title: Streptococcus parasagnuinis , bacterial cells, OD600 0.8, no treatment, bio rep 3

description: Library name: Sample 3

value: No treatment


title: Streptococcus parasagnuinis , bacterial cells, OD600 0.8, no treatment, bio rep 1

status: Public on Feb 01 2026

type: SRA

city: Birmingham

first: Sara

middle: Elizabeth

last: Edmonds

state: AL

address: 1720 2nd Ave South, BBRB 744

department: Microbiology

country: USA

institute: University of Alabama at Birmingham

description: Library name: Sample 1

library_source: transcriptomic

data_processing:
Intermediate RNA Analysis was performed at SeqCenter (Pittsburg, PA), specifically sequencing was done on a NovaSeq 6000 giving 2x51bp reads.
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.0.3).
Assembly: Read mapping was performed with HISAT2 (v2.2.0). Read quantification was performed using Subread’s featureCounts (v2.0.1) functionality. Read counts loaded into R (v4.0.2) and were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (cpm). Differential expression analysis was performed using edgeR’s (v1.14.5) exact test for differences between two groups of negative-binomial counts with an estimated dispersion value of .1.
Supplementary files format and content: The file “All Quantified Genes.tsv” contains the results of the qlfTest for all genes in addition to the normalized counts per million.
Supplementary files format and content: The file “Differentially Expressed Genes.tsv” is a subset of the aforementioned file with |logFC| > 1 and p < .05.

molecule: total RNA

organism: Streptococcus parasanguinis FW213

source_name: Gram-positive Bacteria

growth_protocol: Overnight cultures of S. parasanguinis were subcultured in Todd Hewitt Broth (+/- 2 mM Nitrite) and harvested at a to an optical density of 0.8 at an absorbance of 600nm (OD600 0.8). Cultures were grown in three biological replicates at 37°C with 5% CO2.

extract_protocol:
RNA was extracted utilizing the Direct-zol RNA Miniprep (Zymo Research, Cat: R2052). Samples were DNAse treated with Invitrogen DNAse (RNAse free).
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

tag: cell type

value: Gram-positive Bacteria

tag: genotype

value: WT

tag: treatment

value: No treamtent


title: M, Esr1KO, PBS, Rep 3

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

description:
Library name: GSF3966-3230
s3230

data_processing:
Demultiplexed FASTQ files were assessed for quality using FastQC (v0.11.9) and trimmed for adapters and low-quality bases using Trimmomatic (v0.39).
Assembly: Clean reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR aligner (v2.7), and gene-level counts were quantified using featureCounts (Subread v2.0).
Supplementary files format and content: xls files containing raw counts for each sample and calculations for specific comparisons

organism: Mus musculus

source_name: lung

extract_protocol:
Total RNA was extracted from snap-frozen whole lungs using the Zymo Quick-RNA Miniprep Kit (Zymo Research, Irvine, CA) following the manufacturer’s protocol, including in-column DNase I treatment to remove genomic DNA. RNA purity and concentration were determined with a NanoDrop spectrophotometer (Thermo Fisher Scientific), and integrity was verified using an Agilent 2100 Bioanalyzer. Samples with RNA integrity number (RIN) ≥ 7.0 were used for sequencing.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on an Illumina NovaSeq 6000 at the Indiana University Center for Genomics and Bioinformatics (CGB) using paired-end 150 bp reads. Sequencing was conducted across two independent NovaSeq runs (CGB Project ID GSF3966), generating a total of 2.56 billion pass-filter reads (~30–40 million reads per sample).

tag: tissue

value: lung

value: Esr1 KO

value: PBS

tag: Sex

value: M


title: F, Esr1KO, PBS, Rep 5

description:
Library name: GSF3966-3237
s3237

value: F


title: F, Esr2KO, PBS, Rep 8

description:
Library name: GSF3966-3269
s3269

value: Esr2 KO


title: IL4_C_resub_1

city: Eugene

first: John

last: Postlethwait

state: OR

address: 1210 University Of Oregon

department: Biology

institute: University of Oregon

description:
Library name: C_resub_1
IL4_C_resub_1

data_processing:
Base calling via Bases2Fastq
Adapter clipping with Trimmomatic with the following parameters: "ILLUMINACLIP:/home/msistaff/public/CHURP_Deps/v1/db/all_illumina_adapters.fa:4:15:7:2:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:18"
Trimmed reads were aligned to the reference genome with HISAT2.
Duplicate reads based on alignment position were marked with SAMTools.
Cleaned and name-sorted alignments were processed with the featureCounts tool from the subread package in a strand-specific manner to give the processed data file in this submission.
Assembly: GRCm39
Supplementary files format and content: Gene expression Count Matrix: Maurice_subread_counts_gene_symbol.tsv

molecule: polyA RNA

source_name: CD8 T cells

growth_protocol: Cells were isolated and cultured in RP10 media for 24 hours.

extract_protocol:
Cells were sorted into RLT buffer plus beta-mercaptoethanol and frozen at -80°C. RNA was extracted using Zymo Research Quick-RNA MicroPrep with gDNA digestion.
Watchmaker Stranded mRNA kit

treatment_protocol: Cells were exposed to cytokines (100ng/mL) and/or agonist peptide (SIINFEKL; 1µM) at start of culture. Stimuli included mock, mock+IL-4, IL-12/15, IL-12/15+IL-4, IL-12/15/18, IL-12/15/18+IL-4, SIINFEKL, SIINFEKL+IL-4.

value: CD8 T cells


title: Streptococcus parasagnuinis , bacterial cells, OD600 0.8, no treatment, bio rep 2

description: Library name: Sample 2


title: F, Esr1KO, PBS, Rep 6

description:
Library name: GSF3966-3126
s3126


title: Streptococcus parasagnuinis , bacterial cells, OD600 0.8, 2 mM of Nitrite treatment, bio rep 2

description: Library name: Sample 5

value: 2 mM of Nitrite


title: M, Esr1KO, PBS, Rep 6

description:
Library name: GSF3966-3141
s3141


title: Streptococcus parasagnuinis , bacterial cells, OD600 0.8, 2 mM of Nitrite treatment, bio rep 3

description: Library name: Sample 6


title: F, WT, HDM, Rep 7

description:
Library name: GSF3966-2531
s2531

value: HDM


title: F, Esr2KO, HDM, Rep 7

description:
Library name: GSF3966-2685
s2685


title: M, Esr1KO, HDM, Rep 6

description:
Library name: GSF3966-2793
s2793


title: M, Esr2KO, HDM, Rep 5

description:
Library name: GSF3966-2609
s2609


title: M, Esr1KO, PBS, Rep 4

description:
Library name: GSF3966-2614
s2614


title: M, Esr1KO, PBS, Rep 5

description:
Library name: GSF3966-2755
s2755


title: M, WT, PBS, Rep 6

description:
Library name: GSF3966-2525
s2525


title: M, Esr1KO, HDM, Rep 5

description:
Library name: GSF3966-2509
s2509


title: M, Esr1KO, HDM, Rep 4

description:
Library name: GSF3966-2505
s2505


title: F, Esr1KO, HDM, Rep 6

description:
Library name: GSF3966-2515
s2515


title: F, Esr1KO, PBS, Rep 4

description:
Library name: GSF3966-2511
s2511


title: M, Esr2KO, HDM, Rep 6

description:
Library name: GSF3966-2878
s2878


title: M, Esr2KO, HDM, Rep 4

description:
Library name: GSF3966-2439
s2439


title: F, Esr1KO, HDM, Rep 4

description:
Library name: GSF3966-2489
s2489


title: M, Esr2KO, PBS, Rep 6

description:
Library name: GSF3966-2437
s2437


title: F, Esr1KO, HDM, Rep 5

description:
Library name: GSF3966-2493
s2493


title: M, Esr1KO, HDM, Rep 3

description:
Library name: GSF3966-2416
s2416


title: F, WT, PBS, Rep 6

description:
Library name: GSF3966-2390
s2390


title: F, Esr1KO, PBS, Rep 3

description:
Library name: GSF3966-2417
s2417


title: F, Esr2KO, HDM, Rep 6

description:
Library name: GSF3966-2435
s2435


title: M, WT, HDM, Rep 6

description:
Library name: GSF3966-2391
s2391


title: F, WT, HDM, Rep 5

description:
Library name: GSF3966-2388
s2388


title: F, WT, PBS, Rep 5

description:
Library name: GSF3966-2387
s2387


title: F, WT, HDM, Rep 4

description:
Library name: GSF3966-2332
s2332


title: M, WT, HDM, Rep 5

description:
Library name: GSF3966-2383
s2383


title: M, Esr2KO, PBS, Rep 5

description:
Library name: GSF3966-2320
s2320


title: F, Esr2KO, HDM, Rep 5

description:
Library name: GSF3966-2311
s2311


title: M, Esr2KO, PBS, Rep 4

description:
Library name: GSF3966-2308
s2308


title: M, WT, PBS, Rep 5

description:
Library name: GSF3966-2385
s2385


title: F, Esr2KO, PBS, Rep 7

description:
Library name: GSF3966-2312
s2312


title: M,Esr2KO, PBS, Rep 3

description:
Library name: GSF3966-2306
s2306


title: F, Esr2KO, PBS, Rep 5

description:
Library name: GSF3966-2297
s2297


title: F, Esr2KO, PBS, Rep 6

description:
Library name: GSF3966-2299
s2299


title: F, WT, HDM, Rep 6

description:
Library name: GSF3966-2389
s2389


title: F, Esr2KO, PBS, Rep 4

description:
Library name: GSF3966-2296
s2296


title: F, WT, HDM, Rep 3

description:
Library name: GSF3966-2249
s2249


title: M, WT, HDM, Rep 4

description:
Library name: GSF3966-2382
s2382


title: F, Esr2KO, HDM, Rep 4

description:
Library name: GSF3966-2298
s2298


title: F, Esr2KO, HDM, Rep 2

description:
Library name: GSF3966-2254
s2254


title: F, Esr2KO, PBS, Rep 3

description:
Library name: GSF3966-2259
s2259


title: F, Esr2KO, HDM, Rep 3

description:
Library name: GSF3966-2295
s2295


title: F, WT, HDM, Rep 2

description:
Library name: GSF3966-2245
s2245


title: F, Esr2KO, PBS, Rep 2

description:
Library name: GSF3966-2257
s2257


title: F, WT, HDM, Rep 1

description:
Library name: GSF3966-2244
s2244


title: F, Esr1KO, HDM, Rep 3

description:
Library name: GSF3966-2317
s2317


title: F, WT, PBS, Rep 3

description:
Library name: GSF3966-2242
s2242


title: F, WT, PBS, Rep 2

description:
Library name: GSF3966-2241
s2241


title: F, WT, PBS, Rep 4

description:
Library name: GSF3966-2243
s2243


title: F, WT, PBS, Rep 1

description:
Library name: GSF3966-2224
s2224


title: M, Esr2KO, HDM, Rep 3

description:
Library name: GSF3966-2198
s2198


title: M, Esr2KO, HDM, Rep 2

description:
Library name: GSF3966-2196
s2196


title: M, Esr2KO, HDM, Rep 1

description:
Library name: GSF3966-2195
s2195


title: M, Esr2KO, PBS, Rep 2

description:
Library name: GSF3966-2168
s2168


title: F, Esr2KO, PBS, Rep 1

description:
Library name: GSF3966-2192
s2192


title: M, Esr2KO, PBS, Rep 1

description:
Library name: GSF3966-2167
s2167


title: F, Esr2KO, HDM, Rep 1

description:
Library name: GSF3966-2163
s2163


title: M, WT, HDM, Rep 3

description:
Library name: GSF3966-2149
s2149


title: M, WT, PBS, Rep 4

description:
Library name: GSF3966-2135
s2135


title: M, WT, HDM, Rep 1

description:
Library name: GSF3966-2137
s2137


title: M, WT, PBS, Rep 2

description:
Library name: GSF3966-2132
s2132


title: M, WT, HDM, Rep 2

description:
Library name: GSF3966-2148
s2148


title: M, WT, PBS, Rep 3

description:
Library name: GSF3966-2133
s2133


title: F, Esr1KO, PBS, Rep 1

description:
Library name: GSF3966-2013
s2013


title: F, Esr1KO, HDM, Rep 1

description:
Library name: GSF3966-2012
s2012


title: M, WT, PBS, Rep 1

description:
Library name: GSF3966-2131
s2131


title: CHeller_Marc1-aLd-G7_2 mg/kg_3 Days_liver_U-3_F21

city: Carlsbad

first: Sagar

last: Damle

state: CA

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

description: Library name: 311002

data_processing:
Custom pipeline executed in linux shell
Libraries mapped to human genome using STAR
PCR duplications were removed post-alignment and making use of UMIs introduced during first-strand-synthesis
Read assignment to genes performed in salmon using pseudoalignment mode and default settings
TPM computed by normalizing per-gene read counts by total number of assigned reads
Assembly: human Grch39 and mouse mm10 (ensembl build 96)
Supplementary files format and content: tab-delimited files containing salmon output (gene counts)

