title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB127POY)

description:
https://www.encodeproject.org/experiments/ENCSR188VGU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR188VGU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB127POY

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS479IUC at ENCODE; https://www.encodeproject.org/ENCBS479IUC/


title: DNase-seq from T-cell (ENCLB209JQO)

status: Public on Mar 06 2026

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR130QML/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR130QML
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB209JQO

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens female adult (33 years) T-cell primary cell

value: T-cell

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: dev stage

tag: age

value: 33 year

tag: lab

tag: source

tag: link

value: ENCBS357OXV at ENCODE; https://www.encodeproject.org/ENCBS357OXV/


title: CD8, switched diet fed mice, 4

city: Kyoto

first: Masaki

last: Tajima

address: Yoshidakonoe cho

country: Japan

institute: Kyoto University

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: spleen

growth_protocol: freshely isolated cells

extract_protocol:
RNA was isolated using ISOGEN with Spin Column kit according to the instruction provided by the manufacturer (Nippongene).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

treatment_protocol: cells isolated from mice treated with normal diet (12 weeks), high fat diet (12 weeks),  and switched diet (high fat diet for 6 weeks and then normal diet for 6 weeks)

tag: tissue

value: spleen

tag: cell type

tag: genotype

value: WT

tag: treatment

value: switched diet (12 weeks)


title: GFP negative GC B cells 4

city: Toronto

first: Liam

middle: D

last: Hendrikse

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description: Library name: 30-09-22_6_BN_S5-S7_S106

data_processing:
Reads were QC'ed using fastqc (v 0.11.5) and multiqc (v 1.7) aligned to the GRCm38 (mm10) mouse reference using STAR (v 2.5.2b).
Gene counts and transcripts per million (TPM) normalization were determined using RSEM (v 1.3.0).
Assembly: mm10
Supplementary files format and content: exprMtrx_expected_count.csv: comma-delimited file containing RSEM output expected gene counts for each sample
Supplementary files format and content: exprMtrx_TPM.csv:comma-delimited file containing RSEM output gene TPM values for each sample

extract_protocol:
Spleens from SRBC-injected ChAT-GFP-tg animals were harvested on day 8 after immunization. ChAT-GFP+ and ChAT-GFP- subsets of GC B cells (CD19+, CD95+, CD38lo) and TFH cells (CD3+, PD1+, Cxcr5+) were sorted from splenic single-cell suspensions. Each replicate consisted of pooled (combined using equal parts), equivalent cell subsets derived from the spleens of two mice to ensure sufficient input cell numbers for RNA isolation. Total RNA was extracted using TRIzol (Invitrogen) according to manufacturer instructions.
Library preparation was performed using the NeoPrep Library System (Illumina) following the manufacturer’s instructions.

treatment_protocol: SRBC immunization as outlined in this study.

value: GC B cells

tag: chat-gfp

value: GFP negative


title: GFP positive Tfh cells 4

description: Library name: 30-09-22_8_TP_S5-S7_S108

value: Tfh cells

value: GFP positive


title: AML SU227, scMultiome GEX

city: Baltimore

first: Andrew

middle: P

last: Feinberg

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics

institute: Johns Hopkins University

data_processing:
For each cell analyzed, paired-end reads were mapped to human genome hg38 using Cell Ranger (10x Genomics) for scRNA-seq or Cell Ranger Arc for single-cell multiomics.
For the single-omic scRNA-seq data, cells with number of non-zero genes larger than 1,000; number of reads less than 60,000; and percentage of mitochondria reads less than 25% were retained.
For the multi-omic data, cells were retained if: number of reads larger than 5,000 but smaller than 100,000 from the scATAC-seq data modality; number of reads larger than 1,000 but smaller than 100,000 from the scRNA-seq data modality; and the percentage of mitochondria reads less than 30%.
The gene expression data were then normalized and log-transformed using the R package Seurat.
Samples from different patients or technologies (single or multi-omics) were integrated using Harmony based on the gene expression data.
Assembly: hg38
Supplementary files format and content: Tab-separated files (tsv) containing log-normalized count data.
Library strategy: Single-cell Multiome

molecule: nuclear RNA

source_name: Primary acute myeloid leukemia

extract_protocol:
Cryopreserved samples were used to generate a single cell suspension (for scRNA-seq) or a single nuclei suspension (for single-cell Multiome, according to protocol Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing [10x Genomics]). Single cells (for scRNA-seq) or nuclei (for scMultiome ATAC+Gene Expression) were captured on a 10x Chromium Controller instrument according to manufacturer instructions.
Libraries were generated using Chromium NextGEM Single-cell 3’ Gene Expression reagents (for scRNA-seq) or using the Chromium Next GEM Single-cell Multiome ATAC + Gene Expression reagents (for scMultiome). Quality control on intermediate products and final libraries was performed using the Agilent Bioanalyzer High Sensitivity Kit. The final libraries were quantified via qPCR using KAPA Library Quantification Kits. A spike-in of 1% PhiX control library (Illumina) was used as the technical control.

value: Primary acute myeloid leukemia

value: CEBPA mutation


title: CD8, switched diet fed mice, 5


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB689ACG)

description:
https://www.encodeproject.org/experiments/ENCSR121AEC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR121AEC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB689ACG

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 50 U/mL Interleukin-2 for 24 hours

value: primary cell

value: male

value: adult

value: 38 year

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS971FOY at ENCODE; https://www.encodeproject.org/ENCBS971FOY/


title: GFP positive GC B cells 4

description: Library name: 30-09-22_5_BP_S5-S7_S105


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB379OOP)

description:
https://www.encodeproject.org/experiments/ENCSR033HUY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR033HUY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB379OOP

source_name: Homo sapiens male adult (38 years) stimulated activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-4 for 4 hours

value: John Stamatoyannopoulos, UW

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS921YZT at ENCODE; https://www.encodeproject.org/ENCBS921YZT/


title: AML SU214 Replicate 2, scMultiome GEX

description: SU214 was sequenced with scRNA-seq single-omics and single-cell multiome sequencing (Biological replicates). This record contains the gene expression portion of the single-cell multiomics data.

value: DNMT3A mutation


title: GFP positive Tfh cells 3

description: Library name: 30-09-22_4_TP_S2-S4_S104

value: spleen


title: AML SU075, scMultiome GEX

value: IDH1/2 mutation


title: CD8, switched diet fed mice, 1

value: WT

value: switched diet (12 weeks)


title: DNase-seq from immature natural killer cell (ENCLB165XRX)

description:
https://www.encodeproject.org/experiments/ENCSR309XUP/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR309XUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB165XRX

source_name: Homo sapiens male adult (30 years) immature natural killer primary cell

value: immature natural killer cell

value: 30 year

value: Shelly Heimfeld

value: ENCBS816LNZ at ENCODE; https://www.encodeproject.org/ENCBS816LNZ/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB714FXK)

description:
https://www.encodeproject.org/experiments/ENCSR145ORS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR145ORS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB714FXK

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-7 for 4 hours

value: primary cell

value: male

value: adult

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P13232; treatment_term_name:Interleukin-7; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS946AOI at ENCODE; https://www.encodeproject.org/ENCBS946AOI/


title: AML JH6048, scMultiome GEX

value: Primary acute myeloid leukemia

value: CEBPA mutation


title: GMP-1, scATAC-seq

description: Library name: GMP-1_scATACseq_single

library_source: genomic single cell

data_processing:
Single-cell sequencing data were aligned to the hg38 human reference genome. Multiomic data were processed using Cell Ranger Arc (10x Genomics), and single-omic scATAC-seq data were processed using Cell Ranger ATAC.
Quality control filtering was applied as follows: For multiomic data, cells were retained if they met all of the following criteria: (i) 5,000–100,000 total reads in the scATAC-seq modality, (ii) 1,000–100,000 total reads and <30% mitochondrial reads in the scRNA-seq modality. For single-omic scATAC-seq data, cells with 2,000–100,000 total reads were retained.
For scATAC-seq data processing, we first generated a unified peak set by merging peaks from all samples (both single-omic and multiomic) using Cell Ranger ATAC and Cell Ranger Arc output peak files. Read counts within these unified peak regions were then quantified for each cell using the Signac R package. Peak-level read counts were normalized using term frequency–inverse document frequency (TF-IDF) via the RunTFIDF() function.
Cross-sample integration was performed using Harmony based on gene expression data to correct for batch effects between patients and technologies (single-omic vs. multiomic).
Assembly: hg38
Supplementary files format and content: Tab-separated files (tsv) containing log-normalized count data for each peak.

source_name: Sorted normal GMP cells

extract_protocol:
Cryopreserved samples were used to generate a single cell suspension (for scATAC-seq, according to protocol Nuclei Isolation for Single Cell ATAC Sequencing [10x Genomics]) or a single nuclei suspension (for single-cell Multiome, according to protocol Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing [10x Genomics]). Single cells (for scATAC-seq) or nuclei (for scMultiome ATAC+Gene Expression) were captured on a 10x Chromium Controller instrument according to manufacturer instructions.
Single-cell ATAC libraries were constructed with Chromium Next GEM Single Cell ATAC reagents. Single-cell multiome ATAC libraries were generated using the Chromium Next GEM Single-cell Multiome ATAC + Gene Expression reagents and a 10x Chromium Controller instrument according to the manufacturer’s instructions. A spike-in of 1% PhiX control library (Illumina) was used as the technical control.

value: Sorted normal GMP cells

value: Normal GMP


title: GFP negative Tfh cells 3

description: Library name: 30-09-22_3_TN_S2-S4_S103

value: spleen

value: Tfh cells

value: GFP negative


title: CD8, switched diet fed mice, 2

value: WT

value: switched diet (12 weeks)


title: CD34-1, scATAC-seq

description: Library name: CD34-1_scATACseq_single

source_name: Bone marrow derived CD34+ Stem/Progenitor

value: Normal CD34+


title: GFP negative GC B cells 3

description: Library name: 30-09-22_2_BN_S2-S4_S102

value: GC B cells


title: AML JH5236, scRNA-seq

library_source: transcriptomic single cell

data_processing:
For each cell analyzed, paired-end reads were mapped to human genome hg38 using Cell Ranger (10x Genomics) for scRNA-seq or Cell Ranger Arc for single-cell multiomics.
For the single-omic scRNA-seq data, cells with number of non-zero genes larger than 1,000; number of reads less than 60,000; and percentage of mitochondria reads less than 25% were retained.
For the multi-omic data, cells were retained if: number of reads larger than 5,000 but smaller than 100,000 from the scATAC-seq data modality; number of reads larger than 1,000 but smaller than 100,000 from the scRNA-seq data modality; and the percentage of mitochondria reads less than 30%.
The gene expression data were then normalized and log-transformed using the R package Seurat.
Samples from different patients or technologies (single or multi-omics) were integrated using Harmony based on the gene expression data.
Assembly: hg38
Supplementary files format and content: Tab-separated files (tsv) containing log-normalized count data.

