
Differential expression analysis was performed using the DESeq (2012) R package.P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression.
FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: lung

growth_protocol: Mice were housed with free access to water and diet, and maintained on a 12h light/12h dark cycle at 23°C throughout the study.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000. spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: WT and Slc15a3-/- mice (8 weeks old)  were intratracheally administered BLM (2 mg/kg) in 50 μl of normal saline on day 0. Mice administered with same volume of normal saline served as controls.  The mice were euthanized on day 21.

value: lung

tag: genotype

value: WT

tag: treatment

value: BLM


title: PBS_2

city: Beijing

first: Yuandong

last: Tao

state: --- Select One ---

address: Beijing

institute: Chinese PLA General Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: Hisat2 v2.0.5
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: Kidney

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher). 1.5 μg RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using mRNA-seq Library Prep Kit following manufacture’s protocols.

value: Kidney

value: PBS


title: RNA-Seq of WT MCF-7 - Replicate 1

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description: RNA-Seq of WT MCF-7 - Replicate 1

data_processing:
Quality controls was performed with FastQC
Read alignment on Gencode v32 annotation was performed with STAR
Gene expression quantification was performed with RSEM
Assembly: hg38
Supplementary files format and content: Raw read count table

organism: Homo sapiens

growth_protocol: MCF-7 cell lines were cultured in high glucose Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum.

extract_protocol:
Total RNA was harvested from cultured cells using Qiagen RNeasy Plus Mini Kit according to manufacturer’s instructions.
Triplicates of each condition were sent to BU’s Microarray and Sequencing core for library preparation using Kapa RNA HyperPrep with RiboErase and run on two high output 75-paired end sequencing runs on Illumina NextSeq.

treatment_protocol: GPS2 KO MCF-7 cells were previously made in laboratory using CRISPR/Cas9-mediated genomic recombination using gRNAs against GPS2. Specifically, CRISPR-Cas9 genome editing was performed using two different sets of sgRNAs. In each case, sgRNAs targeted exons 2 and 6 of the human GPS2 sequence. The two sets of sgRNAs each targeting were cloned separately into the LentiCRISPRv2 lentiviral vector (Kindly shared by Dr. Feng Zhang, Addgene plasmid #52961). 3.5 mg of each viral plasmid was co-transfected along with packaging plasmids pCMV-VSV-G and ps.PAX2 (Addgene plasmids #8454 and #12260) into HEK293T cells using Lipofectamine 3000. Media was changed after 24 hours and viral supernatant collected at 60 h. The virus was filtered through a 0.46 μm low protein binding filter membrane and either used immediately or stored at -80°C for later use. Transduction of target cell lines was performed in a six-well plate with 1–1.5 ml of viral supernatant and 8μg/ml polybrene in DMEM with 10% FBS. Media was changed after 24 h and cells split into selection media (puromycin 2.5 μg/ml) at 48 h. The KO lines were maintained as heterogeneous pools without selection of individual clones.

tag: cell line


title: SYZ1


title: WT_ZT22_1

city: HOUSTON

first: Jidong

last: Liu

state: TX

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

data_processing:
Raw sequence reads from each biological replicate of total RNA were aligned to the mouse genome GRCm38 (mm10) with HISAT2 using default parameters.
HTSeq was used to obtain read counts from the aligned reads.
DESeq2 (version 1.8.2) was used to normalized the read counts and perform differential gene analysis.
Assembly: mm10
Supplementary files format and content: Matrix table include FPKM values

source_name: Tibialis Anterior

extract_protocol:
Tibialis Anterior were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Total RNA was extracted from the mouse Tibialis Anterior muscle samples using the RNA extraction kit (RNeasy Mini Kit, Qiagen) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols

value: Tibialis Anterior


title: KO_ZT10_2

value: KO


title: KO_ZT10_1


title: WT_ZT22_2


title: PBS_3


title: KO_ZT22_3


title: WT_ZT22_3


title: 28-01-032-N

city: Woolloongabba

first: Yang

last: Xi

state: QLD

address: 37 Kent St

country: Australia

institute: University of Queensland Diamantina Institute

data_processing:
Raw reads from the 50 bp single-end sequencing libraries were checked using the FastQC tool. All libraries showed a good quality profile with an average quality score per read of 36 (Phred score). A consistent GC content was observed along the reads and no over-represented sequences were found.
The raw reads were trimmed using Trimmomatic v.0.38 to remove poor quality sequence reads, and any reads below a minimum length of 36 bp (ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). Around 98-99% of the reads survived the trimming step.
The reads were mapped to the hg38 human reference genome using the program BWA v0.7.4. Sequence reads were assigned to genes using the program featureCounts from the Subread package v1.6.2 and the hg38 human annotation GTF file (UCSC). The filterbyExpr function in the edgeR package was used to filter genes with low read counts. 11,569 genes had sufficiently large counts to be retained in the subsequent analysis.
Normalisation by the method of trimmed mean of M-values  was performed using the calcNormFactors function in edgeR. Counts were next transformed to log2 counts per million reads (log-CPM) using the voom function from the limma package.
A Principal Component Analysis (PCA) was performed using the normalised data with the mixOmics package. Differential gene expression analysis was performed using Limma . A linear model was fitted for the comparisons of interest using the functions lmFit and contrasts.fit and Empirical Bayes moderation was carried out
Assembly: hg38
Supplementary files format and content: The tsv file gene_features.txt contains the raw count table. The tsv file results.RV1B.AllComparisonSubtypes.txt contains the differential expression results for all genes.

source_name: PBMC

extract_protocol: Cultured cell pellets were cryopreserved in RNAprotectTM (100ul/well) previously, which were then thawed in the room temperature before the extraction. Total RNA was extracted using the RNeasy Micro Kit together with RNase free DNase set (QIAGEN) according to the manufacturer’s instructions. RNA quantity and quality was determined using the Agilent 2100 Bioanalyzer (BGI, Hong Kong NGS Lab, China).

treatment_protocol: Peripheral blood mononuclear cells samples from adults with persistent asthma of different inflammatory subtypes were stimulated with human rhinovirus RV1b in vitro for 24hr

tag: disease state

value: Neutrophilic Asthma

value: Media

value: Human venous blood


title: 295-GAAS-137

value: Healthy control


title: KO_ZT22_2


title: WT_ZT10_3


title: WT_ZT10_2


title: 289r-GAAS-102


title: 292-GAAS-103


title: 291r-GAAS-102


title: 294-GAAS-103


title: 286-GAAS-74


title: 288-GAAS-74


title: KO_ZT22_1


title: 285-GAAS-229


title: 277-GAAS-72


title: 273r-GAAS-147


title: 280-GAAS-77


title: 279-GAAS-72


title: KO_ZT10_3


title: WT_ZT10_1


title: 271r-GAAS-147


title: 297-GAAS-137


title: 252-04-073-E

value: Eosinophilic Asthma


title: 249-04-072-E


title: 265-GAAS-116


title: 256-GAAS-20


title: 247-04-072-E


title: 246-02-030-P

value: Paucigranulocytic Asthma


title: 244-02-030-P


title: 282r-GAAS-77


title: 283-GAAS-229


title: 237-04-065-P


title: 235-04-065-P


title: 232-04-064-E


title: 234-04-064-E


title: 223-01-127-E


title: 216-04-054-P


title: 214-04-054-P


title: 229-01-131-P


title: 225-01-127-E


title: 213-02-021-P


title: 210-01-123-P


title: 211-02-021-P


title: 258-GAAS-20


title: 205-01-106-P


title: 207-01-106-P


title: 250-04-073-E


title: 208-01-123-P


title: 267-GAAS-116


title: 204-04-052-E


title: 202-04-052-E


title: 201-04-051-E


title: 199-04-051-E


title: 195-04-047-P


title: 198-04-049-E


title: 196-04-049-E


title: 193-04-047-P


title: 192-02-022-E


title: 186-04-044-E


title: 190-02-022-E


title: 231-01-131-P


title: 184-04-044-E


title: 183-04-043-N


title: 175r-01-109-E


title: 178-02-019-P


title: 180-02-019-P


title: 177-01-109-E


title: 174-01-101-P


title: 172-01-101-P


title: 163-04-038-E


title: 165-04-038-E


title: 151r-01-098-E


title: 147-01-094-N


title: 153-01-098-E


title: 145-01-094-N


title: 123-01-075-E


title: 144-01-089-P


title: 121-01-075-E


title: 142-01-089-P


title: 139-01-087-N


title: 141-01-087-N


title: 133-01-083-P


title: 135-01-083-P


title: 115-01-061-N


title: 105-01-071-N


title: 117-01-061-N


title: 108-02-007-P


title: 103-01-071-N


title: 181-04-043-N


title: 93-04-030-E


title: 94-04-031-P


title: 91-04-030-E


title: 88-04-029-E


title: 106-02-007-P


title: 67-04-022-E


title: 85-04-028-P


title: 96-04-031-P


title: 64-04-001-E


title: 66-04-001-E


title: 69-04-022-E


title: 87-04-028-P


title: 36-02-001-N


title: 15-01-008-N


title: 13-01-008-N


title: 34-02-001-N


title: 30-01-032-N


title: S,Basement membranes of cochlea,rep1

city: Nanjing, Jiangsu Province, China

first: Jiheng

last: Wu

address: No.371 Heyan Road, Qixia District

institute: Southeast University

description: Library name: Sample2

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every nucleus

molecule: polyA RNA

source_name: Basement membranes of cochlea

extract_protocol:
Single-nucleus were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then nucleus were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single nucleus 3’ Reagent v3 Kits according to the manufacturer’s protocol.

treatment_protocol: P7 mice basement membranes  were isolated in cold HBSS, collected at the bottom of low-adsorption centrifuge tubes, snap-frozen in liquid nitrogen for 1 minute, and subsequently stored at -80°C for single-nucleus RNA sequencing.

value: Basement membranes of cochlea

tag: cell type

value: Hair Cell, Supporting Cell

value: Tamoxifen injection


title: 25-01-030-E


title: Pool 12 of 4 specimens

city: Bar Harbor

first: Daniel

last: Skelly

state: ME

address: 600 Main St

institute: Jackson Laboratory

description: 10X Genomics. First 4 raw files are gene expression, second 4 raw files are cell hashing.

data_processing:
Demultiplexing, alignment, and read counting were performed using version 6.1.1 Cell Ranger count pipeline (10x Genomics)
Cell hashing sequence files were used for demultiplexing pooled biological specimens. Hashing results were processed using CITE-seq-Count v1.4.0 (https://github.com/Hoohm/CITE-seq-Count) using the hashtag sequences in hashtag_sequences.csv.
Splitting of cell hashed samples in each pool used results from CITE-seq-Count and was performed using Seurat v5.0.1
Quality control, filtering, normalization, dimensionality reduction, and clustering were performed using Seurat v5.0.1
Assembly: mm10/GRCm38
Supplementary files format and content: Tab-separated values files and sparse matrix (MTX) files

source_name: tumor

growth_protocol: Using the MC38 tumor cell line, 0.5 million cells were injected subcutaneously into female mice aged 8-12 weeks. Measurements of body weight and tumor size were obtained daily after tumor cell injection.