source_name: liver

extract_protocol:
Total RNA was isolated using a custom silica column–based purification kit similar in principle to Qiagen RNA purification systems. 500ng RNA was used for library construction
Libraries constructed using Lexogen 3'QuantSeq (Rev) kit with custom first-strand-synthesis primers containing UMIs for PCR deduplication

value: liver

tag: treatment dose

value: 2 mg/kg

tag: batch

value: Experiment D - 25-1092


title: mouse bone, microgravity

city: Shimotsuke

first: Makoto

last: Kuro-o

state: Tochigi

address: 3311-1 Yakushiji

country: Japan

institute: Jichi Medical University

description:
Library name: Sample 0
pooled sample from 6 mice

data_processing:
High-throughput RNA sequencing were carried out using Illumina NovaSeq 6000 platform.
Raw data were aligned to the mouse reference genome GRCm38/mm10 with STAR (v2.7.3a).
Assembly and quantification of the transcripts were accomplished with RESM (v1.3.1).
Transcripts Per Million (TPM) were used for the measurements of the relative abundance of the transcripts.
The genes with low expression (TPM lower than 1 in both groups) were eliminated from further analysis.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Bone

growth_protocol: All the mice were housed individually in the Transportetion Cage Unit (TCU) equipped with LED lights for day/night cycles, a temperature/humidity logger, and a syringe-shaped food (containing 1.3% inorganic phosphate) and a drink nozzle to allow the mice free access to food and water.

extract_protocol:
The mice in the TCU were launched using SpaceX-22 from the NASA Kennedy Space Center (KSC) on June 3rd, 2021 (Day 0) and then transferred to Kibo, the Japanese experimental module attached to the International Space Station (ISS). On Day 9 or Day 10, the mice were starved for 5-16 hours, anesthetized by intraperitoneal injection of Ketamine (150mg/kg) and Xylazine (45 mg/kg), and then sacrificed by whole blood sampling with cardiac puncture and cervical dislocation. The carcasses were stored in the -95C freezer. The frozen blood samples and carcasses arrived at KSC on July 20th, 2021 via spaceX-22. The difference in the food weight between before and after the space flight was measured to calculate the average daily food consumption. As a control group for this microgravity group, mice were housed on ground under the same conditions as in the space (the normal gravity group). Six (6) mice with the similar body weight as those sent to the ISS were selected and transferred individually to the TCU. These mice were fed the same amount of food each day as the average daily food intake of the microgravity group. The carcasses were prepared 9 or 10 days later and stored frozen in a -80C freezer.
The bone RNA samples prepared individually from 6 mice each in the microgravity group and the normal gravity group were mixed in equal amounts per group, and subjected to RNA sequencing analysis. Sequencing libraries were constructed using TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Exposure to microgravity or normal gravity for 9-10 days

value: Bone

tag: cell line

value: tissue

value: wild-type

value: microgravity


title: CHeller_PBS_0 mg/kg_3 Days_liver_G-4_C7

description: Library name: 310973


title: M, Esr1KO, HDM, Rep 1

description:
Library name: GSF3966-2014
s2014


title: CHeller_PBS_0 mg/kg_3 Days_liver_G-2_C3

description: Library name: 310960


title: mouse bone, normal gravity

description:
Library name: Sample 1
pooled sample from 6 mice

value: normal gravity


title: CHeller_Marc1-aLd-G7_2 mg/kg_3 Days_liver_U-1_F17

description: Library name: 310962


title: CHeller_Marc1-aLd-G7_10 mg/kg_3 Days_liver_T-3_F15

description: Library name: 310999

value: 10 mg/kg


title: M, Esr1KO, PBS, Rep 1

description:
Library name: GSF3966-2015
s2015

value: lung

value: Esr1 KO


title: CHeller_PBS_0 mg/kg_3 Days_liver_G-3_C5

description: Library name: 311026

value: PBS


title: CHeller_Marc1-aLd-G7_10 mg/kg_3 Days_liver_T-1_F11

description: Library name: 310978


title: CHeller_PBS_0 mg/kg_3 Days_liver_G-1_C1

description: Library name: 310984


title: CHeller_Marc1-aLd-G7_10 mg/kg_3 Days_liver_T-2_F13

description: Library name: 311018


title: CHeller_Marc1-aLd-G7_0.4 mg/kg_3 Days_liver_V-2_G1

description: Library name: 310982

value: 0.4 mg/kg


title: CHeller_Marc1-aLd-G7_0.4 mg/kg_3 Days_liver_V-1_F23

description: Library name: 310985


title: CHeller_Marc1-aLd-G7_2 mg/kg_3 Days_liver_U-2_F19

description: Library name: 310955


title: CHeller_Marc1-aLd-G6_2 mg/kg_3 Days_liver_R-2_F1

description: Library name: 311019


title: CHeller_Marc1-aLd-G6_2 mg/kg_3 Days_liver_R-3_F3

description: Library name: 311016


title: CHeller_Marc1-aLd-G6_10 mg/kg_3 Days_liver_Q-2_E19

description: Library name: 311028


title: CHeller_Marc1-aLd-G6_10 mg/kg_3 Days_liver_Q-1_E17

description: Library name: 311015


title: CHeller_Marc1-aLd-G6_10 mg/kg_3 Days_liver_Q-3_E21

description: Library name: 311008


title: CHeller_Marc1-aLd-G7_0.4 mg/kg_3 Days_liver_V-3_G3

description: Library name: 311027


title: CHeller_Marc1-aLd-G6_0.4 mg/kg_3 Days_liver_S-2_F7

description: Library name: 310993


title: CHeller_Marc1-aLd-G6_0.4 mg/kg_3 Days_liver_S-3_F9

description: Library name: 310961


title: CHeller_Marc1-dx-G7_0.4 mg/kg_3 Days_liver_P-2_E13

description: Library name: 311022


title: CHeller_Marc1-dx-G7_2 mg/kg_3 Days_liver_O-3_E9

description: Library name: 310969


title: CHeller_Marc1-dx-G7_10 mg/kg_3 Days_liver_N-2_E1

description: Library name: 310971


title: CHeller_Marc1-dx-G7_2 mg/kg_3 Days_liver_O-1_E5

description: Library name: 310983


title: CHeller_Marc1-dx-G7_10 mg/kg_3 Days_liver_N-3_E3

description: Library name: 310981


title: CHeller_Marc1-dx-G7_0.4 mg/kg_3 Days_liver_P-3_E15

description: Library name: 311007


title: CHeller_Marc1-dx-G7_10 mg/kg_3 Days_liver_N-1_D23

description: Library name: 310972


title: CHeller_Marc1-dx-G7_0.4 mg/kg_3 Days_liver_P-1_E11

description: Library name: 310957


title: CHeller_Marc1-aLd-G6_0.4 mg/kg_3 Days_liver_S-1_F5

description: Library name: 310998


title: CHeller_Marc1-aLd-G6_2 mg/kg_3 Days_liver_R-1_E23

description: Library name: 310990


title: CHeller_Marc1-dx-G6_2 mg/kg_3 Days_liver_L-1_D11

description: Library name: 310965


title: CHeller_Marc1-dx-G6_2 mg/kg_3 Days_liver_L-2_D13

description: Library name: 311004


title: CHeller_Marc1-dx-G6_2 mg/kg_3 Days_liver_L-3_D15

description: Library name: 311017


title: CHeller_Marc1-dx-G7_2 mg/kg_3 Days_liver_O-2_E7

description: Library name: 311005


title: CHeller_Marc1-dx-G6_0.4 mg/kg_3 Days_liver_M-3_D21

description: Library name: 310991


title: CHeller_Marc1-dx-G6_0.4 mg/kg_3 Days_liver_M-1_D17

description: Library name: 311024


title: CHeller_Marc1-dx-G6_10 mg/kg_3 Days_liver_K-2_D7

description: Library name: 310968


title: CHeller_Marc1-dx-G6_0.4 mg/kg_3 Days_liver_M-2_D19

description: Library name: 310988


title: CHeller_Marc1-dx-G6_10 mg/kg_3 Days_liver_K-3_D9

description: Library name: 310977


title: CHeller_Marc1-parent_2 mg/kg_3 Days_liver_I-1_C17

description: Library name: 311020


title: CHeller_Marc1-dx-G6_10 mg/kg_3 Days_liver_K-1_D5

description: Library name: 310997


title: CHeller_Marc1-parent_2 mg/kg_3 Days_liver_I-3_C21

description: Library name: 310975


title: CHeller_Marc1-parent_10 mg/kg_3 Days_liver_H-2_C11

description: Library name: 310987


title: CHeller_Marc1-parent_10 mg/kg_3 Days_liver_H-4_C15

description: Library name: 311014


title: CHeller_Marc1-parent_0.4 mg/kg_3 Days_liver_J-2_D1

description: Library name: 311001


title: CHeller_Marc1-parent_10 mg/kg_3 Days_liver_H-3_C13

description: Library name: 310970


title: ALow_MD303_Ttr-dx-G6_30 mg/kg_U-3_J7

description: Library name: 181618

value: 30 mg/kg

value: Experiment B - 23-0b40


title: CHeller_Marc1-parent_10 mg/kg_3 Days_liver_H-1_C9

description: Library name: 310976


title: ALow_MD303_Ttr-dx-G6_30 mg/kg_U-4_J8

description: Library name: 181620


title: ALow_MD303_Ttr-dx-G6_30 mg/kg_U-2_J6

description: Library name: 181676


title: CHeller_Marc1-parent_2 mg/kg_3 Days_liver_I-2_C19

description: Library name: 310958


title: ALow_MD303_Ttr-dx-G6_100 mg/kg_V-3_J11

description: Library name: 181695

value: 100 mg/kg


title: ALow_MD303_Ttr-dx-G6_100 mg/kg_V-4_J12

description: Library name: 181619


title: ALow_MD303_Ttr-dx-G6_10 mg/kg_T-2_J2

description: Library name: 181669


title: CHeller_Marc1-parent_0.4 mg/kg_3 Days_liver_J-1_C23

description: Library name: 311023


title: ALow_MD303_Ttr-dx-G6_30 mg/kg_U-1_J5

description: Library name: 181670


title: CHeller_Marc1-parent_0.4 mg/kg_3 Days_liver_J-3_D3

description: Library name: 310964


title: ALow_MD302_Ttr-aLd-A7_30 mg/kg_7 Days_liver_U-4_E8

description: Library name: 181431

value: Experiment A - 23-0b0e


title: ALow_MD303_Ttr-dx-G6_10 mg/kg_T-3_J3

description: Library name: 181656

value: liver


title: ALow_MD303_Ttr-dx-G6_10 mg/kg_T-4_J4

description: Library name: 181652


title: ALow_MD303_Ttr-dx-G6_10 mg/kg_T-1_J1

description: Library name: 181637


title: ALow_MD302_Ttr-aLd-A7_30 mg/kg_7 Days_liver_U-1_E5

description: Library name: 181449


title: liver tissue,BPAF, female day28,rep3

city: Shanghai

first: Xiaoyu

last: Zhao

state: Shanghai

address: Shangda Road, no.99, Shanghai University

department: School of Environmental and Chemical Engineering

country: China

institute: Shanghai University

data_processing:
Illumina Casava1.8 software used for basecalling
The quality of the sequenced raw data was analyzed using Fastp.
The processed reads were then mapped to the reference zebrafish genome using the HISAT tool (version 2.1.0).
The assembled reads were then compared with known transcripts using Cufflinks or String Tie
reads were mapped to the reference zebrafish genome using HISAT2 (version 2.1.0).
The expression levels of each gene were calculated using RSEM and quantified in terms of Read Counts for each sample gene or transcript
Differential gene expression analysis was performed using DEGSeq2, with a threshold of fold-change ≥ 2 and adjusted P-value ≤ 0.05 to identify genes that showed significant differences between the control and treatment groups.
Assembly: Teleostei
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

growth_protocol: Wild-type zebrafish of the TU strain were housed in a temperature-controlled flow-through aquarium system at a temperature of 28 ± 0.5°C, with a 14 hour light: 10 hour dark cycle and were fed with brine shrimp twice daily.