molecule: polyA RNA

value: IDH1/2 mutation


title: GFP positive GC B cells 3

description: Library name: 30-09-22_1_BP_S2-S4_S101

value: GFP positive


title: AML SU344, scATAC-seq

description: Library name: SU344_scATACseq_single

value: DNMT3A mutation


title: AML JH5205, scMultiome GEX


title: AML SU270, scATAC-seq

description: Library name: SU270_scATACseq_single

value: TET2 mutation


title: CD8, normal diet fed mice, 6

value: normal diet (12 weeks)


title: CD8, normal diet fed mice, 5


title: CD8, switched diet fed mice, 3


title: AML JH4639, scMultiome GEX


title: AML SU214 Replicate 1, scATAC-seq

description:
Library name: SU214_scATACseq_single
SU214 was sequenced with scATAC-seq single-omics and single-cell multiome sequencing (Biological replicates). This record contains scATAC-seq single-omics data.


title: GFP positive Tfh cells 2

description: Library name: 30-09-22_16_TP_S10_S116


title: AML JH4316, scMultiome GEX


title: GFP negative Tfh cells 2

description: Library name: 30-09-22_15_TN_S10_S115


title: CD8, normal diet fed mice, 3


title: AML SU209, scATAC-seq

description: Library name: SU209_scATACseq_single


title: CD8, normal diet fed mice, 2


title: GFP negative GC B cells 2

description: Library name: 30-09-22_14_BN_S10_S114


title: AML SU204, scATAC-seq

description: Library name: SU204_scATACseq_single


title: CD8, normal diet fed mice, 4


title: CD8, normal diet fed mice, 1


title: AML SU070, scATAC-seq

description: Library name: SU070_scATACseq_single


title: GFP positive GC B cells 2

description: Library name: 30-09-22_13_BP_S10_S113


title: Leukemia cells from  Iron-overload AML BM

city: Nanjing

first: feifei

last: yang

address: Changle Road 68

country: China

institute: Nanjing first hospital,Nanjing medical university

data_processing:
Base calling was done by Illumina NovaSeq6000
Read pairs with low quality in either read were filtered out (10% bases with N or 50% bases with Q5)
Alignment was performed against RefSeq by bowtie2 (version 2.2.5)
FPKM values of each gene for each sample was measured via RSEM (version v1.2.12)
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: BM

extract_protocol:
Sorted macrophages and leukemia cells were harvested and resuspended in 350ul RLT and 3.5ul β-Me.Total RNA is exacted by QIAGEN Rneasy Mini Kit(CAT 74103).
RNA libraries were prepared for sequencing using illumina NovaSeq6000 protocols

value: BM

tag: cell line

value: AML cells

value: Iron,leukemia


title: AML JH5034, scMultiome GEX

value: Primary acute myeloid leukemia


title: GFP positive Tfh cells 1

description: Library name: 30-09-22_12_TP_S8-S9_S112


title: AML SU050, scATAC-seq

description: Library name: SU050_scATACseq_single


title: Leukemia cells from  AML BM

description: Leukemia cells from  AML BM

value: Leukemia cells from  AML BM

value: PBS,leukemia


title: XXV_C26_H3K27me3

city: Cleveland

first: Yaw

last: Asante

state: OH

address: 10900 Euclid Ave

department: Department of Nutrition

institute: Case Western Reserve University

data_processing:
HiChIP data was processed by first trimming the bridge sequence (AGGTTCGTCCATCGATCGATGGACGAACCT), followed by use of the HiC-Pro pipeline (https://github.com/nservant/HiC-Pro) where the enzymatic digestion enzyme parameter was left blank, to account for MNase digestion methodology.
Processed file for Juicebox visualization was generated by hicpro2juicebox.sh (HiC-Pro tools) and Juicer tools (https://github.com/aidenlab/juicer).
Assembly: Hg38
Supplementary files format and content: hic files are provided at the chromosome-level.
Library strategy: HiChIP

source_name: SU-DIPG-XXV

growth_protocol: XXV cells were grown in T75 ultra-low attachment flasks with standard neurosphere media (TSM base supplemented with B27 minus vitamin A, EGF, FGF, PDGF-AA, PDGF-BB, heparin).

extract_protocol:
For HiChIP, the Dovetail MNase HiChIP kit (Catalogue #21007) was used. Briefly, cells were then thawed and fixed with DSG and 1% formaldehyde, then digested with MNase for 15 minutes at 22˚C and stopped with EGTA. Cells were then lysed with RIPA buffer, and chromatin was evaluated for digestion efficiency, achieving 50-70% mononucleosomes.  Immunoprecipitation was carried out with anti-H3K27ac (Millipore, MABE647) and anti-H3K27me3 (Cell Signaling Technology, 9733). Spike-in for AQuA-normalization was performed by adding chromatin extracted from C2C12 cells, a mouse muscle myoblast cell line, at a defined and conserved ratio of 1:10 mouse chromatin to human chromatin.
Standard Illumina barcodes were introduced during library preparation.

treatment_protocol: For HiChIP experiments, XXV cells were treated with DMSO or 8uM of C26 for 24 hours. Cells were then spun down, washed, and flash frozen for further processing.

value: SU-DIPG-XXV


title: XXV_C26_H3K27ac


title: Macrophages from  Iron-overload AML Spleen

source_name: Spleen

value: Spleen

value: Macrophage


title: GFP negative Tfh cells 1

description: Library name: 30-09-22_11_TN_S8-S9_S111

value: spleen

value: Tfh cells

value: GFP negative


title: GFP negative GC B cells 1

description: Library name: 30-09-22_10_BN_S8-S9_S110

value: GC B cells


title: XXV_DMSO_H3K27me3

value: DMSO


title: AML SU048, scATAC-seq

description: Library name: SU048_scATACseq_single


title: Macrophages from  AML Spleen

description: Macrophages from  AML Spleen

value: Macrophages from  AML Spleen


title: GMP-1, WGBS

description: Library name: GMP-1_WGBS

data_processing:
Following DNA sequencing, fastq files were trimmed using TrimGalore. Trimmed reads were aligned to the hg19 genome using Bismark. Samtools was used to merge, sort, and deduplicate bam files. Finally, the informME analysis pipeline was applied to quantify methylation stochasticity within individual samples and to compare methylation stochasticity between samples.
Assembly: hg19
Supplementary files format and content: bigwig format. Tracks include mean methylation level (MML), normalized methylation entropy (NME), and Jensen Shannon Distance (JSD) to measure methylation stochasticity between samples.
Supplementary files format and content: Processed data for AML samples and normal CD34+ and GMP controls includes comparison to WGBS data from a previously published LMPP sample (GSM4036933).

source_name: Sorted normal GMP

extract_protocol:
Primary AML samples were collected from peripheral blood or bone marrow.
WGBS libraries for CMP and MEP normal controls were generated using the IDT Methyl-Seq Kit. For primary AML samples, and CD34+ and GMP normal controls, WGBS libraries were generated using NEBNext Ultra DNA library Prep kit for Illumina according to the manufacturer's instructions with modifications. Input gDNA was spiked with 1% unmethylated Lambda DNA (Promega) to monitor bisulfite conversion efficiency. Size selection was performed using SPRIselect beads and insert sizes of 300-400bp were isolated. Samples were bisulfite converted after size selection using EZ DNA Methylation-Lightning Kit (Zymo). Libraries were sequenced on an Illumina HiSeq4000 or NovaSeq6000 instruments.

value: Sorted normal GMP

value: Normal GMP


title: AML JH4198, scRNA-seq

value: IDH1/2 mutation


title: XXV_DMSO_H3K27ac


title: Macrophages from Normal Spleen

description: Macrophages from Normal Spleen

value: Macrophages from Normal Spleen

value: PBS


title: RPMI8226 cells, shHNRNPC

source_name: Peripheral blood

extract_protocol:
Multiple myeloma cells were harvested and resuspended in 350ul RLT and 3.5ul β-Me.Total RNA is exacted by QIAGEN Rneasy Mini Kit(CAT 74103).
RNA libraries were prepared for sequencing using illumina NovaSeq6000 protocols

value: Peripheral blood

value: Multiple myeloma cells

value: HNRNPC knockdown


title: long read RNA-seq from C2C12 (ENCLB122YYB)

description:
https://www.encodeproject.org/experiments/ENCSR160HKZ/
***************
biological replicate number: 1
technical replicate number: 1
description: myoblast C2C12 direct rna
experiment encode accession: ENCSR160HKZ
assay title: long read RNA-seq
assembly: GRCm39
encode release date: 2025-06-05
lab: Ali Mortazavi, UCI
library encode accession: ENCLB122YYB
size range: 5-470674
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

source_name: Mus musculus C2C12 cell line

tag: line

value: cell line

tag: description

value: C2C12 single-cell myoblasts

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: ATCC

value: ENCBS521YWL at ENCODE; https://www.encodeproject.org/ENCBS521YWL/

value: Derived from ENCODE donor ENCDO321TZV; https://www.encodeproject.org/ENCDO321TZV/


title: RPMI8226 cells, shControl

value: WT


title: Aged+SMNV-ATAC-seq

city: hangzhou

first: Zhao

last: lan

state: Zhejiang Province

address: Dinglan Street

institute: Hangzhou Traditional Chinese Medicine Hospital

description: Library name: sample2

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
ATAC-seq reads were aligned to the hg38 genome using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig

organism: Rattus norvegicus

source_name: Rat mesenchymal stem cells

growth_protocol: Rat mesenchymal stem cells were cultured in a high-glucose DMEM medium containing 10% serum at 37°C and 5% CO2 in an incubator.

extract_protocol:
cells were harvested from cell culture and lysed in lysis buffer. The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer’s manual. 50 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃.
The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen).

treatment_protocol: Rat mesenchymal stem cells were incubated with 200 nM doxorubicin for 24 hours, followed by replacement with fresh complete medium for an additional 6 days to induce senescence. During this subsequent period, cells were treated with either 100 µg/ml SMNV or a vehicle control.

value: Rat mesenchymal stem cells

value: Doxorubicin-induced senescence


title: Aged-ATAC-seq

description: Library name: sample1


title: Macrophages from Iron-overload Normal Spleen

value: Spleen

value: Macrophage

value: Iron


title: long read RNA-seq from C2C12 (ENCLB518XCK)

description:
https://www.encodeproject.org/experiments/ENCSR160HKZ/
***************
biological replicate number: 1
technical replicate number: 3
description: myoblast C2C12 direct rna
experiment encode accession: ENCSR160HKZ
assay title: long read RNA-seq
assembly: GRCm39
encode release date: 2025-06-05
lab: Ali Mortazavi, UCI
library encode accession: ENCLB518XCK
size range: 5-306886
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

tag: biosample encode accession


title: Ctrl_L_2

status: Public on Mar 05 2026

city: Madison

first: Hongtae

last: Park

state: Wisconsin

address: 2015 Linden Drive

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

description:
Library name: Ctrl_L_2
Replicate 2

data_processing:
Bulk RNA-seq: Raw Ensembl-level gene counts were filtered using NOISeq (CPM > 1, CV < 100) and normalized using the size-factor scaling method in TCC.
scRNA-seq: Raw sequencing data processed using Cell Ranger. Quality control, filtering, and dimensional reduction (PCA, UMAP) performed using Seurat (v5).
Assembly: mm10
Supplementary files format and content: Bulk RNA-seq data is provided as a combined, normalized count matrix CSV. scRNA-seq data is provided as filtered feature-barcode matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) generated by Cell Ranger.