extract_protocol:
Tumors were harvested and frozen in DMEM/10% FCS with 10% DMSO. We isolated RNA using the RNeasy (QIAGEN) RNA extraction kit.
Library preparation was performed using NextGEM single cell 5’ version 2 chemistry and according to the manufacturer’s protocol (10x Genomics, CG000330). Four biological specimens were pooled in each library using TotalSeq-A hashing antibiodies (BioLegend).

treatment_protocol: When tumors reached a size of 75-110mm3, a single dose of isotype control (Bioxcell, 2A3) or aPD1 antibody (Bioxcell, 29F.1A12) was injected intraperitoneally at 200ug per mouse, and the mice were euthanized 48 hours later.

value: tumor

value: sorted tumor 90% CD45+ and 10% CD45-

value: C57BL/6J x CC001/UncJ,C57BL/6J x CC001/UncJ,C57BL/6J x CC002/UncJ,C57BL/6J x CC002/UncJ


title: 90-04-029-E


title: LS,Basement membranes of cochlea,rep1

description: Library name: Sample1


title: Pool 6 of 4 specimens

value: C57BL/6J,C57BL/6J,C57BL/6J x CC007/UncJ,C57BL/6J x CC007/UncJ


title: Pool 11 of 4 specimens

value: C57BL/6J x CC075/UncJ,C57BL/6J x CC075/UncJ,C57BL/6J x CC080/TauUncJ,C57BL/6J x CC080/TauUncJ


title: Pool 2 of 4 specimens

value: C57BL/6J x CC001/UncJ,C57BL/6J x CC001/UncJ,C57BL/6J x CC079/TauUncJ,C57BL/6J x CC079/TauUncJ


title: Pool 3 of 4 specimens

value: C57BL/6J x CC002/UncJ,C57BL/6J x CC002/UncJ,C57BL/6J x CC080/TauUncJ,C57BL/6J x CC080/TauUncJ


title: Pool 9 of 4 specimens

value: C57BL/6J x CC075/UncJ,C57BL/6J x CC075/UncJ,C57BL/6J x CC036/UncJ,C57BL/6J x CC036/UncJ


title: Pool 8 of 4 specimens

value: C57BL/6J x CC036/UncJ,C57BL/6J x CC036/UncJ,C57BL/6J,C57BL/6J


title: Pool 5 of 4 specimens

value: C57BL/6J x CC002/UncJ,C57BL/6J x CC002/UncJ,C57BL/6J x CC079/TauUncJ,C57BL/6J x CC079/TauUncJ


title: Pool 10 of 4 specimens


title: MC38, C57BL/6J x CC075/UncJ host + isotype control, biol rep 2

description: fresh frozen spatial transcriptome sequencing

data_processing:
FASTQ files and associated OMETIFF corresponding to each capture area were aligned to the GRCm38 reference assembly with vM23 annotations from GENCODE (10x Genomics mm10 reference 2020-A) using the version 1.3.1 Space Ranger count pipeline (10x Genomics)
We normalized spot gene expression using the SCTransform algorithm implemented in Seurat v5.0.1.
To test for colocalization of cell types: cytotoxic T lymphocytes (CTLs) with dendritic cells (DCs) or Cxcl9+ macrophages) we computed binary indicators of nonzero expression of the marker genes mentioned (main text) for each spot and deemed two cell types as colocalized within a spot if markers of both cell types were expressed in that spot.
Assembly: mm10/GRCm38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of th tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image-.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png - low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol:
After resection, each tissue was blotted dry with an RNase-free laboratory towel then immediately submerged in fresh isopentane chilled over liquid nitrogen for approximately one minute and transferred to a cryovial pre-cooled on dry ice for long term storage at -80C.  Tissue was subsequently submerged in Optimal Cutting Temperature compound (OCT) in a prechilled cryomold using prechilled forceps, and the cryomold was immediately placed on powdered dry ice and allowed to completely freeze. OCT blocks were stored at -80C until quality control and processing.
Five 10µm sections from each block were used for total RNA extraction (RNeasy Mini Kit, Qiagen) and determination of RNA integrity (RINe score) using an automated electrophoresis (Tapestation 4200, Agilent) and High Sensitivity RNA ScreenTape. Blocks with RINe greater than 7 were optimized for ideal permeabilization time following the vendor protocol (10x Genomics, CG000238). Sections from four tissue blocks were placed on Visium Gene Expression slide for H&E staining and brightfield imaging via NanoZoomer SQ (Hamamatsu), block-specific tissue permeabilization, mRNA capture, and subsequent library generation per the manufacturer's protocol (10x Genomics, CG000239). Libraries were quantified by automated electrophoresis (Tapestation 4200, Agilent) and High Sensitivity D5000 reagents and fluorometry (Qubit, Invitrogen) and the presence of Illumina adapters was verified via qPCR (QuantStudio 7 Flex, Applied Biosystems).

treatment_protocol: When tumors reached a size of 75-110mm3, a single dose of isotype control (Bioxcell, 2A3) was injected intraperitoneally at 200ug per mouse, and the mice were euthanized 48 hours later.

value: bulk tumor

value: C57BL/6J x CC075/UncJ

value: isotype control


title: MC38, C57BL/6J x CC080/TauUncJ host + isotype control, biol rep 1

value: C57BL/6J x CC080/TauUncJ


title: 27-01-030-E

value: Eosinophilic Asthma

value: Human venous blood


title: CC75xB6 MC38, isotype control biol rep 5

data_processing:
We constructed transcriptomes for each CC founder strain using GENCODE vM23 annotations by using g2gtools v0.2.9 (https://github.com/churchill-lab/g2gtools) to alter sites that differed from the mouse reference genome according to Mouse Genomes Project SNP and indel release version 5
We mapped reads to these transcriptomes using bowtie v1.2.3, followed by converting to EMASE format and using gbrs v0.1.6, which can account for reads mapping to multiple or divergent haplotypes, to quantify multiway expression across the eight founder haplotypes.
We used total expected read counts across each gene for our analyses
Assembly: mm10/GRCm38
Supplementary files format and content: 20240429_24-liu-003_processed_matrix.tsv is a tab-separated file with ensembl gene IDs in rows and samples in columns. Values in the matrix were obtained according to the data processing steps in this record.

extract_protocol:
Tumors were harvested and frozen in DMEM/10% FCS with 10% DMSO. We isolated RNA using the RNeasy (QIAGEN) RNA extraction kit.
Poly(A) RNA-seq libraries were constructed using the KAPA mRNA HyperPrep Kit (KAPA Biosystems).

treatment_protocol: Mice were treated with aGMCSF (clone MP1-22E9, Bioxcell, 100ug intraperitoneally [i.p.]),  aIl2rb (clone TM-Beta 1, BioXcell, 200ug i.p.), or corresponding isotype controls (same isotype and dose amount as corresponding blocking antibody, Bioxcell) starting immediately after tumor engraftment and given every third day until tumors reached 75-110mm3. When tumors reached a size of 75-110mm3, a single dose of isotype control (Bioxcell, 2A3) or aPD1 antibody (Bioxcell, 29F.1A12) was injected i.p. at 200ug per mouse, and the mice were euthanized 48 hours later.

value: CC075/UncJ x C57BL/6J F1


title: Pool 7 of 4 specimens

value: tumor


title: Pool 4 of 4 specimens

value: sorted tumor 90% CD45+ and 10% CD45-

value: C57BL/6J x CC001/UncJ,C57BL/6J x CC001/UncJ,C57BL/6J x CC080/TauUncJ,C57BL/6J x CC080/TauUncJ


title: CC75xB6 MC38, isotype control biol rep 4


title: CC75xB6 MC38, aPD1 + aGMCSF biol rep 9

value: aPD1 + aGMCSF


title: Pool 1 of 4 specimens


title: MC38, C57BL/6J x CC080/TauUncJ host + isotype control, biol rep 2


title: MC38, C57BL/6J x CC075/UncJ host + isotype control, biol rep 1


title: CC75xB6 MC38, aPD1 biol rep 6


title: CC75xB6 MC38, aPD1 + aGMCSF biol rep 7


title: CC75xB6 MC38, aPD1 biol rep 5


title: CC75xB6 MC38, aPD1 + aIL2RB biol rep 11

value: aPD1 + aIL2RB


title: CC75xB6 MC38, aPD1 + aGMCSF + aIL2RB biol rep 8

value: aPD1 + aGMCSF + aIL2RB


title: CC75xB6 MC38, aPD1 + aGMCSF + aIL2RB biol rep 11


title: CC75xB6 MC38, aPD1 + aGMCSF + aIL2RB biol rep 10


title: CC75xB6 MC38, aPD1 + aIL2RB biol rep 9


title: CC75xB6 MC38, aPD1 + aGMCSF biol rep 8


title: CC75xB6 MC38, isotype control biol rep 3


title: CC75xB6 MC38, aPD1 + aGMCSF + aIL2RB biol rep 7


title: CC75xB6 MC38, aPD1 + aGMCSF biol rep 6


title: CC75xB6 MC38, isotype control biol rep 2


title: CC75xB6 MC38, aPD1 + aGMCSF biol rep 5


title: CC75xB6 MC38, aPD1 + aIL2RB biol rep 10


title: CC75xB6 MC38, aPD1 + aIL2RB biol rep 6


title: CC75xB6 MC38, aPD1 + aGMCSF + aIL2RB biol rep 6


title: CC75xB6 MC38, aPD1 + aIL2RB biol rep 5


title: CC75xB6 MC38, aPD1 + aGMCSF + aIL2RB biol rep 9


title: CC75xB6 MC38, aPD1 + aIL2RB biol rep 8


title: CC75xB6 MC38, aPD1 + aIL2RB biol rep 7


title: CC75xB6 MC38, aPD1 + aGMCSF + aIL2RB biol rep 5


title: CC75xB6 MC38, aPD1 + aGMCSF biol rep 4


title: CC75xB6 MC38, aPD1 biol rep 4


title: CC75xB6 MC38, isotype control biol rep 1


title: CC75xB6 MC38, aPD1 + aIL2RB biol rep 2


title: CC75xB6 MC38, aPD1 + aGMCSF + aIL2RB biol rep 1


title: CC75xB6 MC38, aPD1 + aIL2RB biol rep 4


title: CC75xB6 MC38, aPD1 + aIL2RB biol rep 1


title: CC75xB6 MC38, aPD1 biol rep 2


title: CC75xB6 MC38, aPD1 + aGMCSF biol rep 2


title: CC75xB6 MC38, aPD1 + aGMCSF + aIL2RB biol rep 2


title: CC75xB6 MC38, aPD1 + aGMCSF biol rep 3


title: CC75xB6 MC38, aPD1 + aGMCSF + aIL2RB biol rep 4


title: CC75xB6 MC38, aPD1 + aGMCSF biol rep 1


title: CC75xB6 MC38, aPD1 + aIL2RB biol rep 3


title: MC38, C57BL/6J x CC079/TauUncJ host + isotype control biol rep 2

data_processing:
We constructed transcriptomes for each CC founder strain using GENCODE vM23 annotations by using g2gtools v0.2.9 (https://github.com/churchill-lab/g2gtools) to alter sites that differed from the mouse reference genome according to Mouse Genomes Project SNP and indel release version 5
We mapped reads to these transcriptomes using bowtie v1.2.3, followed by converting to EMASE format and using gbrs v0.1.6, which can account for reads mapping to multiple or divergent haplotypes, to quantify multiway expression across the eight founder haplotypes.
We used total expected read counts across each gene for our analyses
Assembly: mm10/GRCm38
Supplementary files format and content: R_NR_processed_matrix.tsv is a tab-separated file with ensembl gene IDs in rows and samples in columns. Values in the matrix were obtained according to the data processing steps in this record.

