title: SMARCA5 Mnase Chip-seq in WT BMDM, 2h LPS 10ng/ml, replicate2

description: Library name: SMARCA5_WT_LPS_R2

value: wild type

tag: treatment

value: 2h LPS 10 ng/ml


title: Hep3B cells, Hypoxia, oxamate sodium

status: Public on Sep 18 2025

type: SRA

city: GUANGZHOU

first: jiamin

last: chen

address: WAIHUAN EAST ROAD

country: China

institute: SOUTH CHINA UNIVERSITY OF TECHNOLOGY

description:
Library name: sample3
Hypoxia_oxamate

library_source: transcriptomic

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Read counts were adjusted using the edgeR R package (3.22.5) by scaling normalization factors to eliminate differences in sequencing depth between samples, followed by differential expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes FPKM value for each sample

molecule: total RNA

organism: Homo sapiens

source_name: liver

growth_protocol: Hep3B cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃. Normal condition: 20% O2; Hypoxic condition: 1% O2.

extract_protocol:
RNA was harvested using TRIzol Reagent. A total amount of 3 µg of RNA per sample was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Hypoxia exposure was achieved by placing cells into a modular chamber flushed with a gas mixture consisting of 1% O2, 5% CO2 and 94% N2 at 37 ℃.

tag: tissue

value: liver

tag: cell line

tag: cell type

value: liver cancer cell

tag: genotype

value: WT

value: Hypoxic condition, oxamate sodium


title: Hep3B cells, Hypoxia

description:
Library name: sample2
Hypoxia

value: Hypoxic condition


title: mmNrf2KO4

city: Baltimore

first: Zhenhua

last: Xu

state: MD

address: 400 North Broadway Smith BLDG 3001 Smith BLDG 3001

country: USA

institute: Johns Hopkins University

description: Library name: mmNrf2KO4

data_processing:
Raw paired-end RNA-seq reads (200 bp) were quality-checked and aligned to the mouse reference genome using STAR with default parameters.
Only uniquely mapped reads were retained for downstream analysis. Gene-level read counts were generated, and differential expression analysis was performed using edgeR in R.
Assembly: Raw reads of RNA-seq were uniquely mapped to the GRCm38/mm10 genome assembly using STAR
Supplementary files format and content: csv file including FKPM values for all samples

organism: Mus musculus

source_name: retina

extract_protocol:
RNA was extracted using RNeasy Micro kit (Qiagen).
NEBNext Poly (A) Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina were used to generate libraries.

value: retina

value: Muller cells

value: Muller-specific Nrf2 cKO

value: OIR

tag: time


title: SMARCA5 Mnase Chip-seq in SMARCA5 KOBMDM, untreated, replicate2

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: Library name: SMARCA5_KO_UT_R2

library_source: genomic

data_processing:
ChIP-seq workflow, which was also used for MNase-seq and MNase ChIP-seq, is available at https://github.com/fgualdr/mmchipseq
FASTQ files were filtered and trimmed using FASTP (v0.23.2)
Reads were aligned to the mouse genome (mm39; GCA_000001635.9) using STAR (v2.7.9a) with parameters: --runMode alignReads, --alignIntronMax 1, --alignMatesGapMax 100000, --alignEndsType EndToEnd, --outSAMtype BAM Unsorted, and --outSAMattributes All.
Duplicate reads were identified and marked using PICARD (v2.27.4).
Multi-mapped reads were assigned using a custom Bayesian EM algorithm (https://github.com/fgualdr/mmatac).
Peaks were called using MACS2 (v2.2.7.1) with parameters: --nomodel --keep-dup all and the narrowPeak setting enabled.
Reference peak set were created by selecting peaks with q-value ≤ 10⁻³ and ≥ 40% overlap between replicates.
Bigwig files were generated using deeptools (v3.5.1).
Normalization was performed using invariant peaks with GeneralNormalizer (https://github.com/fgualdr/GeneralNormalizer).
Unsupervised clustering was done using PCA (FactoMineR, v2.11), UMAP (uwot, v0.1.16), k-nearest neighbor (FNN, v1.1.4.1), and Louvain clustering (igraph, v1.4.2).
Heatmaps were generated using ComplexHeatmap (v2.14.0).
Assembly: mm39
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: BMDM

growth_protocol: Bone marrow-derived macrophages (BMDMs) were harvested from Csf1r-Cre wild-type (WT) and SMARCA5 knockout Smarca5lox/lox Csf1r-Cre (KO) mice and cultured under standard conditions. Cells were differentiated into BMDMs over 7 days with daily treatment of 4-hydroxytamoxifen (4-OHT).