source_name: Lung

extract_protocol:
For bulk RNA-seq, total RNA was extracted from lung tissues using the Direct-zol RNA Miniprep Plus Kit. For scRNA-seq, single-cell suspensions from lung tissues were stained with NP366 tetramer and sorted using a FACSAria III with >95% purity.
For bulk RNA-seq, mRNA libraries were prepared using poly-A enrichment and strand-specific protocols. For scRNA-seq, sorted cells were loaded into the Chromium Controller using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1.

treatment_protocol: Mice were vaccinated intranasally with recombinant nucleoprotein (NP) of the influenza A/Puerto Rico/8/34/H1N1 strain formulated with ADJ+GLA, ADJ+CDN, or ADJ+CpG, or infected with a sublethal dose of IAV-PR8.

value: Lung

value: Unvaccinated Control


title: ACPG_Sec_L_2

description:
Library name: ACPG_Sec_L_2
Replicate 2

value: ADJ+CpG Secondary (Prime and Boost)


title: Ctrl_L_3

description:
Library name: Ctrl_L_3
Replicate 3


title: ACDN_Sec_L_3

description:
Library name: ACDN_Sec_L_3
Replicate 3

value: ADJ+CDN Secondary (Prime and Boost)


title: long read RNA-seq from C2C12 (ENCLB538FHP)

description:
https://www.encodeproject.org/experiments/ENCSR160HKZ/
***************
biological replicate number: 1
technical replicate number: 2
description: myoblast C2C12 direct rna
experiment encode accession: ENCSR160HKZ
assay title: long read RNA-seq
assembly: GRCm39
encode release date: 2025-06-05
lab: Ali Mortazavi, UCI
library encode accession: ENCLB538FHP
size range: 5-377370
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: cell line

value: C2C12 single-cell myoblasts


title: SLC22A18-/-, liver tissues

city: Shanghai

first: Jing

last: Li

address: No.1678 Dongfang Road

institute: Shanghai Children's Medical Center

description:
Library name: Sample1
one sample from murine liver tissue

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

source_name: liver tissues

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

value: liver tissues


title: Ctrl_L_1

description:
Library name: Ctrl_L_1
Replicate 1


title: ACPG_Sec_L_3

description:
Library name: ACPG_Sec_L_3
Replicate 3


title: ACDN_Sec_L_1

description:
Library name: ACDN_Sec_L_1
Replicate 1


title: AGLA_Sec_L_1

description:
Library name: AGLA_Sec_L_1
Replicate 1

value: ADJ+GLA Secondary (Prime and Boost)


title: ACPG_Pri_L_2

description:
Library name: ACPG_Pri_L_2
Replicate 2

value: ADJ+CpG Primary (Single Dose)


title: AGLA_Sec_L_2

description:
Library name: AGLA_Sec_L_2
Replicate 2


title: ACPG_Pri_L_1

description:
Library name: ACPG_Pri_L_1
Replicate 1


title: ACPG_Pri_L_3

description:
Library name: ACPG_Pri_L_3
Replicate 3


title: ACDN_Pri_L_1

description:
Library name: ACDN_Pri_L_1
Replicate 1

value: ADJ+CDN Primary (Single Dose)


title: ACDN_Pri_L_3

description:
Library name: ACDN_Pri_L_3
Replicate 3


title: SLC22A18+/+, liver tissues

description:
Library name: Sample2
one sample from murine liver tissue


title: ACDN_Pri_L_2

description:
Library name: ACDN_Pri_L_2
Replicate 2


title: ACPG_Sec_L_1

description:
Library name: ACPG_Sec_L_1
Replicate 1


title: AGLA_Pri_L_2

description:
Library name: AGLA_Pri_L_2
Replicate 2

value: ADJ+GLA Primary (Single Dose)


title: AGLA_Pri_L_3

description:
Library name: AGLA_Pri_L_3
Replicate 3


title: male C57BL/6NJ mice 12, rectal tissue, IBM, Day7

city: Akabanedai

first: Takumi

last: Iwasawa

state: KIta

department: Institute of Life Innovation Studies

institute: Toyo University

description:
Library name: IBM sample 6
Column name in raw_counts_All_Samples.csv: 512RC

data_processing:
Adapter trimming, quality trimming, and downsampling were conducted using FASTQ Toolkit (v2.2.6). For downsampling, 20 million reads per sample were randomly selected. Secondary transcriptome analysis was performed using DRAGEN Differential Expression (v4.3.7) (Illumina) with mm10 as the reference genome. Differential expres-sion was assessed within the DESeq2 framework (DESeq2 v1.38.3); for each gene, p-values were calculated using the Wald test based on raw counts.
Assembly: mm10
Supplementary files format and content: Processed data are provided as text-based tables in TSV/CSV format and include:  1. Gene-level raw count matrix (rows: genes; columns: samples; values: integer counts).  2. Normalized expression matrix (e.g., DESeq2-normalized counts and/or variance-stabilized/rlog values; rows: genes; columns: samples).  3. Differential expression results table(s) comparing IBM vs vehicle (gene ID/symbol, log2 fold change, standard error, Wald statistic, p-value, FDR-adjusted p-value).  4. Sample metadata table describing group assignment, dose, and collection time point.

source_name: rectal

growth_protocol: Male C57BL/6NJ mice (8 weeks old) were maintained under specific pathogen-free conditions with ad libitum access to standard chow and water. Mice were acclimated for at least 7 days prior to treatment and housed under a 12 h light/12 h dark cycle at controlled temperature and humidity.

extract_protocol:
At day 7, mice were euthanized and rectal tissue was collected, rinsed briefly in cold PBS to remove luminal contents, and immediately preserved by snap-freezing in liquid nitrogen (or immersion in RNAlater) and stored at −80°C until processing. Total RNA was extracted from rectal tissue using FastGene RNA Premium Kit (FastGene, FG-81050) according to the manufacturer’s instructions, including on-column (or in-solution) DNase treatment. RNA quantity was measured by Qubit and RNA integrity was assessed using Bioanalyzer; samples with RIN ≥ 9.0 were used for library preparation.
NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA)

treatment_protocol: Mice were randomly assigned to receive intestinal bacterial metabolites (IBM) or vehicle once daily by oral gavage for 7 consecutive days. IBM is a cell-free fermented soybean extract generated by co-culturing 31 Lactobacillus/Bifidobacterium-related strains (strain list provided in Supplementary Table S1 of the associated manuscript). The administered dose was 2 mL/kg/day. Control mice received an equivalent volume of vehicle.

value: rectal

value: male

value: IBM

tag: time

value: Day 7


title: male C57BL/6NJ mice 11, rectal tissue, IBM, Day7

description:
Library name: IBM sample 5
Column name in raw_counts_All_Samples.csv: 511RC

tag: Sex


title: AGLA_Sec_L_3

description:
Library name: AGLA_Sec_L_3
Replicate 3


title: AGLA_Pri_L_1

description:
Library name: AGLA_Pri_L_1
Replicate 1


title: male C57BL/6NJ mice 9, rectal tissue, IBM, Day7

description:
Library name: IBM sample 3
Column name in raw_counts_All_Samples.csv: 509RC


title: male C57BL/6NJ mice 10, rectal tissue, IBM, Day7

description:
Library name: IBM sample 4
Column name in raw_counts_All_Samples.csv: 510RC


title: male C57BL/6NJ mice 8, rectal tissue, IBM, Day7

description:
Library name: IBM sample 2
Column name in raw_counts_All_Samples.csv: 508RC


title: male C57BL/6NJ mice 6, rectal tissue, control, Day7

description:
Library name: Control sample 6
Column name in raw_counts_All_Samples.csv: 506RC

value: Control


title: male C57BL/6NJ mice 4, rectal tissue, control, Day7

description:
Library name: Control sample 4
Column name in raw_counts_All_Samples.csv: 504RC


title: male C57BL/6NJ mice 5, rectal tissue, control, Day7

description:
Library name: Control sample 5
Column name in raw_counts_All_Samples.csv: 505RC


title: male C57BL/6NJ mice 1, rectal tissue, control, Day7

description:
Library name: Control sample 1
Column name in raw_counts_All_Samples.csv: 501RC


title: ACDN_Sec_L_2

description:
Library name: ACDN_Sec_L_2
Replicate 2


title: male C57BL/6NJ mice 3, rectal tissue, control, Day7

description:
Library name: Control sample 3
Column name in raw_counts_All_Samples.csv: 503RC


title: Rps19flox/+ Ter119+ polysome replicate 3

city: Manhasset

first: Lionel

last: Blanc

state: New York

address: 350 Community Drive

department: Pediatric Hematology/Oncology

institute: Feinstein Institutes for Medical Research

description: Library name: Sample_46

data_processing:
Reads were aligned to the mouse transcriptome mm10. Gene expression was corrected for sequencing depth with the variance stabilization transformation. The 1000 most variable genes across the dataset were used to embed the samples in a principal components analysis (PCA) space. Samples whose PCA embeddings were dominated by artifacts from poor sequencing depth, and genes found fewer than ten times among the polysome samples, were excluded from the final gene expression table.
Assembly: mm10
Supplementary files format and content: filtred_gene_norm_counts rShiny.csv
Library strategy: Ribo-Seq

source_name: Liver

growth_protocol: Female mice heterozygous for VavCre were mated with male mice homozygous for flox mutations in Rpl5 or Rps19. Fifteen days after observation of the copulation plug, the pregnant dam was euthanized by CO2 inhalation. Each fetus was extracted from the uterus, euthanized by decapitation, and dissected to obtain the liver and an extremity. Livers were homogenized in warm IMDM while genotypes were determined by PCR of DNA from the extremity.

extract_protocol:
Cell lysates were loaded on top of linear gradients of 10-50% w/v sucrose, 20 mM HEPES-KOH (pH 7.4), 5 mM MgCl2, 100 mM KCl, 2 mM dithiothreitol prepared with a Biocomp Gradient Master 108 in polyallomer tubes (Seton Scientific). The gradients were subjected to ultracentrifugation at 41000 rpm for 2 hr at 4 degC in a Beckman Coulter SW-41Ti rotor. Gradients were fractionated and analyzed for absorbance at 260 nm with a Biocomp Piston Gradient Fractionator. RNA was isolated from the cytoplasm and polysome fractions with Trizol LS (Thermo Fisher Scientific).
Magnetic mRNA capture, reverse transcription, adapter ligation, and library amplification were accomplished with the Watchmaker mRNA Library Prep Kit (Watchmaker Genomics). Samples were sequenced on an Illumina NovaSeq X Plus for 100 bp paired-end reads.

treatment_protocol: Liver homogenates were treated for 15 min in IMDM, 10% v/v FBS, 25 μg/mL emetine dihydrochloride (Sigma-Aldrich) at 37 degC. The c-Kit+ portion of each liver homogenate and the Ter119+ portion was isolated of the c-Kit- effluent were immunomagnetically isolated with Miltenyi MACS beads and columns. For each immunophenotype, cells were pooled by genotype in equal number for lysis in 10 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 100 mM KCl, 1% v/v Triton X-100, 2 mM dithiothreitol, 1X EDTA-free protease inhibitors (Selleck Chemical), and 1000 U/mL RNase inhibitors (Meridian Bioscience), for 10 min on ice. Lysates were clarified by centrifugation at 1300 rcf for 10 min at 4 degC.

