title: Jejunum_CD

city: Cologne

first: F

middle: Thomas

last: Wunderlich

address: Gleueler Str. 50

department: Obesity and Cancer

institute: MPI for Metabolism Research

description: 10x Genomics

data_processing:
Raw sequencing data were demultiplexed, aligned to the mouse reference genome GRCm38 and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-separated files for barcodes (cells) and features (genes) and matrix file for raw counts corresponding to the Cellranger output.

source_name: Jejunum

extract_protocol:
The small intestine was removed from mice and divided into three parts representing the duodenum, jejunum and ileum from proximal to distal. Intestines were washed in ice-cold PBS by vortexing. Then, the samples were incubated for 30 min at 37 °C with horizontal rotation in 20 ml predigestion solution (1× HBSS without magnesium/calcium, 10 mM HEPES, 5 mM EDTA, 1 mM DTT and 2% FCS). IECs were detached by intensive vortexing and harvested on ice using a 100μm cell strainer (Greiner). To increase the IEC yield, samples were vortexed a second time in 10 ml predigestion solution, and cell suspensions were pooled. Afterwards, IECs were collected by centrifugation (10 min at 50 g and 4 °C) and resuspended in 1X HBSS/2%FCS solution. Isolated cells from three 12-week-old male mice were pooled in order to minimize artefacts originating from individual mice. IECs and intraepithelial immune cells were resuspended in 2% FCS in PBS and counterstained using propidium iodide (PI). Live cell sorting was performed with a BD FACSAria Fusion and BD FACSAria IIIu at 4°C using a 100 μm nozzle and sheath pressure set at 20 psi. Live single cells were gated based on PI fluorescence. Sorted, PI negative cells were collected in 1xPBS buffer containing 0.04% BSA for 10X genomics single cell sequencing.
Isolated cells were processed using a 10X Genomics Chromium Controller. cDNA was prepared using the Chromium single-cell 3′ reagent kit v3 according to the manufacturer’s protocol (10X Genomics).

value: Jejunum

value: intestinal epithelial cells

value: WT


title: Combination, rep 3

status: Public on Jan 15 2024

type: SRA

city: Boston

first: Dan

last: Duda

state: MA

address: 55 Fruit St

department: Radiation Oncology

country: USA

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
The quality control of RNA-Seq raw data was performed by FastQC.
After quality control, the low-quality bases and adaptors contamination was removed by Cutadapt.
The quality of clean yield data was examined again by FastQC software.
Next, the clean data were aligned to mouse reference genome mm10 by Hisat2 with a maximum of 2 mismatches per read.
After data mapping, samtools and HTSeq-count were used to count the number of reads aligned to the gene features.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: tumor (Intrahepatic cholangiocarcinoma)

extract_protocol:
Total RNA was extracted from the 425-ICC tumor tissues using Qiagen kits.
RNA libraries for RNA-seq were prepared using Qiagen Stranded RNA Library Kits following manufacturer's protocols.

tag: tissue

value: tumor (Intrahepatic cholangiocarcinoma)

tag: treatment

value: Combination


title: Ileum_CD

country: Germany

description: 10x Genomics

library_source: transcriptomic single cell

source_name: Ileum

value: Ileum

tag: cell type

tag: genotype


title: FD treated, RNAseq, replicate 4

city: Bethesda

first: Luis

middle: A

last: Fernandez de Castro Diaz

state: Maryland

address: 30 Convent Drive

department: SDMHS

institute: NIDCR/NIH

data_processing:
base-called demultiplexed (fastq) read qualities were determined using FastQC (v0.11.2)
Sequenced reads were mapped to GENCODE M23 mouse genome (GRCm38.M23)
Gene counts were generated with STAR (v2.7.3a) built-in counting option
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression between groups was performed using DESeq2.
Assembly: GRCm38.M23
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized counts per million, using edgeR built-in cpm() function, tab-delimited txt format.

source_name: Distal radius and ulna

extract_protocol:
Samples were snap-frozen, pulverized and immediately transferred to Trizol. Phenol-chloroform RNA extraction was carried out. cDNA synthesis, library construction and sequencing were performed by Novogene
mRNA libraries were prepared using the polyA TruSeq method (Illumina) and sequenced on an Illumina NovaSeq 6000 sequencer using 150 x 150 paired-end mode.

value: Distal radius and ulna

tag: age

value: skeletal tissue


title: FD treated, RNAseq, replicate 6


title: FD treated, RNAseq, replicate 5


title: Duodenum_CD

description: 10x Genomics

source_name: Duodenum

value: Duodenum


title: gut, HTO

city: Princeton

first: Sarah

middle: K

last: Walker

state: NJ

address: Lewis-Sigler Institute of Integrative Genomics

institute: Princeton University

description:
220523_SNH_uLIPSTIC_gut_HTO_S4
sample and biotin HTOs for gut IEL
gut_barcodes.tsv.gz
gut_features.tsv.gz
gut_matrix.mtx.gz

library_source: other

data_processing:
*library strategy: CITE-seq
FASTQ files from both scRNA and hashtag (HTO) sequencing were processed by “cellranger count” using reference transcriptome refdata-gex-mm10-2020-A (for gut data, CellRanger v6.0.1 was used, for LCMV data v7.0.1 was used).
FASTQ files from TCR sequencing were processed by "cellranger vdj" using mm10_vdj_refdata using CellRanger v6.0.1
Assembly: mm10
Supplementary files format and content: CellRanger output files: gut_barcodes.tsv.gz, gut_features.tsv.gz, gut_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: SNH1_barcodes.tsv.gz, SNH1_features.tsv.gz, SNH1_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: SNH3_barcodes.tsv.gz, SNH3_features.tsv.gz, SNH3_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: SNH4_barcodes.tsv.gz, SNH4_features.tsv.gz, SNH4_matrix.mtx.gz
Supplementary files format and content: gut_filtered_contig_annotations.csv is a CSV file with metadata about cell TCR sequence analysis outputted directly from "cellranger vdj"

molecule: protein

source_name: gut

extract_protocol:
Intestinal intraepithelial leukocytes were isolated as follows: small intestines were harvested and washed in PBS. Peyer’s patches were surgically removed and the intestine was segmented in ~1 cm pieces prior to incubation with 1 mM dithiothreitol for 10 min at room temperature followed by addition of 30 mM EDTA and incubation for 30 min at 37oC. Intraepithelial cells were recovered from the supernatant of dithiothreitol and EDTA washes and mononuclear cells were isolated by collecting the middle ring after 40% and 80% gradient Percoll centrifugation. Immune cells from the lymph nodes, lungs, spleen, and liver were isolated by incubating the fragmented tissue in 1.5 ml HBSS supplemented with collagenase D at 400 U ml-1, 0.1 mg ml-1 Dnase 1 (Sigma) and 0.8 mg ml-1 dispase 1 (Sigma) for 30 min at 37oC. After digestion, tissue was forced 5 times through a 21-gauge needle and filtered through a 70 µm strainer into a 15 ml falcon tube with PBE.
In addition to fluorescent antibodies, cells were co-stained prior to sorting with hashtag oligonucleotide (HTO)-labeled antibodies to CD45 and MHC-I for sample separation (two hashtags per sample) and HTO-anti-biotin for detection of the uLIPSTIC signal. Sorted cells were collected into a microfuge tube with 300 μl PBS supplemented with 0.4% BSA. After the sort, tubes were topped with PBS 0.4% BSA, centrifuged and the buffer was carefully reduced by removing the volume with a pipette to a final volume of 40 μl. Cells were counted for viability and immediately submitted to library preparation. The scRNA-seq library was prepared using the 10X Single Cell Chromium system, according to the manufacturer’s instructions.

treatment_protocol: Gut samples: SrtA expression in gut epithelial cells was induced by daily intraperitoneal injections of tamoxifen (2 mg per injection) for 5 consecutive days, starting 14 days before the end point. LCMV samples: Mice received adoptive transfers of mSrtA+ P14 T cells and were infected the next day intraperitoneally with 2x10^5 PFU of LCMV Armstrong strain. For both groups, mice were injected with LIPSTIC substrate (biotin-LPETG) intraperitoneally (100 μl of 20 mM solution in PBS) six times, 20 min apart.

value: gut

value: immune cells

value: Tamoxifen

tag: library type

value: HTO

tag: hto


title: lcmv,HTO, lung + spleen

description:
SNH4_lcmv_HTO_S3_lane1
sample, biotin, and donor HTOs for LCMV Med LN SNH4
SNH4_barcodes.tsv.gz
SNH4_features.tsv.gz
SNH4_matrix.mtx.gz

source_name: lung, spleen

value: lung, spleen

value: LCMV WT + mut


title: gut, GEX

description:
220523_SNH_uLIPSTIC_gut_ex_S3
GEX mRNA library for gut IEL

molecule: polyA RNA

value: mRNA


title: lcmv,GEX,medLN + liver +  lung

description:
SNH3_lcmv_ex_S5_lane1
GEX mRNA library for LCMV Med LN SNH3

source_name: med LN, liver, lung

value: med LN, liver, lung


title: FD treated, RNAseq, replicate 3


title: lcmv,HTO,medLN only

description:
SNH1_lcmv_HTO_S1_lane1
sample, biotin, and donor HTOs for LCMV Med LN SNH1
SNH1_barcodes.tsv.gz
SNH1_features.tsv.gz
SNH1_matrix.mtx.gz

source_name: med LN

value: med LN


title: lcmv,GEX,medLN only

description:
SNH1_lcmv_ex_S4_lane1
GEX mRNA library for LCMV Med LN SNH1


title: lcmv,GEX, lung + spleen

description:
SNH4_lcmv_ex_S6_lane1
GEX mRNA library for LCMV Med LN SNH4


title: gut, TCR

description:
220523_SNH_uLIPSTIC_gut_TCR_S5
TCR sequencing for gut IEL

value: TCR


title: FD treated, RNAseq, replicate 2


title: FD treated, RNAseq, replicate 1


title: FD control, RNAseq, replicate 5


title: FD control, RNAseq, replicate 4


title: FD control, RNAseq, replicate 3


title: FD control, RNAseq, replicate 2


title: WT control, RNAseq, replicate 6

value: WT

value: not applicable


title: WT control, RNAseq, replicate 5


title: FD control, RNAseq, replicate 1


title: lcmv,HTO,medLN + liver + lung

description:
SNH3_lcmv_HTO_S2_lane1
sample, biotin, and donor HTOs for LCMV Med LN SNH3
SNH3_barcodes.tsv.gz
SNH3_features.tsv.gz
SNH3_matrix.mtx.gz


title: WT control, RNAseq, replicate 3


title: WT control, RNAseq, replicate 4


title: WT control, RNAseq, replicate 1


title: IgD- Ighg2A10, WT_CSP27, VDJ

city: Canberra

first: Xin

last: Gao

state: ACT

address: 131 Garran Rd

department: Immunology

country: Australia

institute: The Australian National University

data_processing:
Data processing was performed by CellRanger V6.0 under default settings
Assembly: mm10
Supplementary files format and content: Sample1_MD4_CSP9_Processed.tar.gz
Supplementary files format and content: Sample2_MD4_CSP27_Processed.tar.gz
Supplementary files format and content: Sample3_WT_CSP9_Processed.tar.gz
Supplementary files format and content: Sample4_WT_CSP27_Processed.tar.gz

source_name: IgD- Ighg2A10, WT_CSP27

extract_protocol:
Mouse splenocytes were incubated with CITE-seq antibodies and flow cytometry antibodies, washed, and resuspend in sorting buffer (PBS+2% FBS) for sorting IgD- Ighg2A10 B cells. The sorted cells were pooled into 4 samples for library construction according to protocols by 10X Genomics
Library was performed according to 10X Genomic's instructions
scRNA-seq, CITE-seq, VDJ-seq

value: Mouse B cells


title: IgD- Ighg2A10, WT_CSP9, Antibody_Capture

source_name: IgD- Ighg2A10, WT_CSP9


title: IgD- Ighg2A10, WT_CSP9, VDJ


title: IgD- Ighg2A10, MD4_CSP27, Antibody_Capture

source_name: IgD- Ighg2A10, MD4_CSP27


title: IgD- Ighg2A10, WT_CSP27, Antibody_Capture


title: IgD- Ighg2A10, WT_CSP27, Transcriptome


title: IgD- Ighg2A10, WT_CSP9, Transcriptome


title: IgD- Ighg2A10, MD4_CSP27, Transcriptome


title: Colon, 28 Months, Rep14 [28M.N14]