extract_protocol:
For ChIP-seq, nuclear extracts were prepared as described in Gualdrini et al., 2022. Chromatin was sheared by sonication (Branson Ultrasonics Sonifier or Diagenode Bioruptor Pico). For SMARCA5 MNase ChIP-seq, nuclei were digested with MNase (9 U; Roche) in digestion buffer (20 mM Tris-HCl, pH 7.6; 5 mM CaCl₂) at 37°C for 2 hours, followed by EDTA quenching (50 mM). Digested chromatin was sonicated in lysis buffer (10 mM Tris-HCl, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% sodium deoxycholate; 0.5% sodium lauroyl sarcosinate) to promote nuclear lysis. Immunoprecipitations were performed with target-specific antibodies prebound to Dynabeads™ Protein G. Beads were washed with RIPA buffer and TE buffer, and DNA was eluted, de-crosslinked, and purified using Qiagen kits (QIAquick PCR purification or MinElute PCR purification).
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB) or following Gualdrini et al., 2022, protocols. Libraries were assessed for size and quality using the Agilent TapeStation High Sensitivity D5000 assay. Libraries were diluted to 4 nM and sequenced as paired-end reads (51-bp or 61-bp) on an Illumina NextSeq6000 platform.

treatment_protocol: Individual Chip-seq were performed on mouse primary BMDMs derived from wild-type or SMARCA5-deleted cells under untreated, LPS-stimulated, or IFNβ-stimulated conditions for 1 and 2 hours. For specific details, refer to individual sample metadata. Cells were either processed directly for ChIP-seq or treated with 1% formaldehyde for 10 minutes at room temperature for chromatin crosslinking, followed by quenching with 0.125 mM Tris-HCl (pH 7.6).

value: BMDM

tag: chip antibody

value: SMARCA5:Abcam, Cat# ab3749


title: Hep3B cells, Normoxia

description:
Library name: sample1
Normoxia

value: Normal condition


title: mmNrf2KO3

description: Library name: mmNrf2KO3


title: Sol_6M_WT6

city: EVRY-COURCOURONNES

first: Tao

last: WANG

state: France

address: 1 bis, rue de l’Internationale

department: R & D

country: France

institute: genethon

description:
Library name: Sol_6M_WT6
Sol6

data_processing:
paired-end reads were aligned to the reference transcriptome using STAR version  2.7.11b using default settings and Gene expression was measured by featureCounts version 2.0.6
Read count extraction was performed using R 4.4.1 and the tximport package (v1.28.0)
genes with more than 50 reads per samples were kept
Differential gene expression was performed using R and the package DESeq2 (v1.48.1) and using arguments lfcThreshold = 0, pAdjustMethod = "fdr", independentFiltering = T
Assembly: Rattus_norvegicus. mRatBN7.2
Supplementary files format and content: Tab-delimited text file (.tsv) containing counts per gene (rows) and samples (columns), generated by featureCounts (v2.0.6).

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Sol

growth_protocol: Cells/muscles were maintained and processed under standard laboratory conditions (details can be added if necessary).

extract_protocol:
Total RNA extraction was performed from muscle lysates using the RNeasy Plus kit (Qiagen). Total RNA concentration was quantified using a Nanodrop spectrophotometer (ND8000 Labtech, Wilmington Delaware). The RNA quality was evaluated using an Agilent RNA 6000 Pico Kit on a 2100 Bioanalyzer instrument (Agilent Technologies) and Illumina RNA seq was performed on three replicates of each selected clone.
The sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced according to the Illumina NovaSeq™ 6000 protocol.