extract_protocol:
The liver samples were processed for RNA extraction using the TRIzol®Reagent
Illumina TruseqTM RNA Sample Preparation Kit method for library construction

treatment_protocol:
Adult male and female zebrafish, aged four months, were exposed to BPAF at an ambient concentration of 10 μg/L or a solvent control (0.0001% DMSO) for 28 days, respectively.
After 28 days of exposure, the zebrafish were anesthetized with ice, and their livers were carefully dissected using sterile scissors and forceps.

value: female

tag: strain

value: TU

value: WT

value: BPAF


title: ALow_MD302_Ttr-aLd-A7_30 mg/kg_7 Days_liver_U-3_E7

description: Library name: 181451


title: ALow_MD302_Ttr-aLd-A7_100 mg/kg_7 Days_liver_V-2_E10

description: Library name: 181472


title: liver tissue,BPAF, female day28,rep1


title: liver tissue,BPAF, female day28,rep2


title: ALow_MD303_Ttr-dx-G6_100 mg/kg_V-1_J9

description: Library name: 181641


title: ALow_MD303_Ttr-dx-G6_100 mg/kg_V-2_J10

description: Library name: 181645


title: ALow_MD302_Ttr-aLd-A7_100 mg/kg_7 Days_liver_V-4_E12

description: Library name: 181424


title: ALow_MD302_Ttr-aLd-A7_100 mg/kg_7 Days_liver_V-1_E9

description: Library name: 181417


title: liver tissue,DMSO control, female day28, rep3

value: DMSO


title: ALow_MD302_Ttr-aLd-A7_10 mg/kg_7 Days_liver_T-1_E1

description: Library name: 181462


title: ALow_MD302_Ttr-aLd-A7_30 mg/kg_7 Days_liver_U-2_E6

description: Library name: 181429


title: liver tissue,DMSO control, female, day28,rep2


title: ALow_MD302_Ttr-aLd-A7_100 mg/kg_7 Days_liver_V-3_E11

description: Library name: 181465


title: liver tissue,BPAF, male day28,rep3

value: male


title: liver tissue,DMSO control, female, day28,rep1


title: liver tissue,BPAF, male day28,rep2


title: ALow_MD302_Ttr-aLd-A7_10 mg/kg_7 Days_liver_T-2_E2

description: Library name: 181414


title: ALow_MD302_Ttr-aLd-A7_10 mg/kg_7 Days_liver_T-3_E3

description: Library name: 181410


title: liver tissue,BPAF, male day28,rep1


title: ALow_MD302_Ttr-aLd-A7_10 mg/kg_7 Days_liver_T-4_E4

description: Library name: 181448


title: liver tissue,DMSO control, male day28, rep2


title: ALow_MD302_Ttr-parent_30 mg/kg_7 Days_liver_G-3_B23

description: Library name: 181430

value: Ttr-parent


title: IBD_940770, colon

city: Chapel Hill

first: Terrence

last: Furey

state: North Carolina

address: 120 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

description: Library name: IBD_940770

data_processing:
A decoy-aware index was built using a concatenated transcriptome of GENCODE v39 and the predicted lncRNAs using salmon index (salmon v.1.6.0)
RNA-seq data was quantified using salmon quant (salmon v.1.6.0) in mapping-based mode.
Assembly: hg38; reads were assembled with GENCODE v39, concatenated with the set of predicted lncRNAs (coordinates are in supplementary GTF file)
Supplementary files format and content: Tab-delimited text file includes raw count data for each sample from Salmon quantification
Supplementary files format and content: Tab-delimited text file includes TPM-normalized count data for each sample from Salmon quantification
Supplementary files format and content: GTF file includes transcript and exon feature annotations for the predicted lncRNA set

organism: Homo sapiens

source_name: colon

extract_protocol:
Samples were collected and stored in RNA-later from macroscopically non-inflamed sections of colonic mucosa for patients undergoing colonoscopy or surgical resection. RNA was isolated using the Qiagen RNeasy Mini Kit.
Total RNA libraries were constructed with the Kapa Total RNA Stranded with Ribo Erase; PolyA libraries were constructed with the Illumina TruSeq polyA+ Sample Prep Kit

value: colon

value: F

tag: inflammation

value: uninflamed

tag: disease status

value: NIBD

value: Female


title: ALow_MD302_Ttr-parent_30 mg/kg_7 Days_liver_G-2_B22

description: Library name: 181479

value: 30 mg/kg


title: liver tissue,DMSO control, male day28, rep3


title: ALow_MD302_Ttr-parent_30 mg/kg_7 Days_liver_G-4_B24

description: Library name: 181461


title: liver tissue,DMSO control, male day28, rep1


title: IBD_616045, colon

description: Library name: IBD_616045

value: Male


title: IBD_145342, colon

description: Library name: IBD_145342


title: ALow_MD302_Ttr-parent_100 mg/kg_7 Days_liver_H-1_C1

description: Library name: 181474

value: 100 mg/kg


title: IBD_734301, colon

description: Library name: IBD_734301

value: CD


title: ALow_MD302_Ttr-parent_30 mg/kg_7 Days_liver_G-1_B21

description: Library name: 181436

value: liver

value: Experiment A - 23-0b0e


title: ALow_MD302_Ttr-parent_100 mg/kg_7 Days_liver_H-3_C3

description: Library name: 181482


title: ALow_MD302_Ttr-parent_100 mg/kg_7 Days_liver_H-2_C2

description: Library name: 181421


title: IBD_165328, colon

description: Library name: IBD_165328


title: IBD_862697, colon

description: Library name: IBD_862697


title: ALow_MD302_Ttr-parent_100 mg/kg_7 Days_liver_H-4_C4

description: Library name: 181413


title: ALow_MD302_Ttr-parent_10 mg/kg_7 Days_liver_F-1_B17

description: Library name: 181419

value: 10 mg/kg


title: ALow_MD302_Ttr-parent_10 mg/kg_7 Days_liver_F-2_B18

description: Library name: 181425


title: IBD_165321, colon

description: Library name: IBD_165321


title: ALow_MD302_Ttr-parent_10 mg/kg_7 Days_liver_F-3_B19

description: Library name: 181433


title: IBD_187565, colon

description: Library name: IBD_187565


title: ALow_MD302_Ttr-parent_10 mg/kg_7 Days_liver_F-4_B20

description: Library name: 181422


title: IBD_363886, colon

description: Library name: IBD_363886


title: IBD_866425, colon

description: Library name: IBD_866425


title: IBD_226236, colon

description: Library name: IBD_226236


title: 28W-KO2

city: Beijing

first: Peng

last: Qu

address: China-Japan Friendship Hospital No. 2 Yinghuayuan East Street, Chaoyang District, Beijing 100029, P.R. China

institute: Institute of Clinical Medical Sciences, China-Japan Friendship Hospital

description:
Library name: Sample 11
Primary podocytes isolated from 28-week-old podocyte-specific Nsd2 knockout mice after HFD/STZ-induced diabetic injury.

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 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 fraction: 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: Primary podocytes

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.

value: Primary podocytes

value: HFD/STZ-induced diabetic model


title: 28W-KO3

description:
Library name: Sample 12
Primary podocytes isolated from 28-week-old podocyte-specific Nsd2 knockout mice after HFD/STZ-induced diabetic injury.


title: IBD_564226, colon

description: Library name: IBD_564226


title: 28W-KO1

description:
Library name: Sample 10
Primary podocytes isolated from 28-week-old podocyte-specific Nsd2 knockout mice after HFD/STZ-induced diabetic injury.


title: IBD_158297, colon

description: Library name: IBD_158297


title: 28W-Con2

description:
Library name: Sample 8
Primary podocytes isolated from 28-week-old floxed control mice after HFD/STZ-induced diabetic injury.


title: IBD_213942, colon

description: Library name: IBD_213942

value: G


title: IBD_332149, colon

description: Library name: IBD_332149


title: 28W-Con1

description:
Library name: Sample 7
Primary podocytes isolated from 28-week-old floxed control mice after HFD/STZ-induced diabetic injury.


title: 28W-Con3

description:
Library name: Sample 9
Primary podocytes isolated from 28-week-old floxed control mice after HFD/STZ-induced diabetic injury.


title: IBD_212365, colon

description: Library name: IBD_212365


title: 20W-KO3

description:
Library name: Sample 6
Primary podocytes isolated from 20-week-old podocyte-specific Nsd2 knockout mice after HFD/STZ-induced diabetic injury.


title: IBD_827477, colon

description: Library name: IBD_827477

value: H


title: 20W-KO2

description:
Library name: Sample 5
Primary podocytes isolated from 20-week-old podocyte-specific Nsd2 knockout mice after HFD/STZ-induced diabetic injury.


title: IBD_651640, colon

description: Library name: IBD_651640


title: IBD_380476, colon

description: Library name: IBD_380476


title: IBD_469904, colon

description: Library name: IBD_469904


title: 20W-Con3

description:
Library name: Sample 3
Primary podocytes isolated from 20-week-old floxed control mice after HFD/STZ-induced diabetic injury.


title: IBD_203023, colon

description: Library name: IBD_203023


title: 20W-KO1

description:
Library name: Sample 4
Primary podocytes isolated from 20-week-old podocyte-specific Nsd2 knockout mice after HFD/STZ-induced diabetic injury.


title: 20W-Con2

description:
Library name: Sample 2
Primary podocytes isolated from 20-week-old floxed control mice after HFD/STZ-induced diabetic injury.


title: 20W-Con1

description:
Library name: Sample 1
Primary podocytes isolated from 20-week-old floxed control mice after HFD/STZ-induced diabetic injury.


title: IBD_155019, colon

description: Library name: IBD_155019


title: IBD_204164, colon

description: Library name: IBD_204164


title: WT, rep3

city: La Jolla

first: Zhouting

last: Zhu

address: 9500 Gilman Drive MC 0762

institute: UC San Diego

description: Library name: WT-3

data_processing:
Raw RNA-seq reads were evaluated for quality using FASTQC to ensure overall sequencing quality and data integrity.
Adapter sequences and low-quality bases were removed using Trimmomatic.
Cleaned reads were aligned to the mouse reference genome (mm10) using HISAT2 with default parameters unless otherwise specified.
Gene-level read counts were generated using HTSeq to obtain raw count data for each gene in each sample.
Assembly: mm10
Supplementary files format and content: raw gene counts for each sample

source_name: Cell line

growth_protocol: B16F10 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from at least two biological replicates per condition using standard column-based purification according to the manufacturer’s instructions. RNA concentration and integrity were assessed prior to library preparation.
RNA-seq libraries were prepared from total RNA following the manufacturer’s protocol for Illumina library construction and sequenced on a NovaSeq 6000 platform at the IGM Genomics Center, University of California, San Diego.


title: WT, rep1

description: Library name: WT-1


title: IBD_117528, colon

description: Library name: IBD_117528


title: WT, rep2

description: Library name: WT-2


title: IBD_322211, colon

description: Library name: IBD_322211


title: miR25 single clone knockout 38, rep3

description: Library name: singleclone38-3


title: IBD_592152, colon

description: Library name: IBD_592152


title: miR25 single clone knockout 38, rep2

description: Library name: singleclone38-2


title: miR25 single clone knockout 38, rep1

description: Library name: singleclone38-1


title: IBD_780248, colon

description: Library name: IBD_780248


title: miR25 single clone knockout 32, rep2

description: Library name: singleclone32-2


title: IBD_980747, colon

description: Library name: IBD_980747


title: miR25 single clone knockout 32, rep1

description: Library name: singleclone32-1


title: miR25 single clone knockout 14, rep3

description: Library name: singleclone14-3


title: IBD_304272, colon

description: Library name: IBD_304272


title: miR25 single clone knockout 14, rep2

description: Library name: singleclone14-2


title: IBD_694599, colon

description: Library name: IBD_694599


title: IBD_418271, colon

description: Library name: IBD_418271


title: IBD_750138, colon

description: Library name: IBD_750138


title: IBD_388822, colon

description: Library name: IBD_388822


title: IBD_255857, colon

description: Library name: IBD_255857


title: miR25 sgRNA1, pooled knockout, rep3

description: Library name: sgRNA1-3_S30_L002


title: miR25 single clone knockout 14, rep1

description: Library name: singleclone14-1


title: miR25 sgRNA1, pooled knockout, rep2

description: Library name: sgRNA1-2_S29_L002


title: miR25 single clone knockout 32, rep3

description: Library name: singleclone32-3


title: IBD_803522, colon

description: Library name: IBD_803522


title: IBD_821572, colon

description: Library name: IBD_821572


title: miR25 sgRNA1, pooled knockout, rep1

description: Library name: sgRNA1-1_S28_L002


title: IBD_676592, colon

description: Library name: IBD_676592


title: IBD_856637, colon

description: Library name: IBD_856637


title: IBD_682714, colon

description: Library name: IBD_682714


title: MC38 tumor, Control, rep4

description: Library name: NTC1358_S2_L003

library_source: transcriptomic single cell

data_processing:
Sequencing data were demultiplexed and converted to read counts using the Cell Ranger pipeline (10× Genomics). Read count data were imported into the Seurat R package (version 5) for analysis. Low-quality cells (fewer than 200 detected genes or mitochondrial gene counts exceeding 20%) were excluded. Gene expression values were normalized and scaled using LogNormalize. Cell clustering was performed using the Louvain algorithm based on the first 50 principal components of gene expression data. Marker genes for each cluster were identified, with the top markers defined as genes upregulated in at least 25% of cells within a cluster.
Assembly: mm10
Supplementary files format and content: h5 & rds files

source_name: Tumor, day18

growth_protocol: MC38 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C. C57BL/6J Mice were injected s.c. with 5 × 10⁵ MC38 cells on day 0. Anti-PD-1 antibody therapy (10 mg/kg, i.p.) was initiated on day 9 and continued until sacrifice.