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

institute: Christian-Albrechts-University Kiel

data_processing:
RNA was isolated using the QIAzol/chloroform extraction method. RNA quality was determined via an Agilent Bioanalyzer 2100 using the RNA 6000 nano kit (Agilent Technologies, Santa Clara, CA, USA). An RNA Integrity Number (RIN) value of greater than 7 was considered to be the minimum quality for sequencing.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions. All libraries were sequenced on an NovaSeq 6000 machine (Illumina, San Diego, CA, USA) with an average of 36 million paired-end reads (2x100 bp) at Competence Centre for Genomic Analysis (CCGA, Kiel, Germany) .
Illumina TruSeq adapter sequences were trimmed from forward and reverse reads using Cutadapt (2.8) with minimum sequence overlap of 3 bp, at most 10% mismatches allowed and minimum read length filter for 20 bp, as well as a two-color-chemistry aware, 3’-end quality trimming for a phred-score >= 25 (nextseq-trim=25).
An additional quality filter was applied with Prinseq lite (0.20.4) for at most 8 unknown nucleotides (‘N’) per read, an overall mean read quality of at least phred-score 15 and a minimum quality trim from both end of the read for a minimum phred-score of 12.
Filtered reads were then mapped against Mus musculus reference genome (GRCm38.p6, mm10) via Hisat2 (2.1.0) with RNA strandedness set to FR, employing non-deterministic random seeds and suppressing the mixed alignments of read pairs. Only primary alignments for each read were kept, via a filtering step (-F 256) with Samtools (1.9).
Gene counts were extracted using the tool featureCounts from the subread package (2.0.1) with reverse stranded information, while ignoring chimeric fragments and allowing only properly mapped read pairs with feature sizes in between 50 bp to 600 bp.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: Tabular delimited matrix text files of read counts per GRCm38 gene (rows) and sample (columns).

source_name: Colon

growth_protocol: All the mice were kept solely for aging in a controlled environment and health status.

extract_protocol:
RNA was isolated using the QIAzol/chloroform extraction method.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions.

value: Colon

tag: strain

tag: Sex

value: Male

value: 28 Months

tag: library batch

value: Prep  2


title: Colon, 28 Months, Rep17 [28M.N17]


title: Colon, 28 Months, Rep16 [28M.N16]

value: Prep  3


title: IgD- Ighg2A10, MD4_CSP27, VDJ


title: Colon, 28 Months, Rep12 [28M.N12]


title: Colon, 28 Months, Rep15 [28M.N15]


title: Colon, 28 Months, Rep18 [28M.N18]

value: Prep  1


title: Colon, 28 Months, Rep13 [28M.N13]


title: Colon, 28 Months, Rep10 [28M.N10]


title: IgD- Ighg2A10, MD4_CSP9, Antibody_Capture

source_name: IgD- Ighg2A10, MD4_CSP9


title: Colon, 28 Months, Rep9 [28M.N9]


title: Colon, 28 Months, Rep7 [28M.N7]


title: WT control, RNAseq, replicate 2

value: Distal radius and ulna

value: skeletal tissue


title: Colon, 28 Months, Rep6 [28M.N6]


title: Colon, 28 Months, Rep4 [28M.N4]


title: Colon, 28 Months, Rep5 [28M.N5]


title: Colon, 28 Months, Rep3 [28M.N3]


title: Colon, 28 Months, Rep2 [28M.N2]


title: Colon, 28 Months, Rep1 [28M.N1]


title: IgD- Ighg2A10, MD4_CSP9, VDJ


title: Colon, 24 Months, Rep15 [24M.N15]

value: 24 Months


title: Colon, 24 Months, Rep17 [24M.N17]


title: IgD- Ighg2A10, MD4_CSP9, Transcriptome


title: Colon, 24 Months, Rep16 [24M.N16]


title: Colon, 28 Months, Rep11 [28M.N11]


title: Colon, 24 Months, Rep10 [24M.N10]


title: Colon, 24 Months, Rep13 [24M.N13]


title: Colon, 24 Months, Rep12 [24M.N12]


title: Colon, 28 Months, Rep8 [28M.N8]


title: Colon, 24 Months, Rep9 [24M.N9]


title: Colon, 24 Months, Rep5 [24M.N5]


title: Colon, 24 Months, Rep8 [24M.N8]


title: Colon, 24 Months, Rep4 [24M.N4]


title: Colon, 24 Months, Rep2 [24M.N2]


title: Colon, 24 Months, Rep7 [24M.N7]


title: Colon, 24 Months, Rep6 [24M.N6]


title: Colon, 15 Months, Rep16 [15M.N16]

value: 15 Months


title: Colon, 24 Months, Rep3 [24M.N3]


title: Colon, 15 Months, Rep15 [15M.N15]


title: Colon, 24 Months, Rep1 [24M.N1]


title: Colon, 15 Months, Rep14 [15M.N14]


title: Colon, 15 Months, Rep13 [15M.N13]


title: Colon, 15 Months, Rep9 [15M.N9]


title: Colon, 15 Months, Rep12 [15M.N12]


title: Colon, 15 Months, Rep5 [15M.N5]


title: Colon, 24 Months, Rep14 [24M.N14]


title: Colon, 15 Months, Rep7 [15M.N7]


title: Colon, 15 Months, Rep10 [15M.N10]


title: Colon, 15 Months, Rep8 [15M.N8]


title: Colon, 15 Months, Rep6 [15M.N6]


title: Colon, 24 Months, Rep11 [24M.N11]


title: Colon, 15 Months, Rep4 [15M.N4]


title: Colon, 15 Months, Rep3 [15M.N3]


title: Colon, 15 Months, Rep11 [15M.N11]


title: Colon, 9 Months, Rep16 [9M.N16]

value: 9 Months


title: Colon, 9 Months, Rep15 [9M.N15]


title: Colon, 9 Months, Rep14 [9M.N14]


title: Colon, 9 Months, Rep13 [9M.N13]


title: Colon, 15 Months, Rep1 [15M.N1]


title: Colon, 9 Months, Rep10 [9M.N10]


title: Colon, 9 Months, Rep8 [9M.N8]


title: Colon, 15 Months, Rep2 [15M.N2]


title: Colon, 9 Months, Rep11 [9M.N11]


title: Colon, 9 Months, Rep9 [9M.N9]


title: Colon, 9 Months, Rep12 [9M.N12]


title: Colon, 9 Months, Rep7 [9M.N7]


title: Colon, 9 Months, Rep6 [9M.N6]


title: Colon, 9 Months, Rep5 [9M.N5]


title: Colon, 9 Months, Rep3 [9M.N3]


title: Colon, 9 Months, Rep4 [9M.N4]


title: Colon, 9 Months, Rep2 [9M.N2]


title: Colon, 9 Months, Rep1 [9M.N1]


title: Colon, 3 Months, Rep16 [3M.N16]

value: 3 Months


title: Colon, 3 Months, Rep13 [3M.N13]


title: Colon, 3 Months, Rep12 [3M.N12]


title: Colon, 3 Months, Rep11 [3M.N11]


title: Colon, 3 Months, Rep9 [3M.N9]


title: Colon, 3 Months, Rep10 [3M.N10]


title: Colon, 3 Months, Rep15 [3M.N15]


title: Colon, 3 Months, Rep4 [3M.N4]


title: Colon, 3 Months, Rep8 [3M.N8]


title: Colon, 3 Months, Rep2 [3M.N2]


title: Colon, 3 Months, Rep1 [3M.N1]


title: Colon, 3 Months, Rep3 [3M.N3]


title: Colon, 3 Months, Rep6 [3M.N6]


title: lung, D14 after orthotopic implantation of K7M2 cells in balb/c mice, biol rep 1

city: Guangzhou

first: Chuangzhong

last: Deng

state: Guangdong China

address: 651 Dongfeng East Rd

department: Department of Musculoskeletal Oncology

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTP
mRNA-seq reads were aligned to the GRCm38.102 genome assembly using Hisat2 version 2.1.0 with default parameters
Gene abundance measurements were generationed and normalized  using stringtie version 1.3.4b Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR function package in R program version 3.4.3
Assembly: GRCm38.102
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: lungs

extract_protocol:
Total RNA from BMDMs were isolated by TRIzol (Thermo Fisher Scientific, USA) and extracted by chloroform.
Sequencing libraries were generated using NEBNest UltraTM RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: lungs

value: balb/c


title: lung, D0 after orthotopic implantation of K7M2 cells in balb/c mice, biol rep 1


title: lung, D14 after orthotopic implantation of K7M2 cells in balb/c mice, biol rep 3


title: DBA mice, NS_Input, rep6

city: Kyoto

first: Shusaku

last: Uchida

state: Kyoto

address: 53 Kawaharamachi, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the mouse reference genome (mm10) using Tophat 2.0.13 (bowtie2-2.2.3), which can adequately align reads onto the location including splice sites in the genome sequence.
The aligned reads were subjected to downstream analyses using StrandNGS 2.6 software (Agilent Technologies). The read counts allocated for each gene and transcript (UCSC version 2013.3.6) were quantified using a Trimmed Mean of M-value (TMM) method.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count for each sample

extract_protocol:
mPFC tissues were removed, flash frozen on dry ice, and immunoprecipitation was performed with antibody against GFP. Then, RNA was extracted using Direct-zol RNA kit.
RNA sequencing libraries were prepared using SMART-Seq™ v4 Ultra™ Low Input RNA Kit (Takara-Bio) and TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s instructions. Libraries were sequenced on a NovaSeq 6000 (Illumina) with a configuration of 2 × 100 bp

value: Brain (mPFC)

value: mPFC (Bulk)

tag: subtype

value: NS

tag: rip antibody


title: lung, D0 after orthotopic implantation of K7M2 cells in balb/c mice, biol rep 3


title: DBA mice, NS_Input, rep3


title: lung, D14 after orthotopic implantation of K7M2 cells in balb/c mice, biol rep 2


title: DBA mice, NS_Input, rep5


title: DBA mice, NS_Input, rep4


title: Colon, 3 Months, Rep14 [3M.N14]

value: Colon


title: DBA mice, NS_Input, rep2


title: DBA mice, NS_Input, rep1


title: DBA mice, Subtype RES_Input, rep5

source_name: Subtype RES_Input

value: RES


title: DBA mice, Subtype RES_Input, rep6


title: DBA mice, Subtype RES_Input, rep4


title: DBA mice, Subtype RES_Input, rep3


title: DBA mice, Subtype RES_Input, rep2


title: Colon, 3 Months, Rep7 [3M.N7]

value: Male


title: Colon, 3 Months, Rep5 [3M.N5]

value: Prep  2


title: DBA mice, Subtype ANH_Input, rep6

source_name: Subtype ANH_Input

value: ANH


title: lung, D0 after orthotopic implantation of K7M2 cells in balb/c mice, biol rep 2


title: DBA mice, Subtype ANH_Input, rep2


title: DBA mice, Subtype ANH_Input, rep3


title: DBA mice, Subtype RES_Input, rep1


title: DBA mice, Subtype ANH_Input, rep5


title: DBA mice, Subtype SA:ANH_Input, rep6

source_name: Subtype SA:ANH_Input


title: DBA mice, Subtype ANH_Input, rep1


title: DBA mice, Subtype SA:ANH_Input, rep2


title: DBA mice, Subtype SA:ANH_Input, rep3


title: DBA mice, Subtype SA:ANH_Input, rep4


title: DBA mice, Subtype SA:ANH_Input, rep5


title: DBA mice, Subtype SA_Input, rep4

source_name: Subtype SA_Input

value: SA


title: DBA mice, Subtype SA_Input, rep6


title: DBA mice, Subtype SA:ANH_Input, rep1


title: DBA mice, Subtype SA_Input, rep2


title: DBA mice, Subtype SA_Input, rep1


title: DBA mice, NS_IP, rep6

value: aPVT projector

value: anti-GFP


title: DBA mice, NS_IP, rep4


title: DBA mice, NS_IP, rep3


title: DBA mice, NS_IP, rep2


title: DBA mice, Subtype RES_IP, rep6

source_name: Subtype RES_IP


title: DBA mice, NS_IP, rep1


title: DBA mice, Subtype ANH_Input, rep4


title: DBA mice, Subtype RES_IP, rep5


title: DBA mice, Subtype RES_IP, rep4


title: DBA mice, Subtype RES_IP, rep1


title: DBA mice, Subtype RES_IP, rep2


title: DBA mice, Subtype ANH_IP, rep6

description: ANH _IP_6

source_name: Subtype ANH_IP


title: DBA mice, Subtype ANH_IP, rep4

description: ANH _IP_4


title: DBA mice, Subtype RES_IP, rep3


title: DBA mice, Subtype ANH_IP, rep5

description: ANH _IP_5


title: DBA mice, Subtype ANH_IP, rep3

description: ANH _IP_3


title: DBA mice, Subtype SA_Input, rep5


title: DBA mice, Subtype SA_Input, rep3


title: DBA mice, Subtype SA:ANH_IP, rep6

source_name: Subtype SA:ANH_IP


title: DBA mice, Subtype SA:ANH_IP, rep5


title: DBA mice, Subtype ANH_IP, rep2

description: ANH _IP_2


title: DBA mice, Subtype ANH_IP, rep1

description: ANH _IP_1


title: DBA mice, Subtype SA:ANH_IP, rep3


title: DBA mice, Subtype SA:ANH_IP, rep4


title: DBA mice, NS_IP, rep5


title: DBA mice, Subtype SA:ANH_IP, rep1


title: DBA mice, Subtype SA_IP, rep6

source_name: Subtype SA_IP


title: DBA mice, Subtype SA_IP, rep4


title: DBA mice, Subtype SA_IP, rep3


title: DBA mice, Subtype SA_IP, rep2


title: DBA mice, Subtype SA_IP, rep1


title: Sample2_D21_Transcriptome

description: 10x Genomics

data_processing:
Cell Ranger (10X Genomics) was used to process the V(D)J, Feature Barcode and GEX sequences and prepare them for downstream analysis.
Seurat (version 3.1) (Butler et al., 2018) was used for graph-based clustering and visualizations of the gene expression data and demultiplexing.
The Immcantation portal were used to convert the 10X V(D)J output from CellRanger into an AIRR community standardized format to allow for further downstream analysis.
Assembly: mm10
Supplementary files format and content: Standard Cellranger output.