treatment_protocol: untreated

value: Sol

value: untreated


title: mmNrf2KO1

description: Library name: mmNrf2KO1


title: SMARCA5 Mnase Chip-seq in SMARCA5 KOBMDM, untreated, replicate1

description: Library name: SMARCA5_KO_UT_R1


title: Wildtype, day 0, rep 3

city: Westmead

first: Riley

last: McMahon

address: 214 Hawkesbury Road

country: Australia

institute: Children's Medical Research Institute

description: Library name: Sample 3

data_processing:
Nucleotide sequences were mapped to the Mus Musculus (mm10) reference genome using the splice-aware aligner, STAR v020201
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Day 0 EB

growth_protocol: Naïve ESCs were grown on gelatin coated plates for two passages before being passaged and counted for embryoid body differentiation. AggreWell™ 400 24-wells (Stem Cell Technologies) were filled with 1 mL of EB media (DMEM, 15% FBS, 1x NEAA, 1x pen/strep, 0.1 mM  b-mercaptoethanol) and spun at 3000 g for 30 seconds to remove air bubbles. 2 x 106 ESCs per Aggrewell in 1mL of EB media were then added and the plate was spun at 500 g for 3 minutes. The plates were incubated at 37°C, 5% CO2 for 24 hours before the EBs were gently dislodged from the wells using a 1 mL pipette and transferred to a non-adherence 10 cm plate in 10mL of EB media. EBs were then incubated on a rocking plate and media was replaced every two days.

extract_protocol:
Total RNA was extracted using RNA Mini kit (Qiagen). 3ug of RNA was used for sequencing libraries
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).

value: Day 0 EB

value: R1 ESC

value: mouse embryonic stem cell


title: FAP33 6 months of diet (T2) RNA-Seq

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

description:
Library name: FAP33_6mo-T2
FAP33 6 months of diet (T2) RNA-Seq

data_processing:
Sequencing reads were preprocessed with fastp v0.21.0 (Chen et al., 2018) in default settings to remove reads associated with a low quality (phred quality <Q15), shorter than 15 nt reads, or with more than 5 Ns.
Reads passing the filtering step were aligned to the human Gencode v36 transcriptome using Salmon v1.4.0 (Patro et al., 2017) with option --validateMappings, --seqBias, and --gcBias.
Gene expression levels were normalized using tximport v.1.18 while DESeq2 v1.30.1 was applied for the differential expression analysis.
Assembly: hg38
Supplementary files format and content: Table of gene expression levels as raw counts.

source_name: PBMC

extract_protocol:
RNA was extracted from peripheral blood mononuclear cells (PBMCs) and formalin-fixed paraffin-embedded (FFPE) intestinal tissue, including both mucosa and polyps from FAP patients, using the RNeasy Kit (Qiagen, Germany).
RNA quality was assessed using an Agilent Bioanalyzer (Agilent, USA). cDNA library preparation was carried out using the Illumina Stranded Total RNA Prep following the manufacturer’s instructions.

value: PBMC

tag: disease

value: FAP

tag: patient

value: 6 months of diet


title: Pso_6M_DMD1

description:
Library name: Pso_6M_DMD1
Pso1

source_name: Pso

value: Pso

value: DMD


title: CEBPb Chip-seq in WT BMDM, untreated, replicate1

description: Library name: WT_CEBPb_R1

value: wild type

value: C/EBPβ:Bethyl, Cat# A302-739A


title: FAP33 3 months of diet (T1) RNA-Seq

description:
Library name: FAP33_3mo-T1
FAP33 3 months of diet (T1) RNA-Seq

value: 3 months of diet


title: Pso_6M_WT6

description:
Library name: Pso_6M_WT6
Pso6

value: WT


title: mmWT5

description: Library name: mmWT5

value: retina

value: Muller cells

value: OIR


title: Heart_12M_WT23

description:
Library name: Heart_12M_WT23
Cr23

source_name: Heart

value: Heart


title: FAP33 Before diet (T0) RNA-Seq

description:
Library name: FAP33_PRE-T0
FAP33 Before diet (T0) RNA-Seq

value: Before diet


title: Heart_6M_DMD1

description:
Library name: Heart_6M_DMD1
Cr1

value: untreated


title: mmWT4

description: Library name: mmWT4


title: SMARCA5 Mnase Chip-seq in SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate2