extract_protocol:
Tumors were mechanically dissociated and enzymatically digested using the Mouse Tumor Dissociation Kit (Miltenyi Biotec) following the manufacturer’s instructions. Spleens were collected, minced with a razor blade, and passed through a 70 μm cell strainer. Cells were washed in culture medium containing 10% fetal bovine serum (FBS; Gibco) and treated with ammonium chloride solution (STEMCELL) to lyse red blood cells (RBCs).
Approximately 20,000 single cells per sample were loaded onto the 10× Chromium system for barcoding and cDNA synthesis, following the manufacturer’s instructions. Quality control of cDNA and libraries was assessed using TapeStation before sequencing on the NovaSeq platform (Illumina), targeting a median read depth of 30,000 reads per cell.

value: Tumor, day18


title: IBD_573202, colon

description: Library name: IBD_573202

value: colon


title: IBD_371731, colon

description: Library name: IBD_371731


title: MC38 tumor, Control, rep3

description: Library name: NTC1356_S1_L003


title: MC38 tumor, miR-25 KO, rep3

description: Library name: KO1355_S8_L003


title: MC38 tumor, miR-25 KO, rep2

description: Library name: KO1343_S7_L003


title: KO_IFN_rep2

description: Library name: KO4_IFN_S78

treatment_protocol: IFN-γ was added at final concentration of 100ng/mL for 48 hours. Cells were harvested at 80-90% confluency.


title: IBD_159242, colon

description: Library name: IBD_159242


title: MC38 tumor, Control, rep1

description: Library name: NTC1346_S4_L003


title: MC38 tumor, Control, rep2

description: Library name: NTC1348_S3_L003


title: IBD_549590, colon

description: Library name: IBD_549590

value: F


title: IBD_143257, colon

description: Library name: IBD_143257

value: uninflamed


title: IBD_189841, colon

description: Library name: IBD_189841


title: IBD_422479, colon

description: Library name: IBD_422479


title: KO_noIFN_rep3

description: Library name: KO4_noIFN_S72-86


title: IBD_602882, colon

description: Library name: IBD_602882


title: KO_noIFN_rep2

description: Library name: KO3_noIFN_S71-85


title: KO_IFN_rep1

description: Library name: KO3_IFN_S77-83


title: KO_noIFN_rep1

description: Library name: KO2_noIFN_S70-84


title: IBD_534278, colon

description: Library name: IBD_534278

value: NIBD


title: NTC_IFN_rep3

description: Library name: NTC3_IFN_S75


title: MC38 tumor, miR-25 KO, rep1

description: Library name: KO1341_S5_L003


title: IBD_996969, colon

description: Library name: IBD_996969

value: Female


title: IBD_434298, colon

description: Library name: IBD_434298


title: NTC_IFN_rep1

description: Library name: NTC1_IFN_S73-87


title: IBD_299477, colon

description: Library name: IBD_299477


title: IBD_986087, colon

description: Library name: IBD_986087


title: Human, TD group,13

city: Jinan

first: Ziyun

last: Li

address: No. 9-7 Jiangshuiquan Road, Lixia District,Jinan, Shandong

institute: Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University

description:
Library name: sample26
/uploads/0009000513273168@orcid_aTK1S2AW

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp (0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis.
Assembly: Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome.
Supplementary files format and content: xls files include FPKM value for each sample

source_name: Serum

extract_protocol:
Total RNA was extracted by the chloroform method.
RNA-seq library was constructed by using NEBNext Ultra Ⅱ RNA Library Prep Kit for Illumina.

value: Serum


title: IBD_681891, colon

description: Library name: IBD_681891


title: NTC_noIFN_rep2

description: Library name: NTC2_noIFN_S68


title: Human, TD group,12

description:
Library name: sample25
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_309068, colon

description: Library name: IBD_309068


title: IBD_421195, colon

description: Library name: IBD_421195

value: Male


title: NTC_IFN_rep2

description: Library name: NTC2_IFN_S74


title: IBD_341124, colon

description: Library name: IBD_341124


title: IBD_109714, colon

description: Library name: IBD_109714


title: IBD_930121, colon

description: Library name: IBD_930121


title: NTC_noIFN_rep1

description: Library name: NTC1_noIFN_S67


title: Human, TD group,10

description:
Library name: sample23
/uploads/0009000513273168@orcid_aTK1S2AW


title: Human, TD group,9

description:
Library name: sample22
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_286558, colon

description: Library name: IBD_286558


title: Tumor_NTC_rep3

description: Library name: NTC_368_S55_L001

source_name: Tumor, day15

growth_protocol: B16F10 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C. C57BL/6J mice were subcutaneously (s.c.) injected with 0.5 × 10⁵ B16 cells into the left flank on day 0. Mice then received 10⁶ irradiated (100 Gy) B16-GM-CSF cells (GVAX) injected into the contralateral flank on days 1 and 4. Anti-PD-1 therapy (rat monoclonal anti-mouse PD-1 antibody, Bio X Cell, clone 29F.1A12) was administered intraperitoneally (i.p.) at 10 mg/kg (200 μg/mouse) on days 6, 9, and 12. GVAX are irradiated B16 melanoma cells genetically engineered to secrete granulocyte-macrophage colony-stimulating factor (GM-CSF). Mice were euthanized by CO₂ inhalation followed by cervical dislocation when tumors reached a maximum diameter of 2.0 cm.

value: Tumor, day15


title: Tumor_NTC_rep5

description: Library name: NTC_366_S53_L001


title: Human, TD group,8

description:
Library name: sample21
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_309065, colon

description: Library name: IBD_309065


title: IBD_998061, colon

description: Library name: IBD_998061


title: Tumor_NTC_rep2

description: Library name: NTC_369_S56_L001


title: Human, TD group,11

description:
Library name: sample24
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_906136, colon

description: Library name: IBD_906136

value: I

value: CD


title: Human, TD group,7

description:
Library name: sample20
/uploads/0009000513273168@orcid_aTK1S2AW


title: Tumor_NTC_rep1

description: Library name: NTC_370_S57_L001


title: IBD_333644, colon

description: Library name: IBD_333644


title: IBD_727829, colon

description: Library name: IBD_727829


title: Tumor_NTC_rep4

description: Library name: NTC_367_S54_L001


title: IBD_965724, colon

description: Library name: IBD_965724


title: IBD_933581, colon

description: Library name: IBD_933581


title: IBD_618849, colon

description: Library name: IBD_618849


title: Tumor_25KO_rep5

description: Library name: 25KO_376_S58_L001


title: Human, TD group,6

description:
Library name: sample19
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_955826, colon

description: Library name: IBD_955826


title: Tumor_25KO_rep4

description: Library name: 25KO_377_S59_L001


title: Human, TD group,5

description:
Library name: sample18
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_949169, colon

description: Library name: IBD_949169


title: Human, TD group,4

description:
Library name: sample17
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_112415, colon

description: Library name: IBD_112415


title: IBD_420609, colon

description: Library name: IBD_420609


title: IBD_845356, colon

description: Library name: IBD_845356


title: IBD_187482, colon

description: Library name: IBD_187482


title: Human, TD group,2

description:
Library name: sample15
/uploads/0009000513273168@orcid_aTK1S2AW


title: Tumor_25KO_rep2

description: Library name: 25KO_379_S61_L001


title: Human, TD group,1

description:
Library name: sample14
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_346821, colon

description: Library name: IBD_346821


title: Human, TD group,3

description:
Library name: sample16
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_564849, colon

description: Library name: IBD_564849


title: Tumor_25KO_rep1

description: Library name: 25KO_380_S62_L001


title: IBD_631005, colon

description: Library name: IBD_631005


title: IBD_268458, colon

description: Library name: IBD_268458


title: IBD_118727, colon

description: Library name: IBD_118727


title: Tumor_25KO_rep3

description: Library name: 25KO_378_S60_L001


title: Tumor_Control_rep3

description: Library name: Tumor_Control_328_SmallRNA_S4

source_name: Tumor, day13

value: Tumor, day13


title: IBD_850257, colon

description: Library name: IBD_850257


title: Human, ASD group,13

description:
Library name: sample13
/uploads/0009000513273168@orcid_aTK1S2AW


title: Tumor_Control_rep2

description: Library name: Tumor_Control_677_SmallRNA_S6


title: IBD_560473, colon

description: Library name: IBD_560473


title: Human, ASD group,12

description:
Library name: sample12
/uploads/0009000513273168@orcid_aTK1S2AW


title: Tumor_Control_rep1

description: Library name: Tumor_Control_680_SmallRNA_S7


title: IBD_954059, colon

description: Library name: IBD_954059


title: IBD_193721, colon

description: Library name: IBD_193721


title: IBD_135118, colon

description: Library name: IBD_135118


title: IBD_301690, colon

description: Library name: IBD_301690


title: Tumor_GVAX_rep3

description: Library name: Tumor_GVAX_321_SmallRNA_S10


title: Human, ASD group,10

description:
Library name: sample10
/uploads/0009000513273168@orcid_aTK1S2AW


title: Human, ASD group,11

description:
Library name: sample11
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_484581, colon

description: Library name: IBD_484581


title: IBD_555519, colon

description: Library name: IBD_555519


title: Human, ASD group,9

description:
Library name: sample9
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_919154, colon

description: Library name: IBD_919154


title: Tumor_Comb_rep3

description: Library name: Tumor_Comb_318_SmallRNA_S17


title: Tumor_GVAX_rep1

description: Library name: Tumor_GVAX_682_SmallRNA_S12


title: IBD_839147, colon

description: Library name: IBD_839147


title: IBD_794755, colon

description: Library name: IBD_794755


title: IBD_467982, colon

description: Library name: IBD_467982


title: Tumor_GVAX_rep2

description: Library name: Tumor_GVAX_325_SmallRNA_S11


title: Human, ASD group,7

description:
Library name: sample7
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_771279, colon

description: Library name: IBD_771279


title: IBD_654224, colon

description: Library name: IBD_654224


title: Tumor_Comb_rep1

description: Library name: Tumor_Comb_701_SmallRNA_S20


title: Tumor_Comb_rep2

description: Library name: Tumor_Comb_335_SmallRNA_S19


title: IBD_816534, colon

description: Library name: IBD_816534


title: Human, ASD group,5

description:
Library name: sample5
/uploads/0009000513273168@orcid_aTK1S2AW


title: Human, ASD group,6

description:
Library name: sample6
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_849039, colon

description: Library name: IBD_849039


title: Human, ASD group,8

description:
Library name: sample8
/uploads/0009000513273168@orcid_aTK1S2AW


title: F121-9 WT, NPC status, replicate 1

city: San Diego

first: David

middle: M

last: Gilbert

address: 3525 John Hopkins Ct., Ste. 200

institute: San Diego BioMEd

description:
Library name: F121-9_NPC
nascent RNA

data_processing:
RNA-seq reads were aligned to an mm10 genome with masked 129/Cas SNPs, using the STAR RNA-seq aligner (Dobin et al., 2013). Reads aligned to mm10 were subsequently parsed into 129 and Cas specific reads using SNPsplit. Browser tracks were generated using the inputAlignmentsFromBAM function of the STAR RNA-seq aligner (Dobin et al., 2013).
Assembly: mm10
Supplementary files format and content: bedgraph files, STAR RNA-seq aligner output for each allele (129 or cas)

source_name: neural precursor cell

growth_protocol: mESC was maintained in 2i media.