source_name: Spleen

extract_protocol:
2x10^4 probe+ CD19+ Ighg2A10 B cells were transferred into recipient mice. 1-2 days later mice were immunized IV with 5x10^4 irradiated Pb-PfCSP sporozoites. At either 7 or 21 days post immunization mice were euthanized, spleens collected and probe+ IgD- Ighg2A10 B cells stained with TotalSeq-C feature and hashtag antibodies were isolated and sorted. Cells were then loaded into a Chromium (10x Genomics).
Indexed V(D)J, Feature Barcode and GEX libraries of sorted samples were prepared according to the protocol for Single Indexed 10X Genomics V(D)J 5' kit for mice with Feature barcoding kit (10X Genomics).Libraries were then sequenced using an Illumina NovaSeq6000.

value: Spleen

value: B cell (probe+ IgD- Ighg2A10)

value: Immunized with irradiated sporozoites

tag: time point


title: Sample2_D21_VDJ

description: 10x Genomics


title: Sample2_D21_Antibody_Capture

description: 10x Genomics


title: Sample1_D7_VDJ

description: 10x Genomics


title: Sample1_D7_Antibody_Capture

description: 10x Genomics


title: DBA mice, Subtype SA:ANH_IP, rep2


title: Untrained,replicate 2, scRNAseq

city: Suzhou

first: Yaobo

last: Liu

state: Jiangsu

address: 199 Ren-Ai Road, Suzhou Industrial Park

department: Institute of neuroscience

institute: Soochow University

data_processing:
FPKM
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: Spinal cord

extract_protocol:
Spinal cord motoneurons of mice in the sham group (n = 3 mice), untrained group (n = 3 mice), 10-20 Hz SBES group (n = 3 mice), were labeled with TRDA and sacrificed 4 weeks after SCI. The freshly isolated spinal cord was sliced on a Vibratome (Leica, Germany) into 200- to 300-μm-thick coronal sections. Fluorescence-labeled motoneurons were visualized under a fluorescence microscope (Zeiss) using a miniature operating system (Eppendorf, Germany), and the motoneurons were aspirated by glass electrodes and placed in preservation solution (Invitrogen, USA).
First, reference genome sequences and gene model annotation files of related species were downloaded from genome websites such as UCSC, NCBI, and ENSEMBL. Second, Hisat2 software (v2.0.1, http://daehwankimlab.github.io/hisat2/) was used to index the reference genome sequence. Finally, clean data were aligned to the reference genome via Hisat2 software (v2.0.1). Then, transcripts in FASTA format were converted from known gff annotation files and indexed properly. Then, with the file that served as the reference genome file, HTSeq (v0.6.1, https://htseq.readthedocs.io/en/master/) was used to estimate gene and isoform expression levels from the paired-end clean data. Differential expression analysis was performed using the DESeq2 Bioconductor package, a model based on a negative binomial distribution. The estimates of dispersion and logarithmic fold changes incorporated data-driven prior distributions 63, and the adjusted p-value of the genes was set to <0.05 to detect differentially expressed genes.

value: Spinal cord

tag: cell line

value: Motorneuron

value: Neuron

value: WT

value: Spinal cord injury


title: Untrained,replicate 1, scRNAseq


title: SBES 20Hz, replicate 3, scRNAseq

value: Spinal cord injury,Synergistic bidirectional electrical stimulation


title: SBES 15Hz, replicate 2, scRNAseq


title: Untrained,replicate 3, scRNAseq


title: SBES 10Hz, replicate 1, scRNAseq


title: Sham, replicate 3, scRNAseq


title: Liver, Semaglutide, rep 8

city: Suwon-si

first: Hyeong min

last: Lee

address: 304, Sinwon-ro

department: Reasearch

country: South Korea

institute: Glaceum

data_processing:
RNA quality was assessed using an Agilent Bioanalyzer, and the samples had average RNA Integrity Number (RIN) value of 8.1 ± 0.7 and 7.3 ± 0.9, respectively
Alignment to human reference genome using HISAT2 program for read mapping
Transcript assembly was performed with StringTie program. DESeq2 was used to identify differentially expressed genes
Assembly: StringTie
Supplementary files format and content: tab-delimited text files include FPKM for each Sample

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
The libraries were prepared with the Illumina TruSeq Stranded mRNA kit and sequenced using the high output on NovaSeq 6000 platform yielding 101bp paired end reads

value: Liver

value: Semaglutide


title: Liver, Semaglutide, rep 7


title: Liver, Semaglutide, rep 6


title: Liver, Semaglutide, rep 5


title: DBA mice, Subtype SA_IP, rep5

value: Brain (mPFC)


title: Liver, Semaglutide, rep 4


title: Liver, Semaglutide, rep 3


title: Liver, Semaglutide, rep 2


title: Liver, Semaglutide, rep 1


title: Liver, Vutiglabridin, rep 8

value: Vutiglabridin


title: Liver, Vutiglabridin, rep 7


title: Liver, Vutiglabridin, rep 6


title: Liver, Vutiglabridin, rep 5


title: Liver, Vutiglabridin, rep 4


title: Sample1_D7_Transcriptome

description: 10x Genomics


title: Liver, Vutiglabridin, rep 3


title: Liver, Vutiglabridin, rep 2


title: Liver, Vutiglabridin, rep 1


title: Sham, replicate 2, scRNAseq


title: Liver, Vehicle, rep 8

value: Vehicle


title: Liver, Vehicle, rep 1


title: Liver, Vehicle, rep 2


title: Sham, replicate 1, scRNAseq


title: Liver, Vehicle, rep 3


title: Liver, Vehicle, rep 6


title: PS-COOH-1

city: Anyang

first: Junjie

last: Zhao

address: No.38 of Huanghe Street

institute: Institute of Cotton Research

data_processing:
Illumina Hiseq platform used for basecalling.
Clean Reads was compared with the reference genome using HISAT2 software to obtain the localization information of Reads on the reference genome.
Fragments per kilobase of transcript per million fragments (FPKM) mapped was applied to measure the expression level of a gene or transcript using StringTie
Assembly: ftp://ftp.bioinfo.wsu.edu/species/Gossypium_hirsutum/UTX-TM1_v2.1/genes/
Supplementary files format and content: Tab-delimited text files include FPKM values for all Samples.

organism: Gossypium hirsutum

source_name: Root

extract_protocol:
Roots cultured on 0 and 300 mg/l PS-COOHs concentrations for 9 days are used to extract RNA.The total RNA was extracted using TRIzol reagent (Invitrogen, California, USA). Then, the RNAs’ purity and quantity were checked using an RNA Nano 6000 Assay Kit for the Bioanalyzer 2100 system (Agilent Technologies, California, USA). Afterwards, approximately 10 µg of total RNA was used for RNA-seq library  construction.
RNA libraries were prepared for sequencing using standard Illumina protocols. And 150-bp paired-end reads were produced.

value: Root


title: PS-COOH-2


title: CK-3


title: Liver, Vehicle, rep 7


title: CK-2


title: CK-1


title: Liver, Vehicle, rep 5


title: PS-COOH-3


title: Liver, Vehicle, rep 4


title: Hippocampus, Trem2 KO, rep 2

city: Rozzano

first: Simona

last: Lodato

address: via Manzoni 56

country: Italy

institute: IRCCS Humanitas Research Hospital

description:
2 Males
10x Genomics

data_processing:
The demultiplexing was made using the BCL Convert software v3.8.2 (https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html)
The  barcoded processing and gene counting were made using the Cell Ranger software v6.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Freshly collected hippocampi from Trem2 P1 pups were dissected into ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.3) to remove fibers. Single cell dissociation was performed by incubation of tissue with papain dissociation solution according to the manufactured instructions (Papain Dissociation System Worthington #LK003150) in a shaking incubator for 30 minutes at 37°C. After incubation the tissue was mechanically dissociated into single cell suspension and the cells were washed and re-suspended in PBS supplemented with 0.02% w/v BSA for cell counting and viability assessment.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, single-end constructs with P5 and P7 sequences and a sample index were added.

value: Hippocampus

value: Trem2 knock-out

tag: number of_mice

value: male and female


title: Hippocampus, Trem2 WT, rep 2

description:
2 Males
10x Genomics

value: wild type


title: Hippocampus, Trem2 KO, rep 3

description:
1 Female  +1 Male
10x Genomics


title: Male Aedes albopictus-3

first: Jinbao

last: Gu

state: Guangdong

address: No. 1023, Shatai South Road

department: Department of Pathogen Biology, School of Public Health

institute: Southern Medical University

description:
TMM_normalized_CPM.txt
circRNA_reads_count.txt

data_processing:
TMM (trimmed mean of M-values) was used to normalize the circRNA expression
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence, then mapped to Aedes albopictus whole genome using Bowtie2 v2.1.0
Assembly: Aedes albopictus
Supplementary files format and content: tab-delimited txt file includes TMM values for each Sample
Supplementary files format and content: Matrix table with circRNA reads count for every circRNA and every sample

organism: Aedes albopictus

source_name: whole body

extract_protocol:
total RNA  was extracted with Takara RNAiso Plus (Takara, Dalian, China)
circRNA-seq library was prepared with approximately 1μg of total RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina® (Kapa Biosystems, Inc., Woburn, MA) and using RNase R (geneseed, Inc., Guangzhou, China) to digest linear RNA . Briefly, ribosomal RNA was removed from the total RNA. Next, the ribominus RNAs were fragmented and then first strand and directional second strand synthesis were performed. Then the A tailing and adapter ligation were performed with the purified cDNA. Finally, the purified, adapter-ligated DNA was amplified. The library quality and concentration was assessed by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer.
HiSeq X10 PE150
circRNA-seq

value: whole body

value: Foshan

value: Male


title: S63del-4 [A12]

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
Illumina Pipeline  Casava 1.9
Reads were aligned to GRCm38/mm10 genome using the STAR aligner
Data were analyzed using DEseq2
Assembly: mm10
Supplementary files format and content: TPM_values wt Xbp1ko.csv is TPM values for wild type and Xbp1ko samples
Supplementary files format and content: Differential_expression_analysis_table wt Xbp1 ko.csv is differential expression analysis for Xbp1ko samples vs. wild type
Supplementary files format and content: TPM_values wt S63del.csv is TPM samples  for wild type and Xbp1ko samples
Supplementary files format and content: Differential_expression_analysis_table wt S63del.csv is differential expression analysis of S63del vs. wild type samples
Supplementary files format and content: TPM_values S63del S63delXbp1ko.csv is TPM values for S63del and S63del/Xbp1ko samples
Supplementary files format and content: Differential_expression_analysis_table S63del S63delXbp1ko.csv  is differential expression analysis forS63del/Xbp1ko vs. S63del samples

source_name: sciatic nerve

growth_protocol: Mice were housed with a normal light/dark cycles and ad libitum access to chow and water.

extract_protocol:
Total RNA was purified from sciatic nerve using Zymo RNA Clean & Concentrator-5 (#R1013)
Illumina, RNA with PolyA selection,
Illumina HiSeq 2x150bp, performed by Genewiz (South Plainfield, NJ)

treatment_protocol: We initially crossed  Mpz S63del  mice with XBP1f/f mice to obtain S63del/XBP1f/+ and P0Cre/XBP1f/+ mice that were then intercrossed to obtain the four experimental groups WT, P0Cre/XBP1f/f (for the Schwann cell specific ablation of XBP1, XBP1SC-KO mice herein), S63del and S63del/P0Cre/XBP1f/f (S63del/XBP1SC-KO herein).S63del were maintained on the FVB/N background, whereas P0Cre, XBP1f/f and ROSA26-XBP1s were on C57BL/6 genetic background. The analysis of all experimental genotypes was performed in F1 hybrid background FVB // C57BL6.

value: sciatic nerve

value: Mpz S63del


title: Hippocampus, Trem2 WT, rep 1

description:
1 Female  +1 Male
10x Genomics


title: S63del//XBPKO-1 [B1]


title: S63del//XBPKO-3 [B3]


title: S63del//XBPKO-2 [B2]


title: S63del-3 [A11]


title: Male Aedes albopictus-1


title: S63del-2 [A10]


title: Female Aedes albopictus-3

value: Female


title: S63del//XBPKO-4 [B4]


title: Hippocampus, Trem2 WT, rep 3

description:
1 Female  +1 Male
10x Genomics


title: Female Aedes albopictus-1


title: S63del-1 [A9]


title: XBPKO-3 [A7]


title: wt-4 [A4]


title: C5S7

city: Stockholm

first: David

last: Brodin

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.7).
Reads were aligned to a reference built from Ensembl GRCh38 genome sequences using STAR (v2.6.1d).
Counts for each gene were obtained using featureCounts (v1.5.1) using the GRCm38.101 GTF file from Ensembl.
Bioconductor package DESEq2 was used for count normalization and sample group comparisons, generating log2 fold changes, Wald test p-values and p-value adjustments for multiple testing (Benjamini-Hochberg method).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited matrix of raw counts for all samples

organism: Homo sapiens

source_name: Monocyte-derived dendritic cells

growth_protocol: Peripheral blood mononuclear cells were isolated from buffy coats of six healthy donors in Copenhagen, Denmark, using Ficoll separation. Monocytes were positively selected with anti-CD14 antibodies via magnetic cell sorting (MACS, Miltenyi). After viability assessment using trypan blue dye exclusion, monocytes were seeded at 1.25 x 10^6 cells/mL in R10 medium (RPMI medium with 10% FBS and 1% penicillin). They were then cultured in a flask at 37°C with 5% CO2 for four days in the presence of IL-4 and GM-CSF (both at a concentration of 12.5 ng/mL, R&D Systems).