description: Library name: SMARCA5_KO_LPS_R2

value: BMDM

value: 2h LPS 10 ng/ml

value: SMARCA5:Abcam, Cat# ab3749


title: Heart_6M_WT6

description:
Library name: Heart_6M_WT6
Cr6


title: SMARCA5 Mnase Chip-seq in SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate1

description: Library name: SMARCA5_KO_LPS_R1


title: Sol_6M_DMD1

description:
Library name: Sol_6M_DMD1
Sol1

value: Sol


title: FAP32 6 months of diet (T2) RNA-Seq

description:
Library name: FAP32_6mo-T2
FAP32 6 months of diet (T2) RNA-Seq

value: PBMC

value: FAP

value: 6 months of diet


title: Dia_6M_DMD1

description:
Library name: Dia_6M_DMD1
Dia1

source_name: diaphragm

value: diaphragm

value: DMD


title: mmWT3

description: Library name: mmWT3


title: SMARCA5 Mnase Chip-seq in WT BMDM, 2h LPS 10ng/ml, replicate1

description: Library name: SMARCA5_WT_LPS_R1

value: wild type


title: FAP32 3 months of diet (T1) RNA-Seq

description:
Library name: FAP32_3mo-T1
FAP32 3 months of diet (T1) RNA-Seq

value: 3 months of diet


title: PU1 Chip-seq in SMARCA5 KOBMDM, untreated, replicate2

description: Library name: KO_PU1_R2

value: PU.1:Cell Signaling, Cat# 2258


title: mmWT1

description: Library name: mmWT1

value: retina

value: Muller cells

value: WT


title: Dia_6M_WT6

description:
Library name: Dia_6M_WT6
Dia6


title: PU1 Chip-seq in SMARCA5 KOBMDM, untreated, replicate1

description: Library name: KO_PU1_R1


title: CEBPb Chip-seq in SMARCA5 KOBMDM, untreated, replicate1

description: Library name: KO_CEBPb_R1

value: C/EBPβ:Bethyl, Cat# A302-739A


title: CEBPb Chip-seq in SMARCA5 KOBMDM, untreated, replicate2

description: Library name: KO_CEBPb_R2


title: FAP31 6 months of diet (T2) RNA-Seq

description:
Library name: FAP31_6mo-T2
FAP31 6 months of diet (T2) RNA-Seq


title: S5-X rep2

city: Beijing

first: Ruoqi

last: Cheng

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

description:
Library name: Sample 54
column name in counts.txt: S5-X-2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low quality data by Trimmomatic v0.39, then mapped to mm10 whole genome using STAR v2.7.10b and annotated using gencode vm25 gtf file.
sam file generated by STAR was converted to bam and counts were generated using featureCounts v2.0.6.
Assembly: mm10
Supplementary files format and content: txt file with raw gene counts for every gene and every sample.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit
RNA sequencing libraries were constructed by using magnetic beads with oligo (DT) enriched mRNA. After that, fragment buffer was added to break the mRNA into short segments. Using mRNA as template, a strand of cDNA was synthesized using six base random primers. Then buffer, dNTPs, DNA polymer I and RNase H were added to synthesize a two strand cDNAs, which were purified using AMPURE XP beads. The purified double stranded cDNAs were repaired, a-tailed and sequenced, and then the fragment size was selected by AMPURE XP beads. Finally, PCR amplification was carried out and PCR products were purified with AMPURE XP beads to obtain the final library. The fragmented and randomly primed 2 × 100- bp paired-end libraries were sequenced using an Illumina HiSeq 2500.

value: S4 on day 1 were treated by peri-implantation medium minus XAV 939 for 3 days on Aggrewell.


title: H3K27ac Chip-seq in WT BMDM, untreated, replicate2

description: Library name: H3K27Ac_UT_WT_R2

value: BMDM

value: H3K27ac:Abcam, Cat# ab47290


title: S5-F rep2

description:
Library name: Sample 52
column name in counts.txt: S5-F-2

value: S4 on day 1 were treated by peri-implantation medium minus FGF4 for 3 days on Aggrewell.