value: Liver

tag: developmental stage

tag: immunophenotype

tag: cellular component

value: Polysome

tag: batch


title: Rps19flox/+ Ter119+ cytoplasm replicate 3

description: Library name: Sample_71

value: Cytoplasm


title: male C57BL/6NJ mice 7, rectal tissue, IBM, Day7

description:
Library name: IBM sample 1
Column name in raw_counts_All_Samples.csv: 507RC


title: VavCre Rps19flox/+ Kit+ polysome replicate 3

description: Library name: Sample_44

value: Kit+

value: VavCre Rps19flox/+


title: VavCre Rps19flox/+ Ter119+ polysome replicate 3

description: Library name: Sample_48


title: VavCre Rps19flox/+ Ter119+ cytoplasm replicate 3

description: Library name: Sample_72


title: Rps19flox/+ Kit+ polysome replicate 3

description: Library name: Sample_42


title: Rps19flox/+ Kit+ cytoplasm replicate 3

description: Library name: Sample_69


title: VavCre Rps19flox/+ Ter119+ cytoplasm replicate 2

description: Library name: Sample_68


title: Rps19flox/+ Ter119+ cytoplasm replicate 2

description: Library name: Sample_67


title: VavCre Rps19flox/+ Kit+ cytoplasm replicate 2

description: Library name: Sample_66


title: VavCre Rps19flox/+ Kit+ polysome replicate 2

description: Library name: Sample_36


title: VavCre Rps19flox/+ Ter119+ polysome replicate 2

description: Library name: Sample_40


title: VavCre Rps19flox/+ Ter119+ cytoplasm replicate 1

description: Library name: Sample_64


title: Rps19flox/+ Kit+ polysome replicate 2

description: Library name: Sample_34


title: Rps19flox/+ Ter119+ cytoplasm replicate 1

description: Library name: Sample_63


title: Rps19flox/+ Kit+ cytoplasm replicate 2

description: Library name: Sample_65


title: Rps19flox/+ Ter119+ polysome replicate 1

description: Library name: Sample_30


title: VavCre Rps19flox/+ Ter119+ polysome replicate 1

description: Library name: Sample_32


title: Rps19flox/+ Ter119+ polysome replicate 2

description: Library name: Sample_38


title: VavCre Rps19flox/+ Kit+ polysome replicate 1

description: Library name: Sample_28


title: male C57BL/6NJ mice 2, rectal tissue, control, Day7

description:
Library name: Control sample 2
Column name in raw_counts_All_Samples.csv: 502RC


title: Rps19flox/+ Kit+ cytoplasm replicate 1

description: Library name: Sample_61


title: VavCre Rpl5flox/+ Ter119+ cytoplasm replicate 3

description: Library name: Sample_60

value: VavCre Rpl5flox/+


title: VavCre Rpl5flox/+ Ter119+ polysome replicate 3

description: Library name: Sample_24


title: Rps19flox/+ Kit+ polysome replicate 1

description: Library name: Sample_26


title: Rpl5flox/+ Kit+ cytoplasm replicate 3

description: Library name: Sample_57


title: VavCre Rps19flox/+ Kit+ cytoplasm replicate 3

description: Library name: Sample_70


title: VavCre Rpl5flox/+ Kit+ cytoplasm replicate 3

description: Library name: Sample_58


title: VavCre Rps19flox/+ Kit+ cytoplasm replicate 1

description: Library name: Sample_62


title: Rpl5flox/+ Kit+ polysome replicate 3

description: Library name: Sample_18


title: VavCre Rpl5flox/+ Ter119+ polysome replicate 2

description: Library name: Sample_16


title: VavCre Rpl5flox/+ Ter119+ cytoplasm replicate 2

description: Library name: Sample_56


title: VavCre Rpl5flox/+ Kit+ cytoplasm replicate 2

description: Library name: Sample_54


title: Rpl5flox/+ Ter119+ cytoplasm replicate 3

description: Library name: Sample_59


title: Rpl5flox/+ Ter119+ cytoplasm replicate 2

description: Library name: Sample_55


title: VavCre Rpl5flox/+ Kit+ polysome replicate 2

description: Library name: Sample_12


title: Rpl5flox/+ Kit+ cytoplasm replicate 2

description: Library name: Sample_53


title: Rpl5flox/+ Ter119+ polysome replicate 2

description: Library name: Sample_14


title: VavCre Rpl5flox/+ Ter119+ polysome replicate 1

description: Library name: Sample_8


title: VavCre Rpl5flox/+ Ter119+ cytoplasm replicate 1

description: Library name: Sample_52


title: Rpl5flox/+ Ter119+ polysome replicate 1

description: Library name: Sample_6


title: Rpl5flox/+ Kit+ polysome replicate 2

description: Library name: Sample_10


title: Rpl5flox/+ Ter119+ cytoplasm replicate 1

description: Library name: Sample_51


title: Rpl5flox/+ Kit+ cytoplasm replicate 1

description: Library name: Sample_49


title: VavCre Rpl5flox/+ Kit+ cytoplasm replicate 1

description: Library name: Sample_50


title: Rpl5flox/+ Kit+ polysome replicate 1

description: Library name: Sample_2


title: SCIMP_coculture with T cells, rep1

city: Wuhan

first: You

last: yongqiang

address: 1277, Jiefang road

institute: Wuhan union hospital

description:
Library name: Sample6
SCIMP_1

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bladder

extract_protocol:
Total RNAs were extracted from xxx（samples） using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 or Illumina HiSeq 2500 sequencer.

value: bladder

value: bladder cancer cells

value: SCIMP overexpression

value: cocultured with CD8+ T cells


title: SCIMP_coculture with T cells, rep2

description:
Library name: Sample7
SCIMP_2


title: Vector_coculture with T cells, rep3

description:
Library name: Sample5
Vector_3

value: Vector


title: Vector_coculture with T cells, rep1

description:
Library name: Sample3
Vector_1


title: Nala_1, HepG2 cells, Nala treated, 48 h

city: Changchun

first: enwei

last: Wei

address: Xinjiang Street

institute: the first hospital of Jilin University

description: Library name: RNA-seq Nala_1

data_processing:
RNA-seq: The raw data was filtered with SOAPnuke (v1.4.0) by 1) Removing readscontaining adapters (adapter contamination); 2) Removing reads whose unknown base('N' base) ratio is more than 5%; 3) Removing reads whose low-quality base ratio(Base quality less than or equal to 15) is more than 20%, afterwards clean reads wereobtained and stored in FASTQ format. The clean data were mapped to the reference genome by HISAT (v2.1.0). The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5) . The expression level of genes was calculated by RSEM (v1.2.8). Within-group differential gene analysis was performed using DESeq.  ChIP-seq and ATAC-seq: Raw data were filtered using fastp (v0.23.1). Clean reads were mapped to the human reference genome (hg38) using STAR software (v2.7.6a). Read distribution analysis was performed using RSeQC (v4.0.0). Peak calling was carried out with MACS2 software (v2.2.7.1). Genes associated with peaks were annotated using HOMER (v4.8.3).
Assembly: hg38
Supplementary files format and content: bam, bai, bigwig

source_name: HepG2 cell line

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were maintained in a humidified atmosphere with 5% CO2 at 37 °C for subsequent cellular experiments.

extract_protocol:
For RNA-seq assay, total RNA was extracted using the RNAiso Plus reagent (Takara Bio, Shiga, Japan, catalog no. 9109) according to the manufacturer’s protocol. For ChIP-seq assay, HepG2 cells were cross-linked with 37% formaldehyde solution (final concentration 1%) for 10 minutes. The cross-linking reaction was quenched with 2.5 M glycine (final concentration 125 mM) for 5 minutes. Cells were washed with cold PBS, and the pellets were resuspended in SDS lysis buffer containing 100× PMSF (final concentration 1×) and 100× PIC (final concentration 1×). The samples were sheared by sonication at 80% amplitude in 1% SDS lysis buffer to generate chromatin fragments of 200–400 bp. For ATAC-seq assay, after treatment, 5 × 104 cells were treated with cell lysis buffer, and the nuclei were collected by centrifugation at 500 × g for 5 minutes.
RNA-seq library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Catalog No. ND607, Vazyme) and then sequenced on the DNBSEQ-T7 sequencer (MGI Tech Co., Ltd., China) with the PE150 model. For ATAC-seq library construction protocol, transposition and high-throughput DNA sequencing libraries were generated using the TruePrep DNA Library Prep Kit V2 for Illumina (Catalog No. TD501, Vazyme), and the libraries were sequenced on the DNBSEQ-T7 sequencer (MGI Tech Co., Ltd., China) using the PE150 model.

value: HepG2 cell line

value: hepatocellular carcinoma

value: WT

value: Nalaatocellular carcinoma


title: Nala_3, HepG2 cells, Nala treated, 48 h

description: Library name: RNA-seq Nala_3

value: Nala


title: Vector_coculture with T cells, rep2

description:
Library name: Sample4
Vector_2


title: NC, Hepg2 cells, untreated, 48 h

description: Library name: ATAC-seq NC


title: 2-DG, Hepg2 cells, 2-DG treated, 48 h

description: Library name: ATAC-seq 2-DG


title: 2-DG_Input, HepG2 cells, 2-DG treated, 48 h

description: Library name: ChIP-seq 2-DG_Input


title: 2-DG_2, HepG2 cells, 2-DG treated, 48 h

description: Library name: RNA-seq 2-DG_2


title: 2-DG_H3K18la, HepG2 cells, 2-DG treated, 48 h

description: Library name: ChIP-seq 2-DG_H3K18la


title: Nala_2, HepG2 cells, Nala treated, 48 h

description: Library name: RNA-seq Nala_2


title: NC_3, HepG2 cells, untreated, 24 h

description: Library name: RNA-seq NC_3


title: NC_BRD9, Hepg2 cells, untreated, 48 h

description: Library name: ChIP-seq NC_BRD9


title: NC_H3K18la, Hepg2 cells, untreated, 48 h

description: Library name: ChIP-seq NC_H3K18la


title: 2-DG_1, HepG2 cells, 2-DG treated, 48 h

description: Library name: RNA-seq 2-DG_1


title: NC_Input, Hepg2 cells, untreated, 48 h

description: Library name: ChIP-seq NC_Input


title: 2-DG_3, HepG2 cells, 2-DG treated, 48 h

description: Library name: RNA-seq 2-DG_3


title: SCIMP_coculture with T cells, rep3

description:
Library name: Sample8
SCIMP_3


title: NC_2, HepG2 cells, untreated, 24 h

description: Library name: RNA-seq NC_2


title: Nematostella vectensis replicate 2 clicktags

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

description:
Library name: Sample 4
Clicktag barcodes reads necessary to demultiplex conditions. See Readme_ClickTag_demultiplexing.xlsx file for detailed description and barcodes used.