extract_protocol:
RNA was isolated with the RNAeasy kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. RLT buffer was added to the cells, loaded to the RNAeasy spin minicolumn and the RNA eluted in RNA-free water. RNA quality was verified by gel electrophoresis. RNA concentration and purity were evaluated by Nanodrop (Thermo Fisher) with a mean concentration RNA level of 71.7 ng/μL and a mean A260/A280 ratio of 2.0.
Samples were normalized to 50 ng/μl and the RNAseq libraries were prepared using the mRNA seq Illumina TrueSeq

treatment_protocol: MoDCs were plated at 10^6 cells per well in 24-well plates, and stimulated for 20 minutes with Al-CPI at concentrations of 0.1 µM or 1 µM, or with Ascaris body fluid (ABF) at 50 µg/mL. For wells stimulated with LPS (alone or Al-CPI + LPS), LPS was added at a final concentration of 10 ng/mL. Stimulated moDCs were cultured for 5 hours at 37°C, and cell pellets were stored at -80°C until RNA extraction.

value: Monocyte-derived dendritic cells

value: LPS + ABF


title: C6S7


title: C4S7


title: C3S7


title: XBPKO-1 [A5]


title: XBPKO-4 [A8]


title: wt-3 [A3]


title: C2S7


title: C1S7


title: wt-2 [A2]


title: Male Aedes albopictus-2


title: C5S6

value: LPS + Al-CPI 0.1 uM


title: wt-1 [A1]


title: C6S6


title: SA:ANH-KDM5Ci_2

source_name: DBA mice, SA:ANH subtype_KDM5Ci

extract_protocol:
mPFC tissues were removed, flash frozen on dry ice, and RNA was extracted using Direct-zol RNA kit.
SureSelect Strand-Specific RNA Library Prep for Illumina (Agilent Technology) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: Brain (mPFC)

value: smSDS_SA:ANH subtype_KDM5Ci


title: SA:ANH-KDM5Ci_3


title: C4S6


title: SA:ANH-KDM5Ci_1


title: Female Aedes albopictus-2


title: XBPKO-2 [A6]


title: SA:ANH-vehicle_3

source_name: DBA mice, SA:ANH subtype_saline

value: smSDS_SA:ANH subtype_Saline


title: C3S6


title: SA:ANH-vehicle_2


title: SA:ANH-vehicle_1


title: C2S6


title: NS_2

source_name: DBA mice, non-stress_saline


title: C6S5

value: LPS + Al-CPI 1 uM


title: C5S5


title: C3S5


title: C4S5


title: C1S5


title: C2S5


title: C6S4

value: Al-CPI 0.1 uM


title: NS_1


title: C4S4


title: C5S4


title: C3S4


title: C2S4


title: C1S4


title: C1S6


title: C6S3

value: Al-CPI 1 uM


title: NS_3


title: C5S3


title: SymptomaticCMV_8

type: RNA

city: Nagoya city

first: Yuka

last: Torii

address: Showa-ku Tsurumai-cho 65

institute: Nagoya University

description: miRNA expression of urine exosomes

hyb_protocol: Cy3-labelled RNA was hybridized at 55°C for 20 hr using miRNA Complete Labeling and Hyb Kit according to the manufacturer’s instructions.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Urine Exosome

label_protocol: Samples were processed with the miRNA Complete Labeling & Hybridization Kit (Agilent Technologies) according to the manufacturer's instructions.

extract_protocol: Urine exosomes were extracted from 1.5 mL of urine using an Exo-urine EV Isolation kit (System Biosciences, Palo Alto, CA, USA) according to the manufacturer’s instructions. CSF exosomes were extracted from 1000 µL CSF using a miRCURY Exosome Cell/Urine/CSF kit (Qiagen, Hilden, Germany). MiRNAs were extracted from urine exosomes using an EVery EV RNA Isolation Kit (System Biosciences) according to the manufacturer’s instructions.

value: Urine

tag: age,days

tag: molecule subtype

value: microRNA

tag: subject status

value: SymptomaticCMV


title: SymptomaticCMV_7

description: miRNA expression of urine exosomes

tag: tissue


title: SymptomaticCMV_6

description: miRNA expression of urine exosomes


title: C4S3

tag: cell type

tag: treatment


title: SymptomaticCMV_11

description: miRNA expression of urine exosomes


title: SymptomaticCMV_9

description: miRNA expression of urine exosomes


title: SymptomaticCMV_10

description: miRNA expression of urine exosomes


title: C2S3


title: C3S3


title: Late-OnsetSymptomaticCMV_1

description: miRNA expression of urine exosomes

value: Late-OnsetSymptomaticCMV


title: SymptomaticCMV_4

description: miRNA expression of urine exosomes


title: SymptomaticCMV_3

description: miRNA expression of urine exosomes


title: SymptomaticCMV_5

description: miRNA expression of urine exosomes


title: C1S3


title: SymptomaticCMV_1

description: miRNA expression of urine exosomes


title: C6S2

value: LPS


title: AsymptomaticCMV_7

description: miRNA expression of urine exosomes

value: AsymptomaticCMV


title: C5S2


title: C4S2


title: AsymptomaticCMV_6

description: miRNA expression of urine exosomes


title: C3S2


title: AsymptomaticCMV_5

description: miRNA expression of urine exosomes


title: AsymptomaticCMV_4

description: miRNA expression of urine exosomes


title: AsymptomaticCMV_3

description: miRNA expression of urine exosomes


title: C1S2


title: C2S2


title: SymptomaticCMV_2

description: miRNA expression of urine exosomes


title: C4S1

value: Control


title: AsymptomaticCMV_1

description: miRNA expression of urine exosomes


title: HealthyControl_11

description: miRNA expression of urine exosomes

value: HealthyControl


title: C2S1

value: Monocyte-derived dendritic cells


title: HealthyControl_10

description: miRNA expression of urine exosomes


title: AsymptomaticCMV_2

description: miRNA expression of urine exosomes


title: HealthyControl_7

description: miRNA expression of urine exosomes


title: HealthyControl_9

description: miRNA expression of urine exosomes


title: HealthyControl_8

description: miRNA expression of urine exosomes


title: C5S1


title: Liver ECs, WT, ABP615

city: Madrid

first: Elena

last: Piñeiro-Yáñez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description:
ABP615
counts.tsv
normalizedcounts.tsv

data_processing:
RNA sequencing data was analyzed using the cluster_RNAseq pipeline (https://github.com/cnio-bu/cluster_rnaseq) as follows:
Quality control of fastq files was done using FastQC (version 0.11.9) and FastQ-Screen (version 0.15.2)
PolyA tails and adapters were removed using BBDuk (BBMap version 39.01-1) (parameters used were k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20)
Resulting reads were aligned to the GRCm39 version of the mouse reference genome using STAR (version 2.7.10b) (parameters used were –outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate)
Genomic feature counts were obtained using featureCounts (Subread version 2.0.0) (with -s 1 option)
For differential expression analysis, DESeq2 (version 1.30.1) was used
Gene set enrichment analysis was performed with GSEA (version 4.2.2). The parameters used for the GSEA analysis were the default ones except for: -collapse No_Collapse, -permute gene_set, -plot_top_x 100, and -set_min 10
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text file including raw counts from DESeq2 for each sample
Supplementary files format and content: tab-delimited text file including normalized counts from DESeq2 for each sample

source_name: liver

extract_protocol:
RNA was extracted using Direct-zol RNA Minipreps Kits (ZYMO RESEARCH #R2050)
Total RNA samples (300ng; RQS/RIN average 6.8, range 5.7-7.8) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq V2 Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 191). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina instrument by following manufacturer's protocols.

value: liver

value: Primary endothelial cells

tag: genotype

value: WT

tag: age


title: Liver ECs, WT, ABP617

description:
ABP617
counts.tsv
normalizedcounts.tsv


title: C3S1


title: HealthyControl_6

description: miRNA expression of urine exosomes


title: C1S1


title: Liver ECs, WT, ABP613

description:
ABP613
counts.tsv
normalizedcounts.tsv


title: HealthyControl_5

description: miRNA expression of urine exosomes


title: HealthyControl_3

description: miRNA expression of urine exosomes


title: C6S1


title: Liver ECs, WT, ABP611

description:
ABP611
counts.tsv
normalizedcounts.tsv


title: HealthyControl_2

description: miRNA expression of urine exosomes


title: Liver ECs, WT, ABP609

description:
ABP609
counts.tsv
normalizedcounts.tsv


title: HealthyControl_1

description: miRNA expression of urine exosomes


title: p119-bc_028_HiC

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description: mOSN

library_source: genomic

data_processing:
RNA reads were mapped to mm10 transcriptome reference using hisat2.
Gene expression were quantified using RSEM.
Hi-C reads were processed and analysed using Dip-C and hickit package.
We generated three replicate structures (_1.3dg.gz, _2.3dg.gz and _3.3dg.gz) per cell reconstructed with different random seeds (1-3).
We pooled Hi-C samples for each group.
Assembly: mm10
Supplementary files format and content: .hic
Supplementary files format and content: .3dg
Supplementary files format and content: .allValidPairs.txt.gz

molecule: genomic DNA

source_name: mouse olfactory epithelium

extract_protocol:
The main olfactory epithelium was dissected and minced to small pieces, then was dissociated into single cell suspension with the Papain Dissociation System (Worthington Biochemical, Cat. #LK003150) at 37°C for 15 min, during incubation, titration every 5 min with wide-bore pipette tip according to previously described2. Then filtered with 30 μm strainer (MACS), then wash twice with ice-cold 1 x PBS.
simultaneous 3D genome and gene expression by LiMCA
Smart-seq2 for LiMCA RNA library; Dip-C protocol for LiMCA Hi-C library

value: mouse olfactory epithelium

value: postnatal day 119

value: bc


title: p119-bc_027_HiC

description: mOSN


title: Liver ECs, Li-TSC1 KO RagA GTP, ABP608

description:
ABP608
counts.tsv
normalizedcounts.tsv

value: Li-TSC1 KO RagA GTP


title: Liver ECs, Li-TSC1 KO RagA GTP, ABP606

description:
ABP606
counts.tsv
normalizedcounts.tsv


title: p119-bc_026_HiC

description: mOSN


title: p119-bc_025_HiC

description: iOSN


title: p119-bc_024_HiC

description: iOSN


title: p119-bc_023_HiC

description: mOSN


title: p119-bc_022_HiC

description: mOSN


title: Liver ECs, Li-TSC1 KO RagA GTP, ABP614

description:
ABP614
counts.tsv
normalizedcounts.tsv


title: Skin, KO, Naïve

city: Seoul

first: Soon Young

last: Shin

address: 120 Neungdong-ro, Gwangjin-gu,

institute: Konkuk university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: skin

growth_protocol: All mice were housed at a temperature of 20 ± 2°C, and the relative humidity was maintained at 50 ± 10% under a 12 h-12 h light-dark cycle. Egr1-/- mice generated on a C57BL6 background. Offsprings produced by intercrosses between homozygous and heterozygous mice were genotyped by PCR to identify both wild-type and Egr1 knockout mice.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Egr1+/+ and Egr1-/- mice were randomly divided into two groups: naive and HDM creams. After the hair on the ear-neck skin was shaved, sodium dodecyl sulfate (SDS) solution was evenly applied on the shaved skin and both ears of the skin to create skin barrier disruption. After 2-3 h, the solution was dried, and 100 mg of the HDM cream was uniformly dispersed on the shaved neck and ear surfaces. All procedures were conducted twice per week for three weeks.