title: FAP32 Before diet (T0) RNA-Seq

description:
Library name: FAP32_PRE-T0
FAP32 Before diet (T0) RNA-Seq

value: Before diet


title: S5-F rep1

description:
Library name: Sample 51
column name in counts.txt: S5-F-1


title: H3K27ac Chip-seq in WT BMDM, untreated, replicate1

description: Library name: H3K27Ac_UT_WT_R1


title: Methyl jasmonate-treated, Pieris, biological replicate 1

city: Madrid

first: Lucia

last: Talavera

address: Parque Científico y Tecnológico, UPM Campus de Montegancedo, Ctra, M-40, km 38

country: Spain

institute: CBGP

description:
Library name: AT_MJ_P1
Column name in raw_counts.txt: AT_MJ_P1_count

data_processing:
Raw reads were trimmed for adapters, poly-N sequences (N>10%) and low quality reads (Qscore of over 50% bases of the read <=5)
Clean reads were mapped against the TAIR10 reference genome of A. thaliana using HISAT2 software.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: cvs files include fpkm values for each sample

organism: Arabidopsis thaliana

source_name: Rosette

extract_protocol:
RNA was isolated and purified using the RNeasy Plant Miki Kit (Qiagen) and including the on-column DNA I (Qiagen) digestion. 2 ug of total RNA was used for the construction of sequencing libraries.
Libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.

value: Rosette

value: Methyl jasmonate


title: Methyl jasmonate-treated, Pieris, biological replicate 2

description:
Library name: AT_MJ_P2
Column name in raw_counts.txt: AT_MJ_P2_count


title: Methyl jasmonate-treated, Pieris, biological replicate 3

description:
Library name: AT_MJ_P3
Column name in raw_counts.txt: AT_MJ_P3_count


title: Methyl jasmonate-treated, Pieris, biological replicate 4

description:
Library name: AT_MJ_P4
Column name in raw_counts.txt: AT_MJ_P4_count


title: FAP30 6 months of diet (T2) RNA-Seq

description:
Library name: FAP30_6mo-T2
FAP30 6 months of diet (T2) RNA-Seq

value: PBMC

value: FAP

value: 6 months of diet


title: S5-B rep2

description:
Library name: Sample 50
column name in counts.txt: S5-B-2

value: S4 on day 1 were treated by peri-implantation medium minus BMP4 for 3 days on Aggrewell.


title: S5-X rep1

description:
Library name: Sample 53
column name in counts.txt: S5-X-1


title: H3K27ac Chip-seq in SMARCA5 KOBMDM, untreated, replicate2

description: Library name: H3K27Ac_UT_KO_R2


title: Non-Primed, Pieris, biological replicate 4

description:
Library name: AT_NP_P4
Column name in raw_counts.txt: AT_NP_P4_count


title: FAP31 Before diet (T0) RNA-Seq

description:
Library name: FAP31_PRE-T0
FAP31 Before diet (T0) RNA-Seq


title: FAP30 3 months of diet (T1) RNA-Seq

description:
Library name: FAP30_3mo-T1
FAP30 3 months of diet (T1) RNA-Seq

value: 3 months of diet


title: S5-B rep1

description:
Library name: Sample 49
column name in counts.txt: S5-B-1


title: Non-Primed, Pieris, biological replicate 3

description:
Library name: AT_NP_P3
Column name in raw_counts.txt: AT_NP_P3_count


title: H3K27ac Chip-seq in SMARCA5 KOBMDM, untreated, replicate1

description: Library name: H3K27Ac_UT_KO_R1


title: FAP30 Before diet (T0) RNA-Seq

description:
Library name: FAP30_PRE-T0
FAP30 Before diet (T0) RNA-Seq


title: H3K27ac Chip-seq in WT BMDM, 2h LPS 10ng/ml, replicate2

description: Library name: H3K27Ac_2hLPS_WT_R2

value: wild type

value: 2h LPS 10 ng/ml


title: S5-A rep2

description:
Library name: Sample 48
column name in counts.txt: S5-A-2

value: S4 on day 1 were treated by peri-implantation medium minus Activin A for 3 days on Aggrewell.