value: C57BL/6J x CC079/TauUncJ


title: MC38, C57BL/6J x CC036/UncJ host + isotype control biol rep 1

value: C57BL/6J x CC036/UncJ


title: MC38, C57BL/6J x CC036/UncJ host + isotype control biol rep 2


title: CC75xB6 MC38, aPD1 + aGMCSF + aIL2RB biol rep 3


title: MC38, C57BL/6J x CC075/UncJ host + aPD1 biol rep 1


title: MC38, C57BL/6J x CC075/UncJ host + isotype control biol rep 2


title: MC38, C57BL/6J x CC075/UncJ host + isotype control biol rep 1


title: CC75xB6 MC38, aPD1 biol rep 1


title: MC38, C57BL/6J x CC080/TauUncJ host + isotype control biol rep 2


title: MC38, C57BL/6J x CC002/UncJ host + aPD1 biol rep 1

value: C57BL/6J x CC002/UncJ


title: MC38, C57BL/6J x CC001/UncJ host + isotype control biol rep 1

value: C57BL/6J x CC001/UncJ


title: Spleen 4FsA_3

city: Lausanne

first: Alejandro

last: Ocampo

address: Rue du Bugnon 27

country: Switzerland

institute: University of Lausanne

data_processing:
Data was processed using nf-core/rnaseq v3.14.0 (doi:https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows, using reproducible software environments from the Bioconda and Biocontainers projects.
Assembly: RNA-seq reads were aligned to the Mus musculus reference genome GRCm39 (GCA_000001635.9), and gene annotation was obtained from the Ensembl release.
Supplementary files format and content: tab delimited text files containing raw counts
Supplementary files format and content: tab delimited text files containing normalized counts generated using DESeq2

source_name: Spleen

extract_protocol:
Total RNA was extracted from mouse tissues and organs using TRIzol (Invitrogen, 15596018). Briefly, 500 µl of TRIzol was added to 20-30 µg of frozen tissue into a tube (Fisherbrand 2 ml 1.4 Ceramic, Cat 15555799) and homogenized at 7000 g for 1 min using a MagNA Lyser (Roche diagnostic) at 4ºC. Subsequently, 200 µl of chloroform was added to the samples and samples were vortexed for 10 sec and placed on ice for 15 min. Next, samples were centrifuged for 15 min at 12000 rpm at 4°C and supernatants were transferred into a 1.5 ml vial with 200 µl of 100% ethanol. Finally, RNA extraction was performed using the Monarch total RNA Miniprep Kit (NEB, T2010S) following the manufacture recommendations and RNA samples were stored at -80°C until use.
Processed by Novogene UK. Eukaryotic RNASeq  （cDNA library）https://www.novogene.com/us-en/technology/platforms/

value: Spleen


title: Spleen 4FsA_2


title: MC38, C57BL/6J x CC080/TauUncJ host + isotype control biol rep 1

value: bulk tumor


title: MC38, C57BL/6J x CC079/TauUncJ host + aPD1 biol rep 1


title: MC38, C57BL/6J x CC079/TauUncJ host + aPD1 biol rep 2


title: Spleen control_3

value: WT


title: Spleen control_1


title: MC38, C57BL/6J x CC079/TauUncJ host + isotype control biol rep 1

value: isotype control


title: Skeletal muscle 4FsA_2

source_name: Skeletal muscle

value: Skeletal muscle


title: MC38, C57BL/6J x CC036/UncJ host + aPD1 biol rep 2


title: MC38, C57BL/6J x CC036/UncJ host + aPD1 biol rep 1


title: Skeletal muscle 4Fk_2


title: CC75xB6 MC38, aPD1 biol rep 3


title: MC38, C57BL/6J x CC002/UncJ host + aPD1 biol rep 2


title: MC38, C57BL/6J x CC002/UncJ host + isotype control biol rep 1


title: Skeletal muscle 4FsB_3


title: Skeletal muscle 4FsA_1


title: MC38, C57BL/6J x CC075/UncJ host + aPD1 biol rep 2

value: C57BL/6J x CC075/UncJ


title: Skeletal muscle 4Fj_2


title: Skeletal muscle 4FsB_2


title: Skeletal muscle 4FsB_1


title: MC38, C57BL/6J x CC002/UncJ host + isotype control biol rep 2


title: Skeletal muscle 4Fj_1


title: MC38, C57BL/6J x CC080/TauUncJ host + aPD1 biol rep 1

value: C57BL/6J x CC080/TauUncJ


title: Skeletal muscle control_2


title: Brain 4FsA_3

source_name: Brain

value: Brain


title: Skeletal muscle control_1


title: Brain 4Fk_2


title: Brain 4FsB_3


title: Brain 4FsB_2


title: MC38, C57BL/6J x CC001/UncJ host + aPD1 biol rep 2

value: tumor


title: MC38, C57BL/6J x CC001/UncJ host + isotype control biol rep 2


title: MC38, C57BL/6J x CC001/UncJ host + aPD1 biol rep 1


title: Brain 4FsB_1


title: Skeletal muscle 4Fj_3


title: Brain control_2


title: Brain control_3


title: Brain 4Fj_1


title: Heart 4FsA_3

source_name: Heart

value: Heart


title: Heart 4FsA_2


title: Spleen 4FsA_1


title: Heart 4Fk_3


title: Spleen 4Fj_1


title: Heart 4Fk_2


title: Skeletal muscle 4Fk_3


title: Skeletal muscle 4Fk_1


title: Skeletal muscle 4FsA_3


title: Heart 4FsB_3


title: induced melanocytes from induced pluripotent stem cells, Day 44

city: Zhenjiang

first: Jie

last: Yang

state: Jiangsu

address: 301 Xuefu Road

institute: Jiangsu University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (10x Genomics).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: PSCs were maintained in a feeder-free culture system with mTeSR on Matrigel. Single-cell suspensions of PSCs were prepared using ACCUTASE™. Approximately 5×105 cells were seeded in each well of an Elplasia™ plate (24-well), and Y27632 was added to a final concentration of 10 μM. AggreWell EB Formation Medium was used. After 24 hours, the resulting aggregates were collected and further cultured in ultra-low attachment plates for 5-10 days. The EBs were then collected and transferred to melanocyte differentiation medium, which contained 50% conditioned medium from L-Wnt3a cells, 30% low-glucose DMEM, 20% MCDB 201 medium, 0.05 μM Dexamethasone, 1× insulin-transferrin-selenium, 1× linoleic acid-bovine serum albumin, 10−4 M L-ascorbic acid, 50 ng/mL SCF, 100 nM Endothelin-3, 20 pM cholera toxin, 50 nM 12-O-tetradecanoyl-phorbel 13-acetate, and 4 ng/mL bFGF. The cultures were maintained in ultra-low attachment plates, with half of the medium replaced every 2-3 days. After two weeks, the differentiated EBs were collected and plated on a fibronectin-coated plate. The cells were cultured for another 7 days and then dissociated using TrypLE Express Enzyme and passaged. Differentiation medium with 0.5% FBS was used, but without TPA. Subsequently, the induced melanocytes were passaged every 3-4 days.

extract_protocol:
The induced melanocytes were dissociated into single cells using TrypLE digestion. After digestion, the cell suspension was filtered through a 40-micron cell strainer to remove any cell clumps. The cell suspension was centrifuged, and the supernatant was discarded. The cells were resuspended in cryopreservation solution (Stem Cell Baker). Cell counting was performed, and the cell concentration was adjusted to 5-10 million cells per milliliter. The cells suspension was aliquoted into cryovials and stored at -80°C overnight. After overnight storage, the cryovials werer transferred to liquid nitrogen for long-term preservation.
The single-cell samples were shipped to BGI Genomics and libraries were prepared according to DNBSEQ protocol.

value: Melanocytes


title: Spleen control_2


title: Heart 4FsB_2


title: Heart 4FsB_1


title: induced melanocytes from induced pluripotent stem cells, Day 32

description: 10x Genomics


title: human arteriole snRNA-seq

city: Tucson

first: Yong

state: AZ

address: The University of Arizona

department: Physiology

institute: University of Arizona

description:
Library name: human arteriole snRNA-seq
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery

data_processing:
Raw fastq files were processed using CellRanger (v7.0.0) to generate feature matrices using 10x Genomics reference genome assembly hg38 (refdata-gex-GRCh38-2020-A). DoubletFinder R package (v2.0.3) was used to remove potential doublets, with the doublet rate set to max(0.3, #cells*8*1e-6). Cells with less than 200 genes or a mitochondrial percentage larger than 20% were excluded from the analysis.
For quality-controlled snRNA-seq data, the gene count matrix was log-transformed and scaled. The top 2000 most variable genes were identified using the FindVariableFeatures function from Seurat R package (v4.3.0.1), and then were used for principal component analysis (PCA). Clustering was performed using the top 20 principal components and the Louvain algorithm, with resolution adjusted from 0.5 to 2 in increments of 0.5. The optimal resolution was selected based on Clustree (v0.5.1) analysis. To annotate identified clusters, differentially expressed genes (DEGs) between clusters were identified by Wilcoxon rank sum test using FindAllMarkers function (logfc.threshold = 0.25, min.pct = 0.25, only.pos = TRUE). Statistical significance was determined as a Bonferroni-adjusted p-value <0.05 and an average log2 fold change >0.25. Canonical markers from PanglaoDB and CellMarker were referenced to annotate major cell types.
Assembly: hg38
Supplementary files format and content: R file for cluster

molecule: nuclear RNA

source_name: arteriole

extract_protocol:
Human arterioles were broken up using a beads method, and nuclei were extracted using the 'Frankenstein' protocol.  Briefly, the arterioles were broken up in 0.5 ml Nuclei EZ Lysis buffer with Precellys Evolution Touch and tissue homogenizing ceramic beads at a setting of 6,500rpm for 20 seconds.  Another 3.5 ml Nuclei EZ Lysis buffer was added to tissue homogenized buffer and incubated for 5 minutes on ice before being filtered through a 70 µm strainer mesh.  The extracted nuclei were washed once with Nuclei Wash and Suspension Buffer.
Single-nucleus RNA-seq libraries were prepared using Chromium Single Cell 3’ Reagent Kits V3 (10x Genomics, Pleasanton, CA), following the manufacturer's user guide.