extract_protocol:
Direct-zol RNA MiniPrep (Zymo research R2050) was used according to the manufacturer's instruction.
Starting from approximately 300ng total RNA, ribosomal RNA was depleted using NEBNext® rRNA Depletion Kit v1 (NEB E6310). The entire resulting RNA was used for 1st strand synthesis by NEBNext Ultra II RNA First Strand Synthesis Module (NEB E7771), following “Directional RNA-seq Workflows“. Second strand was synthesized using NEBNext Ultra II Directional Second Strand Synthesis Kit (NEB E7550) then cDNA was made into sequencing library using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645).

treatment_protocol: mESC was differentiated to NPC using  RHB-A.  Detailed differentiation method has been described in PMC5991511.

value: neural precursor cell

value: biol rep 1


title: Human, ASD group,4

description:
Library name: sample4
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_961597, colon

description: Library name: IBD_961597


title: IBD_143391, colon

description: Library name: IBD_143391


title: IBD_396332, colon

description: Library name: IBD_396332


title: Heterozygous Ptn E/P deletion from F121-9, NPC status, replicate 1

description:
Library name: D9_NPC
nascent RNA


title: IBD_602009, colon

description: Library name: IBD_602009


title: IBD_328631, colon

description: Library name: IBD_328631


title: Human, ASD group,3

description:
Library name: sample3
/uploads/0009000513273168@orcid_aTK1S2AW


title: Homozygous Ptn E/P deletion from F121-9, NPC status,  replicate 1

description:
Library name: B8_NPC
nascent RNA


title: IBD_336603, colon

description: Library name: IBD_336603


title: IBD_614970, colon

description: Library name: IBD_614970


title: Human, ASD group,2

description:
Library name: sample2
/uploads/0009000513273168@orcid_aTK1S2AW


title: IBD_415959, colon

description: Library name: IBD_415959


title: Human, ASD group,1

description:
Library name: sample1
/uploads/0009000513273168@orcid_aTK1S2AW


title: Wild type leptotene/zygotene spermatocytes_rep2

first: Hanzhen

state: Shandong

address: 44 Wenhua West Road

institute: Shandong University

description: Library name: Sample 5

data_processing:
quality control (FASTQC), adapter trimming (Trim Galore v0.6.4), alignment to the GRCm38 genome (HISAT2 v2.0.5)
Assembly: Mouse reference genome GRCm38 (mm10) assembly.
Supplementary files format and content: The file “counts.txt”contains the raw read counts for all samples

source_name: testis

extract_protocol:
Testes were dissected, decapsulated to remove the tunica albuginea, and placed in Dulbecco’s phosphate-buffered saline (DPBS) on ice. Then, seminiferous tubules were incubated in digestion buffer containing 120 U/mL of collagenase type I in DPBS at 35 °C for 10 minutes with gentle shaking to dissociate interstitial cells. Tubules were subsequently digested in a second buffer containing 0.25% trypsin and 5mg/mL DNase I at 35 °C for 8 minutes to obtain a single-cell suspension.
mRNA reverse transcription, and cDNA amplification were performed using the Discover-sc WTA Kit V2 (Vazyme, N711). cDNA fragmentation and adapter ligation were subsequently carried out using the TruePrep Flexible DNA Library Prep Kit for Illumina (Vazyme, TD504).

value: testis

value: spermatocytes

value: Wild type


title: IBD_105888, colon

description: Library name: IBD_105888


title: Wild type leptotene/zygotene spermatocytes_rep3

description: Library name: Sample 6


title: Srp68 SKO leptotene/zygotene spermatocytes_rep3

description: Library name: Sample 3

value: Srp68 SKO


title: IBD_462979, colon

description: Library name: IBD_462979

value: colon


title: HFF treated with Oleic Acid, Rep 2

first: Jiayi

last: Cai

address: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road

description:
Library name: HFF_OA_2
HFF treated with OA

data_processing:
Raw data (fastq) of fast format were processed using fastp (or Trimmomatic). In this step, clean data were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data.
Paired-end clean reads were aligned to the reference genome (Homo_sapiens GRCh38) using HISAT2 software.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Tab-delimited text files containing raw read counts for each gene (generated by featureCounts).

source_name: Human foreskin fibroblasts

growth_protocol: Human foreskin fibroblasts (HFFs) were cultured in standard cell culture medium (e.g., DMEM supplemented with 10% FBS) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from the cells using TRIzol reagent (Invitrogen) following the manufacturer's instructions. RNA integrity and concentration were assessed using the Agilent 2100 Bioanalyzer.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations. Index codes were added to attribute sequences to each sample. The libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads.

treatment_protocol: Cells were treated with Palmitic Acid (PA) or Oleic Acid (OA) compared to a Vehicle control group for 48 hours to induce inflammatory responses.

value: Human foreskin fibroblasts

value: Fibroblasts

value: Oleic Acid (OA)


title: HFF treated with Oleic Acid, Rep 3

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description:
Library name: HFF_OA_3
HFF treated with OA


title: Wild type leptotene/zygotene spermatocytes_rep1

description: Library name: Sample 4


title: IBD_150644, colon

description: Library name: IBD_150644

value: F

value: uninflamed

value: Female


title: IBD_268860, colon

description: Library name: IBD_268860

value: Male


title: IBD_745873, colon

description: Library name: IBD_745873

value: NIBD


title: IBD_664409, colon

description: Library name: IBD_664409

value: CD


title: IBD_699081, colon

description: Library name: IBD_699081


title: HFF treated with Palmitic Acid, Rep 3

description:
Library name: HFF_PA_3
HFF treated with PA

value: Palmitic Acid (PA)


title: HFF treated with Oleic Acid, Rep 1

description:
Library name: HFF_OA_1
HFF treated with OA


title: IBD_888189, colon

description: Library name: IBD_888189


title: Srp68 SKO leptotene/zygotene spermatocytes_rep1

description: Library name: Sample 1


title: IBD_565921, colon

description: Library name: IBD_565921


title: IBD_102541, colon

description: Library name: IBD_102541


title: IBD_621989, colon

description: Library name: IBD_621989


title: HFF treated with Palmitic Acid, Rep 2

description:
Library name: HFF_PA_2
HFF treated with PA


title: HFF treated with Palmitic Acid, Rep 1

description:
Library name: HFF_PA_1
HFF treated with PA


title: IBD_124014, colon

description: Library name: IBD_124014

value: I


title: IBD_571968, colon

description: Library name: IBD_571968


title: Srp68 SKO leptotene/zygotene spermatocytes_rep2

description: Library name: Sample 2


title: IBD_900592, colon

description: Library name: IBD_900592


title: Kidney Slc7a9-/- male L-Ergothioneine treated 3

city: Hospitalet de Llobregrat

first: Clara

last: Mayayo

state: Barcelona

address: Gran Via Hospitalet, 199

country: Spain

institute: IDIBELL

description: Library name: UDP0019

data_processing:
Raw reads underwent quality assessment with FastQC (v0.11.9) and adapter/low-quality trimming using Trim Galore (v0.6.7) with Cutadapt (v3.4).
The nf-core/rnaseq pipeline (v3.12.0, Nextflow v22.10.7) was employed for downstream processing.
Reads were aligned to the Mus musculus GRCm38 reference genome using STAR (v2.7.10a) within the STAR-RSEM workflow.
Gene-level quantification was performed with RSEM (v1.3.1), complemented by pseudoalignment-based quantification using Salmon (v1.10.1). Additional processing included duplicate marking with Picard (v3.0.0), BAM sorting and indexing with Samtools (v1.17), and transcript assembly with StringTie (v2.2.1). Quality control metrics were generated using Qualimap RNA-seq (v2.2.2-dev) and RSeQC (v3.0.1), while coverage and biotype summaries were obtained with Bedtools (v2.30.0) and MultiQC. Gene-level counts were also computed using featureCounts (Subread v2.0.1). Differential expression analysis was carried out with DESeq2.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Text file that include raw counts for each sample
Supplementary files format and content: Text file that include genes tpm for each sample

source_name: kidney

extract_protocol:
Total RNA was extracted from frozen kidney tissue using TRIzol Reagent (Ambion®, Thermo Fisher Scientific, MA, USA) and a Polytron PT-1200 homogenizer (Kinematica, Switzerland) following the protocol provided by the Direct-zol™ RNA MiniPrep Plus Kit (Zymo Research, CA, USA).
RNA libraries were prepared for sequencing using the kits Illumina® Ribo-Zero plus (20036696), Illumina® Stranded mRNA Prep, Ligation (20040534) and IDT® for Illumina® RNA UD Indexes Set A, Ligation (20040553), following manufacturer's instructions and 10 cycles of amplification.

treatment_protocol: 16 mg/kg/day of L-Erg was delivered for orally via drinking water.

value: kidney

tag: age

value: 6 months

value: L-Ergothioneine 16 mg/kg/day


title: Kidney Slc7a9-/- male L-Ergothioneine treated 4

description: Library name: UDP0014


title: IBD_296868, colon

description: Library name: IBD_296868


title: HFF treated with Vehicle, Rep 2

description:
Library name: HFF_Vehicle_2
HFF treated with Vehicle

value: Wild type

value: Vehicle (Control)


title: IBD_154177, colon

description: Library name: IBD_154177

value: colon

value: H


title: Kidney Slc7a9-/- male 3

description: Library name: UDP0015


title: HFF treated with Vehicle, Rep 1

description:
Library name: HFF_Vehicle_1
HFF treated with Vehicle

value: Human foreskin fibroblasts

value: Fibroblasts


title: HFF treated with Vehicle, Rep 3

description:
Library name: HFF_Vehicle_3
HFF treated with Vehicle


title: IBD_413522, colon

description: Library name: IBD_413522

value: F


title: IBD_974304, colon

description: Library name: IBD_974304

value: uninflamed


title: ACTN1_ACTN1-dx-G6_repAtx1_5.000000uM_K1_techrep2

description: Library name: 205721

value: Experiment C - 23-1629


title: Kidney Slc7a9-/- male L-Ergothioneine treated 2

description: Library name: UDP0023

value: Male


title: Kidney Slc7a9-/- male L-Ergothioneine treated 1

description: Library name: UDP0044


title: IBD_697394, colon

description: Library name: IBD_697394

value: NIBD

value: Female


title: ACTN1_ACTN1-dx-G6_repAtx1_5.000000uM_K1_techrep1

description: Library name: 205769


title: Kidney Slc7a9-/- male 1

description: Library name: UDP0049


title: A2780 cells, lycorine treatment-1

city: jiangsu Huai an

first: Yao yao

last: Tang

address: No. 9 Keji Avenue, Qingjiangpu District,

institute: Jiangsu College of Nursing

description: Library name: LYC-1

data_processing:
Raw reads were quality-assessed with FastQC v0.11.9 and adapter-trimmed/quality-filtered using Trimmomatic v0.39. Clean reads were aligned to the GRCh38.p13 human reference genome using STAR v2.7.10b. Gene-level counts were generated using featureCounts (from Subread package v2.0.3) with the GENCODE v40 annotation. Differential expression analysis was performed using DESeq2 v1.30.1, with genes having an adjusted p-value (padj) < 0.05 and |log2FoldChange| > 1 considered significantly differentially expressed. The normalized counts from DESeq2 are provided as the expression dataset.
Assembly: Clean reads were aligned to the GRCh38.p13 primary genome assembly (downloaded from GENCODE) using STAR v2.7.10b with the corresponding GENCODE v40 comprehensive gene annotation. Gene-level quantification was performed using featureCountsagainst the same annotation.
Supplementary files format and content: CSV file including Reads count for each sample

source_name: ovarian

extract_protocol:
Total RNA was extracted using TRIzol reagent (15596018CN, Thermo Fisher Scientiffc, MA, USA).
Using Oligo dT magnetic beads, mRNA is enriched from total RNA. After fragmentation, the first strand of cDNA is synthesized using random hexamer primers, followed by the synthesis of the second strand of cDNA. After end repair, A-tailing, adapter ligation, fragment selection, amplification, and purification, the library is ready.