value: skin

tag: developmental stage

value: adult

value: Egr1 knockout

value: SDS


title: Skin, KO, HDM-challenged

tag: strain

value: SDS+HDM extract


title: Skin, WT, HDM-challenged

value: Wild type


title: p119-bc_020_HiC

description: mOSN


title: p119-bc_019_HiC

description: iOSN


title: 3T3 HNF4OE-ATAC

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

data_processing:
All reads were mapped to the mm10 genome using the BWA-MEM aligner version 0.7.13.
BAM files were filtered using the encode_task_filter.py script from the ENCODE chip-seq-pipeline2.
MACS2 was used to call peaks using the parameters “-p 0.01 -f BAMPE  -g hs” for the CUT&RUN and CUT&Tag data, and “-p 0.01 -g hs --nomodel --shift -75 --extsize 150” for the ATAC-seq data.
Bigwig files were generated from the filtered BAM files using MACS2 bdgcmp using the fold enrichment option for the ATAC-seq data and deepTools bamCoverage with the options "--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2864785220 --extendReads" for the CUT&Tag and CUT&RUN data
Assembly: mm10
Supplementary files format and content: Track in Bigwig format

extract_protocol:
3T3 cells were treated with accutase and harvested for CUT&Tag and ATAC-seq. For liver samples, 3-5mg For liver samples, 3-5mg of liver tissues was pulverized using liquChIP-seq, CUT&Tag and ATAC-seq.ogen and used for CUT&Tag
NEBnext DNA Ultra ii (New England Biolabs)

value: Mouse fibriblast

value: NIH3T3 cells with HNF4A Ectopic expression


title: 3T3 HNF4OE-MLL4-CT

data_processing:
All reads were mapped to the mm10 genome using the BWA-MEM aligner version 0.7.13.
BAM files were filtered using the encode_task_filter.py script from the ENCODE chip-seq-pipeline2.
MACS2 was used to call peaks using the parameters “-p 0.01 -f BAMPE  -g hs” for the CUT&RUN and CUT&Tag data, and “-p 0.01 -g hs --nomodel --shift -75 --extsize 150” for the ATAC-seq data.
Bigwig files were generated from the filtered BAM files using MACS2 bdgcmp using the fold enrichment option for the ATAC-seq data and deepTools bamCoverage with the options "--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2864785220 --extendReads" for the CUT&Tag and CUT&RUN data
Assembly: mm10
Supplementary files format and content: Track in Bigwig format
Library strategy: CUT&Tag

tag: antibody


title: Skin, WT, Naïve


title: p119-bc_017_HiC


title: 3T3 Control-ATAC

value: NIH3T3 cells with empty vector


title: 3T3 Control-MLL4-CT


title: p119-bc_016_HiC


title: Liver ECs, Li-TSC1 KO RagA GTP, ABP607

description:
ABP607
counts.tsv
normalizedcounts.tsv


title: 3T3 HNF4OE-H3K27ac-CT


title: 3T3 Control-H3K27ac-CT


title: p119-bc_015_HiC

description: mOSN


title: 3T3 HNF4OE-H3K4me1-CT


title: 3T3 Control-H3K4me1-CT


title: p119-bc_012_HiC


title: p119-bc_021_HiC

description: mOSN


title: 3T3 HNF4a-CT


title: p119-bc_013_HiC

description: mOSN


title: KO-liver-MLL4-CT

value: Liver


title: WT-liver-MLL4-CT


title: p119-bc_011_HiC


title: p119-bc_010_HiC

description: mOSN


title: KO-liver-H3K27ac-CT


title: p119-bc_009_HiC

description: mOSN


title: p119-bc_008_HiC

description: mOSN


title: WT-liver-H3K27ac-CT


title: p119-bc_006_HiC

description: mOSN


title: p119-bc_007_HiC

description: mOSN


title: KO-liver-ATAC


title: WT-liver-ATAC


title: KO-liver-H3K4me1-ChIP


title: HealthyControl_4

description: miRNA expression of urine exosomes

value: Urine

value: microRNA

value: HealthyControl


title: p119-bc_018_HiC

value: mouse olfactory epithelium

value: WT


title: p119-bc_004_HiC

value: postnatal day 119

value: bc


title: WT-liver-H3K4me1-ChIP


title: E95_Brd4_cKO2 (NextSeq500)

city: San Francisco

first: Angelo

last: Pelonero

state: CA

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

description: Single cell transcriptomes from cardiogenic region from E9.5 Brd4 flox homozygous; Mef2c-AHF-Cre heterozygous mouse embryo

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger Suite (3.0.2) from 10X genomics
Additional filtering, quality control and doublet removal was done using Seurat v3 according to specifications in the tutorials (https://satijalab.org/seurat/pbmc3k_tutorial.html)
Genome_build: mm10
Supplementary_files_format_and_content: normalized gene-cellbarcode expression matrix in csv format

source_name: Embryonic mouse heart at E9.5

growth_protocol: Timed matings were set up between male mice that were compound heterozygous for the Brd4 floxed allele and Mef2c-AHF-cre allele and Brd4 floxed homozygous female mice. Morning of plug detection was considered E0.5 and embryos were harvested at embryonic day (E)9.5

extract_protocol:
35ul of single cell suspensions were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN- 1000121) and Chromium i7 Multiplex Kit (PN-120262).

treatment_protocol: Embryos were dissected in PBS and 1% FBS on ice. Cardiogenic tissue regions were microdissected and dissociated in 200ul TryplE for 5 minutes at 37C followed by brief trituration and incubation for an additional 5 minutes. TryplE was quenched with 600ul PBS/1% FBS and centrifuged at 150 rcf for 3 minutes and resuspended in 35ul of PBS/1% FBS

value: Embryonic mouse heart at E9.5

value: Brd4 flox/flox; Mef2c-AHF-cre

tag: specific heart region

value: Cardiogenic region

tag: additional cell lineages present in dataset

value: Non-cardiac mesoderm, ectoderm and endoderm


title: p119-bc_014_HiC

description: mOSN


title: p119-bc_001_HiC

description: mOSN


title: p119-bc_002_HiC

description: iOSN


title: E95_Brd4_flox2 (NextSeq500)

description: Single cell transcriptomes from cardiogenic region from E9.5 Brd4 flox homozygous mouse embryo

value: Brd4 flox/flox


title: E95_Brd4_cKO1 (NextSeq500)


title: p111-bc_006_HiC

value: postnatal day 111


title: p111-bc_007_HiC

description: iOSN


title: Library_286_S8

description: Brd4 2nd HF deletion using Isl1-Cre; Micro-dissected RV and OFTs of E9.5-E10.5 embryos

data_processing:
Raw reads were trimmed with Trimmomatic v0.32
aligned to mm10 genome using STAR (10) (version 2.6.0c)
filtered using samtools view with ‘-F 4 -q 10’ parameters
reads quantified with Rsubread featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: gene-cellbarcode expression matrix in txt (tab-delimited) format

source_name: Embryonic mouse heart

growth_protocol: NA - freshly dissected cardiac tissue as described below

extract_protocol:
Microdissected E9.5 hearts and the pharyngeal mesoderm immediately posterior to the outflow tract and anterior to the neural tube were isolated into Trizol and RNA was obtained using Qiagen RNeasy spin columns, with on-column DNAse I digestion following manufacturer’s directions.
Bulk RNA libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) to enrich poly-A tailed RNA molecules. Libraries were PCR’ed with single end barcodes using Illumina Multiplex Oligos (NEB).

value: Embryonic mouse heart

value: micro-dissected RV and OFT

value: Isl1-Cre; Brd4flox/flox

tag: group

value: Mutant


title: p111-bc_004_HiC

description: mOSN


title: p119-bc_005_HiC

description: mOSN


title: p111-bc_005_HiC

description: mOSN


title: Library_285_S2


title: p111-bc_003_HiC

description: mOSN


title: Library_292_S10

value: Isl1-Cre; Brd4flox/+

value: Control


title: p111-bc_002_HiC

description: mOSN


title: Library_291_S1


title: p111-bc_001_HiC

description: mOSN


title: Chp1-GFP yeast SeRP, total translatome, rep1

status: Public on Jan 16 2024

city: Heidelberg

first: Ilgin

last: Kotan

address: Im Neuenheimer Feld 329

institute: Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)

description: Chp1 SeRP total

data_processing:
3’ Adapters were trimmed using Cutadapt v 3.2 with the following command: cutadapt --cores=8 --nextseq-trim=20 -m23 --discard-untrimmed -O6 -a ATCG-TAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o '/'outfile.fastq.gz' '/infile.fastq.gz' 1> '/'Cutadapt_report.txt. Unique molecular identifiers (UMI) were removed using a custom Julia script (Script 1). julia -p 8 '.jl' '<input_path>/'infile.fastq.gz' '<input_path>/outfile.fastq.gz' --umi3 5 --umi5 2.
To remove rRNA, the reads were aligned to S. cerevisiae rRNA sequences with bowtie2 v 2.4.2 and only the reads that do not align were kept: bowtie2 -p8 -t -x '<ref_file_path>' -q infile.fastq.gz' --un '<outfile_path>/outfile.fastq' -S /dev/null 2> '<outfile_path>/Bowtie2_report.txt'.
The remaining rRNA depleted reads were aligned to the S. cerevisiae S288C Genome (Assembly: GCA_000146045.2) with STAR v 2.7.7a. The TEF2 entry in the fasta file was removed to allow both TEF1 and TEF2 reads to align to the TEF1 sequence. The STAR index with the modified fasta file was generated using the following command: STAR --runMode genomeGenerate --runThreadN 8 --genomeDir <input_path> --genomeFastaFiles infile.dna.toplevel.fa --genomeSAindexNbases 10 --sjdbGTFfile <out-file_path>/outfile.gtf. As TEF1 and TEF2 differ from each other by two mutations at position 762 (T->C), and position 834 (T->C), the threshold for the allowed maximum number of mismatches per pair was set to 2. The alignment was performed with the following command: STAR --runThreadN 7 --genomeDir '<ref_file_path>' --readFilesIn '<infile_path>/infile.fastq' --outSAMmultNmax 1 --outFilterType BySJout --outFilterMismatchNmax 2 --alignIntronMin 5 --outFileNamePrefix '<outfile_path>' --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All XS --quantMode GeneCounts --twopassMode Basic --limitBAMsortRAM 1185598524.
Reads from PCR duplicates were collapsed to a single read and positions of ribosomal a, p, and e-sites on footprints were assigned with a custom Julia script (Script 2): julia -p 8 script.jl -g /annotation_file.gff3 -o //infile.bam" -u -c 1.
The data was analyzed using a custom R package RiboSeqTools (accessible from: https://github.com/ilia-kats/RiboSeqTools). The analysis was performed exclusively using p-site assigned reads for all datasets.
Assembly: SGD R64-1-1GCA_000146045.2
Supplementary files format and content: Processed data are stored in HDF5 files. Each HDF5 file contains one data set per gene. Each data set consists of a 2-row matrix, with the first row containing the 1-based position within the CDS, and the second row the number of detected P-site reads at this position. Additional information is stored in the data set attributes, including: gene and protein names, length of the coding sequence, chromosome and strand location of the gene. In this study the p-site assignments stored in such HDF5 files were further analyzed using RiboSeqTools
Library strategy: Ribosome Profiling

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cultures were grown for roughly 6 hours at 30 °C until they have reached early log phase in YPD media (in 1 L for SeRP and in 200 mL for total translatomes)

extract_protocol:
RNA from ribosomes precipitated via sucrose cushion, or from ribosomes that co-IP with GFP-binder coupled beads were extracted using the hot acid phenol method as described in Galmozzi and Merker et al. 2019, for total translatome and IP samples respectively.
Libraries were constructed as decribed in Galmozi and Merker et al. 2019

treatment_protocol: Cells were harvested by rapid filtration and frozen in liquid nitrogen. The frozen cell pellets were lysed by cryo-milling. Lysates were thawed,and treated with10U/A260 RNase I for 30 min at 4 °C.

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 CHP1-sfGFP::kanMX

tag: fraction

value: total translatome


title: Library_289_S15


title: p070-bdf1_015_HiC

description: mOSN

value: mouse olfactory epithelium

value: postnatal day 70

value: WT


title: p070-bdf1_014_HiC

description: mOSN


title: p070-bdf1_012_HiC

description: mOSN


title: p070-bdf1_013_HiC

description: mOSN


title: OHT_lib108

description: CMV-CreERT2; Brd4flox/flox mouse ESCs treated with tamoxifen at the CPC stage of cardiac differentiation

data_processing:
Raw reads were trimmed with Trimmomatic v0.32
aligned to mm10 genome using STAR (10) (version 2.6.0c)
filtered using samtools view with ‘-F 4 -q 10’ parameters
reads quantified with Rsubread featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: gene-cellbarcode expression matrix in txt (tab-delimited) format
Raw reads were trimmed with Trimmomatic v0.32

source_name: mouse embryonic stem cells

growth_protocol: Embryonic stem cells (ESCs) were derived from CMV-CreERT2; Brd4flox/flox mice.

extract_protocol:
RNA was isolated isolated using Qiagen RNeasy spin columns following manufacturer’s directions
Bulk RNA libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) to enrich poly-A tailed RNA molecules. Libraries were PCR’ed with single end barcodes using Illumina Multiplex Oligos (NEB).