value: arteriole


title: Skeletal muscle control_3


title: Heart 4Fj_3


title: endothelium-denuded arterioles (EDA) _4

description:
Library name: endothelium-denuded arterioles (EDA) RRBS_4
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed

data_processing:
Bisulfite-converted reads were processed using Trim Galore with non-directional and paired setting to remove adapters and low-quality sequences. The trimmed reads were aligned to the human genome (hg38) using bismark (v0.23.1dev). Next, PCR duplicates were removed by identifying and collapsing reads with identical UMI tags. Then, Bismark_methylation_extractor was employed to extract methylation calls for individual CpG sites.  Bisulfite conversion efficiency was assessed using methylated and unmethylated spike-in controls. Finally, for each CpG site, DNA methylation rate was calculated as the percentage of unconverted cytosines within each RRBS library. To visualize global methylation profiles in these iPSC-derived cells, the top 1% of most variable CpG sites across all samples were selected for unsupervised hierarchical clustering and principal component analysis (PCA). Promoter is defined as 2kbp upstream and 200bp downstream of the transcription start site (TSS). DMRs were identified using Metilene, a preferred tool specifically designed for RRBS data. Metilene applies a binary segmentation algorithm combined with a two-dimensional Kolmogorov–Smirnov test to de novo identify genomic regions that maximize methylation differences between two groups. For this analysis, a minimum mean methylation difference between groups of 0.05 and a minimum of five CpGs within a region were required. Statistical significance of DMRs was determined using an FDR threshold of < 0.05.
Assembly: hg38
Supplementary files format and content: methylation calls for individual CpG sites were extracted from Bismark_methylation_extractor.

source_name: endothelium-denuded arterioles (EDA)

extract_protocol:
Genomic DNA of tissue/cell was extracted following Diagenode’s Premium RRBS protocol (https://www.diagenode.com/).
RRBS libaries wer made following Diagenode’s Premium RRBS protocol (https://www.diagenode.com/). In brief, genomic DNA was digested using Msp1, followed by end-repair. Next, premium Methyl Unique Dual Indexes (UDI) and Unique Molecular Identifiers (UMI) Adapters were ligated to the resulting fragments. Then, UDI-UMI-tagged fragments are size-selected to enrich CpG-rich regions with gene regulatory potential. Finally, the enriched DNA underwent bisulfite conversion, followed by sequencing on an Illumina Novaseq 6000 platform with paired-end 50 bp reads

value: endothelium-denuded arterioles (EDA)


title: Brain 4FsA_2


title: Heart 4Fj_2


title: Brain 4FsA_1


title: Brain 4Fj_3


title: Brain 4Fk_1


title: endothelium-denuded arterioles (EDA) _2

description:
Library name: endothelium-denuded arterioles (EDA) RRBS_2
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed


title: Heart 4Fj_1


title: endothelium-denuded arterioles (EDA) _1

description:
Library name: endothelium-denuded arterioles (EDA) RRBS_1
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed


title: Heart control_2


title: human arteriole _3

description:
Library name: human arteriole RRBS_3
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery


title: Brain control_1


title: Heart 4FsA_1


title: Brain 4Fk_3


title: Small intestine 4FsA_2

source_name: Small Intestine

value: Small Intestine


title: Heart 4Fk_1


title: A549 cells, RARa AHT + CIM7 Rep3

city: Bronx

first: Mericka

last: McCabe

state: NY

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

description: Library name: RAC3

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and Gccontent the clean data were calculated.
Index of the reference genome (GRCh38) was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: GRCh38
Supplementary files format and content: Excel worksheet containing gene counts

growth_protocol: Cells were maintained in RPMI with 10% FBS and 1% antibiotic at 37C with 5% CO2.

extract_protocol:
RNA was extracted with Qiagen RNeasy Plus Mini Kit as per the manufacturer's protocol. RNA quality was checked with the Agilent Bioanalyzer 2100 system.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Cells were transfected with WT or AHT RARa. Sixteen hours later, cells were treated with compound or DMSO. After three hours, RNA was extracted.

value: Adenocarcinoma alveolar epithelial

value: RARa AHT

value: 5 µM CIM7

tag: replicate

value: Replicate 3


title: human arteriole _1

description:
Library name: human arteriole RRBS_1
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery


title: A549 cells, RARa AHT + DMSO Rep1

description: Library name: RAD1

value: Replicate 1


title: Heart control_1

value: WT


title: induced melanocytes from induced pluripotent stem cells, Day 23

description: 10x Genomics


title: human endothelial cell _3

description:
Library name: human endothelial cell RRBS_3
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery

source_name: endothelial cell

value: endothelial cell


title: Brain 4Fj_2


title: A549 cells, RARa WT + CIM7 Rep3

description: Library name: RWC3

value: RARa WT


title: A549 cells, RARa WT + CIM7 Rep1

description: Library name: RWC1


title: human arteriole _4

description:
Library name: human arteriole RRBS_4
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery


title: Small intestine 4FsA_3


title: A549 cells, RARa AHT + CIM7 Rep2

description: Library name: RAC2

value: Replicate 2


title: human arteriole _2

description:
Library name: human arteriole RRBS_2
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery


title: Small intestine 4FsA_1


title: Small intestine 4FsB_3


title: A549 cells, RARa AHT + DMSO Rep2

description: Library name: RAD2


title: A549 cells, RARa AHT + CIM7 Rep1

description: Library name: RAC1


title: human endothelial cell _1

description:
Library name: human endothelial cell RRBS_1
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: A549 cells, RARa WT + DMSO Rep1

description: Library name: RWD1


title: Small intestine 4Fk_2


title: Small intestine 4Fk_1


title: Small intestine 4FsB_2


title: human endothelial cell _4

description:
Library name: human endothelial cell RRBS_4
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: NA12878, Kriukiene method, Rep-2

city: Birmingham

first: Robert

last: Neely

address: 97 Vincent Drive

country: United Kingdom

institute: Tagomics LTD

data_processing:
Adapter and quality trimming: BBTools
Alignment: BWA-MEM2
Filtering of reads MAPQ<40: Samtools
Duplicate removal: Sambamba
Coverage bigWig generation: deepTools, bamCoverage tool
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: Blood

extract_protocol:
Genomic DNA was obtained from the Coriell Institute (https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=NA12878&Product=DNA)
Genomic DNA was sheared to an average of 180 bp in 8 microTube-50 AFA Fiber V2 Strips using a Covaris E220 evolution sonicator. 10 ng of input DNA was tagged using the Tagomics Active-Seq reaction kit and according to the manufacturer’s instructions. DNA was mixed with the methyltransferase enzyme and tagging compound and incubated at 37 °C for 1 hour. The reaction was stopped using the reaction termination buffer, with an incubation at 55°C for 15 mins. Without purification, the sample was cooled to 10°C. To this, was added 9 µL of End Repair & A-Tailing Master Mix (3.5 µL KAPA End Repair & A-Tailing Buffer, 1.5 µL KAPA End Repair & A-Tailing Enzyme and 4 µL water). The mixture was mixed thoroughly by pipette aspiration and incubated at 20°C for 30 mins followed by a 65°C incubation for a further 30 mins. The sample was cooled to 10°C, and to it were added IDT xGen Stubby Adapters (2.5 µL of 15µM Stocks) and 22.5 µL of Ligation Master Mix were added (15 µL KAPA Ligation Buffer, 5 µL KAPA DNA Ligase and 2.5 µL water). The mixture was thoroughly mixed by aspiration then incubated at 20 °C for 30 minutes.Without purification, DNA mixed with Tagomics Active-seq capture compound and the mixture was incubated at 37 °C for 1 hour with shaking at 500 rpm. The DNA was purified from the reaction mixture using AMPure Beads (Beckman Coulter) (washing with 150 µL 80% Ethanol) with final elution in 30 µL PBST (10mM Phosphate Buffer, 1M NaCl, pH 7.5, 0.005 % Tween-20). 5 µL Dynabeads MyOne Streptavidin C1 beads (ThermoFisher) were washed with 150 µL of PBST. Capture-ready DNA was added to the beads (29 µL - 1 µL was taken for QC) and mixed with by aspiration until a homogenous mixture was achieved. The mixture was further incubated at 23 °C for 15 minutes, with shaking at 1000 rpm. Once completed, the beads were washed twice with 150 µL of PBST. Finally, the beads were resuspended in 20 µL of Tagomics Active-seq Release Buffer and incubated at 50 °C for 30 minutes at 1000 rpm. After release of the DNA, the beads were placed on the magnet and left for 3 minutes. The supernatant containing the unmodified DNA fraction was transferred to a sterile tube and can be stored at this point or used directly for amplification. A mixture of KAPA HiFi HotStart ReadyMix (2x, 25 µL), IDT Unique Dual Index Primer Pairs (5 µL of 10 µM Stock) and the enriched DNA library (20 µL) was prepared and subjected to amplification by PCR (up to 13 cycles). The amplified library was purified using 1X AMPure XP Beads (washed with 150 µL 80% ethanol) and eluted in 10mM Tris-HCl (pH 8.5), 0.01% Tween-20.

value: Blood

tag: cell line_source

tag: biomaterial provider

value: B-Lymphocyte

value: Kriukiene method


title: human endothelial cell _2

description:
Library name: human endothelial cell RRBS_2
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: A549 cells, RARa WT + CIM7 Rep2

description: Library name: RWC2


title: human endothelium-denuded arterioles (EDA) RNA-seq_3

description:
Library name: H197vrmR
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed

data_processing:
Raw RNA-Seq sequence reads were pre-processed using Trim Galore (v0.6.2) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Adapters and reads with low quality (base quality < 20) were removed prior to further analysis.
Reads longer than 20bp after the trimming were aligned to the human genome (hg38) using hisat2 (v2.2.1).
Transcript assembly and quantification were performed using StringTie2 (v2.2.1), based on the GENCODE reference annotation (v38).
DESeq2 package (1.46.0) was used to perform differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: FPKM file include FPKM for each sample

extract_protocol:
Total RNA was extracted from tissue samples using the TRIzol reagent
Poly(A)-dependent RNA-seq libraries were prepared following protocol of Novogene (https://www.novogene.com/us-en/services/research-services/transcriptome-sequencing/mrna-sequencing/).


title: NA12878, Kriukiene method, Rep-1


title: A549 cells, RARa WT + DMSO Rep2

description: Library name: RWD2


title: A549 cells, RARa WT + DMSO Rep3

description: Library name: RWD3


title: A549 cells, RARa AHT + DMSO Rep3

description: Library name: RAD3


title: Small intestine 4Fj_3


title: Small intestine 4FsB_1


title: Vilanterol 100 nM + RNO -treated rep3

city: Calgary

first: Radhika

last: Joshi

state: Alberta

address: 3300 Hospital Drive NW

department: Department of Physiology and Pharmacology

country: Canada

institute: University of Calgary

data_processing:
Basecalls were performed using RTA v2
demultiplexing FASTQ conversion was performed using bcl2fastq v2.18.0.12
Sequenced reads were mapped to the reference human transcriptome (GRCh37/hg19) and quantified using Kallisto with 100 bootstraps per sample
Differential expression analysis was performed using the R package Sleuth and transcripts per million (TPM) values were calculated
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes transcripts per million (TPM) values for each sample for each gene described by its HGNC symbol

source_name: Lung

growth_protocol: BEAS-2B cells were grown to confluence in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 (DMEM/F12) supplemented with 10 % Canada origin FBS, L-glutamine (2.5 mM) and NaHCO3 (0.15 % w/v) followed by overnight incubation in serum-free medium.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA kit (MACHEREY-NAGEL GmbH & Co. KG, Düren, Germany) and quantified using NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE) according to manufacturer's instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra II Directional kit (New England Biolabs Inc., Ipswich, MA) with the poly(A) mRNA magnetic isolation module according to the manufacturer’s instructions. The prepared libraries were validated using the D1000 Screen Tape assay on an Agilent 2200 TapeStation system (Agilent Technologies, Santa Clara, CA) and quantified by Kapa qPCR Library Quantification kit for Illumina (Kapa Biosystems, Boston, MA).