data_processing:
scRNA-seq: We used CellRanger 6.1.1 (10X Genomics) to map reads and count unique molecular identifiers (UMIs) per gene per cell. We used the --force-cells flat to set a constant number of 20,000 per experiment (well in excess of the expected number cells for each case, as we intended to remove non-cells from the dataset using our own procedure; see below). We used whole gene bodies to guide the mapping of reads to the genome (--transcriptome flag). For details on clicktag barcode demultiplexing see Readme_ClickTag_demultiplexing.xlsx file.
Assembly: Nematostella vectensis: GCF_932526225.1
Supplementary files format and content: For ATAC-seq and ChIP-seq: bigWig coverage files (bw extension)
Supplementary files format and content: For scRNA_seq: TSV file with CellIDs and associated metadata, including treatment condition, metacell cluster, and replicate (in the same order as in the UMI matrix)
Supplementary files format and content: For scRNA_seq: MTX file containin gene x cell UMI counts

organism: Nematostella vectensis

source_name: Whole adult specimens

extract_protocol:
Embryos were fixed, dissociated and pooled before sorting single-cells for scRNAseq.
See Protocols column in Samples

value: Whole adult specimens

value: RLRb::mCherry transgenic line


title: wt

city: Heidelberg

first: Nicoletta

last: Petridou

state: BW

address: Meyerhofstrasse 1

department: DB

country: Germany

institute: EMBL

description:
Library name: wt
10x Genomics

data_processing:
Reads were processed using CellRanger-6.1.1 with default settings.
Assembly: GRCz11
Supplementary files format and content: features.tsv.gz : Tab-separated values, gzipped text (.tsv.gz); 3 columns: gene ID, gene name, type. Gene annotations (gene IDs and names)
Supplementary files format and content: matrix.mtx.gz : Matrix Market format, gzipped text (.mtx.gz); contains triplets: row, column, value. Sparse matrix of gene expression counts
Supplementary files format and content: barcodes.tsv.gz : Tab-separated values, gzipped text (.tsv.gz); 1 column of barcode strings. List of cell barcodes (one per line).
Supplementary files format and content: filtered_feature_bc_matrix.h5 : cellRanger output with features as rows, barcodes as columns, couonts (UMIs) as values in a sparse amtrix.
Supplementary files format and content: cds-wt_wnt11-processed.rds : R dataset  from analysis for both samples.

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish (Danio rerio) were raised at 28.5°C under a 14 h light / 10 h dark cycle. After eggs collection, the embryos were kept at 28.5°C in E3 solution.

extract_protocol:
ACME (ACetic-MEthanol), a dissociation protocol for single-cell transcriptomics, which simultaneously fixes the tissue, was used to avoid potential effects of the dissociated tissue architecture to gene expression (García-Castro et al., 2021). Briefly, shield-stage wildtype and MZwnt11/slb embryos were dechorionated and treated with the ACME solution. Dissociated cells were cryopreserved by adding 10% DMSO and stored at −80 °C.
cDNA libraries targeting ~10,000 cells per sample were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) following the manufacturer’s instructions.

value: whole embryo

tag: Stage

value: shield

value: wildtype


title: Nematostella vectensis replicate 2

description: Library name: Sample 2

extract_protocol:
Cells were fixed using the ACME protocol (10.1186/s13059-021-02302-5), FACS sorted, and processed with the 10X Genomics Chromium Single Cell 3' scRNAseq v3.1 kit.
Embryos were fixed, dissociated and pooled before sorting single-cells for scRNAseq.
See Protocols column in Samples

tag: tissue


title: wnt11

description:
Library name: wnt11
10x Genomics


title: Nematostella vectensis replicate 1 clicktags

description:
Library name: Sample 3
Clicktag barcodes reads necessary to demultiplex conditions. See Readme_ClickTag_demultiplexing.xlsx file for detailed description and barcodes used.

tag: cell type


title: 2-DG_BRD9, HepG2 cells, 2-DG treated, 48 h

description: Library name: ChIP-seq 2-DG_BRD9

tag: genotype


title: NC_1, HepG2 cells, untreated, 24 h

description: Library name: RNA-seq NC_1

tag: treatment


title: MCF7, PNA25, rep3

city: Kobe

first: Tamai

last: Endoh

address: 7-1-20, Minatojima-minamimachi, Chuo-ku

department: FIRST/FIBER

institute: Konan University

description:
Library name: PNA25_3
Column name in raw_CPM.txt: PNA25_3

data_processing:
CLC Genomics Workbench Version 25.0.1
Trimed sequencing reads were analyzed according to workflows provided by the manufacturer using mirBase_v22 as reference miRNAs data.
A total of 421 mature miRNAs, in which expression levels counted as counts per million reads (CPM) were more than 4 in control cells without PNA treatment, were analysed to quantify Log(2) fold change caused by the PNA treatment.
Statistical analyses were performed using NGS data obtained from triplicate experiments.
Assembly: mirBase_v22
Supplementary files format and content: Values of raw CPM values obtained from all samples in text format.
Supplementary files format and content: miRNA expression levels summalized in excel format. Values of Log(2) fold change obtained from samples with PNA treatment comparing to control sample without PNA treatment and Log(10) FDR-p-values obtained from triplicate experiments.

growth_protocol: MCF7 cells were cultured in Eagle′s minimum essential medium (EMEM) with non-essential amino acids (NEAA), supplemented with 10% fetal bovine serum and antibiotics (100 U/mL penicillin and 100 μg/mL streptomycin), and maintained at 37 °C under 5% CO2.

extract_protocol:
Cellular total RNA was purified using the miRNeasy Mini Kit (Qiagen) and a robotic workstation for automated purification (QIAcube, Qiagen) according to the standard program without optional DNase treatment.
A library for RNA-seq analysis was prepared from 100 ng total RNA using QIAseq miRNA Library Kit for Thermo Fisher Scientific NGS Systems (Qiagen) according to the manufacturer’s protocol. QIAseq miRNA 12 Index TF (Qiagen) was used to distinguish samples.

treatment_protocol: PNA (400 pmol) was mixed MCF7 (4 × 105 cells) in a solution of 4D-Nucleofector X Kit S (Lonza) and introduced into the cells using 4D-nucleofector (Lonza) with the optimal program for each cell line provided by the manufacturer. After the electroporation, 1/2 of the cells used for the electroporation were replated in each of the 2 wells of a collagen-coated 24-well plate (Iwaki). Cells were continuously cultured for 66 hours at 37 °C under 5% CO2.

value: breast carcinoma

value: electroporation with PNA25


title: MCF7, PNA23, rep3

description:
Library name: PNA23_3
Column name in raw_CPM.txt: PNA23_3

value: electroporation with PNA23


title: MCF7, PNA22, rep3

description:
Library name: PNA22_3
Column name in raw_CPM.txt: PNA22_3

value: electroporation with PNA22


title: MCF7, PNA23, rep2

description:
Library name: PNA23_2
Column name in raw_CPM.txt: PNA23_2


title: MCF7, PNA24, rep3

description:
Library name: PNA24_3
Column name in raw_CPM.txt: PNA24_3

value: electroporation with PNA24


title: MCF7, PNA25, rep2

description:
Library name: PNA25_2
Column name in raw_CPM.txt: PNA25_2


title: MCF7, PNA24, rep2

description:
Library name: PNA24_2
Column name in raw_CPM.txt: PNA24_2


title: MCF7, without PNA, rep2

description:
Library name: w/o_PNA_2
Column name in raw_CPM.txt: w/o_PNA_2

value: electroporation without PNA


title: MCF7, PNA21, rep2

description:
Library name: PNA21_2
Column name in raw_CPM.txt: PNA21_2

value: electroporation with PNA21


title: MCF7, PNA25, rep1

description:
Library name: PNA25_1
Column name in raw_CPM.txt: PNA25_1


title: Nematostella vectensis replicate 1

description: Library name: Sample 1


title: MCF7, without PNA, rep1

description:
Library name: w/o_PNA_1
Column name in raw_CPM.txt: w/o_PNA_1


title: MCF7, PNA22, rep1

description:
Library name: PNA22_1
Column name in raw_CPM.txt: PNA22_1


title: MCF7, PNA23, rep1

description:
Library name: PNA23_1
Column name in raw_CPM.txt: PNA23_1


title: P-spheroids on PS-Day35

first: YASUAKI

last: IWAMA

address: 2-1-8, Minatojimaminamimachi, Chuo-ku

department: Research Center

institute: Kobe City Eye Hospital

description:
Library name: D35_P
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1.
Assembly: GRCh38 v. 2020-A
Supplementary files format and content: Tab-separated values files and matrix files (10X Genomics Chromium Raw Gene BC Cellular Barcodes, Cellular Genes, and Cellular Matrix)

source_name: ES-cell line derived retinal spheroid

extract_protocol:
Ten to fifteen spheroids collected at each time point were dissociated using dispersed solutions for neuronal cells. Dissociated cells were subjected to the standard 10X workflow for Single Cell 3’ Reagent Kits v3.1. Single Index Kits were used on PS-D05 and PS-D09, whereas Dual Index Kits were used on PS-D15 and PS-D35.
Library Strategy: RNA-Seq, Library Source: transcriptomic (single cell), Library Selection: cDNA.

value: ES-cell line derived retinal spheroid

value: Rax::Venus (hESC-KhES-1)


title: NL-spheroids on PS-Day35

description:
Library name: D35_NL
10X Genomics


title: MCF7, PNA21, rep3

description:
Library name: PNA21_3
Column name in raw_CPM.txt: PNA21_3


title: WL-spheroids on PS-Day35

description:
Library name: D35_WL
10X Genomics


title: MCF7, PNA22, rep2

description:
Library name: PNA22_2
Column name in raw_CPM.txt: PNA22_2


title: MCF7, without PNA, rep3

description:
Library name: w/o_PNA_3
Column name in raw_CPM.txt: w/o_PNA_3


title: NL-spheroids on PS-Day15

description:
Library name: D15_NL
10X Genomics


title: P-spheroids on PS-Day09

description:
Library name: D09_P
10X Genomics


title: WL-spheroids on PS-Day15

description:
Library name: D15_WL
10X Genomics


title: WL-spheroids on PS-Day09

description:
Library name: D09_WL
10X Genomics


title: Well-Layered Retinal spheroids (WL-spheroids) on PS-Day05

description:
Library name: D05_WL
10X Genomics


title: MCF7, PNA24, rep1

description:
Library name: PNA24_1
Column name in raw_CPM.txt: PNA24_1


title: Non-Layered Retinal spheroids (NL-spheroids) on post-sorting (PS)-Day05

description:
Library name: D05_NL
10X Genomics


title: Polarized Retinal spheroids (P-spheroids) on PS-Day05

description:
Library name: D05_P
10X Genomics


title: MCF7, PNA21, rep1

description:
Library name: PNA21_1
Column name in raw_CPM.txt: PNA21_1


title: NL-spheroids on PS-Day09

description:
Library name: D09_NL
10X Genomics


title: P-spheroids on PS-Day15

description:
Library name: D15_P
10X Genomics


title: tumor, entinostat, TCR, rep2

city: Portland

first: Lisa

last: Coussens

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description:
Library name: Ent2_T
10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting and TCR/BCR identifcation were made using the multi function of Cell Ranger software v7.1.0
Assembly: mm10
Supplementary files format and content: CellRanger output files: mRNA_filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files: T_filtered_contig_annotations.csv
Supplementary files format and content: CellRanger output files: B_filtered_contig_annotations.csv

source_name: mammary gland primary tumor

extract_protocol:
Tumors were minced into 2mm pieces and digested with collagenase A and a simultaneous 150rpm homogenizatino process for 30 min at 37°C. Cells were washed twice with cold PBS 2% FBS and centrifugated 5min at 400 x g to stop the lysis reaction.
Single cell suspensions were counted and submitted to 5’ single-cell RNA sequencing using the 10x Genomics Single Cell 5' v2.