treatment_protocol: Cardiac differentiation of these cells was adapted from published protocols as previously described by our group and others (Christoforou et al. 2008; Kattman et al. 2011; Jain et al. 2015; Poleshko et al. 2017). Briefly, ESCs were cultured and maintained on a feeder layer of mitotically inactivated MEFs in DMEM with 15% FBS (Fisher Scientific #SH3007003) and ESGRO LIF. Differentiation through the hanging droplets method was initiated following ESC dissociation and suspension at 5e4 cells/ml in DMEM with 10% FBS (Atlanta Biologicals #S11550) without LIF in 20 µl drops. Two days after droplet formation, embryoid bodies (EBs) were transferred in suspension onto poly-HEMA coated dishes. After another two days, EBs were plated on gelatin-coated dishes in cardiac differentiation media (StemPro-34 SF medium, Invitrogen #10639-011) supplemented with 5 ng/ml VEGF (R&D systems), 10 ng/ml bFGF (R&D systems), 12.5 ng/ml FGF10 (R&D systems), 2.5 µM XAV939 (Cayman Chemical #13596), 1 mM Ascorbic Acid (Sigma #A4403) and 2 mM Glutamax (Invitrogen #35050-061). Beating cells were visible within 24-48 hours. Brd4 knockout in CMV-CreERT2; Brd4flox/flox ESCs were performed using 4-hydroxytamoxifen (TAM) (Sigma #T176) dissolved in 100% ethanol. Cells were treated with 1 µg/ml 4-hydroxytamoxifen (dissolved in 100% ethanol) to delete Brd4 starting on Day 5 and samples were collected on Day 10.

value: mouse embryonic stem cells

value: tamoxifen

tag: cell stage

value: cardiac progenitor

value: Brd4flox/flox; CMV-CreERT2


title: E95_Brd4_flox1 (NextSeq500)

value: Embryonic mouse heart at E9.5

value: Brd4 flox/flox

value: Cardiogenic region

value: Non-cardiac mesoderm, ectoderm and endoderm


title: p070-bdf1_011_HiC

description: mOSN


title: OHT_lib105


title: Library_287_S14

value: Embryonic mouse heart

value: micro-dissected RV and OFT

value: Isl1-Cre; Brd4flox/flox


title: Library_290_S16

value: Isl1-Cre; Brd4flox/+

value: Control


title: p070-bdf1_010_HiC

description: mOSN


title: OHT_lib107


title: p070-bdf1_008_HiC

description: mOSN


title: p070-bdf1_009_HiC


title: Ctrl_lib103

description: CMV-CreERT2; Brd4flox/flox mouse ESCs treated with vehicle only at the CPC stage of cardiac differentiation

value: vehicle


title: Ctrl_lib101


title: p119-bc_003_HiC

description: mOSN

value: mouse olfactory epithelium

value: postnatal day 119

value: bc


title: p070-bdf1_007_HiC

description: mOSN

value: postnatal day 70

value: WT


title: p070-bdf1_006_HiC

description: mOSN


title: Library_288_S5


title: p070-bdf1_004_HiC

description: mOSN


title: p070-bdf1_003_HiC

description: mOSN


title: GM12878_cell_219_HiC

description: Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice

data_processing:
RNA reads were mapped to hg38 transcriptome reference using hisat2.
Hi-C reads were processed and analysed using Dip-C and hickit package.
Files with .e.allValidPairs.gz and .e.hic suffixes were generated using the human genome assembly corrected for Philadelphia chromosome (ehap.hg38.genome.fa.gz).
We pooled Hi-C samples for each cell line.
We generated three replicate structures (_1.3dg.gz, _2.3dg.gz and _3.3dg.gz) per cell reconstructed with different random seeds (1-3).
Assembly: hg38
Supplementary files format and content: .hic
Supplementary files format and content: .3dg
Supplementary files format and content: .allValidPairs

source_name: blood

extract_protocol:
Viable cells were picked into a single tube containing 7 μL soft cell lysis buffer (25 mM Tris pH8.3, 30 mM NaCl, 0.45% IGEPAL-CA630, 1 U/μL SUPERaseIn) supplemented with 0.25 μL magnetic beads, then incubate on ice for 30 min, after incubation, vortex for 1 min. Centrifuge at 500 x g for 5 min at 4°C, then take 5 μL supernatant to a new tube. The supernatant was proceeded to Smart-seq2 reverse transcription and amplification5. Nuclei was proceeded to chromosome conformation capture.
simultaneous 3D genome and gene expression by LiMCA
Smart-seq2 for LiMCA RNA library; Dip-C protocol for LiMCA Hi-C library

value: blood

tag: cell line

value: Lymphoblastoid


title: GM12878_cell_221_HiC


title: p070-bdf1_002_HiC

description: mOSN


title: GM12878_cell_220_HiC


title: GM12878_cell_222_HiC


title: p070-bdf1_001_HiC

description: mOSN


title: p060-bdf1_051_HiC

description: mOSN

value: postnatal day 60


title: p060-bdf1_050_HiC

description: mOSN


title: Ctrl_lib102

value: mouse embryonic stem cells

value: cardiac progenitor

value: Brd4flox/flox; CMV-CreERT2


title: GM12878_cell_217_HiC


title: GM12878_cell_215_HiC


title: GM12878_cell_218_HiC


title: GM12878_cell_216_HiC


title: GM12878_cell_214_HiC


title: p060-bdf1_047_HiC

description: iOSN


title: p060-bdf1_046_HiC


title: GM12878_cell_212_HiC


title: p060-bdf1_049_HiC

description: iOSN


title: GM12878_cell_213_HiC


title: p060-bdf1_048_HiC

description: mOSN


title: p070-bdf1_005_HiC

description: iOSN


title: p060-bdf1_044_HiC

description: iOSN


title: p060-bdf1_045_HiC

description: mOSN


title: GM12878_cell_209_HiC


title: p060-bdf1_043_HiC

description: iOSN


title: GM12878_cell_210_HiC


title: GM12878_cell_211_HiC


title: p060-bdf1_042_HiC

description: mOSN


title: GM12878_cell_207_HiC


title: GM12878_cell_205_HiC


title: p060-bdf1_041_HiC

description: mOSN


title: p060-bdf1_038_HiC

description: iOSN


title: p060-bdf1_039_HiC

description: mOSN


title: GM12878_cell_204_HiC


title: GM12878_cell_206_HiC


title: p060-bdf1_036_HiC

description: mOSN


title: p060-bdf1_037_HiC

description: mOSN


title: GM12878_cell_201_HiC


title: p060-bdf1_034_HiC

description: mOSN


title: p060-bdf1_033_HiC

description: mOSN


title: GM12878_cell_203_HiC


title: p060-bdf1_035_HiC

description: mOSN


title: GM12878_cell_202_HiC


title: GM12878_cell_199_HiC


title: p060-bdf1_032_HiC

description: iOSN


title: p060-bdf1_031_HiC

description: mOSN


title: GM12878_cell_196_HiC


title: GM12878_cell_198_HiC


title: p060-bdf1_040_HiC

description: mOSN


title: GM12878_cell_197_HiC


title: GM12878_cell_195_HiC


title: p060-bdf1_028_HiC

description: mOSN


title: p060-bdf1_030_HiC

description: mOSN


title: p060-bdf1_029_HiC

description: mOSN


title: GM12878_cell_194_HiC


title: GM12878_cell_193_HiC


title: C21

city: Shanghai

first: Wei

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

data_processing:
We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads for further analysis. Then, we aligned the reads to reference sequences by bowtie. To assess the expression levels of the miRNAs, the 3’ ends of miRNA with ≤ 3 nt deletions or additional sequences derived from pri-miRNAs were counted as miRNAs. The miRNA expression level was normalized by size factor from DEseq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include log2-transformed normalized read counts for each sample

source_name: Extracellular vesicle

extract_protocol:
Frozen plasma samples were thawed in thermostat water bath for 2 min at 37 °C and then centrifuged at 2,500 × g for 15 min at 4 °C to remove precipitated proteins and lipids. ~0.5-1 ml plasma was used as the starting material for each EVs isolation by exoRNeasy Midi kit (Qiagen; Cat#77144) according to the manufacturer’s instructions. For EV-RNA extraction, 1 ml Trizol reagent (Invitrogen; Cat#15596026) was added to the column and centrifuged at 3,000 × g for 1 min. Total EV-RNA was isolated by Trizol reagent according to manufacturer’s recommendations.
A total amount of 0.5-1 ng RNA per sample was used as input material for the RNA sample preparations. The cDNA libraries establishment of small RNAs included adaptor ligation, adapter depletion, first-strand cDNA synthesis, Cas9/sgRNA in vitro cleavage treatment, PCR amplification and gel purification.

treatment_protocol: For each blood collection, 2 ml venous blood was collected into 10 ml BD K2EDTA Vacutainer tubes to prevent coagulation. The anticoagulant-treated blood samples were immediately inverted several times and transferred to 2 ml conical tubes (Eppendorf; Cat# 0030120094). To obtain plasma, blood samples were centrifuged at 1,300 × g for 10 min at room temperature (RT). The upper layer containing plasma was transferred to new tubes and centrifuged twice at 2,500 × g for 15 min at RT to obtain platelet poor plasma (PPP). Each plasma supernatant was carefully transferred to 1 ml fresh tubes and then stored at -80 °C until further use.