treatment_protocol: Confluent BEAS-2B cells were treated for two hours with vehicle, RNO (1 µM), a maximal concentration of ONO-AE1-329 (1 µM), two sub-maximal concentrations of ONO-AE1-329 (0.1 nM and 1 nM), a maximal concentration of Vilanterol (100 nM) and their combination with RNO (ONO0.1 + RNO, ONO1 + RNO, ONO1000 + RNO, Vil100 + RNO).

value: Lung

value: BEAS-2B human airway epithelial cell line

value: Vilanterol 100 nM + RNO


title: human arteriole RNA-seq_3

description:
Library name: H197namR
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery

value: arteriole


title: Vilanterol 100 nM + RNO -treated rep4


title: Vilanterol 100 nM + RNO -treated rep2


title: human endothelial cell RNA-seq_3

description:
Library name: H197ecmR
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: Pool1_Trex1iKO1-KO4_mixed sample

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Immunologie

country: Germany

institute: Universitätklinikum Heidelberg

description: 10x Genomics

data_processing:
Raw data were processed all with the Cell Ranger-7.1.0 software
include-introns: false; nosecondary: false; nobam: false; multiplexing cmo-set: Biolegend_hashtag_feature_reference.csv
Assembly: cellranger/mus_musculus/GRCm39.e104
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Skin implanted tumor B16-F10

growth_protocol: Eight to twelve week-old male Trex1Fl/Fl R26CreERT2 or Trex1Fl/WT R26CreERT2  mice were used in this study.

extract_protocol:
Tumors were harvested at day 14 post-tumor implantation and were cut into ~4-5 mm pieces. Tissue was digested with an enzyme mixture containing Liberase (25µg/ml, LiberaseTM Research Grade, Sigma Aldrich), Hyaluronidase (0.5 mg/ml Sigma, 100mg Hyaluronidase from bovine testes, Sigma Aldrich ), and DNaseI (200U/µl, DNase I grade II, from bovine pancreas, Sigma Aldrich) in DMEM/20mM Hepes buffer for 30 min at 37°C with agitation (1300rpm). Digested tumor tissue was minced, filtered through 100 µm mesh, then washed with FACS buffer (0.5% BSA/2mM EDTA/PBS). CD45+ cells were enriched from bulk tumor cell suspension using Miltenyi CD45 (TIL) mouse Microbeads kit followed by magnetic separation with LS column (Miltenyi). The cell was then blocked in Fc blocking medium (5 µg/ml Purified anti-mouse CD16/32 Antibody, Biolegend in FACS buffer), and then stained with anti-mouse CD45 (PerCP-Cy5.5 conjugated, clone 30-F11, eBioscience) and DAPI. Living CD45-positive lymphocytes after FACS sorting were further used for downstream single-cell RNAseq preparation.
10x Genomics: Chromium Next GEM Single Cell 3’ Reagent Kits v3 (Dual Index) with Feature Barcode technology for Cell Surface Protein prototal combine with Biolegend TotalSeqA hashtag sample multiplexing protocol

treatment_protocol: 1x10^3 B16-F10 cells cells were mixed with an equal volume of Matrigel (BD Biosciences) and intradermally injected on both legs of male mice on day 0. Mice received 1 mg of Tamoxifen (in 100 ul Sunflower oil/5% ethanol) (Sigma #T5648) by i.p. injection on day 5 for three consecutive days.

value: Skin implanted tumor B16-F10

tag: Sex

value: male

value: tumor inflitrated lymphocytes

value: Trex1 fl/fl-R26CreERT2-ki/wt

value: tumor implantation and i.p. injection

value: Tamoxifen


title: Vilanterol 100 nM -treated rep4

value: Vilanterol 100 nM


title: endothelium-denuded arterioles (EDA) _3

description:
Library name: endothelium-denuded arterioles (EDA) RRBS_3
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed

value: endothelium-denuded arterioles (EDA)


title: Pool2_Trex1Ctrl1-Ctrl4_mixed sample

description: 10x Genomics

value: Trex1 wt/fl-R26CreERT2-ki/wt


title: human endothelial cell RNA-seq_2

description:
Library name: H169ecmR
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery

value: endothelial cell


title: Vilanterol 100 nM + RNO -treated rep1


title: Small intestine 4Fj_1

value: Small Intestine


title: Small intestine control_2

value: WT


title: Vilanterol 100 nM -treated rep2


title: human endothelium-denuded arterioles (EDA) RNA-seq_1

description:
Library name: H064vrmR
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed


title: ONO-AE1-329 1µM + RNO -treated rep3

value: ONO-AE1-329 1 µM + RNO


title: Small intestine 4Fk_3


title: human arteriole RNA-seq_2

description:
Library name: H169namR
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery


title: Vilanterol 100 nM -treated rep3

value: Lung


title: Small intestine control_3


title: human endothelium-denuded arterioles (EDA) RNA-seq_2

description:
Library name: H169vrmR
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed


title: Vilanterol 100 nM -treated rep1

value: BEAS-2B human airway epithelial cell line


title: Small intestine control_1


title: ONO-AE1-329 1µM + RNO -treated rep4


title: ONO-AE1-329 1µM + RNO -treated rep2


title: human arteriole RNA-seq_1

description:
Library name: H064namR
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery


title: ONO-AE1-329 1 nM + RNO -treated rep4

value: ONO-AE1-329 1 nM + RNO


title: ONO-AE1-329 1µM + RNO -treated rep1


title: human arteriole Pan-promoter capture Micro-C_round1

description:
Library name: huEVRVCMCC_1
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery

data_processing:
The data was analyzed following Dovetail Promoter Panel Data Processing Guide to generate mapped.PT.bam file. Direct chromatin interactions were then identified by CHiCAGO at different resolutions with the mapped.PT.bam file.
Assembly: hg38
Supplementary files format and content: hic contact map file

extract_protocol:
Using Dovetail  Micro-C Kit following the manufacturer’s User Guide.
Pan-promoter capture Micro-C library was created using the Micro-C libraries generated using Dovetail Micro-C Kit following manufacturer’s User Guide for Tissue and Blood to create Micro-C libraries.Dovetail® human Pan Promoter Enrichment panel, and Dovetail Target Enrichment kit. The panel included 161,144 probes designed to cover 84,643 promoters for 19725 protein-coding genes and 7,630 long noncoding genes in human based on Ensembl GRCh38 version 86. The libraries were sequenced using the Illumina NovaSeq sequencers.

value: arteriole


title: Small intestine 4Fj_2


title: ONO-AE1-329 1 nM + RNO -treated rep2


title: Liver 4Fk_2

source_name: Liver

value: Liver


title: human endothelial cell RNA-seq_1

description:
Library name: H064ecmR
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: ONO-AE1-329 1µM -treated rep4

value: ONO-AE1-329 1 µM


title: ONO-AE1-329 1µM -treated rep3


title: ONO-AE1-329 1µM -treated rep2


title: ONO-AE1-329 1 nM + RNO -treated rep1


title: human endothelium-denuded arterioles (EDA) Pan-promoter capture Micro-C_round2

description:
Library name: huEVRVCMCB_2
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed


title: ONO-AE1-329 1µM -treated rep1


title: human arteriole Pan-promoter capture Micro-C_round3

description:
Library name: huEVRVCMCC_3
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery


title: Liver 4FsA_1


title: RBL-2H3 cells, PIO, 6h, rep 1 [airpio1]

city: Shanghai

first: Weihua

last: Wang

address: 150 Jimo Road

department: Otolaryngology-Head & Neck Surgergy

institute: School of Medicine, Tongji University

data_processing:
Trimmomatic V0.36 LEADING:3 TRAILING:3 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8:true SLIDINGWINDOW:4:15 MINLEN:50
RseQC V2.6.4;fastqc v0.11.5 ; hisat2 V2.2.1.0 ; stringtie2 V1.3.3b; bwa V0.7.5a; samtools V1.3.1; bcftools V1.3.1
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the human genome (GRCh38) using HISAT2. FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count. Differential expression analysis was performed using the DESeq (2012) R package. P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of differentially expressed genes (DEGs) was performed to demonstrate the expression pattern of genes in different groups and samples. GO enrichment and KEGG pathway enrichment analysis of DEGs were performed respectively using R based on the hypergeometric distribution.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

growth_protocol: RBL-2H3 cells were maintained in MEM (Corning Cellgro, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco; Thermo Fisher Scientific, USA), 100 U/ml penicillin G, and 100 μg/mL streptomycin in a humidified atmosphere of 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: RBL-2H3 cells were treated with or without PIO (10 μM) for 6 h.

value: rat basophilic leukemia cells

value: PIO treated


title: human arteriole Pan-promoter capture Micro-C_round2

description:
Library name: huEVRVCMCC_2
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery


title: RBL-2H3 cells, Control, rep 3 [airc3]

value: control


title: Liver 4Fk_3


title: Liver 4FsA_3


title: human endothelium-denuded arterioles (EDA) Pan-promoter capture Micro-C_round3

description:
Library name: huEVRVCMCB_3
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed


title: ONO-AE1-329 1 nM-treated rep4

value: ONO-AE1-329 1 nM


title: human endothelial cell Pan-promoter capture Micro-C_sample3

description:
Library name: huEVRVCMCA_3
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: RBL-2H3 cells, PIO, 6h, rep 3 [airpio3]


title: ONO-AE1-329 1 nM-treated rep3


title: Liver 4Fk_1


title: RBL-2H3 cells, PIO, 6h, rep 2 [airpio2]


title: RBL-2H3 cells, Control, rep 1 [airc1]


title: Liver 4FsA_2


title: ONO-AE1-329 1 nM + RNO -treated rep3


title: Liver 4FsB_2


title: human endothelium-denuded arterioles (EDA) Pan-promoter capture Micro-C_round1

description:
Library name: huEVRVCMCB_1
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed


title: RBL-2H3 cells, Control, rep 2 [airc2]


title: Liver 4FsB_1


title: human endothelial cell Pan-promoter capture Micro-C_sample2

description:
Library name: huEVRVCMCA_2
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: Liver 4Fj_3


title: ONO-AE1-329 1 nM-treated rep1


title: human arteriole Micro-C_sample2

description:
Library name: HNV323MC
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery

data_processing:
Pair-end sequencing reads were cleaned with Trim Galore to remove adaptor and low-quality reads. We used JuicerBox, which was a one-click pipeline for processing HiC or Micro-C data, to generate hic file for direct visualization. We followed Dovetail Micro-C Data Processing Guide to generate .mcool file and used it for loop calling with Mustache.
Assembly: hg38
Supplementary files format and content: hic contact map file

extract_protocol:
Using Dovetail  Micro-C Kit following the manufacturer’s User Guide.
Micro-C assay was performed using Dovetail Micro-C Kit following manufacturer’s User Guide for Tissue and Blood to create Micro-C libraries. Briefly, tissues were ground into fine powder with CryoGrinder. The ground tissue was crosslinked with disuccinimidyl glutarate and formaldehyde sequentially. The genomic DNA was digested in situ with MNase Enzyme mix to 20%-40% mononucleosomes.  Genomic DNA was released from cells and put through a sequential process of binding to chromatin capture beads, end polishing, bridge ligation, intra-aggregate ligation, crosslink reversal, and DNA purification. Library was made from the purified DNA and subject to sequencing with Novaseq 6000 platform for approximately 800M 150PE reads.