value: ovarian

value: human ovarian adenocarcinoma cell line


title: ACTN1_ACTN1-dx-G6_repAtx1_1.000000uM_K3_techrep1

description: Library name: 205847


title: A2780 cells, lycorine treatment-2

description: Library name: LYC-2


title: A2780 cells, Control-3

description: Library name: NC3


title: A2780 cells, Control-2

description: Library name: NC2


title: KO2

description:
Library name: Sample 4
Primary podocytes isolated from 28-week-old podocyte-specific Nsd2 knockout mice after HFD/STZ-induced diabetic injury.

library_source: genomic

data_processing:
Raw FASTQ files were quality-trimmed using fastp to obtain clean reads.
Clean reads were aligned to the reference genome using Bowtie2.
Peak calling was performed with SEACR using the “stringent” setting.
eaks were annotated with ChIPseeker. Peak visualization was performed using IGV. Motif enrichment was conducted with MEME and DREME.
Assembly: GRCm39
Supplementary files format and content: bigWig
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Podocytes

extract_protocol:
CUT&Tag was performed following the protocol of the Hyperactive™ In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD903-TD904). Briefly, cells were bound to concanavalin A–coated magnetic beads and permeabilized with digitonin. Bead-bound cells were sequentially incubated with primary antibody (H3K36me2), secondary antibody, and Hyperactive pA-Tn5 transposase for targeted chromatin tagmentation.
Tagmented chromatin fragments containing inserted P5 and P7 adapters were PCR-amplified using index primers. The amplified libraries were purified and quality-checked using an Agilent 2100 Bioanalyzer. Final libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads.

value: Podocytes

value: Primary podocytes

value: HFD/STZ-induced diabetic model


title: A2780 cells, Control-1

description: Library name: NC1


title: A2780 cells, lycorine treatment-3

description: Library name: LYC-3


title: Kidney Slc7a9-/- male 2

description: Library name: UDP0050

value: kidney

value: 6 months


title: IBD_271984, colon

description: Library name: IBD_271984

value: colon

value: CD


title: ACTN1_ACTN1-dx-G6_repAtx1_0.200000uM_K5_techrep2

description: Library name: 205787


title: 220V1PL

city: Dublin

first: Walter

last: Kolch

address: School of Medicine, University College Dublin, Belfield, Dublin 4.

country: Ireland

institute: Systems Biology Ireland

description: Library name: 20-559-036

data_processing:
The reads were aligned and quantified  to the Genome Reference Consortium Human Build 38 using the R package Rsubread with default settings.
Assembly: Assembly: hg38
Supplementary files format and content: Txt file with raw gene counts for each sample

source_name: skin

extract_protocol:
RNA isolation was then performed using a Fibrous RNA isolation kit (Qiagen) following the manufacturer’s instruction.
cDNA was created from 100ng of input RNA using theTruSeq Stranded mRNA input kit, sequencing 50 bp paired end stranded

value: skin

tag: disease

value: Atopic dermatitis

tag: lesional (ls)_or_nonlesional_(nl)

value: NL


title: 220V1L

description: Library name: 20-559-035

value: LS


title: KO1

description:
Library name: Sample 3
Primary podocytes isolated from 28-week-old podocyte-specific Nsd2 knockout mice after HFD/STZ-induced diabetic injury.

data_processing:
Raw FASTQ files were quality-trimmed using fastp to obtain clean reads.
Clean reads were aligned to the reference genome using Bowtie2.
Peak calling was performed with SEACR using the “stringent” setting.
eaks were annotated with ChIPseeker. Peak visualization was performed using IGV. Motif enrichment was conducted with MEME and DREME.
Assembly: GRCm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag


title: 219V1L

description: Library name: 20-559-033


title: ACTN1_ACTN1-dx-G6_repAtx1_0.200000uM_K5_techrep1

description: Library name: 205753

value: Experiment C - 23-1629


title: 216V1L

description: Library name: 19-508-077


title: K-STZ4

description:
Library name: Sample 16
Renal cortex tissue isolated from 24-week-old HFD/STZ-induced diabetic mice.

source_name: kidney cortex tissue

value: kidney cortex tissue

value: WT


title: 216V12PL

description: Library name: 19-508-076


title: ACTN1_ACTN1-aLd-A7_repAtx1_5.000000uM_I1_techrep1

description: Library name: 205764


title: 216V1PL

description: Library name: 19-508-078


title: 219V1PL

description: Library name: 20-559-034


title: Con2

description:
Library name: Sample 2
Primary podocytes isolated from 28-week-old floxed control mice after HFD/STZ-induced diabetic injury.


title: ACTN1_ACTN1-aLd-A7_repAtx1_5.000000uM_I1_techrep2

description: Library name: 205710


title: ACTN1_ACTN1-dx-G6_repAtx1_1.000000uM_K3_techrep2

description: Library name: 205771


title: 215V1L

description: Library name: 19-508-073


title: 216V12L

description: Library name: 19-508-075


title: Con1

description:
Library name: Sample 1
Primary podocytes isolated from 28-week-old floxed control mice after HFD/STZ-induced diabetic injury.


title: 214V1L

description: Library name: 19-508-071


title: 215V1PL

description: Library name: 19-508-074


title: K-STZ2

description:
Library name: Sample 14
Renal cortex tissue isolated from 24-week-old HFD/STZ-induced diabetic mice.


title: ACTN1_ACTN1-aLd-A7_repAtx1_0.200000uM_I5_techrep1

description: Library name: 205782


title: K-STZ1

description:
Library name: Sample 13
Renal cortex tissue isolated from 24-week-old HFD/STZ-induced diabetic mice.


title: 212V1PL

description: Library name: 19-508-070


title: ACTN1_ACTN1-aLd-A7_repAtx1_0.200000uM_I5_techrep2

description: Library name: 205821


title: 212V1L

description: Library name: 19-508-069


title: 211V1PL

description: Library name: 19-508-068


title: 211V1L

description: Library name: 19-508-067


title: K-Con4

description:
Library name: Sample 12
Renal cortex tissue isolated from 24-week-old control mice

value: control


title: K-STZ3

description:
Library name: Sample 15
Renal cortex tissue isolated from 24-week-old HFD/STZ-induced diabetic mice.


title: ACTN1_ACTN1-aLd-A7_repAtx1_1.000000uM_I3_techrep2

description: Library name: 205845


title: ACTN1_ACTN1-aLd-A7_repAtx1_1.000000uM_I3_techrep1

description: Library name: 205839


title: 214V1PL

description: Library name: 19-508-072


title: 211V12L

description: Library name: 19-508-065


title: 210V1PL

description: Library name: GTG-360-B2-79


title: 211V12PL

description: Library name: 19-508-066


title: ACTN1_ACTN1-parent_repAtx1_5.000000uM_A1_techrep2

description: Library name: 205844


title: K-Con2

description:
Library name: Sample 10
Renal cortex tissue isolated from 24-week-old control mice


title: ACTN1_ACTN1-parent_repAtx1_5.000000uM_A1_techrep1

description: Library name: 205751


title: K-Con1

description:
Library name: Sample 9
Renal cortex tissue isolated from 24-week-old control mice


title: K-Con3

description:
Library name: Sample 11
Renal cortex tissue isolated from 24-week-old control mice


title: 209V1PL

description: Library name: GTG-360-B1-82


title: 210V1L

description: Library name: GTG-360-B2-78


title: 208V1PL

description: Library name: GTG-360-B2-77


title: 207V12L

description: Library name: GTG-360-B1-77


title: 206V1L

description: Library name: GTG-360-B2-73


title: ACTN1_ACTN1-parent_repAtx1_1.000000uM_A3_techrep1

description: Library name: 205852


title: 208V12L

description: Library name: GTG-360-B2-75


title: G-Con4

description:
Library name: Sample 4
Isolated glomeruli collected from 24-week-old control mice.

source_name: Glomeruli

value: Glomeruli


title: 208V1L

description: Library name: GTG-360-B2-76


title: G-STZ4

description:
Library name: Sample 8
Isolated glomeruli collected from 24-week-old HFD/STZ-induced diabetic mice.


title: 209V1L

description: Library name: GTG-360-B1-81


title: G-STZ2

description:
Library name: Sample 6
Isolated glomeruli collected from 24-week-old HFD/STZ-induced diabetic mice.


title: 205V12L

description: Library name: GTG-360-B2-69


title: 205V1PL

description: Library name: GTG-360-B2-72


title: 207V1L

description: Library name: GTG-360-B1-79


title: G-STZ3

description:
Library name: Sample 7
Isolated glomeruli collected from 24-week-old HFD/STZ-induced diabetic mice.


title: G-Con3

description:
Library name: Sample 3
Isolated glomeruli collected from 24-week-old control mice.


title: ACTN1_ACTN1-parent_repAtx1_0.200000uM_A5_techrep2

description: Library name: 205719


title: 207V12PL

description: Library name: GTG-360-B1-78


title: ACTN1_ACTN1-parent_repAtx1_1.000000uM_A3_techrep2

description: Library name: 205706


title: G-STZ1

description:
Library name: Sample 5
Isolated glomeruli collected from 24-week-old HFD/STZ-induced diabetic mice.


title: 205V1L

description: Library name: GTG-360-B2-71


title: HT1080 Control

city: Ann Arbor

first: Stephen

middle: J

last: Weiss

state: MI

address: 210 Washtenaw Ave

institute: University of Michigan

description:
Library name: 7841-AO_1
10X Genomics

data_processing:
Libraries were subjected to 151bp paired-end sequencing using Illumina NovaSeq to a depth of ~60,000-150,000 reads/cell and BCL Convert Conversion Software (v4.0, Illumina) was used to generate de-multiplexed FASTQ files.
Assembly: Sequencing data were processed using the 10X Genomics CellRanger pipeline (7.1.0) and align to the GRCh38-2020-A human reference genome to generate gene expression counts.
Supplementary files format and content: Following alignment and initial quality control, 3478 and 1567 cells from control and 4B4-treated HT1080 spheroids, respectively, were included in the analysis using the Seurat package (5.0.1) in R (4.3.2). Following additional filtering for cells with 12000 > nFeature_RNA > 3000 and percent mitochondrial RNA < 17.5 percent, 3327 and 1273 cells were included in the final analysis using Seurat.

source_name: Cell Line

growth_protocol: Spheroids were prepared at 2,000 cells per droplet, and ~50 spheroids per sample were embed in 500µl collagen, allowing for 72 hours of 3D spheroid invasion.

extract_protocol:
At this time, media were aspirated, and collagen hydrogels were gently removed from their well and transferred to a 1.7ml tube. Using small surgical scissors, gels were cut into pieces before adding sterilized digestion buffer (2mg/ml Type 7 Collagenase (Worthington) in HBSS) at a 2:1 buffer to gel ratio. Samples were incubated at 37°C for 10 minutes before lightly vortexing and pipetting the samples. After an additional 5-10 minutes, when collagen was no longer visible, cells were pelleted in a microcentrifuge at 300g. Digestion buffer was aspirated, and the isolated cells were resuspended in 100ul trypsin (0.25%) and incubated at 37°C for an additional three minutes before 1ml of complete media was added to inhibit proteolysis. Samples were filtered into a 5ml falcon tube with a cell strainer cap before being pelleted by centrifugation (300g). Media was aspirated and cells were resuspended in 50µl FACS buffer (PBS + 0.5% BSA) for sequencing.
Prepared single-cell suspensions were used for library preparation with 10X Genomics Chromium Single-Cell 3’ v3 Chemistry following manufacturer’s protocols.

treatment_protocol: 4B4-treated cells were cultured in the presence of 2 µg/ml media.