value: mammary gland primary tumor

value: MMTV-PyMT

value: Entinostat


title: tumor, entinostat, mRNA, rep2

description:
Library name: Ent2_mRNA
10x Genomics


title: tumor, entinostat, BCR, rep1

description:
Library name: Ent1_B
10x Genomics


title: tumor, entinostat, BCR, rep2

description:
Library name: Ent2_B
10x Genomics


title: Six2Cre, Replicate 1

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description: Library name: JP1573

data_processing:
Sequencing reads were aligned to UCSC mouse genome mm10 using hisat2. Only uniquely mapped reads were retained for downstream analysis.
Differential gene analysis was performed using cuffdiff.
Assembly: mm10
Supplementary files format and content: Excel file containing cuffdiff differential analysis results and FPKM for each sample

source_name: kidney

extract_protocol:
Total RNA from FACS isolated cells were prepared using Single Cell RNA Purification Kit (Norgen). From total RNA, mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs) following manufacturer’s instructions. Fragmentation of RNA followed by reverse transcription and second strand cDNA synthesis was done using NEBNext RNA First Strand Synthesis Module (E7525L) and NEBNext RNA Second Strand Synthesis Module (E6111L) following manufacturer’s instructions.
The resulting double-stranded cDNA’s were further processed to DNA sequencing libraries using ThruPLEX DNA-seq 12S Kit (R400428, Clontech Laboratories). Libraries were size-selected by gel purification for an average size of 350bp.

value: kidney

value: mesenchymal nephron progenitors

value: Six2 Cre/+

value: isolated by FACS


title: Six2Cre, Replicate 2

description: Library name: JP1574


title: tumor, entinostat, TCR, rep1

description:
Library name: Ent1_T
10x Genomics


title: tumor, entinostat, mRNA, rep1

description:
Library name: Ent1_mRNA
10x Genomics


title: tumor, untreated, BCR, rep2

description:
Library name: NT2_B
10x Genomics

value: Untreated


title: tumor, untreated, TCR, rep2

description:
Library name: NT2_T
10x Genomics


title: tumor, untreated, mRNA, rep2

description:
Library name: NT2_mRNA
10x Genomics


title: tumor, untreated, BCR, rep1

description:
Library name: NT1_B
10x Genomics


title: tumor, untreated, TCR, rep1

description:
Library name: NT1_T
10x Genomics


title: tumor, untreated, mRNA, rep1

description:
Library name: NT1_mRNA
10x Genomics


title: WT-3dpi-Glycerol-4

city: Gainesville

first: Yangyi

middle: Edward

last: Luo

state: FL

address: 1864 Stadium Road

institute: University of Florida

description: Library name: WT-3dpi-Glycerol-4

data_processing:
adaptor sequence removed with fastp
Alignment were performed using Salmon
gene quantification used featureCounts
differentital gene expression performed with DESeq2 in R
Assembly: GRC39 Mus Musculus
Supplementary files format and content: CSV files. Reads per sample

source_name: TA Muscle

extract_protocol:
RNA isolation on freshly isolated FAPs using Qiagen RNeasy Micro Kit
NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490L) was used for Poly A enrichment, and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (E7760L) was used for library Prep. 50ng of total RNA was used as the input to start.

value: TA Muscle

value: Primary FAPs

value: Mesenchymal Stromal Cell

value: WT

value: Glycerol


title: WT-3dpi-Glycerol-3

description: Library name: WT-3dpi-Glycerol-3


title: WT-3dpi-Glycerol-2

description: Library name: WT-3dpi-Glycerol-2


title: WT-3dpi-Glycerol-1

description: Library name: WT-3dpi-Glycerol-1


title: SMA-3dpi-Glycerol-4

description: Library name: SMA-3dpi-Glycerol-4

value: SMA


title: SMA-3dpi-Glycerol-3

description: Library name: SMA-3dpi-Glycerol-3


title: SMA-3dpi-Glycerol-2

description: Library name: SMA-3dpi-Glycerol-2


title: ARDS018

type: genomic

city: Little Rock

first: Akhilesh

last: Kaushal

state: Arkansas

address: One Children’s Way, Slot 512-43

department: Hematology/Oncology

institute: University of Arkansas for Medical Sciences

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing: The raw iDAT files were imported and processed using the minfi and sesame R packages. The data were normalized using the Subset-quantile Within Array Normalization (SWAN) package. The SWAN method is known to reduce technical variability between probe types while maintaining biological differences. DNAm levels for each probe were quantified as beta (β) values, calculated as the proportion of methylated signal (M) to the methylated plus unmethylated (U) signal from probes, with a constant c = 100 (β=  M⁄((M+U+c))). Probes with cross-hybridization, high detection p-values (> 0.01), β > 0.8 or < 0.2 across all samples, and those near single-nucleotide polymorphisms were excluded from the downstream analyses. The preprocessed and filtered β-values were log-transformed to M values using the approximation 〖log〗_2 [β⁄((1-β)]), to ensure a better fit to statistical model assumptions. The limma4 package in R was used to assess the statistical significance of differences in DNAm across groups. Probes with an absolute percentage difference in β-values > 5% and FDR p-value < 0.05 were considered significant.

label: Cy3 and Cy5

source_name: Nasal brushings

label_protocol: Standard Illumina Protocol

extract_protocol: Brushes were thawed on ice with 1:100 Beta-mercaptoethanol to reduce mucus disulfide bonds. The resulting suspension was then passed through a QIAShredder (Qiagen) and treated with DNAse. DNA and RNA were then extracted using an AllPrep DNA/RNA Mini-Kit (Qiagen). DNA was quantified using the Qubit Flex Fluorometer (ThermoFisher Scientific). The DNA was then sent to the CCHMC DNA core and run on an Illumina Infinium MethylationEPIC v2.0 microarray platform.

value: male

tag: group

tag: subject status

value: ARDS

value: Nasal brushings


title: SMA-3dpi-Glycerol-1

description: Library name: SMA-3dpi-Glycerol-1

tag: cell line


title: CONTROL022

value: CONTROL


title: WT-FAPs-3

description: Library name: WT-FAPs-3


title: WT-FAPs-2

description: Library name: WT-FAPs-2


title: ARDS036

value: female


title: SMA-FAPs-3

description: Library name: SMA-FAPs-3


title: SMA-FAPs-1

description: Library name: SMA-FAPs-1


title: pHSCs day 7-2

city: Daejeon

first: Thi Nga

last: Ha

address: 282 Munhwa-ro Jung-gu

department: Medical Science

country: South Korea

institute: Chungnam National University

description: Library name: Sample 6

data_processing:
Raw paired-end sequencing reads (100 nt) were quality-checked and trimmed to remove low-quality bases and adapter sequences using Trimmomatic. Clean reads were aligned to the Mus musculus reference genome (mm10/GRCm38) using HISAT2 (v2.0.5). HISAT2 alignment was performed using both a global whole-genome index and multiple local indexes downloaded from the UCSC Table Browser.
Transcript assembly and abundance estimation were performed using StringTie (v1.3.3b), generating gene- and transcript-level expression values as fragments per kilobase of exon per million mapped fragments (FPKM).
Expression values were transformed as log2(FPKM + 1) and normalized using quantile normalization to reduce systematic bias.
Assembly: Mus musculus genome assembly mm10 (GRCm38).
Supplementary files format and content: Tab-delimited text file containing gene-level expression values (FPKM) for each sample. Rows represent genes and columns represent individual samples (Day1, Day4, Day7 biological replicates).

extract_protocol:
Total RNA was extracted from primary hepatic stellate cells using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions. Briefly, cells were lysed in TRIzol, followed by phase separation with chloroform and RNA precipitation with isopropanol. The RNA pellet was washed with 70% ethanol and resuspended in RNase-free water. RNA concentration and purity were assessed using spectrophotometry, and RNA integrity was evaluated prior to library preparation.
Libraries were generated from 1.3 µg of total RNA using the TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) (Illumina) following the manufacturer’s protocol (Part #15031048 Rev. E). Ribosomal RNA was depleted prior to cDNA synthesis. Libraries were PCR-amplified, purified, and quality-checked before sequencing.

value: Liver

value: Primary liver cells


title: pHSCs day 7-1

description: Library name: Sample 5


title: SMA-FAPs-2

description: Library name: SMA-FAPs-2


title: ARDS032


title: ARDS030


title: WT-FAPs-1

description: Library name: WT-FAPs-1


title: ARDS004


title: ARDS015


title: pHSCs day 4-2

description: Library name: Sample 4


title: pHSCs day 4-1

description: Library name: Sample 3


title: ARDS001


title: ARDS039


title: CONTROL023


title: pHSCs day 1-2

description: Library name: Sample 1


title: pHSCs day 1-3

description: Library name: Sample 2


title: FLU_CD8_RECALL Vascular Tag (Anti-CD45.2 TotalSeq-B)

description:
Library name: FLU_CD8_RECALL_ADT
FB: Intravascular labeling with anti-CD45.2 TotalSeq-B antibody

library_source: other

value: Lung

value: Sorted NP366+ CD8 T cells

value: IAV-PR8 Recall


title: ARDS029


title: AG_CD8_RECALL Vascular Tag (Anti-CD45.2 TotalSeq-B)

description:
Library name: AG_CD8_RECALL_ADT
FB: Intravascular labeling with anti-CD45.2 TotalSeq-B antibody

value: ADJ+GLA Recall


title: ARDS019


title: FLU_CD8_RECALL, GEX

description:
Library name: FLU_CD8_RECALL_mRNA
GEX: transcriptome profiles


title: FLU_MEMORY

description:
Library name: FLU_MEMORY
10x Genomics

value: IAV-PR8 Memory


title: AG_CD8_RECALL, GEX

description:
Library name: AG_CD8_RECALL_mRNA
GEX: transcriptome profiles


title: FLU_PEAK

description:
Library name: FLU_PEAK
10x Genomics

value: IAV-PR8 Peak Effector


title: AG_MEMORY

description:
Library name: AG_MEMORY
10x Genomics

value: ADJ+GLA Memory


title: IM3

first: Lisen

last: Lu

address: Hongshan District, Wuhan City, Hubei Province, No. 1 Shizishan Street

institute: Huazhong agriculture university

description:
Library name: sample6
IM3_fpkm

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork (parameter-Qualitylimit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork（parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8 similarity faction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lymph node

growth_protocol: M2 macrophage were maintained in DMEM supplemented with 10% fetalbovine serum(FBS)and antibiotics in humidifed atmosphere with 5% CO2 at 37C