title: S5-A rep1

description:
Library name: Sample 47
column name in counts.txt: S5-A-1

value: WT


title: FAP31 3 months of diet (T1) RNA-Seq

description:
Library name: FAP31_3mo-T1
FAP31 3 months of diet (T1) RNA-Seq


title: H3K27ac Chip-seq in WT BMDM, 2h LPS 10ng/ml, replicate1

description: Library name: H3K27Ac_2hLPS_WT_R1


title: S5 rep2

description:
Library name: Sample 46
column name in counts.txt: S5-2

value: S4 on day 1 were treated by peri-implantation medium for 3 days on Aggrewell.


title: H3K27ac Chip-seq in SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate2

description: Library name: H3K27Ac_2hLPS_KO_R2


title: Non-Primed, Pieris, biological replicate 1

description:
Library name: AT_NP_P1
Column name in raw_counts.txt: AT_NP_P1_count


title: FAP29 3 months of diet (T1) RNA-Seq

description:
Library name: FAP29_3mo-T1
FAP29 3 months of diet (T1) RNA-Seq


title: Methyl jasmonate-treated, Tetranychus, biological replicate 4

description:
Library name: AT_MJ_T4
Column name in raw_counts.txt: AT_MJ_T4_count


title: S5 rep1

description:
Library name: Sample 45
column name in counts.txt: S5-1


title: H3K27ac Chip-seq in SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate1

description: Library name: H3K27Ac_2hLPS_KO_R1


title: S3-CD rep2

description:
Library name: Sample 44
column name in counts.txt: S3-CD-2

value: S2 cell aggeregates were treated by 4C-64C medium minus CD1530 for 1 day.


title: Methyl jasmonate-treated, Tetranychus, biological replicate 3

description:
Library name: AT_MJ_T3
Column name in raw_counts.txt: AT_MJ_T3_count


title: FAP28 3 months of diet (T1) RNA-Seq

description:
Library name: FAP28_3mo-T1
FAP28 3 months of diet (T1) RNA-Seq


title: H3K27ac Chip-seq in WT BMDM, 2h IFN 100U/ml, replicate2

description: Library name: H3K27Ac_2hIFN_WT_R2

value: BMDM

value: 2h IFNb 100 U/ml


title: S3-CD rep1

description:
Library name: Sample 43
column name in counts.txt: S3-CD-1


title: FAP29 Before diet (T0) RNA-Seq

description:
Library name: FAP29_PRE-T0
FAP29 Before diet (T0) RNA-Seq


title: Methyl jasmonate-treated, Tetranychus, biological replicate 1

description:
Library name: AT_MJ_T1
Column name in raw_counts.txt: AT_MJ_T1_count


title: H3K27ac Chip-seq in WT BMDM, 2h IFN 100U/ml, replicate1

description: Library name: H3K27Ac_2hIFN_WT_R1

value: H3K27ac:Abcam, Cat# ab47290


title: FAP28 6 months of diet (T2) RNA-Seq

description:
Library name: FAP28_6mo-T2
FAP28 6 months of diet (T2) RNA-Seq


title: Methyl jasmonate-treated, Tetranychus, biological replicate 2

description:
Library name: AT_MJ_T2
Column name in raw_counts.txt: AT_MJ_T2_count


title: FAP28 Before diet (T0) RNA-Seq

description:
Library name: FAP28_PRE-T0
FAP28 Before diet (T0) RNA-Seq

value: Before diet


title: S3-C10 rep2

description:
Library name: Sample 42
column name in counts.txt: S3-C10-2

value: S2 cell aggeregates were treated by 4C-64C medium minus CHIR-99021 for 1 day.