value: Cell Line

value: Fibrosarcoma

value: Wildtype

value: Control


title: 204V12PL

description: Library name: GTG-360-B1-76


title: ACTN1_ACTN1-parent_repAtx1_0.200000uM_A5_techrep1

description: Library name: 205793

data_processing:
Custom pipeline executed in linux shell
Libraries mapped to human genome using STAR
PCR duplications were removed post-alignment and making use of UMIs introduced during first-strand-synthesis
Read assignment to genes performed in salmon using pseudoalignment mode and default settings
TPM computed by normalizing per-gene read counts by total number of assigned reads
Assembly: human Grch39 and mouse mm10 (ensembl build 96)
Supplementary files format and content: tab-delimited files containing salmon output (gene counts)


title: 205V12PL

description: Library name: GTG-360-B2-70


title: Exogenous human skin equivalent, replicate 3

city: Napoli

first: Paolo

middle: Antonio

last: Netti

address: Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53

department: IIT - Center for Advanced Biomaterials for Healthcare

country: Italy

institute: IIT

description: Library name: exoft3

data_processing:
Raw data preprocessing involved several steps. Quality check was performed through the FastQC tool, which screens for low-quality samples as it provides useful information about the goodness and the reliability of sequenced reads. A MultiQC report was generated which included FastQC reports in order to integrate quality check results for all the samples. Cutadapt was used to remove residual Illumina Universal Adapter sequences from each file, and Hisat2 was used to align the trimmed sequences to the reference genome (genome build: GRCh38). The BAM files obtained were processed for quantification of gene expression using the Rsubread package in the R environment. Raw counts data were then normalized, and Differential Gene Expression analysis was carried out using the DESeq2 R package. Additionally, over-representation analysis (ORA) was implemented with reference gene sets retrieved from Gene Ontology database (BP: Biological Process, CC: Cellular Component, MF: Molecular Function) and Molecular Signatures Database (Hallmark gene sets).
Assembly: GRCh38
Supplementary files format and content: xlsx files containing raw counts

source_name: 3D skin model

extract_protocol:
Tissues were thawed, then they were cut and resuspended in a lysis buffer containing 1% β-Mercaptoethanol. The tissues were mechanically disrupted by vortexing in a 2 ml Eppendorf tube with a stainless-steel bead (7 mm in diameter). Tissue lysate was loaded onto the QIAshredder (Qiagen) homogenizer placed in a collection tube and centrifuged. The homogenized lysate was then collected. The RNA was extracted by using the RNeasy Mini Kit (Qiagen).
Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific). Libraries were prepared from 125 ng of total RNA using the mRNA 3′ DGE research grade sequencing service (Next Generation Diagnostics srl) which included library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing platform using a single-end, 100 cycle strategy (Illumina Inc.).

value: 3D skin model


title: G-Con2

description:
Library name: Sample 2
Isolated glomeruli collected from 24-week-old control mice.


title: HT1080 4B4-Treated

description:
Library name: 7841-AO_2
10X Genomics

value: 2ug/ml 4B4 Antibody


title: Exogenous human skin equivalent, replicate 2

description: Library name: exoft2


title: G-Con1

description:
Library name: Sample 1
Isolated glomeruli collected from 24-week-old control mice.


title: 203V1PL

description: Library name: 19-508-064


title: siNRF2 rep3

city: Rome

first: Daniela

last: Barilà

address: Via Cracovia, 90

department: Department of Biology

institute: Università Tor Vergata

description:
Library name: TorV-MGT13-siNRF2-003
tpm_Ctrl_siNRF2.tsv

data_processing:
Data processed using the nf-core/rnaseq pipeline with default parameters
Assembly: hg19
Supplementary files format and content: tab-delimited text file including TPM values for each sample

source_name: mammary gland tumor

growth_protocol: MGT cell lines, derived from MMTV-R26Met mice, were grown in DMEM/F12 (Dulbecco’s modified Eagle’s media/F12, 1/1, Sigma) supplemented with: 10% fetal bovine serum (FBS, Sigma), 100 U/mL penicillin, and 100 mg/mL streptomycin (P/S, Sigma), L-glutamine (2mM, Sigma), glucose (0,25%, Sigma), insulin (10 µg/mL, Sigma), transferrin (10 µg/mL, Sigma), sodium selenite (5 ng/mL, Sigma), hydrocortisone (0,5 µg/mL, Sigma), EGF (20 ng/mL, Sigma) and HGF (10 ng/mL, Thermo Fisher Scientific), at 37° in a 5% of CO₂ atmosphere. All MGT cells were routinely negative tested for Mycoplasma contamination

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, IT), purified from DNA contamination through a DNase I (Qiagen, IT) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen, IT). Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and by Agilent TapeStation (Agilent Technologies, CA), respectively
RNA libraries for sequencing were generated using the same amount of RNA for each sample according to the Illumina Stranded Total RNA Prep kit with an initial ribosomal depletion step using Ribo-Zero Plus (Illumina, CA). The libraries were quantified by qPCR and sequenced in paired-end mode (2x100 bp) with NovaSeq 6000 (Illumina, CA)

value: mammary gland tumor

value: Epithelial cell


title: 203V1L

description: Library name: 19-508-063

value: skin


title: 204V12L

description: Library name: GTG-360-B1-75

value: Atopic dermatitis


title: Endogenous human skin equivalent, replicate 4

description: Library name: endoft4


title: Endogenous human skin equivalent, replicate 3

description: Library name: endoft3


title: Exogenous human skin equivalent, replicate 1

description: Library name: exoft1


title: 206V1PL

description: Library name: GTG-360-B2-74

value: NL


title: 201V1PL1

description: Library name: GTG-360-B2-68


title: 201V1PL2

description: Library name: GTG-360-B1-74


title: siNRF2 rep1

description:
Library name: TorV-MGT13-siNRF2-001
tpm_Ctrl_siNRF2.tsv


title: Endogenous human skin equivalent, replicate 2

description: Library name: endoft2


title: siNRF2 rep2

description:
Library name: TorV-MGT13-siNRF2-002
tpm_Ctrl_siNRF2.tsv


title: Endogenous human skin equivalent, replicate 1

description: Library name: endoft1


title: 201V1L1

description: Library name: GTG-360-B2-67

value: LS


title: 201V12PL

description: Library name: GTG-360-B2-66


title: 201V1L2

description: Library name: GTG-360-B1-73


title: 203V12PL

description: Library name: 19-508-062


title: 141V1PL

description: Library name: 20-559-032

value: Psoriasis


title: Control rep2

description:
Library name: TorV-MGT13-Ctr-002
tpm_Ctrl_siNRF2.tsv


title: 201V12L

description: Library name: GTG-360-B2-65


title: white_D3-rep2

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: Library name: Sample_10-wD3-rep2-22511

data_processing:
ATAC-seq reads were filtered by removing low-quality reads using fastp v0.23.2 (Chen et al. 2018).
Reads were mapped to the hg38 genome with Bowtie2 v2.4.1.
Duplicates were removed using Picard MarkDuplicates along with mitochondrial reads and alignments with a mapping quality below 10 using samtools v1.9
Genrich v0.6.1 was used to calling peaks for each sample . Normalized read counts tracks  were generated using Deeptools
Assembly: hg38
Supplementary files format and content: Bed files with 4 columns: chromosome, start position, end position, score
Supplementary files format and content: Bigwig file using bamCoverage from deeptools 3.5.1.

source_name: subcutaneous abdominal adipose

growth_protocol: Primary ASCs were isolated from subcutaneous fat obtained by liposuction from a female donor (age 45; BMI 20,9 kg/m2). ASCs were cultured in DMEM/F12 (17.5 mM glucose) with 10% fetal calf serum and 20 ng/ml basic fibroblast growth factor (proliferation medium).

extract_protocol:
ATAC-seq was performed following the Omni-ATAC protocol {Corces, 2017}. Cells on D0, D1 and D3 were trypsinized and 50000 viable cells per condition were pelleted at 500 g for 5 min at 4⁰C. Nuclei were isolated by lysing cell pellets in 50 µl of ice-cold RSB buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, 0.01% digitonin) and ending lysis with 1 ml RSB buffer lacking NP40 and digitonin, followed by centrifugation at 500 g for 10 min at 4⁰C. Supernatants were removed and nuclei pellets were carefully resuspended in 50 µl of transposition mixture (25 µl 2X TD buffer and 2.5 µl transposase (Illumina, 20034197), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O) to carry out the transposition reaction at 37⁰C for 30 min on a Thermomixer at 1000 rpm. Cells on D15 were washed with PBS and treated 30 min with 200U/ml DNAse I (Worthington Biochemical, LS002139) in DMEM/F12 10% FBS at 37ºC. After 4 washes with warm PBS, cells were lysed directly on the culture dish on ice using RSB containing 1% NP40, 0.1% Tween-20 and 0.01% digitonin. After a 5 min centrifugation at 500 g 4ºC, pelleted nuclei were resuspended in RSB lacking NP40 and digitonin, and then stained with Trypan Blue and counted on a Neubauer chamber. 50000 nuclei were transferred to 1ml of the same buffer to be pelleted during a 10 min centrifugation at 500g 4ºC. Tagmentation was performed as for the rest of the cells. Total tagmented DNA was purified using the Zymo DNA Clean and Concentrator-5 kit (Zymo Research, D4014) and eluted in 20 µl elution buffer.
Libraries were amplified initially for 5 cycles using dual indexes for tagmented libraries from Diagenode (C01011034) with NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541). Further amplification was adjusted to the input material as assessed by qPCR using primer pair UDI 1 (Diagenode) for all samples. Library clean-up was done by performing a double-sided selection twice using AMPure XP beads (Beckman Coulter). Clean libraries were quantified with the KAPA Library Quantification Kit (Roche KK4824) and quality assessed using the Agilent TapeStation System, before sequencing at > 200 million read depth per sample with 150 bp paired-end reads on an Illumina NovaSeq.

treatment_protocol: Upon confluency, fibroblast growth factor was removed, and cells cultured for 72 h in DMEM/F12 (17.5 mM glucose) with 10% fetal calf serum (basal medium) before induction of differentiation (day 0: D0). For white adipogenic differentiation, ASCs were induced with a cocktail of 0.5 µM 1-methyl-3 isobutyl xanthine, 1 µM dexamethasone, 10 µg/ ml insulin and 200 µM indomethacin in basal medium. Differentiation media was renewed every 3 days until day 9, after which cells were maintained in DMEM/F12 (17.5 mM glucose) with 10% fetal calf serum and 10 µg/ ml insulin. For beige adipogenic differentiation, media were supplemented with 1 µM Rosiglitazone (Sigma, R2408) until day 15 (D15) when samples were harvested.

value: subcutaneous abdominal adipose

value: primary adipose stem cells

tag: time

value: white adipogenic differentiation

tag: replicate


title: Control rep3

description:
Library name: TorV-MGT13-Ctr-003
tpm_Ctrl_siNRF2.tsv


title: 141V1L

description: Library name: 20-559-031


title: 140V1PL

description: Library name: 20-559-030


title: Control rep1

description:
Library name: TorV-MGT13-Ctr-001
tpm_Ctrl_siNRF2.tsv


title: 131V1L

description: Library name: 20-559-027


title: white_D3-rep1

description: Library name: Sample_3-wD3-rep1-22504


title: 140V1L

description: Library name: 20-559-029


title: 131V1PL

description: Library name: 20-559-028


title: scRNAseq of mus muscles: adult male femoral artery,injury

first: Jialing

last: Mou

address: NO.320 Yueyang Road

institute: CEMCS

description: Library name: LC_337340_FA_VEI

data_processing:
Raw sequencing data were processed with Cell Ranger (v9.0.1), including alignment to a customized mouse reference based on the database (Ensembl release 105), alignment filtering, barcode processing, and unique molecular identifier (UMI) quantification.
Assembly: Ensembl release 105 reference genome
Supplementary files format and content: matrix format, including cell counts and features

source_name: femoral artery

extract_protocol:
Aortic tissues were collected from the mice perfused with PBS, finely minced and subsequently transferred to a digestion mixture (DMEM; 1.5 mg/ml collagenase, Type 1 [Gibco, 17100-017]; 1.5 mg/ml collagenase, Type 2 [Worthington, LS004177]; 2 U/ml elastase [Worthington, LS002279]; and 10% fetal bovine serum [Thermo Fisher], 10099141c]). Aortic tissues were incubated in the digestion mixture at 37°C for 40 min on a shaker at a speed of 120 rpm. After digestion, the cell suspension was filtered through a 70 μm cell strainer and then pelleted by centrifugation at 500g for 5 minutes. 1X RBC lysis buffer (eBioscience, 00-4333-57) was added for blood cell clearance if necessary. After the cells were washed with PBS, they were centrifuged at 500g for 5 min, after which the supernatant was discarded. The cell precipitate was resuspended in PBS.
Femoral artery single-cell suspensions were processed on the 10x Genomics Chromium Controller using the Chromium Single Cell 3′ Reagent Kits v3, following the manufacturer’s instructions. cDNA amplification and library construction were performed according to the standard protocol. Sequencing was carried out on an Illumina NovaSeq 6000 platform (paired-end, 150 bp, multiplexed) by LC-Bio Technology Co., Ltd. (Hangzhou, China)

value: femoral artery


title: beige_D3-rep1

description: Library name: Sample_6-bD3-rep1-22507

value: beige adipogenic differentiation


title: scRNAseq of mus muscles: adult male femoral artery,control

description: Library name: LC_337340_FA_sham


title: 129V12L

description: Library name: 19-508-057


title: 127V1PL

description: Library name: 19-508-056


title: 127V1L

description: Library name: 19-508-055


title: 127V12L

description: Library name: 19-508-053


title: wild type F121-9, NPC status, early S fraction, replicate 1

description:
Library name: F121-9_NPC_R1_2_E
nascent DNA from early S fraction

data_processing:
Repli-seq and Bru-seq data processing methods have been described in PMC6546437. Basically, sequencing reads were mapped to mm10 then reads for 129 and cas alleles were parsed using SNPsplit.
Assembly: mm10
Supplementary files format and content: bedgraph files, log2(E/L) for each allele (129 or cas), scaled and LOESS smoothed in 300kb bins

growth_protocol: 2i media for mESC maintenance and RHB-A for NPC differentiation. Both have been described in PMC5991511.