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

treatment_protocol: DMSO stimulation for control group with 24 hour , IU1 (10 µM) stimulation for IM group with 24 hour

value: lymph node


title: IM2

description:
Library name: sample5
IM2_fpkm


title: IM1

description:
Library name: sample4
IM1_fpkm


title: ARDS003


title: AG_PEAK

description:
Library name: AG_PEAK
10x Genomics

extract_protocol:
For bulk RNA-seq, total RNA was extracted from lung tissues using the Direct-zol RNA Miniprep Plus Kit. For scRNA-seq, single-cell suspensions from lung tissues were stained with NP366 tetramer and sorted using a FACSAria III with >95% purity.
For bulk RNA-seq, mRNA libraries were prepared using poly-A enrichment and strand-specific protocols. For scRNA-seq, sorted cells were loaded into the Chromium Controller using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1.

value: ADJ+GLA Peak Effector


title: ACDN_PEAK

description:
Library name: ACDN_PEAK
10x Genomics

value: ADJ+CDN Peak Effector


title: control2

description:
Library name: sample2
control2_fpkm


title: Perk KO, ZsGreen1-, 4 weeks WD, CMO

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

description:
Library name: ML039M
10x Genomics cell multiplexing library

data_processing:
Fastq files from each sequencing run was processed by Cell Ranger 6.1.2 using cellranger multi pipeline. A custom mouse genome was used  that included mm10 reference genome and ZsGreen1 sequence. Duplicate gene symbols were suffixed with numbers. Cell Ranger output files were provided for each replicate of the demultiplexed samples.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz (linked to the corresponding GEX sample records)

molecule: protein

source_name: Aorta

growth_protocol: Mice were housed with free access to water and chow until 6 week of age, tamoxifen-induced with 5-day IP, then allowed to rest for one week. At 8 weeks of age, chow was replace with western diet for the duration of the treatment.

extract_protocol:
At the end of each treatment timepoint, 3 mice of each genotype was euthanized following IACUC guidelines and the vasculature was immediately perfused with ice-cold PBS containing  actinomycin D. Working quickly, the ascending aorta of each mouse was isolated and independently enzymatically digested to single-cell suspensions, hashed, and sorted to separate viable ZsGreen+ and ZsGreen-populations. Cells were then pooled by Perk genotype and ZsGreen expression in a manner that ensured that all mice in each pool  were equally sampled, then pelleted and counted. A final pooling of the ZsGreen+ and ZsGreen- populations of each genotype was completed immediately before input into the 10x Genomics Chromium system to ensure equal numbers of SMC-derived and non-SMC-derived cells could be detected by scRNA-seq.
Libraries were prepared according to manufacturer’s instructions (Single Cell 3' v3 protocol, 10X Genomics).

treatment_protocol: Mice were treated with 0, 4, 8, 12, or 16 weeks of western diet, and were bled and weighed every two weeks during this time to track weight gain and serum cholesterol levels.

value: Aorta

value: Myh11(Cre), ROSA(ZsGreen1), Ldlr(-/-), Perk(-/-)

value: 4-week western diet

tag: cmo


title: control1

description:
Library name: sample1
control1_fpkm


title: ARDS037

value: male

value: ARDS

value: Nasal brushings


title: ARDS023

value: female


title: Perk KO, ZsGreen1+, 4 weeks WD, CMO

description:
Library name: ML038M
10x Genomics cell multiplexing library


title: Perk KO, ZsGreen1-, 4 weeks WD, GEX

description:
Library name: ML039
10x Genomics 3' mRNA library


title: ARDS031


title: Perk WT, ZsGreen1-, 4 weeks WD, CMO

description:
Library name: ML037M
10x Genomics cell multiplexing library

value: Myh11(Cre), ROSA(ZsGreen1), Ldlr(-/-)


title: Perk KO, ZsGreen1+, 4 weeks WD, GEX

description:
Library name: ML038
10x Genomics 3' mRNA library


title: Perk WT, ZsGreen1+, 4 weeks WD, CMO

description:
Library name: ML036M
10x Genomics cell multiplexing library


title: ARDS016


title: ARDS034


title: Perk KO, ZsGreen1-, 12 weeks WD, CMO

description:
Library name: ML035M
10x Genomics cell multiplexing library

value: 12-week western diet


title: Perk WT, ZsGreen1+, 4 weeks WD, GEX

description:
Library name: ML036
10x Genomics 3' mRNA library


title: Perk KO, ZsGreen1-, 12 weeks WD, GEX

description:
Library name: ML035
10x Genomics 3' mRNA library


title: ARDS010


title: ARDS002


title: Perk WT, ZsGreen1-, 4 weeks WD, GEX

description:
Library name: ML037
10x Genomics 3' mRNA library


title: Perk KO, ZsGreen1+, 12 weeks WD, GEX

description:
Library name: ML034
10x Genomics 3' mRNA library


title: Perk WT, ZsGreen1-, 12 weeks WD, CMO

description:
Library name: ML033M
10x Genomics cell multiplexing library


title: Perk WT, ZsGreen1+, 12 weeks WD, CMO

description:
Library name: ML032M
10x Genomics cell multiplexing library


title: Perk KO, ZsGreen1-, 8 weeks WD, CMO

description:
Library name: ML031M
10x Genomics cell multiplexing library

value: 8-week western diet


title: Perk WT, ZsGreen1-, 8 weeks WD, CMO

description:
Library name: ML029M
10x Genomics cell multiplexing library


title: Perk KO, ZsGreen1+, 8 weeks WD, CMO

description:
Library name: ML030M
10x Genomics cell multiplexing library


title: Perk WT, ZsGreen1+, 12 weeks WD, GEX

description:
Library name: ML032
10x Genomics 3' mRNA library


title: Perk KO, ZsGreen1+, 8 weeks WD, GEX

description:
Library name: ML030
10x Genomics 3' mRNA library


title: Perk WT, ZsGreen1+, 8 weeks WD, CMO

description:
Library name: ML028M
10x Genomics cell multiplexing library


title: Perk WT, ZsGreen1-, 8 weeks WD, GEX

description:
Library name: ML029
10x Genomics 3' mRNA library


title: Perk KO, ZsGreen1-, 8 weeks WD, GEX

description:
Library name: ML031
10x Genomics 3' mRNA library


title: Perk WT, ZsGreen1+, 8 weeks WD, GEX

description:
Library name: ML028
10x Genomics 3' mRNA library


title: Perk KO, ZsGreen1-, 0 week WD, CMO

description:
Library name: ML027M
10x Genomics cell multiplexing library

value: 0-week western diet


title: Perk WT, ZsGreen1-, 12 weeks WD, GEX

description:
Library name: ML033
10x Genomics 3' mRNA library


title: ARDS026


title: CONTROL001

value: CONTROL


title: Perk KO, ZsGreen1-, 0 week WD, GEX

description:
Library name: ML027
10x Genomics 3' mRNA library


title: Perk KO, ZsGreen1+, 0 week WD, CMO

description:
Library name: ML026M
10x Genomics cell multiplexing library


title: Perk KO, ZsGreen1+, 0 week WD, GEX

description:
Library name: ML026
10x Genomics 3' mRNA library


title: Perk WT, ZsGreen1+, 0 week WD, CMO

description:
Library name: ML024M
10x Genomics cell multiplexing library


title: Perk WT, ZsGreen1-, 0 week WD, GEX

description:
Library name: ML025
10x Genomics 3' mRNA library


title: ARDS045


title: ARDS021


title: Perk WT, ZsGreen1-, 0 week WD, CMO

description:
Library name: ML025M
10x Genomics cell multiplexing library


title: Perk KO, ZsGreen1-, 16 weeks WD, CMO

description:
Library name: ML023M
10x Genomics cell multiplexing library

value: 16-week western diet


title: Perk WT, ZsGreen1+, 0 week WD, GEX

description:
Library name: ML024
10x Genomics 3' mRNA library


title: Perk KO, ZsGreen1-, 16 weeks WD, GEX

description:
Library name: ML023
10x Genomics 3' mRNA library


title: Perk KO, ZsGreen1+, 16 weeks WD, CMO

description:
Library name: ML022M
10x Genomics cell multiplexing library


title: Perk WT, ZsGreen1-, 16 weeks WD, CMO

description:
Library name: ML021M
10x Genomics cell multiplexing library


title: male_femur_27 months_1409356

city: Tarrytown

first: Kun

last: Xiong

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

description: Library name: 1409356

data_processing:
Sequencing reads were processed with ArrayStudio (11.7.4) RNA-seq pipeline to quantify gene expression levels
Assembly: mm10
Supplementary files format and content: Tab-separated raw counts

source_name: femur

extract_protocol:
Mice were sacrificed by CO2 asphyxiation. Organs were removed, tissues were dissected on ice, preserved in RNAlater® solution (Thermo Fisher Scientific) and stored at -80℃ until further processing. RNA was extracted using MagMax-96 total RNA isolation kit (Termo Fisher). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies), and the integrity was assessed using Fragment Analyzer (Agilent).
Strand-specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen). RNA-seq libraries were sequenced at 100 million reads using Illumina Novo-Seq 6000 platforms in paired-end mode to a length of 2×76 bp base-pairs