title: ONO-AE1-329 1 nM-treated rep2


title: Liver control_2


title: human endothelial cell Pan-promoter capture Micro-C_sample1

description:
Library name: huEVRVCMCA_1
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: human arteriole Micro-C_sample1round1

description:
Library name: HNV197MC_1
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery


title: Liver 4FsB_3


title: A5-/-_16 hpf

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

description:
Library name: Sample1
10x Genomics

data_processing:
Illumina sequencing reads were aligned to the zebrafish mRNA reference genome (GRCz11) using the 10x Genomics CellRanger pipeline (version 3.0.2) with default parameters.
Assembly: GRCz11
Supplementary files format and content: tar compressed  files include filtered_gene_bc_matrices after running CellRanger pipeline

organism: Danio rerio

source_name: embryonic cells

growth_protocol: The angptl5Δ10/Δ10 embryos were raised in 0.3× Danieau Buffer and harvested at 16 hpf

extract_protocol:
RNA from the barcoded cells was reverse-transcribed  reagents from a Chromium Single Cell reagent kit (10X Genomics)
Libraries were prepared using Single Cell 3′Library & gel Bead kit v3 (10x Genomics, Cat# PN-1000268) according to the manufacturer’s protocol for 7350 cell recovery.

treatment_protocol: Collected samples were digested with trypsin into single cell suspension and set to Novogene for single cell sequencing.

value: embryonic cells

tag: strain

value: AB

value: angptl5 mutant

value: CRISPR/Cas9 knockout

tag: batch


title: SplitSeq_Cortex_GEX

city: Lyon

first: Guillaume

last: Marcy

address: 8 avenue Rockefeller

country: France

institute: Universite Lyon 1

description:
Library name: Visual_Cortex_mRNA
multiplexed_library (CTL_1, CTL_2, LPS_J2, LPS_J7)
read1 file contain cell barcode and UMI; read2 contains trancript

data_processing:
Reads were aligned and counted using Parse Biosciences demultiplexing pipeline v1.1.2 using standard parameters
Seurat version 4.4.0 was used to analyze data
Low-quality nuclei were filtered out of the dataset: percentage mitochondrial genes >1%, nCount >15,000 UMI or <100 genes. Doublets were also removed using scdblFinder.
Assembly: Rattus_norvegicus.mRatBN7.2
Supplementary files format and content: PARSE DGE filtered outputs: anndata.h5ad with features (rows) and nuclei (columns)
Supplementary files format and content: PARSE DGE filtered outputs: all genes, cell metadata and count matrix

source_name: cortex (brain)

extract_protocol:
Nuclei from visual cortex were obtained from one rat, anesthetized with isoflurane and sacrificed. The dissected visual cortex tissue was immediately placed in a dry-ice-cold tube for immediate freezing until processing for nuclei isolation. Dissected frozen cortex was resuspended and mechanically homogenized using dounce homogeneizer to release nuclei following the Salty EZ 10 protocol (dx.doi.org/10.17504/protocols.io.bx64prgw). Nuclei were resuspended in 500μL of resuspension buffer and were then fixed with the Evercode Nuclei Fixation kit (#ECF2003) according to manufacturer instructions (Parse Biosciences) and FACS-sorted based on DAPI intensity to remove debris (BD ARIA). Sorted nuclei were finally frozen down. All steps were carried on ice or at 4°C.
Nuclei were thawed and loaded in round 1, 2 and 3 plates for combinatorial barcoding according to manufacturer instructions (#UMWT3300 , Parse Biosciences). Six sub-libraries of 12,500 nuclei were prepared to target 75,000 nuclei and 12,000 nuclei per condition. Libraries were sequenced using the Novaseq 6000 platform (Illumina). Libraries were prepared according to Parse Biosciences version 3 chemistry & Illumina protocols

treatment_protocol: Treated Animals received bilateral injections of 4 µl of LPS solution at a rate of 0.4 µl/min into the primary visual cortex

value: cortex (brain)

value: cortical nuclei

value: wild type

tag: development satge

value: Postnatal day 45

value: mixed samples (CTRL versus LPS at 2 and 7 days post injection)

value: male


title: RNA seq of Freshly isolated satellite cells from wild type mice after volunteer exercise (VE) 3

city: Hong Kong

first: Feng

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

department: Chemical Pathology

institute: The Chinese University of Hong Kong

data_processing:
Sequenced fragment were mapped to mouse genome mm9 using TopHat
The differential genes were identifined by cuffdiff
Assembly: mm9

source_name: satellite cell

extract_protocol:
Total RNAs from cells or tissues were extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions.
cDNAs were synthesized under the manufacturer’s instructions of HiScript® II Reverse Transcriptase Kit with gDNA wiper (Vazyme, R223-01). Real-time PCR was performed to quantify the expression level of mRNAs by Luna® Universal qPCR Master Mix (NEB, M3003E) and LightCycler ®480 Real-Time PCR System (Roche). GAPDH (glyceraldehydes 3-phosphate dehydrogenase) or 18s RNA were used as internal controls for normalization.

value: satellite cell

value: volunteer exercise (VE) by running wheel

tag: time

value: 21 days


title: Liver 4Fj_2

value: Liver


title: ONO-AE1-329 0.1 nM + RNO -treated rep4

value: Lung

value: BEAS-2B human airway epithelial cell line

value: ONO-AE1-329 0.1 nM + RNO


title: RNA seq of Freshly isolated satellite cells from wild type mice after endurance exercise (EE) 3

value: endurance exercise (EE) by treadmill

value: 10 days


title: human arteriole Micro-C_sample3

description:
Library name: huV0424MC
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery

value: arteriole


title: ONO-AE1-329 0.1 nM-treated rep4


title: RNA seq of Freshly isolated satellite cells from wild type mice with non-exercise Ctrl (NE) (3 rep mixed)


title: ONO-AE1-329 0.1 nM-treated rep3


title: ONO-AE1-329 0.1 nM + RNO -treated rep2


title: Liver control_3

value: WT


title: RNA seq of Freshly isolated satellite cells from wild type mice after endurance exercise (EE) 1


title: RNA seq of Freshly isolated satellite cells from wild type mice after endurance exercise (EE) 2


title: ONO-AE1-329 0.1 nM + RNO -treated rep3


title: Liver 4Fj_1


title: human arteriole Micro-C_sample1round2

description:
Library name: HNV197MC_2
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery


title: ONO-AE1-329 0.1 nM + RNO -treated rep1


title: Liver control_1


title: human endothelium-denuded arterioles (EDA) Micro-C_sample2

description:
Library name: HVR323MC
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed

value: endothelium-denuded arterioles (EDA)


title: Kidney 4FsA_1

source_name: Kidney

value: Kidney


title: Kidney 4Fk_3


title: Kidney 4FsA_3


title: ONO-AE1-329 0.1 nM-treated rep2


title: ONO-AE1-329 0.1 nM-treated rep1


title: human endothelial cell Micro-C_sample1round4

description:
Library name: HEC197MC_4
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery

value: endothelial cell


title: Kidney 4FsA_2


title: RNO-treated rep3

value: Roflumilast N-oxide (RNO)


title: human endothelial cell Micro-C_sample2

description:
Library name: huEC0424MC
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: Tumor, iKO6

description:
Library name: Sample12
Processed: gene_count column name: iKO6

data_processing:
Raw data were processed through fastq software
Secondary analysis were generated on R studio platform
Assembly: mm10
Supplementary files format and content: counts

source_name: Skin implanted tumor

extract_protocol:
Tumors were harvested at day 14 post-tumor implantation and were cut into ~4-5 mm pieces. Tissue was digested with an enzyme mixture containing Liberase (25µg/ml, LiberaseTM Research Grade, Sigma Aldrich), Hyaluronidase (0.5 mg/ml Sigma, 100mg Hyaluronidase from bovine testes, Sigma Aldrich ), and DNaseI (200U/µl, DNase I grade II, from bovine pancreas, Sigma Aldrich) in DMEM/20mM Hepes buffer for 30 min at 37°C with agitation (1300rpm). Digested tumor tissue was minced, filtered through 100 µm mesh, then washed with FACS buffer (0.5% BSA/2mM EDTA/PBS). The cell was then blocked in Fc blocking medium (5 µg/ml Purified anti-mouse CD16/32 Antibody, Biolegend in FACS buffer), and then stained with anti-mouse CD45 (PerCP-Cy5.5 conjugated, clone 30-F11, eBioscience) and CD31 (PE conjugated, clone MEC13.3, eBioscience). CD45-negative or CD31-negative FACS-sorted cells were further processed to total RNA extraction using RNeasy Mini Kits (Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non strand specific library . Library was ready after end repair, A-tailing, adapter ligation, size selection, amplification,and purification.