value: Blood plasma

tag: disease state

value: Healthy


title: GM12878_cell_200_HiC


title: p060-bdf1_026_HiC

description: mOSN


title: GM12878_cell_192_HiC


title: GM12878_cell_190_HiC


title: p060-bdf1_025_HiC

description: mOSN


title: GM12878_cell_191_HiC


title: GM12878_cell_188_HiC


title: p060-bdf1_021_HiC

description: iOSN


title: p060-bdf1_022_HiC

description: mOSN


title: GM12878_cell_186_HiC


title: GM12878_cell_187_HiC


title: GM12878_cell_189_HiC


title: p060-bdf1_023_HiC

description: mOSN


title: GM12878_cell_185_HiC


title: p060-bdf1_020_HiC

description: mOSN


title: p060-bdf1_027_HiC

description: mOSN


title: GM12878_cell_184_HiC


title: GM12878_cell_208_HiC


title: GM12878_cell_183_HiC


title: p060-bdf1_016_HiC

description: mOSN


title: GM12878_cell_181_HiC


title: p060-bdf1_015_HiC

description: mOSN


title: GM12878_cell_182_HiC


title: p060-bdf1_017_HiC

description: mOSN


title: p060-bdf1_013_HiC

description: iOSN


title: GM12878_cell_179_HiC


title: p060-bdf1_024_HiC

description: iOSN


title: GM12878_cell_180_HiC


title: p060-bdf1_012_HiC

description: mOSN


title: GM12878_cell_178_HiC


title: p060-bdf1_014_HiC

description: mOSN


title: p060-bdf1_011_HiC


title: GM12878_cell_177_HiC


title: p060-bdf1_019_HiC

description: mOSN


title: p060-bdf1_018_HiC

description: mOSN


title: p060-bdf1_009_HiC


title: GM12878_cell_175_HiC


title: GM12878_cell_176_HiC


title: GM12878_cell_174_HiC


title: p060-bdf1_008_HiC

description: mOSN


title: p060-bdf1_010_HiC


title: GM12878_cell_172_HiC


title: p060-bdf1_006_HiC

description: mOSN


title: GM12878_cell_169_HiC


title: p060-bdf1_005_HiC

description: mOSN


title: p060-bdf1_003_HiC


title: GM12878_cell_171_HiC


title: p060-bdf1_004_HiC

description: mOSN


title: GM12878_cell_168_HiC


title: p060-bdf1_002_HiC

description: mOSN


title: p060-bdf1_001_HiC

description: mOSN


title: GM12878_cell_173_HiC


title: p060-bdf1_007_HiC

description: mOSN


title: GM12878_cell_166_HiC


title: p028-bdf1_070_HiC

description: mOSN

value: postnatal day 28


title: GM12878_cell_167_HiC


title: GM12878_cell_165_HiC


title: GM12878_cell_164_HiC


title: GM12878_cell_163_HiC


title: GM12878_cell_162_HiC


title: GM12878_cell_161_HiC


title: p028-bdf1_068_HiC


title: p028-bdf1_064_HiC

description: mOSN


title: p028-bdf1_065_HiC

description: mOSN


title: p028-bdf1_063_HiC

description: mOSN


title: p028-bdf1_062_HiC


title: p028-bdf1_066_HiC

description: mOSN


title: GM12878_cell_159_HiC


title: GM12878_cell_158_HiC


title: p028-bdf1_061_HiC

description: mOSN


title: GM12878_cell_157_HiC


title: p028-bdf1_060_HiC


title: GM12878_cell_170_HiC


title: p028-bdf1_069_HiC

description: mOSN


title: GM12878_cell_155_HiC


title: GM12878_cell_154_HiC


title: p028-bdf1_058_HiC

description: mOSN


title: GM12878_cell_156_HiC


title: p028-bdf1_059_HiC

description: mOSN


title: GM12878_cell_153_HiC


title: GM12878_cell_152_HiC


title: p028-bdf1_057_HiC

description: mOSN


title: GM12878_cell_150_HiC


title: GM12878_cell_151_HiC


title: p028-bdf1_056_HiC

description: mOSN


title: p028-bdf1_067_HiC

description: mOSN


title: p028-bdf1_055_HiC

description: mOSN


title: p028-bdf1_053_HiC

description: mOSN


title: GM12878_cell_160_HiC


title: p028-bdf1_054_HiC

description: mOSN


title: GM12878_cell_149_HiC


title: GM12878_cell_148_HiC


title: GM12878_cell_147_HiC


title: p028-bdf1_052_HiC


title: GM12878_cell_145_HiC


title: p028-bdf1_050_HiC

description: mOSN


title: GM12878_cell_144_HiC


title: p028-bdf1_048_HiC

description: mOSN


title: GM12878_cell_146_HiC


title: p028-bdf1_047_HiC

description: mOSN


title: GM12878_cell_142_HiC


title: GM12878_cell_143_HiC


title: GM12878_cell_141_HiC


title: p028-bdf1_046_HiC


title: p028-bdf1_045_HiC

description: mOSN


title: GM12878_cell_139_HiC


title: p028-bdf1_044_HiC

description: mOSN


title: GM12878_cell_138_HiC


title: p028-bdf1_043_HiC

description: mOSN


title: GM12878_cell_140_HiC


title: p028-bdf1_041_HiC

description: mOSN


title: GM12878_cell_137_HiC


title: GM12878_cell_136_HiC


title: p028-bdf1_042_HiC


title: p028-bdf1_051_HiC

description: iOSN


title: p028-bdf1_039_HiC

description: mOSN


title: GM12878_cell_134_HiC


title: GM12878_cell_135_HiC


title: p028-bdf1_038_HiC


title: p028-bdf1_049_HiC


title: GM12878_cell_132_HiC


title: p028-bdf1_037_HiC

description: mOSN


title: p028-bdf1_036_HiC


title: GM12878_cell_131_HiC


title: p028-bdf1_035_HiC


title: p028-bdf1_040_HiC

description: mOSN


title: GM12878_cell_129_HiC


title: GM12878_cell_128_HiC


title: GM12878_cell_133_HiC


title: p028-bdf1_033_HiC


title: p028-bdf1_030_HiC

description: iOSN


title: p028-bdf1_031_HiC


title: p028-bdf1_032_HiC

description: mOSN


title: GM12878_cell_127_HiC


title: p028-bdf1_029_HiC


title: GM12878_cell_126_HiC


title: GM12878_cell_125_HiC


title: p028-bdf1_028_HiC

description: mOSN


title: GM12878_cell_123_HiC


title: GM12878_cell_124_HiC


title: p028-bdf1_027_HiC


title: GM12878_cell_122_HiC


title: p028-bdf1_026_HiC


title: GM12878_cell_121_HiC


title: p028-bdf1_025_HiC


title: p028-bdf1_024_HiC


title: GM12878_cell_130_HiC


title: p028-bdf1_023_HiC


title: GM12878_cell_119_HiC


title: p028-bdf1_022_HiC


title: GM12878_cell_117_HiC


title: p028-bdf1_021_HiC


title: p028-bdf1_019_HiC


title: GM12878_cell_118_HiC


title: p028-bdf1_020_HiC


title: GM12878_cell_120_HiC


title: GM12878_cell_115_HiC


title: GM12878_cell_114_HiC


title: GM12878_cell_116_HiC


title: GM12878_cell_113_HiC


title: p028-bdf1_034_HiC

description: iOSN


title: p028-bdf1_018_HiC

description: mOSN


title: p028-bdf1_017_HiC


title: GM12878_cell_112_HiC


title: p028-bdf1_016_HiC

description: mOSN


title: GM12878_cell_111_HiC


title: p028-bdf1_014_HiC

description: mOSN


title: p028-bdf1_015_HiC


title: GM12878_cell_110_HiC


title: GM12878_cell_108_HiC


title: p028-bdf1_012_HiC

description: mOSN


title: GM12878_cell_106_HiC


title: GM12878_cell_107_HiC


title: p028-bdf1_010_HiC


title: p028-bdf1_013_HiC

description: mOSN


title: GM12878_cell_105_HiC


title: p028-bdf1_011_HiC


title: p028-bdf1_007_HiC


title: GM12878_cell_102_HiC


title: p028-bdf1_008_HiC

description: iOSN


title: GM12878_cell_103_HiC


title: GM12878_cell_109_HiC


title: p028-bdf1_006_HiC

description: mOSN


title: p028-bdf1_004_HiC


title: GM12878_cell_100_HiC


title: GM12878_cell_104_HiC


title: p028-bdf1_003_HiC


title: p028-bdf1_009_HiC


title: GM12878_cell_097_HiC


title: GM12878_cell_098_HiC


title: GM12878_cell_099_HiC


title: GM12878_cell_095_HiC


title: p028-bdf1_005_HiC

description: mOSN


title: p028-bdf1_002_HiC


title: p014-bdf1_055_HiC

value: postnatal day 14


title: p014-bdf1_054_HiC


title: p028-bdf1_001_HiC


title: GM12878_cell_096_HiC


title: GM12878_cell_094_HiC


title: GM12878_cell_093_HiC


title: p014-bdf1_052_HiC

description: mOSN


title: p014-bdf1_053_HiC


title: GM12878_cell_092_HiC


title: p014-bdf1_051_HiC


title: GM12878_cell_090_HiC


title: p014-bdf1_049_HiC


title: GM12878_cell_089_HiC


title: GM12878_cell_101_HiC


title: p014-bdf1_047_HiC

description: mOSN


title: GM12878_cell_088_HiC


title: p014-bdf1_046_HiC


title: GM12878_cell_086_HiC


title: p014-bdf1_045_HiC

description: unknown


title: GM12878_cell_085_HiC


title: GM12878_cell_087_HiC


title: p014-bdf1_043_HiC

description: unknown


title: p014-bdf1_042_HiC

description: unknown


title: p014-bdf1_041_HiC

description: unknown


title: GM12878_cell_081_HiC


title: GM12878_cell_082_HiC


title: GM12878_cell_083_HiC


title: p014-bdf1_044_HiC


title: p014-bdf1_050_HiC


title: p014-bdf1_040_HiC

description: unknown


title: GM12878_cell_080_HiC


title: GM12878_cell_091_HiC


title: GM12878_cell_079_HiC


title: GM12878_cell_077_HiC


title: p014-bdf1_048_HiC

description: iOSN


title: p014-bdf1_038_HiC

description: mOSN


title: GM12878_cell_078_HiC


title: p014-bdf1_037_HiC

description: unknown


title: p014-bdf1_035_HiC

description: unknown


title: GM12878_cell_075_HiC


title: p014-bdf1_034_HiC

description: unknown


title: GM12878_cell_084_HiC


title: p014-bdf1_033_HiC


title: GM12878_cell_074_HiC


title: GM12878_cell_073_HiC


title: p014-bdf1_032_HiC

description: unknown


title: GM12878_cell_072_HiC


title: p014-bdf1_039_HiC


title: GM12878_cell_071_HiC


title: p014-bdf1_031_HiC

description: mOSN


title: p014-bdf1_029_HiC

description: iOSN


title: p014-bdf1_030_HiC

description: unknown


title: GM12878_cell_070_HiC


title: p014-bdf1_028_HiC


title: GM12878_cell_068_HiC


title: GM12878_cell_067_HiC


title: p014-bdf1_025_HiC

description: unknown


title: p014-bdf1_027_HiC


title: p014-bdf1_036_HiC

description: unknown


title: GM12878_cell_064_HiC


title: p014-bdf1_023_HiC

description: unknown


title: GM12878_cell_076_HiC


title: GM12878_cell_063_HiC


title: GM12878_cell_066_HiC


title: p014-bdf1_022_HiC

description: unknown


title: p014-bdf1_026_HiC

description: unknown


title: p014-bdf1_024_HiC


title: GM12878_cell_065_HiC


title: GM12878_cell_062_HiC


title: p014-bdf1_020_HiC

description: mOSN


title: p014-bdf1_021_HiC

description: unknown


title: GM12878_cell_059_HiC


title: GM12878_cell_061_HiC


title: GM12878_cell_069_HiC


title: p014-bdf1_017_HiC


title: GM12878_cell_060_HiC


title: GM12878_cell_058_HiC


title: GM12878_cell_056_HiC


title: GM12878_cell_054_HiC


title: p014-bdf1_014_HiC

description: iOSN


title: GM12878_cell_057_HiC


title: p014-bdf1_016_HiC

description: mOSN


title: GM12878_cell_053_HiC


title: p014-bdf1_018_HiC

description: mOSN


title: GM12878_cell_055_HiC


title: p014-bdf1_012_HiC

description: iOSN


title: GM12878_cell_052_HiC


title: p014-bdf1_019_HiC


title: p014-bdf1_009_HiC

description: unknown


title: GM12878_cell_050_HiC


title: GM12878_cell_051_HiC


title: GM12878_cell_046_HiC


title: p014-bdf1_013_HiC

description: iOSN


title: p014-bdf1_010_HiC


title: p014-bdf1_015_HiC

description: unknown


title: p014-bdf1_011_HiC

description: unknown


title: p014-bdf1_008_HiC

description: unknown


title: p014-bdf1_007_HiC


title: p014-bdf1_005_HiC

description: iOSN


title: p014-bdf1_003_HiC

description: mOSN


title: GM12878_cell_047_HiC


title: GM12878_cell_049_HiC


title: p014-bdf1_006_HiC

description: unknown


title: GM12878_cell_044_HiC


title: GM12878_cell_045_HiC


title: GM12878_cell_041_HiC


title: p014-bdf1_001_HiC

description: unknown


title: GM12878_cell_048_HiC


title: GM12878_cell_040_HiC


title: GM12878_cell_043_HiC


title: p014-bc_043_HiC

description: iOSN


title: p014-bc_042_HiC

description: iOSN


title: p014-bc_041_HiC


title: p014-bc_040_HiC

description: iOSN


title: GM12878_cell_039_HiC


title: GM12878_cell_038_HiC


title: GM12878_cell_037_HiC


title: p014-bdf1_004_HiC


title: p014-bc_038_HiC

description: mOSN


title: p014-bc_037_HiC

description: mOSN


title: GM12878_cell_035_HiC


title: GM12878_cell_034_HiC


title: GM12878_cell_042_HiC


title: GM12878_cell_036_HiC


title: p014-bdf1_002_HiC


title: p014-bc_039_HiC

description: iOSN


title: p014-bc_036_HiC

description: iOSN


title: GM12878_cell_031_HiC


title: GM12878_cell_030_HiC


title: p014-bc_035_HiC

description: iOSN


title: GM12878_cell_033_HiC


title: p014-bc_034_HiC

description: iOSN


title: p014-bc_032_HiC


title: GM12878_cell_029_HiC


title: p014-bc_033_HiC


title: p014-bc_031_HiC

description: mOSN


title: p014-bc_027_HiC

description: iOSN


title: GM12878_cell_027_HiC


title: p014-bc_030_HiC

description: iOSN


title: GM12878_cell_025_HiC


title: p014-bc_028_HiC

description: iOSN


title: p014-bc_023_HiC

description: mOSN


title: GM12878_cell_023_HiC


title: p014-bc_026_HiC

description: mOSN


title: p014-bc_029_HiC

description: iOSN


title: GM12878_cell_028_HiC


title: GM12878_cell_018_HiC


title: GM12878_cell_021_HiC


title: p014-bc_021_HiC