tag: strain

value: femur

tag: age

value: 27 months


title: male_femur_24 months_1409351

description: Library name: 1409351

value: 24 months


title: female_femur_24 months_1409354

description: Library name: 1409354


title: female_femur_24 months_1409353

description: Library name: 1409353


title: male_femur_24 months_1409348

description: Library name: 1409348


title: male_femur_24 months_1409349

description: Library name: 1409349


title: Perk WT, ZsGreen1-, 16 weeks WD, GEX

description:
Library name: ML021
10x Genomics 3' mRNA library


title: Perk KO, ZsGreen1+, 16 weeks WD, GEX

description:
Library name: ML022
10x Genomics 3' mRNA library


title: male_femur_24 months_1409347

description: Library name: 1409347


title: male_femur_24 months_1409350

description: Library name: 1409350


title: male_femur_27 months_1409355

description: Library name: 1409355


title: male_femur_24 months_1409346

description: Library name: 1409346


title: male_femur_12 months_1409341

description: Library name: 1409341

value: 12 months


title: male_femur_12 months_1409340

description: Library name: 1409340


title: Perk WT, ZsGreen1+, 16 weeks WD, CMO

description:
Library name: ML020M
10x Genomics cell multiplexing library

value: Aorta


title: female_femur_12 months_1409339

description: Library name: 1409339


title: female_femur_18 months_1409342

description: Library name: 1409342

value: 18 months


title: female_femur_18 months_1409343

description: Library name: 1409343


title: Perk WT, ZsGreen1+, 16 weeks WD, GEX

description:
Library name: ML020
10x Genomics 3' mRNA library


title: female_femur_6 months_1409337

description: Library name: 1409337

value: 6 months


title: female_femur_24 months_1409352

description: Library name: 1409352


title: male_femur_6 months_1409335

description: Library name: 1409335

value: male


title: female_femur_6 months_1409336

description: Library name: 1409336


title: male_femur_6 months_1409334

description: Library name: 1409334


title: female_femur_27 months_1409329

description: Library name: 1409329


title: female_femur_27 months_1409330

description: Library name: 1409330


title: female_femur_24 months_1409327

description: Library name: 1409327


title: male_femur_27 months_1409333

description: Library name: 1409333


title: female_femur_24 months_1409326

description: Library name: 1409326


title: male_femur_27 months_1409332

description: Library name: 1409332


title: female_femur_24 months_1409324

description: Library name: 1409324


title: male_femur_18 months_1409345

description: Library name: 1409345


title: female_femur_24 months_1409325

description: Library name: 1409325


title: female_femur_27 months_1409331

description: Library name: 1409331


title: female_femur_12 months_1409338

description: Library name: 1409338


title: female_femur_24 months_1409328

description: Library name: 1409328


title: female_femur_24 months_1409323

description: Library name: 1409323


title: male_femur_24 months_1409320

description: Library name: 1409320


title: female_femur_24 months_1409322

description: Library name: 1409322


title: male_femur_24 months_1409319

description: Library name: 1409319


title: female_femur_21 months_1409317

description: Library name: 1409317

value: 21 months


title: male_femur_24 months_1409321

description: Library name: 1409321


title: male_femur_24 months_1409318

description: Library name: 1409318


title: female_femur_21 months_1409316

description: Library name: 1409316


title: female_femur_21 months_1409315

description: Library name: 1409315


title: female_femur_21 months_1409313

description: Library name: 1409313


title: female_femur_21 months_1409312

description: Library name: 1409312


title: female_femur_21 months_1409311

description: Library name: 1409311


title: female_femur_21 months_1409314

description: Library name: 1409314


title: male_femur_21 months_1409309

description: Library name: 1409309


title: male_femur_21 months_1409308

description: Library name: 1409308


title: male_femur_21 months_1409306

description: Library name: 1409306


title: female_femur_21 months_1409310

description: Library name: 1409310


title: male_femur_21 months_1409307

description: Library name: 1409307


title: male_femur_21 months_1409305

description: Library name: 1409305


title: male_femur_21 months_1409303

description: Library name: 1409303


title: control3

description:
Library name: sample3
control3_fpkm

value: lymph node


title: male_femur_18 months_1409301

description: Library name: 1409301


title: male_femur_18 months_1409297

description: Library name: 1409297


title: male_femur_18 months_1409299

description: Library name: 1409299


title: male_femur_18 months_1409298

description: Library name: 1409298


title: male_femur_21 months_1409302

description: Library name: 1409302


title: male_femur_18 months_1409296

description: Library name: 1409296


title: female_femur_18 months_1409295

description: Library name: 1409295

value: female


title: female_femur_18 months_1409291

description: Library name: 1409291


title: male_femur_18 months_1409300

description: Library name: 1409300


title: female_femur_18 months_1409292

description: Library name: 1409292


title: female_femur_18 months_1409290

description: Library name: 1409290


title: female_femur_18 months_1409294

description: Library name: 1409294


title: male_femur_21 months_1409304

description: Library name: 1409304


title: male_femur_12 months_1409284

description: Library name: 1409284


title: male_femur_12 months_1409285

description: Library name: 1409285


title: male_femur_12 months_1409288

description: Library name: 1409288


title: male_femur_12 months_1409287

description: Library name: 1409287


title: male_femur_12 months_1409286

description: Library name: 1409286


title: female_femur_12 months_1409283

description: Library name: 1409283


title: female_femur_18 months_1409293

description: Library name: 1409293


title: female_femur_12 months_1409281

description: Library name: 1409281


title: female_femur_12 months_1409280

description: Library name: 1409280


title: female_femur_12 months_1409282

description: Library name: 1409282


title: male_femur_6 months_1409277

description: Library name: 1409277


title: male_femur_6 months_1409273

description: Library name: 1409273


title: male_femur_12 months_1409289

description: Library name: 1409289


title: male_femur_6 months_1409276

description: Library name: 1409276


title: female_femur_12 months_1409279

description: Library name: 1409279


title: female_femur_6 months_1409267

description: Library name: 1409267


title: female_femur_6 months_1409270

description: Library name: 1409270


title: female_femur_6 months_1409269

description: Library name: 1409269


title: male_femur_6 months_1409272

description: Library name: 1409272


title: female_femur_27 months_1408841

description: Library name: 1408841


title: female_femur_6 months_1409271

description: Library name: 1409271


title: female_femur_6 months_1409268

description: Library name: 1409268


title: female_femur_6 months_1409266

description: Library name: 1409266


title: female_femur_27 months_1408842

description: Library name: 1408842


title: male_femur_27 months_1408839

description: Library name: 1408839


title: female_skin_18 months_1407138

description: Library name: 1407138

source_name: skin

value: skin


title: female_skin_18 months_1407139

description: Library name: 1407139


title: male_femur_27 months_1408840

description: Library name: 1408840


title: male_skin_18 months_1407136

description: Library name: 1407136


title: female_gWAT_18 months_1407133

description: Library name: 1407133

source_name: gWAT

value: gWAT


title: female_femur_12 months_1409278

description: Library name: 1409278


title: male_femur_6 months_1409275

description: Library name: 1409275


title: male_skin_18 months_1407134

description: Library name: 1407134


title: male_femur_6 months_1409274

description: Library name: 1409274


title: male_skin_12 months_1407131

description: Library name: 1407131


title: male_skin_18 months_1407132

description: Library name: 1407132


title: male_skin_12 months_1407128

description: Library name: 1407128


title: male_skin_18 months_1407126

description: Library name: 1407126


title: male_skin_24 months_1407127

description: Library name: 1407127


title: male_skin_6 months_1407129

description: Library name: 1407129


title: male_skin_6 months_1407124

description: Library name: 1407124


title: male_skin_12 months_1407122

description: Library name: 1407122


title: male_skin_12 months_1407119

description: Library name: 1407119


title: male_skin_21 months_1407120

description: Library name: 1407120


title: female_gWAT_27 months_1407115

description: Library name: 1407115


title: male_skin_18 months_1407123

description: Library name: 1407123


title: male_gWAT_27 months_1407116

description: Library name: 1407116


title: male_gWAT_27 months_1407108

description: Library name: 1407108


title: female_gWAT_18 months_1407104

description: Library name: 1407104


title: male_gWAT_27 months_1407117

description: Library name: 1407117


title: male_gWAT_27 months_1407109

description: Library name: 1407109


title: female_gWAT_24 months_1407102

description: Library name: 1407102


title: female_gWAT_27 months_1407106

description: Library name: 1407106


title: female_gWAT_27 months_1407105

description: Library name: 1407105


title: female_gWAT_24 months_1407096

description: Library name: 1407096


title: female_gWAT_27 months_1407099

description: Library name: 1407099


title: female_gWAT_27 months_1407110

description: Library name: 1407110


title: Perk KO, ZsGreen1+, 12 weeks WD, CMO

description:
Library name: ML034M
10x Genomics cell multiplexing library

value: Myh11(Cre), ROSA(ZsGreen1), Ldlr(-/-), Perk(-/-)

value: 12-week western diet


title: female_gWAT_21 months_1407100

description: Library name: 1407100


title: male_gWAT_27 months_1407114

description: Library name: 1407114


title: male_gWAT_24 months_1407098

description: Library name: 1407098


title: female_gWAT_21 months_1407101

description: Library name: 1407101


title: male_gWAT_24 months_1407094

description: Library name: 1407094


title: male_gWAT_27 months_1407112

description: Library name: 1407112


title: female_gWAT_24 months_1407097

description: Library name: 1407097


title: female_gWAT_27 months_1407107

description: Library name: 1407107


title: female_gWAT_27 months_1407111

description: Library name: 1407111


title: female_gWAT_18 months_1407103

description: Library name: 1407103


title: female_gWAT_24 months_1407092

description: Library name: 1407092


title: male_gWAT_24 months_1407090

description: Library name: 1407090


title: female_gWAT_24 months_1407091

description: Library name: 1407091


title: male_gWAT_24 months_1407095

description: Library name: 1407095


title: male_gWAT_24 months_1407093

description: Library name: 1407093


title: female_gWAT_27 months_1407083

description: Library name: 1407083


title: female_gWAT_24 months_1407087

description: Library name: 1407087


title: male_gWAT_27 months_1407084

description: Library name: 1407084


title: male_gWAT_27 months_1407086

description: Library name: 1407086


title: female_gWAT_27 months_1407081

description: Library name: 1407081


title: female_gWAT_27 months_1407082

description: Library name: 1407082


title: female_gWAT_21 months_1407020

description: Library name: 1407020


title: male_gWAT_21 months_1407016

description: Library name: 1407016


title: male_gWAT_21 months_1407017

description: Library name: 1407017


title: male_gWAT_21 months_1407014

description: Library name: 1407014


title: male_gWAT_21 months_1407012

description: Library name: 1407012


title: male_gWAT_21 months_1407009

description: Library name: 1407009


title: female_gWAT_21 months_1407019

description: Library name: 1407019


title: female_gWAT_24 months_1407008

description: Library name: 1407008


title: female_gWAT_24 months_1407011

description: Library name: 1407011


title: male_gWAT_24 months_1407004

description: Library name: 1407004


title: male_gWAT_21 months_1407015

description: Library name: 1407015


title: male_gWAT_24 months_1407005

description: Library name: 1407005


title: female_gWAT_21 months_1407002

description: Library name: 1407002


title: male_gWAT_27 months_1407085

description: Library name: 1407085


title: female_gWAT_24 months_1407007

description: Library name: 1407007


title: female_gWAT_21 months_1407001

description: Library name: 1407001


title: female_gWAT_24 months_1407006

description: Library name: 1407006


title: male_gWAT_21 months_1407013

description: Library name: 1407013


title: female_gWAT_21 months_1407018

description: Library name: 1407018


title: male_gWAT_6 months_1406999

description: Library name: 1406999


title: female_gWAT_6 months_1406998

description: Library name: 1406998


title: male_gWAT_24 months_1407000

description: Library name: 1407000


title: female_gWAT_18 months_1406996

description: Library name: 1406996


title: male_gWAT_24 months_1407088

description: Library name: 1407088


title: female_gWAT_18 months_1406995

description: Library name: 1406995


title: female_gWAT_18 months_1406994

description: Library name: 1406994


title: female_gWAT_12 months_1406993

description: Library name: 1406993


title: male_gWAT_24 months_1407003

description: Library name: 1407003


title: female_gWAT_21 months_1406997

description: Library name: 1406997


title: male_gWAT_12 months_1406991

description: Library name: 1406991


title: male_gWAT_12 months_1406986

description: Library name: 1406986


title: female_gWAT_18 months_1406985

description: Library name: 1406985


title: female_gWAT_12 months_1406989

description: Library name: 1406989


title: male_gWAT_12 months_1406990

description: Library name: 1406990


title: male_gWAT_12 months_1406987

description: Library name: 1406987


title: male_gWAT_18 months_1406978

description: Library name: 1406978


title: male_gWAT_18 months_1406980

description: Library name: 1406980


title: female_gWAT_18 months_1406984

description: Library name: 1406984


title: male_gWAT_6 months_1406976

description: Library name: 1406976


title: male_gWAT_18 months_1406983

description: Library name: 1406983


title: male_gWAT_18 months_1406982

description: Library name: 1406982


title: male_gWAT_18 months_1406988

description: Library name: 1406988


title: male_gWAT_18 months_1406979

description: Library name: 1406979


title: female_gWAT_12 months_1406972

description: Library name: 1406972


title: female_gWAT_12 months_1406974

description: Library name: 1406974


title: female_gWAT_12 months_1406969

description: Library name: 1406969