value: Skin implanted tumor

value: Cd45-negtive Cd31-negative sorted Tumor tissue

value: Wildtype  B16F10 in Trex1 fl/fl-R26CreERT2-ki/wt mouse

value: tumor implantation and i.p. injection


title: RNA seq of Freshly isolated satellite cells from wild type mice after volunteer exercise (VE) 1

value: satellite cell

value: volunteer exercise (VE) by running wheel

value: 21 days


title: human endothelium-denuded arterioles (EDA) Micro-C_sample1

description:
Library name: huVR0424MC
Human arterioles were obtained from discarded subcutaneous adipose tissue from surgery. Endothelial cells were removed


title: Tumor, iKO5

description:
Library name: Sample11
Processed: gene_count column name: iKO5


title: human endothelial cell Micro-C_sample1round3

description:
Library name: HEC197MC_3
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: Tumor, iKO4

description:
Library name: Sample10
Processed: gene_count column name: iKO4


title: Kidney 4Fk_1


title: Tumor, iKO3

description:
Library name: Sample9
Processed: gene_count column name: iKO3


title: human endothelial cell Micro-C_sample1round2

description:
Library name: HEC197MC_2
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: human endothelial cell Micro-C_sample1round1

description:
Library name: HEC197MC_1
Endothelial cells were isolated from human arterioles obtained from discarded subcutaneous adipose tissue from surgery


title: RNO-treated rep2

value: Lung

value: BEAS-2B human airway epithelial cell line


title: RNO-treated rep4


title: Kidney 4FsB_3


title: Tumor, iKO2

description:
Library name: Sample8
Processed: gene_count column name: iKO2


title: RNO-treated rep1


title: Tumor, iKO1

description:
Library name: Sample7
Processed: gene_count column name: iKO1


title: Vehicle-treated rep4

value: Vehicle


title: Kidney 4FsB_2


title: Tumor, Ctrl5

description:
Library name: Sample5
Processed: gene_count column name: CTRL5

value: Wildtype  B16F10 in Trex1 wt/fl-R26CreERT2-ki/wt mouse


title: NA12878, MeDIP, Rep1

value: Blood

value: B-Lymphocyte

value: MeDIP


title: Kidney 4Fj_3

value: Kidney


title: NA12878, Active-seq unbound DNA, RunC-Rep1

data_processing:
*library strategy: Active-Seq (Azide Click Tagging for In Vitro Epigenomic sequencing)
Adapter and quality trimming: BBTools
Alignment: BWA-MEM2
Filtering of reads MAPQ<40: Samtools
Duplicate removal: Sambamba
Coverage bigWig generation: deepTools, bamCoverage tool
Assembly: GRCh38
Supplementary files format and content: bigWig

value: Active-seq


title: Vehicle-treated rep2


title: Kidney 4FsB_1

data_processing:
Data was processed using nf-core/rnaseq v3.14.0 (doi:https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows, using reproducible software environments from the Bioconda and Biocontainers projects.
Assembly: RNA-seq reads were aligned to the Mus musculus reference genome GRCm39 (GCA_000001635.9), and gene annotation was obtained from the Ensembl release.
Supplementary files format and content: tab delimited text files containing raw counts
Supplementary files format and content: tab delimited text files containing normalized counts generated using DESeq2


title: NA12878, Active-seq, RunC-Rep1


title: Tumor, Ctrl4

description:
Library name: Sample4
Processed: gene_count column name: CTRL4


title: Vehicle-treated rep1


title: Vehicle-treated rep3


title: NA12878, Active-seq, RunB-Rep2


title: Kidney 4Fj_2


title: Tumor, Ctrl3

description:
Library name: Sample3
Processed: gene_count column name: CTRL3


title: Kidney 4Fj_1


title: ZT22_Muslce_Input

data_processing:
Raw reads were first cleaned using trim_galore with default parameters.
Bowtie2 was used for alignment of the ChIP-seq data and Picard MarkDuplicates was used to remove duplicate reads from bam files.
Read coverage for every 10 bp bins was calculated using the deepTools bamCoverage function, avoiding blacklist regions of the mouse genome (ENCODE project). Genome browser tracks were visualized in Integrative Genome Browser (IGV version 1.5). Peak calling was performed on unique reads with MACS2 using input as control.
Assembly: mm10
Supplementary files format and content: bigWig file

extract_protocol:
Mouse skeletal muscles were harvested at ZT10 and ZT22. Tissues were ground in liquid N2 and cross-linked in 1% formaldehyde for 20 min. Whole cell extracts were sonicated and immunoprecipitated with antibodies to Rev-erbα (Cell signaling, cat # 13418).
DNA libraries were prepared for sequencing using standard protocols

value: Skeletal muscle

value: WT

tag: antibody


title: NA12878, Whole Genome Sequencing, Rep1

data_processing:
*library strategy: WGS
Adapter and quality trimming: BBTools
Alignment: BWA-MEM2
Filtering of reads MAPQ<40: Samtools
Duplicate removal: Sambamba
Coverage bigWig generation: deepTools, bamCoverage tool
Assembly: GRCh38
Supplementary files format and content: bigWig

value: Whole Genome Sequencing


title: NA12878, Active-seq, RunB-Rep1


title: NA12878, Active-seq, RunA-Rep3


title: Tumor, Ctrl2

description:
Library name: Sample2
Processed: gene_count column name: CTRL2

value: Skin implanted tumor

value: Cd45-negtive Cd31-negative sorted Tumor tissue


title: Kidney control_3

extract_protocol:
Total RNA was extracted from mouse tissues and organs using TRIzol (Invitrogen, 15596018). Briefly, 500 µl of TRIzol was added to 20-30 µg of frozen tissue into a tube (Fisherbrand 2 ml 1.4 Ceramic, Cat 15555799) and homogenized at 7000 g for 1 min using a MagNA Lyser (Roche diagnostic) at 4ºC. Subsequently, 200 µl of chloroform was added to the samples and samples were vortexed for 10 sec and placed on ice for 15 min. Next, samples were centrifuged for 15 min at 12000 rpm at 4°C and supernatants were transferred into a 1.5 ml vial with 200 µl of 100% ethanol. Finally, RNA extraction was performed using the Monarch total RNA Miniprep Kit (NEB, T2010S) following the manufacture recommendations and RNA samples were stored at -80°C until use.
Processed by Novogene UK. Eukaryotic RNASeq  （cDNA library）https://www.novogene.com/us-en/technology/platforms/


title: ZT10_Muslce_Input


title: Kidney 4Fk_2


title: Kidney control_2


title: ZT22_Muslce_ChIP

value: Rev-erbalpha (Cell signaling, cat # 13418)


title: Tumor, Ctrl1

description:
Library name: Sample1
Processed: gene_count column name: CTRL1

value: tumor implantation and i.p. injection


title: NA12878, Active-seq, RunA-Rep2


title: CD8 cells, with or without OVA treatment, HTO

city: Rehovot

first: Anna

last: Rudnitsky

department: Systems Immunology

country: Israel

institute: Weizmann Institute

description:
Library name: FB2_S4
10X genomics

data_processing:
Processing was done using the Cell Ranger ‘multi’ analysis pipeline (10x Genomics version 8.0.1), with the reference data file refdata-gex-mm10-2020-A.
Assembly: mm10
Supplementary files format and content: cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, hashing_config.csv

source_name: small intestine

extract_protocol:
After removal of Peyer's patches, small intestine tissues were treated sequentially with PBS containing 1 mM DTT at room temperature for 10 min, twice with 5 mM EDTA at 37 °C for 10 min to remove epithelial cells, and then minced and dissociated in digestion buffer (RPMI containing collagenase (1 mg ml−1 collagenase D; Roche), DNase I (100 μg ml−1; Sigma), dispase (0.1 U ml−1; Worthington) and 10% FBS) with constant stirring at 37 °C 55 min. Leukocytes were collected at the interface of a 40%–80% Percoll gradient (GE Healthcare). Cells were stained with OVA-H2Kb-PE tetramer and enriched with Miltenyi PE beads. then H2Kb-OVA-Pe positive cells were sorted using FACS with the following gating strategy: Dapi-, B220- CD8b+, OVA-H2Kb+. sort efficiency was above 99%.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsioin (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDCA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: C57BL66 week old female mice were either fed OVA 50mg in 200ul PBS or just PBS by gavage on days 1,2,3 and 4, then on day 13 infected with 10^9 CFU of LmOVA (PMID 11207297)  by gavage.

value: small intestine

value: CD8 T cells

value: OVA fed and then LmOVA infection

tag: library type

value: HTO


title: MDA-MB-231 cells, m6A-IP-rep2

status: Public on May 03 2025

city: xi'an

first: tongtong

last: jiang

address: changle western load

institute: Fourth Military Medical University

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of m6A on genome
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for each group.

source_name: MDA-MB-231 cell line

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNAs were extracted from MDA-MB-231 cells using TRIzol Reagent (Invitrogen, cat. NO 15596026）. DNA digestion was carried out after RNA extraction by DNaseI.5 μg total RNAs were used for meRIP experiment. Briefly，20mM ZnCl2 was added to total RNA and incubated at 94℃ for 5min until the RNA fragments were mainly distributed in 100-200 nt. Then 10% RNA fragments was saved as “Input” and the remaining was used for m6A immunoprecipitation（IP）.The specific anti-m6A antibody (Synaptic Systems, 202203) was applied for m6A immunoprecipitation.
The stranded RNA sequencing library was constructed by using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) with five PCR cycles. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. Then ribosomal cDNA was removed by SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; 634413;Takara/Clontech, Japan) and ten PCR cycles were added . The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on MGISEQ-T7（MGI） with PE150 model .

value: MDA-MB-231 cell line

value: human breast cancer

tag: rip antibody

value: m6A (Synaptic Systems, #202203)


title: MDA-MB-231 cells, input-rep2


title: Kidney control_1

tag: tissue


title: ALI_TFPI_MSC_3

first: Miao

last: Li

state: Shanghai

address: 180 Fenglin Road

institute: Zhongshan Hospital, Fudan University

description: Library name: Sample 19

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Differential expression analysis was performed using the DESeq25.
Based on the hypergeometric distribution, GO6, KEGG7 pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: All mice were raised carefully in specific-pathogen-free cages (SPF) and maintained at temperatures between 20°C and 25° at a relative humidity ranging from 50% to 70% in accordance with the ethical guidelines of the National Institutes of Health on Animal Care.

extract_protocol:
Fresh lung tissue was prepared and added Trizol for lysis and total RNA extraction.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Mice were randomly divided into five groups of 24 animals each (control group, ALI group, ALI+rhTFPI group, ALI+MSC group and ALI+rhTFPI+MSC group). ALI group: 5 mg/kg LPS (Merck & Co., Inc., USA) was dissolved in 50 μl of 0.9% normal saline and slowly instilled through the trachea. ALI+rhTFPI group: rhTFPI (5 mg/kg) (Beijing SinoBiological Co., Ltd) was given through the tail vein. After 30min, LPS (5 mg/kg) was given through the trachea. And rhTFPI (5 mg/kg) was given again through tail vein 30min later. ALI+MSC group: 4 h after administration of the same amount of LPS solution, tail vein injection of 200 μl PBS containing about 1×10^6 MSCs. ALI+rhTFPI+MSC group: 4 h after the same treatment as ALI+rhTFPI group, tail vein injection of 200 μl PBS containing about 1×106 MSCs.