description: mOSN


title: p014-bc_024_HiC

description: mOSN


title: GM12878_cell_017_HiC


title: GM12878_cell_019_HiC


title: GM12878_cell_022_HiC


title: GM12878_cell_020_HiC


title: p014-bc_022_HiC

description: iOSN


title: GM12878_cell_015_HiC


title: p014-bc_020_HiC

description: mOSN


title: GM12878_cell_014_HiC


title: p014-bc_018_HiC

description: iOSN


title: GM12878_cell_016_HiC


title: GM12878_cell_013_HiC


title: p014-bc_019_HiC

description: iOSN


title: p014-bc_025_HiC

description: iOSN


title: GM12878_cell_026_HiC


title: GM12878_cell_024_HiC


title: p014-bc_017_HiC

description: mOSN


title: GM12878_cell_012_HiC


title: p014-bc_016_HiC

description: mOSN


title: p014-bc_015_HiC

description: iOSN


title: p014-bc_014_HiC


title: p014-bc_013_HiC


title: GM12878_cell_007_HiC


title: p014-bc_011_HiC

description: iOSN


title: p014-bc_010_HiC

description: mOSN


title: p014-bc_009_HiC

description: mOSN


title: GM12878_cell_009_HiC


title: GM12878_cell_004_HiC


title: GM12878_cell_005_HiC


title: p014-bc_012_HiC

description: mOSN


title: GM12878_cell_008_HiC


title: GM12878_cell_010_HiC


title: p014-bc_008_HiC

description: mOSN


title: GM12878_cell_006_HiC


title: eHAP_cell_042_HiC

source_name: eHAP

value: eHAP


title: p014-bc_003_HiC

description: mOSN


title: p014-bc_007_HiC

description: iOSN


title: GM12878_cell_001_HiC


title: p014-bc_001_HiC

description: mOSN


title: eHAP_cell_039_HiC


title: eHAP_cell_041_HiC


title: GM12878_cell_003_HiC


title: p007-bdf1_079_HiC

value: postnatal day 7


title: eHAP_cell_036_HiC


title: p014-bc_006_HiC

description: mOSN

value: mouse olfactory epithelium


title: GM12878_cell_002_HiC


title: p007-bdf1_077_HiC


title: p014-bc_005_HiC

description: mOSN


title: p014-bc_004_HiC

description: iOSN


title: GM12878_cell_011_HiC


title: p007-bdf1_081_HiC


title: p014-bc_002_HiC

description: iOSN


title: eHAP_cell_040_HiC


title: p007-bdf1_080_HiC


title: p007-bdf1_075_HiC

description: iOSN


title: eHAP_cell_031_HiC


title: eHAP_cell_038_HiC


title: eHAP_cell_037_HiC


title: p007-bdf1_078_HiC


title: eHAP_cell_035_HiC


title: eHAP_cell_034_HiC


title: p007-bdf1_070_HiC


title: eHAP_cell_032_HiC


title: eHAP_cell_033_HiC


title: p007-bdf1_076_HiC

description: iOSN


title: eHAP_cell_028_HiC


title: p007-bdf1_068_HiC


title: eHAP_cell_026_HiC


title: p007-bdf1_074_HiC


title: eHAP_cell_023_HiC


title: eHAP_cell_024_HiC


title: p007-bdf1_066_HiC

description: iOSN


title: p007-bdf1_073_HiC


title: eHAP_cell_022_HiC


title: p007-bdf1_072_HiC


title: p007-bdf1_064_HiC


title: p007-bdf1_071_HiC


title: eHAP_cell_030_HiC


title: eHAP_cell_029_HiC


title: eHAP_cell_027_HiC


title: eHAP_cell_020_HiC


title: p007-bdf1_069_HiC

description: iOSN


title: p007-bdf1_065_HiC

description: iOSN


title: p007-bdf1_067_HiC


title: eHAP_cell_018_HiC


title: eHAP_cell_019_HiC


title: p007-bdf1_060_HiC


title: p007-bdf1_059_HiC

description: iOSN


title: p007-bdf1_063_HiC

description: iOSN


title: eHAP_cell_017_HiC


title: eHAP_cell_016_HiC


title: eHAP_cell_021_HiC


title: p007-bdf1_062_HiC


title: eHAP_cell_025_HiC


title: eHAP_cell_014_HiC


title: p007-bdf1_061_HiC

description: mOSN


title: p007-bdf1_057_HiC


title: p007-bdf1_055_HiC

description: iOSN


title: eHAP_cell_012_HiC


title: p007-bdf1_058_HiC

description: iOSN


title: p007-bdf1_054_HiC

description: iOSN


title: eHAP_cell_015_HiC


title: eHAP_cell_011_HiC


title: eHAP_cell_009_HiC


title: p007-bdf1_052_HiC

description: iOSN


title: eHAP_cell_010_HiC


title: p007-bdf1_051_HiC


title: p007-bdf1_053_HiC

description: iOSN


title: eHAP_cell_008_HiC


title: p007-bdf1_050_HiC

description: iOSN


title: eHAP_cell_007_HiC


title: eHAP_cell_013_HiC


title: p007-bdf1_048_HiC

description: iOSN


title: p007-bdf1_049_HiC


title: p007-bdf1_056_HiC


title: eHAP_cell_005_HiC


title: K562_cell_063_HiC

source_name: bone marrow

value: bone marrow


title: K562_cell_062_HiC


title: p007-bdf1_047_HiC

description: iOSN


title: p007-bdf1_041_HiC

description: mOSN


title: p007-bdf1_042_HiC

description: iOSN


title: p007-bdf1_046_HiC

description: iOSN


title: K562_cell_060_HiC


title: p007-bdf1_040_HiC

description: iOSN


title: eHAP_cell_004_HiC


title: p007-bdf1_037_HiC


title: eHAP_cell_002_HiC


title: p007-bdf1_038_HiC


title: K562_cell_058_HiC


title: p007-bdf1_045_HiC


title: eHAP_cell_003_HiC


title: p007-bdf1_043_HiC


title: p007-bdf1_044_HiC


title: K562_cell_061_HiC


title: K562_cell_059_HiC


title: p007-bdf1_035_HiC


title: K562_cell_055_HiC


title: p007-bdf1_039_HiC

description: mOSN


title: K562_cell_057_HiC


title: p007-bdf1_036_HiC


title: K562_cell_056_HiC


title: eHAP_cell_006_HiC


title: K562_cell_054_HiC


title: K562_cell_053_HiC


title: p007-bdf1_030_HiC


title: p007-bdf1_034_HiC


title: p007-bdf1_032_HiC


title: eHAP_cell_001_HiC


title: K562_cell_048_HiC


title: K562_cell_049_HiC


title: K562_cell_051_HiC


title: p007-bdf1_028_HiC


title: p007-bdf1_026_HiC


title: p007-bdf1_033_HiC


title: K562_cell_050_HiC


title: p007-bdf1_025_HiC


title: p007-bdf1_031_HiC


title: K562_cell_052_HiC


title: p007-bdf1_024_HiC


title: K562_cell_044_HiC


title: K562_cell_047_HiC


title: K562_cell_046_HiC


title: p007-bdf1_027_HiC


title: K562_cell_043_HiC


title: K562_cell_045_HiC


title: p007-bdf1_023_HiC


title: p007-bdf1_022_HiC


title: K562_cell_041_HiC


title: K562_cell_039_HiC


title: K562_cell_037_HiC


title: K562_cell_038_HiC


title: K562_cell_040_HiC


title: p007-bdf1_020_HiC

description: iOSN


title: p007-bdf1_029_HiC


title: K562_cell_042_HiC


title: K562_cell_035_HiC


title: p007-bdf1_018_HiC

description: iOSN


title: p007-bdf1_019_HiC

description: iOSN


title: K562_cell_034_HiC


title: p007-bdf1_017_HiC


title: p007-bdf1_021_HiC

description: iOSN


title: K562_cell_036_HiC


title: p007-bdf1_014_HiC


title: K562_cell_033_HiC


title: K562_cell_032_HiC


title: p007-bdf1_013_HiC


title: p007-bdf1_015_HiC


title: p007-bdf1_012_HiC


title: p007-bdf1_011_HiC


title: K562_cell_031_HiC


title: K562_cell_030_HiC


title: p007-bdf1_010_HiC

description: iOSN


title: p007-bdf1_008_HiC

description: iOSN


title: K562_cell_029_HiC


title: K562_cell_028_HiC


title: p007-bdf1_007_HiC

description: mOSN


title: p007-bdf1_016_HiC


title: K562_cell_027_HiC


title: K562_cell_024_HiC


title: K562_cell_025_HiC


title: K562_cell_026_HiC


title: p007-bdf1_004_HiC

description: mOSN


title: p007-bdf1_005_HiC


title: p007-bdf1_003_HiC


title: p007-bdf1_006_HiC

description: iOSN


title: K562_cell_023_HiC


title: p007-bdf1_002_HiC


title: K562_cell_020_HiC


title: K562_cell_019_HiC


title: p007-bdf1_009_HiC

description: mOSN


title: p007-bc_020_HiC

description: iOSN

value: bc


title: p007-bc_019_HiC


title: p007-bdf1_001_HiC


title: p007-bc_010_HiC

description: mOSN


title: K562_cell_015_HiC


title: K562_cell_009_HiC


title: p007-bc_014_HiC


title: K562_cell_007_HiC


title: K562_cell_021_HiC


title: K562_cell_006_HiC


title: K562_cell_013_HiC


title: p007-bc_012_HiC


title: p007-bc_006_HiC


title: p007-bc_018_HiC


title: p007-bc_013_HiC


title: K562_cell_022_HiC


title: p007-bc_007_HiC

description: mOSN


title: p007-bc_016_HiC


title: K562_cell_012_HiC


title: K562_cell_017_HiC


title: p007-bc_005_HiC


title: K562_cell_018_HiC


title: p007-bc_011_HiC

description: mOSN


title: p007-bc_009_HiC

description: iOSN


title: K562_cell_011_HiC


title: K562_cell_010_HiC


title: K562_cell_005_HiC


title: K562_cell_004_HiC


title: K562_cell_008_HiC


title: K562_cell_001_HiC


title: K562_cell_002_HiC


title: p007-bc_001_HiC

description: iOSN


title: p003-bdf1_039_HiC

description: iOSN

value: postnatal day 3


title: p007-bc_002_HiC

description: iOSN

value: WT


title: K562_cell_003_HiC


title: p007-bc_004_HiC


title: BJ_cell_063_HiC

source_name: foreskin

value: foreskin

value: human fibroblast cell line

value: BJ


title: p003-bdf1_040_HiC


title: BJ_cell_061_HiC


title: p003-bdf1_038_HiC

description: iOSN


title: p003-bdf1_041_HiC

description: iOSN


title: p007-bc_003_HiC

description: iOSN


title: BJ_cell_060_HiC


title: BJ_cell_059_HiC


title: BJ_cell_057_HiC


title: p007-bc_017_HiC

description: mOSN


title: K562_cell_016_HiC


title: BJ_cell_056_HiC


title: p003-bdf1_037_HiC


title: p003-bdf1_035_HiC

description: mOSN


title: p003-bdf1_033_HiC

description: iOSN


title: BJ_cell_055_HiC


title: p003-bdf1_034_HiC


title: BJ_cell_062_HiC


title: BJ_cell_058_HiC


title: p003-bdf1_032_HiC

description:
progenitor-2
Reconstruction of the 3D genome structure for this cell failed due to the shallow data depth.


title: BJ_cell_054_HiC


title: p007-bc_008_HiC


title: BJ_cell_053_HiC


title: BJ_cell_052_HiC


title: p003-bdf1_031_HiC


title: p003-bdf1_028_HiC


title: p003-bdf1_030_HiC

description: mOSN


title: p007-bc_015_HiC


title: BJ_cell_050_HiC


title: p003-bdf1_029_HiC


title: BJ_cell_051_HiC


title: p003-bdf1_027_HiC


title: BJ_cell_048_HiC


title: p003-bdf1_036_HiC

description: mOSN


title: p003-bdf1_026_HiC

description: iOSN


title: p003-bdf1_025_HiC

description: iOSN


title: BJ_cell_047_HiC


title: BJ_cell_046_HiC


title: BJ_cell_045_HiC


title: BJ_cell_043_HiC


title: p003-bdf1_021_HiC


title: p003-bdf1_023_HiC


title: BJ_cell_044_HiC


title: BJ_cell_040_HiC


title: K562_cell_014_HiC


title: p003-bdf1_017_HiC


title: BJ_cell_041_HiC


title: p003-bdf1_015_HiC


title: p003-bdf1_016_HiC

description: iOSN


title: BJ_cell_049_HiC


title: BJ_cell_037_HiC


title: p003-bdf1_019_HiC


title: p003-bdf1_014_HiC


title: BJ_cell_036_HiC


title: BJ_cell_034_HiC


title: BJ_cell_035_HiC


title: p003-bdf1_013_HiC


title: BJ_cell_039_HiC


title: p003-bdf1_012_HiC


title: p003-bdf1_024_HiC


title: BJ_cell_038_HiC


title: p003-bdf1_022_HiC


title: p003-bdf1_010_HiC


title: BJ_cell_030_HiC


title: BJ_cell_042_HiC


title: BJ_cell_031_HiC


title: p003-bdf1_009_HiC


title: p003-bdf1_008_HiC

description: iOSN


title: p003-bdf1_018_HiC


title: BJ_cell_029_HiC


title: p003-bdf1_007_HiC


title: BJ_cell_028_HiC


title: BJ_cell_027_HiC


title: BJ_cell_025_HiC


title: p003-bdf1_006_HiC


title: p003-bdf1_011_HiC


title: p003-bdf1_004_HiC


title: BJ_cell_024_HiC


title: p003-bdf1_005_HiC

description: iOSN


title: p003-bdf1_003_HiC


title: BJ_cell_023_HiC


title: BJ_cell_033_HiC


title: p119-bc_027_rna

description:
mOSN
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz

value: postnatal day 119


title: BJ_cell_032_HiC


title: p003-bdf1_002_HiC


title: p119-bc_026_rna


title: p003-bdf1_001_HiC

description: iOSN


title: BJ_cell_019_HiC


title: p119-bc_025_rna

description:
iOSN
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz


title: BJ_cell_022_HiC


title: p003-bdf1_020_HiC


title: BJ_cell_018_HiC


title: BJ_cell_017_HiC


title: p119-bc_023_rna


title: p119-bc_022_rna


title: BJ_cell_020_HiC


title: BJ_cell_016_HiC


title: BJ_cell_026_HiC


title: p119-bc_021_rna


title: p119-bc_028_rna


title: BJ_cell_015_HiC


title: p119-bc_020_rna


title: p119-bc_017_rna

description:
progenitor-2
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz


title: p119-bc_018_rna


title: BJ_cell_014_HiC


title: BJ_cell_021_HiC


title: BJ_cell_012_HiC


title: p119-bc_019_rna


title: BJ_cell_013_HiC


title: p119-bc_015_rna


title: p119-bc_024_rna


title: BJ_cell_010_HiC


title: p119-bc_016_rna


title: p119-bc_014_rna


title: p119-bc_013_rna


title: BJ_cell_009_HiC


title: BJ_cell_007_HiC


title: p119-bc_012_rna


title: p119-bc_011_rna


title: BJ_cell_006_HiC


title: BJ_cell_005_HiC


title: p119-bc_010_rna


title: p119-bc_009_rna


title: BJ_cell_004_HiC


title: BJ_cell_011_HiC


title: BJ_cell_003_HiC


title: p119-bc_008_rna


title: BJ_cell_002_HiC


title: p119-bc_007_rna


title: p119-bc_006_rna