title: FAP29 6 months of diet (T2) RNA-Seq

description:
Library name: FAP29_6mo-T2
FAP29 6 months of diet (T2) RNA-Seq


title: Non-Primed, Pieris, biological replicate 2

description:
Library name: AT_NP_P2
Column name in raw_counts.txt: AT_NP_P2_count

value: Rosette


title: Non-Primed, Tetranychus, biological replicate 4

description:
Library name: AT_NP_T4
Column name in raw_counts.txt: AT_NP_T4_count


title: FAP26 6 months of diet (T2) RNA-Seq

description:
Library name: FAP26_6mo-T2
FAP26 6 months of diet (T2) RNA-Seq

value: PBMC


title: H3K27ac Chip-seq in SMARCA5 KOBMDM, 2h IFN 100U/ml, replicate1

description: Library name: H3K27Ac_2hIFN_KO_R1


title: S3-C10 rep1

description:
Library name: Sample 41
column name in counts.txt: S3-C10-1


title: FAP26 3 months of diet (T1) RNA-Seq

description:
Library name: FAP26_3mo-T1
FAP26 3 months of diet (T1) RNA-Seq

value: FAP


title: Non-Primed, Tetranychus, biological replicate 3

description:
Library name: AT_NP_T3
Column name in raw_counts.txt: AT_NP_T3_count


title: S3-8Bira rep2

description:
Library name: Sample 40
column name in counts.txt: S3-Bira-2

value: S2 cell aggeregates were treated by 4C-64C medium minus Birabresib for 1 day.


title: H3K27ac Chip-seq in WT BMDM, 1h LPS 10ng/ml, replicate2

description: Library name: H3K27Ac_1hLPS_WT_R2

value: 1h LPS 10 ng/ml


title: FAP26 Before diet (T0) RNA-Seq

description:
Library name: FAP26_PRE-T0
FAP26 Before diet (T0) RNA-Seq


title: Non-Primed, Tetranychus, biological replicate 2

description:
Library name: AT_NP_T2
Column name in raw_counts.txt: AT_NP_T2_count


title: S3-8Bira rep1

description:
Library name: Sample 39
column name in counts.txt: S3-Bira-1


title: Non-Primed, Tetranychus, biological replicate 1

description:
Library name: AT_NP_T1
Column name in raw_counts.txt: AT_NP_T1_count


title: H3K27ac Chip-seq in WT BMDM, 1h LPS 10ng/ml, replicate1

description: Library name: H3K27Ac_1hLPS_WT_R1


title: H3K27ac Chip-seq in SMARCA5 KOBMDM, 1h LPS 10ng/ml, replicate2

description: Library name: H3K27Ac_1hLPS_KO_R2


title: S3-8Br rep2

description:
Library name: Sample 38
column name in counts.txt: S3-8Br-2

value: S2 cell aggeregates were treated by 4C-64C medium minus 8Br-cAMP for 1 day.


title: S3-8Br rep1

description:
Library name: Sample 37
column name in counts.txt: S3-8Br-1


title: FAP25 6 months of diet (T2) RNA-Seq

description:
Library name: FAP25_6mo-T2
FAP25 6 months of diet (T2) RNA-Seq

value: 6 months of diet


title: H3K27ac Chip-seq in SMARCA5 KOBMDM, 1h LPS 10ng/ml, replicate1

description: Library name: H3K27Ac_1hLPS_KO_R1


title: Methyl jasmonate-treated, Control, biological replicate 4

description:
Library name: AT_MJ_C4
Column name in raw_counts.txt: AT_MJ_C4_count

value: Methyl jasmonate


title: H3K27ac Chip-seq in SMARCA5 KOBMDM, 2h IFN 100U/ml, replicate2

description: Library name: H3K27Ac_2hIFN_KO_R2


title: FAP25 Before diet (T0) RNA-Seq

description:
Library name: FAP25_PRE-T0
FAP25 Before diet (T0) RNA-Seq


title: Methyl jasmonate-treated, Control, biological replicate 3

description:
Library name: AT_MJ_C3
Column name in raw_counts.txt: AT_MJ_C3_count


title: Methyl jasmonate-treated, Control, biological replicate 2

description:
Library name: AT_MJ_C2
Column name in raw_counts.txt: AT_MJ_C2_count


title: FAP25 3 months of diet (T1) RNA-Seq

description:
Library name: FAP25_3mo-T1
FAP25 3 months of diet (T1) RNA-Seq

value: 3 months of diet


title: H3K27ac Chip-seq in WT BMDM, 1h IFN 100U/ml, replicate2

description: Library name: H3K27Ac_1hIFN_WT_R2

value: wild type

value: 1h IFNb 100 U/ml


title: S3 rep1

description:
Library name: Sample 35
column name in counts.txt: S3-1

value: WT

value: S2 cell aggeregates were treated by 4C-64C medium for 1 day.