extract_protocol:
Repli-seq and Bru-seq sample extraction methods have been described in PMC6546437.
Repli-seq and Bru-seq library preparation methods have been described in PMC6546437.

treatment_protocol: For tet promoter activation, doxycycline hyclate was added to the culture media (concentration and duration indicated in the file name or figre legends in PMC11838563).

value: neural precursor cell

value: biol rep 1


title: 129V1PL

description: Library name: 19-508-060


title: wild type F121-9, ESC status, early S fraction, replicate 1

description:
Library name: F121-9_ES_R1_2_E
nascent DNA from early S fraction

source_name: embryonic stem cell

value: embryonic stem cell


title: 122V1PL

description: Library name: 19-508-052


title: white_D15-rep2

description: Library name: Sample_11-wD15-rep2-22512


title: wild type F121-9, NPC status, late S fraction, replicate 1

description:
Library name: F121-9_NPC_R1_2_L
nascent DNA from late S fraction


title: 203V12L

description: Library name: 19-508-061


title: beige_D3-rep2

description: Library name: Sample_13-bD3-rep2-22514


title: 129V1L

description: Library name: 19-508-059


title: wild type F121-9, ESC status, late S fraction, replicate 1

description:
Library name: F121-9_ES_R1_2_L
nascent DNA from late S fraction


title: 127V12PL

description: Library name: 19-508-054


title: beige_D15-rep2

description: Library name: Sample_14-bD15-rep2-22515


title: 122V12PL

description: Library name: 19-508-050


title: 122V12L

description: Library name: 19-508-049


title: 122V1L

description: Library name: 19-508-051


title: beige_D15-rep1

description: Library name: Sample_7-bD15-rep1-22508


title: white_D1-rep2

description: Library name: Sample_9-wD1-rep2-22510


title: Heterozygous Ptn E/P deletion from F121-9, NPC status, late S fraction, replicate 3

description:
Library name: D9NPC_R3_L
nascent DNA from late S fraction

value: biol rep 3


title: white_D1-rep1

description: Library name: Sample_2-wD1-rep1-22503


title: Homozygous Ptn E/P deletion from F121-9, NPC status, late S fraction, replicate 3

description:
Library name: B8NPC_R3_L
nascent DNA from late S fraction


title: 120V1L

description: Library name: 19-508-047


title: beige_D1-rep2

description: Library name: Sample_12-bD1-rep2-22513


title: 119V1L

description: Library name: GTG-360-B1-71


title: 119V12PL

description: Library name: GTG-360-B1-70


title: 129V12PL

description: Library name: 19-508-058


title: 119V1PL

description: Library name: GTG-360-B1-72


title: Heterozygous Ptn E/P deletion from F121-9, NPC status, late S fraction, replicate 2

description:
Library name: D9NPC_R2_L
nascent DNA from late S fraction

value: biol rep 2


title: 119V12L

description: Library name: GTG-360-B1-69


title: 120V1PL

description: Library name: 19-508-048


title: 118V12L

description: Library name: GTG-360-B2-61


title: beige_D1-rep1

description: Library name: Sample_5-bD1-rep1-22506


title: 118V12PL

description: Library name: GTG-360-B2-62


title: D0-rep1

description: Library name: Sample_1-D0-rep1-22502

value: uninduced


title: Heterozygous Ptn E/P deletion from F121-9, NPC status, early S fraction, replicate 3

description:
Library name: D9NPC_R3_E
nascent DNA from early S fraction


title: 118V1PL

description: Library name: GTG-360-B2-64


title: 118V1L

description: Library name: GTG-360-B2-63


title: Heterozygous Ptn E/P deletion from F121-9, NPC status, early S fraction, replicate 2

description:
Library name: D9NPC_R2_E
nascent DNA from early S fraction


title: D0-rep2

description: Library name: Sample_8-D0-rep2-22509


title: 116V1PL

description: Library name: 19-508-046


title: Homozygous Ptn E/P deletion from F121-9, NPC status, late S fraction, replicate 2

description:
Library name: B8NPC_R2_L
nascent DNA from late S fraction


title: 115V1PL

description: Library name: 20-559-024


title: Homozygous Ptn E/P deletion from F121-9, NPC status, early S fraction, replicate 3

description:
Library name: B8NPC_R3_E
nascent DNA from early S fraction


title: 116V1L

description: Library name: 19-508-045


title: beige_D15-rep2

description: Library name: 4-24773

data_processing:
H3K27ac Hi-ChIP was analyzed using MAPS v2.0 as implemented within the Arima Genomics pipeline
MACS2 2.2.9.1was used for H3K27ac peaks calling
Paired-end reads with at least one end overlapping the H3K27ac ChIP–seq peaks were used to identify long-range chromatin interactions at 5 kb resolution.
A positive Poisson model was used for identifying significant interactions (FDR < 0.01).
Assembly: hg38
Supplementary files format and content: broadPeaks: H3K27ac enriched regions from MACS2
Supplementary files format and content: sig3Dinteractions.bedpe: 3D chromatin contacts from MAPS2
Library strategy: HiChIP

extract_protocol:
ASCs were differentiated in 10 cm Petri dishes. Cells were washed twice in warm PBS before lysis in 4 ml Hi-ChIP buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3 mM MgCl2; 0.01% Digitonin, 0.1% Tween 20 and 1.0% NP-40, 20 mM Na-Butyrate). Lysed cells were centrifugated at 500 g for 5 min at 4⁰C. The floating fraction (containing unlysed adipocytes) and the pellet were combined in 5 ml Hi-ChIP buffer and dounced to isolate nuclei. Nuclei were washed twice in Hi-ChIP buffer, followed by centrifugation at 500 g for 5 min at 4⁰C. The nuclei pellet was resuspended in 5 ml Nuclei buffer (10mM HEPES, 1.5 mM MgCl2, 250 mM sucrose, 0.1 % NP-40, 20 mM Na-Butyrate in PBS) and processed for Hi-ChIP according Arima-HiC+ Kit protocol (Cat Nr: A510008), with some adaptations. Briefly, 15 µg DNA equivalent of crosslinked nuclei were lysed in deionized H2O, sonicated for 10 cycles (30s on, 30s off; Bioruptor Pico). The ChIP was performed with 2.5 µg H3K27ac antibody (Diagenode C15410174).
Libraries were quantified (KAPA, KK4824), amplified (KAPA, KK2620) and barcoded with xGen 2S Plus DNA library prep kit (IDT, 10009877 ) in combination with xGen 2S MID Adapter (IDT, 10009900). Libraries were sequenced to an average depth of 355 million 150 bp PE reads on an Illumina NovaSeq instrument.

tag: chip antibody


title: white_D15-rep1

description: Library name: Sample_4-wD15-rep1-22505

tag: cell type


title: Homozygous Ptn E/P deletion from F121-9, NPC status, early S fraction, replicate 2

description:
Library name: B8NPC_R2_E
nascent DNA from early S fraction


title: Heterozygous Ptn E/P deletion from F121-9, ESC status, late S fraction, replicate 3

description:
Library name: D9ESR3_L
nascent DNA from late S fraction


title: white_D15-rep2

description: Library name: 3-24772


title: 115V1L

description: Library name: 20-559-023


title: white_D15-rep1

description: Library name: 1-24770


title: Heterozygous Ptn E/P deletion from F121-9, ESC status, early S fraction, replicate 3

description:
Library name: D9ESR3_E
nascent DNA from early S fraction


title: beige_D15-rep1

description: Library name: 2-24771


title: Homozygous Ptn E/P deletion from F121-9, ESC status, late S fraction, replicate 3

description:
Library name: B8ESR3_L
nascent DNA from late S fraction


title: 114V1L

description: Library name: GTG-360-B1-67


title: 114V12L

description: Library name: GTG-360-B1-65


title: 114V12PL

description: Library name: GTG-360-B1-66


title: 113V1PL

description: Library name: GTG-360-B2-60


title: 113V1L

description: Library name: GTG-360-B2-59


title: Homozygous Ptn E/P deletion from F121-9, ESC status, early S fraction, replicate 3

description:
Library name: B8ESR3_E
nascent DNA from early S fraction


title: 115V12L

description: Library name: 20-559-025


title: Heterozygous Ptn E/P deletion from F121-9, ESC status, late S fraction, replicate 2

description:
Library name: D9ESR2_L
nascent DNA from late S fraction


title: beige_Input_D3

description: Library name: 20-23709_S18

data_processing:
FASTQ sequences from H3K27ac, H3K4me3, H3K4me1, H3K27me3, H3K36me3 and H3K9me3 ChIPs  were aligned to hg38 using Bowtie2 v2.4.5
Peaks were detected using MACS2 v2.2.7.1 with default narrow option for H3K4me3 and H3K27ac and broad option for H3K4me1, H3K36me3 and H3K27me3.  H3K9me3 peaks were called using EDD [protocol].
ChIP-seq read counts were normalized to library size using reads per genome coverage (RPGC) method in deepTools.
Assembly: hg38
Supplementary files format and content: narrowPeak, broadPeak are MACS2 output files, whilst _peaks.bed are bed files showing genomic enrichments output by EDD.
Supplementary files format and content: bigwig files are RPGC normalised coverage tracks.

extract_protocol:
Cells were fixed for 10 min with 1% formaldehyde, lysed in 50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS, protease inhibitors and Na-butyrate, and sonicated in a Picorupter (Diagnode) into ~200 bp fragments. After sedimentation, the supernatant was diluted 10 times in RIPA buffer and incubated with H3K4me3 (Diagenode c15410003), H3K4me1 (Diagenode c15410037) or H3K27ac (Diagenode c15410174) antibodies (each at 2.5 µg/106 cells) coupled to magnetic Dynabeads Protein A/G (Invitrogen) for 2 h at 4°C. ChIP samples were washed, cross-links were reversed and DNA was eluted for 2 h at 68°C in 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 5 mM EDTA, 1% SDS and 50 ng/µl Proteinase K. DNA was purified using phenol-chloroform isoamylalcohol and dissolved in H2O. For Day 15 differentiated white and beige adipocytes, cells were trypsinized, resuspended in HBSS, 0.5% BSA, and centrifuged 200g for 5 min to isolate floating mature adipocytes. Purified nuclei were then fixed and processed as cell samples
ChIP-seq libraries were prepared using a Microplex kit (Diagenode) and sequenced with 150-bp paired-end reads on an Illumina NovaSeq.

treatment_protocol: Upon confluency, fibroblast growth factor was removed, and cells cultured for 72 h in DMEM/F12 (17.5 mM glucose) with 10% fetal calf serum (basal medium) before induction of differentiation (day 0: D0). For white adipogenic differentiation, ASCs were induced with a cocktail of 0.5 µM 1-methyl-3 isobutyl xanthine, 1 µM dexamethasone, 10 µg/ ml insulin and 200 µM indomethacin in basal medium. Differentiation media was renewed every 3 days until day 9, after which cells were maintained in DMEM/F12 (17.5 mM glucose) with 10% fetal calf serum and 10 µg/ ml insulin. For beige adipogenic differentiation, media were supplemented with 1 µM Rosiglitazone (Sigma, R2408) until day 15. Samples were harvested on day (D0), then D1, D3 and D15 after induction.

value: Input


title: white_H3K9me3_D15

description: Library name: 33-22576_S103


title: 115V12PL

description: Library name: 20-559-026

value: skin


title: Homozygous Ptn E/P deletion from F121-9, ESC status, late S fraction, replicate 2

description:
Library name: B8ESR2_L
nascent DNA from late S fraction


title: beige_Input_D1

description: Library name: 19-23708_S5