value: Lung

tag: genotype

value: Wild type

value: Lipopolysaccharide + human recombinant TFPI + human chorion-derived MSC

value: batch 1


title: ALI_TFPI_MSC_4

description: Library name: Sample 20

tag: treatment


title: ALI_TFPI_MSC_2

description: Library name: Sample 18


title: ZT10_Muslce_ChIP

city: HOUSTON

first: Jidong

address: One Baylor Plaza

institute: Baylor College of Medicine

source_name: Skeletal muscle

value: Skeletal muscle

value: WT


title: Tumor, Ctrl6

description:
Library name: Sample6
Processed: gene_count column name: CTRL6

value: Skin implanted tumor

tag: cell line

value: Wildtype  B16F10 in Trex1 wt/fl-R26CreERT2-ki/wt mouse


title: ALI_MSC_3

description: Library name: Sample 15

value: Lipopolysaccharide + human chorion-derived MSC


title: ALI_MSC_2

description: Library name: Sample 14


title: ALI_MSC_1

description: Library name: Sample 13


title: ALI_TFPI_4

description: Library name: Sample 12

value: Lipopolysaccharide + human recombinant TFPI


title: GECD8 cells, with or without OVA treatment

description:
Library name: GEX2_S1
10X genomics

value: small intestine

value: LmOVA infection

value: mRNA


title: MDA-MB-231 cells, m6A-IP-rep1


title: ALI_TFPI_3

description: Library name: Sample 11


title: NA12878, Active-seq, RunA-Rep1

value: Blood

value: B-Lymphocyte

value: Active-seq


title: ALI_TFPI_1

description: Library name: Sample 9


title: ALI_3

description: Library name: Sample 7

value: Lipopolysaccharide


title: Control_3

description: Library name: Sample 3

value: Lung

value: PBS


title: ALI_MSC_4

description: Library name: Sample 16

value: Wild type


title: ALI_TFPI_MSC_1

description: Library name: Sample 17

value: Lipopolysaccharide + human recombinant TFPI + human chorion-derived MSC

value: batch 1


title: ALI_1

description: Library name: Sample 5


title: MDA-MB-231 cells, input-rep1

value: MDA-MB-231 cell line

value: human breast cancer


title: Spleen_CD4_Env126_WT, replicate 1, scRNASeq

city: Milano

first: Pietro

last: Delfino

address: Via Olgettina 58

institute: San Raffaele Scientific Institute

description:
Library name: Spleen_CD4_Env126_WT
Parse Biosciences

data_processing:
Parse Biosciences analysis pipeline split-pipe (v.1.1.0p) was used with default parameters to perform demultiplexing, alignment of sequencing reads against GRCm38.93 genome and generation of the cell-by-gene count matrix (https://support.parsebiosciences.com/hc/en-us/articles/17200056667924-Pipeline-Download-Current-Version).
Assembly: GRCm38.93
Supplementary files format and content: Comma-separated files and matrix files

source_name: Spleen

extract_protocol:
In selected experiments, WT C57BL/6 mice were immunized subcutaneously with 100μg of Env126-138 peptide and 50μg of polyI:C immune adjuvant at three time points every 7 days. Isolation of CD8+ T cells from spleens of Cor93 or Env28 mice and CD4+ T cells from spleens of Env126 transgenic mice have been performed as previously described6. Isolation of CD4+ T cells from spleens of Env126 transgenic mice was performed by negative immunomagnetic selection taking advantage of the EasySepTM Mouse CD4+ T Cell Isolation Kit (StemCell Technologies). Mice were injected i.v. with 106 HBV-specific (Cor93 or Env28) naïve CD8+ T cells and/or HBV-specific effector CD4+ T cells (Env126 TEFF). In indicated experiments, mice were splenectomized and treated i.v. with 200 μg of anti-CD62L mAb (clone MEL-14, BioXcell) 48 and 4 hours prior to cell injection and 24 hours after cell transfer. Splenectomy was performed according to standard procedures72 and as previously described 6. In selected experiments, mice were treated intraperitoneally (i.p.) with Busulfan and reconstituted i.v. with bone marrow from CD11c-iDTR-GFP mice (107). In selected experiments, dendritic cells and Kupffer cells were depleted by injecting i.p. 25 ng/g of diphtheria toxin (Sigma-Aldrich) 3 days and 1 day prior to T cell transfer and 1 day and 3 days after cell transfer. In indicated experiments, Kupffer cells were depleted by i.v. injection of clodronate-containing liposomes (10 μL/g) (Liposoma B’V) 2 days prior to T cell injection73. In indicated experiments, mice were treated i.p. with 250 μg of anti-CD40L mAb (clone MR-1), 250 μg of anti-IL12 p40 mAb (clone C17.8), 250 μg of anti-IL27 p28 mAb (clone MM27.7B1) and 2,5 μg of recombinant IL27 (Fc: LALA-PG-KIH heterodimer, Adipogen). All mAbs were purchased from BioXcell, unless otherwise indicated.
Env126 CD4+ TEFF and Env126 CD4+ TN cells were fixed according to the Evercode Fixation (Parse Biosciences) protocol and single-cell RNA libraries were prepared using the Evercode split-pool combinatorial barcoding technology approach using the ParseBio Evercode WT v2 kit. Sequencing was performed on the Illumina NovaSeq 6000 sequencer with the S4 flow cell 200 cycle kit according to the sequencing protocol provided by the Evercode kit (v1.5) at a desired depth of 30,000 reads/cell.

value: Spleen

value: CD4+ T cells

value: Naive


title: ALI_TFPI_2

description: Library name: Sample 10

value: Lipopolysaccharide + human recombinant TFPI


title: ALI_4

description: Library name: Sample 8


title: Kidney, Hmx3; Hmx2 control, rep4

city: Los Angeles

first: Riana

middle: K

last: Parvez

state: CA

address: 1425 San Pablo St.

department: Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

description:
150bp reads
h32_295

data_processing:
Sequence reads were filtered using fastp (0.20.1) (average quality > 20, length > 20)
Filtered reads were aligned using STAR (2.7.0e)
Read count extraction was performed using featureCount (2.0.1)
Assembly: mm39
Supplementary files format and content: txt files contain read counts for all samples and genes

source_name: embryonic kidney

extract_protocol:
Samples were preserved in RNAlater, incubated overnight at 4°C and stored at -80°C until extraction
Whole embryonic kidney RNA was extracted using Qiagen RNeasy Mini Kit according to manufacturer's protocols. RNA was eluted in 30uL nuclease free water.
Samples were shipped to the Genome Technology Access Center at McDonnell Genomic Institute at Washington University in St. Louis for sequencing. Up to 5ug of RNA were used for library prepration; library preparation was performed using the manufacturer's protocol for polyA selection.

value: embryonic kidney

tag: developmental stage

value: Hmx3; Hmx2 control


title: Kidney, Hmx3; Hmx2 control, rep5

description:
150bp reads
h32_297


title: Kidney, 3XKO, rep1

description:
150bp reads
3xko_112

value: Dmrt2; Hmx3; Hmx2 KO


title: Kidney, Hmx3; Hmx2 control, rep3

description:
150bp reads
h32_88_WT


title: Control_2

description: Library name: Sample 2


title: Control_4

description: Library name: Sample 4


title: Kidney, Hmx3; Hmx2 control, rep2

description:
150bp reads
h32_84_WT


title: Kidney, Hmx3; Hmx2 control, rep1

description:
150bp reads
h32_83_WT


title: ALI_2

description: Library name: Sample 6


title: Kidney, Hmx3; Hmx2 KO, rep4

description:
150bp reads
h32_302

value: Hmx3; Hmx2 KO


title: Control_1

description: Library name: Sample 1


title: Kidney, 3XKO control, rep3

description:
150bp reads
3xko_72

value: Dmrt2; Hmx3; Hmx2 control


title: Kidney, 3XKO control, rep2

description:
150bp reads
3xko_70


title: Kidney, 3XKO, rep3

description:
150bp reads
3xko_115


title: Kidney, 3XKO control, rep1

description:
150bp reads
3xko_57


title: Kidney, Dmrt2 control, rep3

description:
150bp reads
dmrt2_122

value: Dmrt2 Control


title: Kidney, Hmx3; Hmx2 KO, rep2

description:
150bp reads
h32_89_KO


title: Kidney, 3XKO, rep2

description:
150bp reads
3xko_114


title: Kidney, Hmx3; Hmx2 KO, rep6

description:
150bp reads
h32_316


title: Kidney, Hmx3; Hmx2 KO, rep5

description:
150bp reads
h32_303


title: Spleen_Eff_CD4_Env126, replicate 1, scRNASeq

description:
Library name: Spleen_Eff_CD4_Env126
Parse Biosciences

tag: cell type

value: Effector


title: Kidney, Hmx3; Hmx2 control, rep6

description:
150bp reads
h32_315


title: Kidney, Hmx3; Hmx2 KO, rep1

description:
150bp reads
h32_87_KO


title: Kidney, Hmx3; Hmx2 KO, rep3

description:
150bp reads
h32_91_KO


title: Sample_6_Tet2KO_LK_2x

city: Frederick

first: Shweta

last: Singh

state: Maryland

address: 1050 Boyles Street

department: Mouse Cancer Genetics Program

institute: National Cancer Institute

data_processing:
Trimming for adapters and lowquality bases using Cutadap
Alignment using STAR
Quantification using RSEM
Assembly: mm10
Supplementary files format and content: .txt table with RSEM genes counts

source_name: Donor Lin- ckit+ from bone marrow

growth_protocol: Donor Lin- ckit+ cells were sort purified from the bone marrow cells of competitive bone marrow transplantation recipient mice.

extract_protocol:
RNA was purified using the RNeasy Micro Kit (Qiagen)
Illumina® Stranded Total RNA Prep and Ligation with Ribo-Zero Plus ( kits

value: Donor Lin- ckit+ from bone marrow

value: Tet2 KO


title: Kidney, Dmrt2 control, rep2

description:
150bp reads
dmrt2_116


title: Sample_5_WT_LK_2x

value: WT


title: Kidney, Dmrt2 KO, rep2

description:
150bp reads
dmrt2_107

value: Dmrt2 KO


title: Kidney, Dmrt2 control, rep1

description:
150bp reads
dmrt2_115


title: KK-Ay mouse with ligature for 3 weeks 2 [KL2]

city: Fukuoka

first: Takanori

last: Shinjo

state: fukuoka

address: Maidashi 3-1-1

department: Section of Periodontology

country: Japan

institute: Kyushu University

data_processing:
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
Raw counts for each gene were estimated in each sample usingFeatureCount . Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCm38
Supplementary files format and content: excel file includes normalized counts for each Sample with annotation.

source_name: glomeruli

growth_protocol: C57BL/6 and KK-Ay mice were housed under normal diet and ad libitum water.

extract_protocol:
Mouse glomeruli were isolated from the kidneys of perfused mice with Dynabeads M-450 Tosylactivated in PBS. Briefly, the dissected kidneys (1 and 1/2 kidneys) from each mouse were minced and digested in 1 mg/ml of collagenase A (10103578001; Sigma-Aldrich, St-Louis, MO, USA) and 100 U/ml DNase Ⅰ in Hank's Balanced Sult Solution (14175095; Thermo Fisher Scientific, Waltham, MA, USA) at 37℃ for 30 minutes. Then, the digested mixture was passed through a 100 µm cell strainer (542000; Greiner, Kremsmünster, Australia) and placed on a magnet for purification. After washing with PBS twice, glomeruli were collected. The purity of glomeruli was confirmed more than 95% by microscopy.
Glomerular RNA was isolated using PureLink RNA Mini Kit (12183018A; Invitrogen) according to the manufacturer's guidance.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: C57BL/6 and KK-Ay mice at 13 week old were injected with anesthetics containing 4 mg/kg midazolam (LF6476; SANDOZ, Tokyo, Japan), 0.3 mg/kg Dorbene® (9021; Kyoritsu Pharmaceutical, Tokyo, Japan), and 5 mg/kg Vetorphale® (3270952; Meiji Seika Pharma, Tokyo, Japan) at the induction of ligation or euthanasia. Mice were checked for ligatures every week.

value: glomeruli

tag: strain background

value: glomerular cells

value: KK-Ay


title: KK-Ay mouse without ligature 3 [K3]

value: no