title: S3 rep2

description:
Library name: Sample 36
column name in counts.txt: S3-2


title: H3K27ac Chip-seq in WT BMDM, 1h IFN 100U/ml, replicate1

description: Library name: H3K27Ac_1hIFN_WT_R1

value: BMDM


title: Methyl jasmonate-treated, Control, biological replicate 1

description:
Library name: AT_MJ_C1
Column name in raw_counts.txt: AT_MJ_C1_count


title: FAP24 3 months of diet (T1) RNA-Seq

description:
Library name: FAP24_3mo-T1
FAP24 3 months of diet (T1) RNA-Seq


title: FAP24 Before diet (T0) RNA-Seq

description:
Library name: FAP24_PRE-T0
FAP24 Before diet (T0) RNA-Seq


title: Non-Primed, Control, biological replicate 4

description:
Library name: AT_NP_C4
Column name in raw_counts.txt: AT_NP_C4_count


title: H3K27ac Chip-seq in SMARCA5 KOBMDM, 1h IFN 100U/ml, replicate1

description: Library name: H3K27Ac_1hIFN_KO_R1

value: H3K27ac:Abcam, Cat# ab47290


title: S2-CD rep2

description:
Library name: Sample 34
column name in counts.txt: S2-CD-2

value: S1 cell aggeregates were treated by 4C-64C medium minus CD1530 for 1 day.


title: S2-CD rep1

description:
Library name: Sample 33
column name in counts.txt: S2-CD-1


title: Non-Primed, Control, biological replicate 3

description:
Library name: AT_NP_C3
Column name in raw_counts.txt: AT_NP_C3_count


title: FAP23 6 months of diet (T2) RNA-Seq

description:
Library name: FAP23_6mo-T2
FAP23 6 months of diet (T2) RNA-Seq


title: S2-C10 rep2

description:
Library name: Sample 32
column name in counts.txt: S2-C10-2

value: S1 cell aggeregates were treated by 4C-64C medium minus CHIR-99021 for 1 day.


title: FAP23 3 months of diet (T1) RNA-Seq

description:
Library name: FAP23_3mo-T1
FAP23 3 months of diet (T1) RNA-Seq


title: S2-C10 rep1

description:
Library name: Sample 31
column name in counts.txt: S2-C10-1


title: Non-Primed, Control, biological replicate 2

description:
Library name: AT_NP_C2
Column name in raw_counts.txt: AT_NP_C2_count

value: Rosette


title: Non-Primed, Control, biological replicate 1

description:
Library name: AT_NP_C1
Column name in raw_counts.txt: AT_NP_C1_count


title: FAP24 6 months of diet (T2) RNA-Seq

description:
Library name: FAP24_6mo-T2
FAP24 6 months of diet (T2) RNA-Seq

value: PBMC


title: CTCF Chip-seq in WT BMDM, untreated, replicate1

description: Library name: CTCF_WT_R1

value: CTCF:Upstate, Cat# 07-729


title: FAP23 Before diet (T0) RNA-Seq

description:
Library name: FAP23_PRE-T0
FAP23 Before diet (T0) RNA-Seq

value: FAP

value: Before diet


title: CTCF Chip-seq in SMARCA5 KOBMDM, untreated, replicate1

description: Library name: CTCF_KO_R1


title: IP_LHP1_FLAG_rep2

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

description: Library name: Sample 33

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

source_name: Arabidopsis thaliana

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

value: Arabidopsis thaliana

value: Arabidopsis seedlings

value: SIGMA, F1804

value: 1305-LHP1-FLAG transformed plants (in Col-0)


title: FAP22 6 months of diet (T2) RNA-Seq

description:
Library name: FAP22_6mo-T2
FAP22 6 months of diet (T2) RNA-Seq

value: 6 months of diet


title: S2-8Br rep2

description:
Library name: Sample 28
column name in counts.txt: S2-8Br-2

value: S1 cell aggeregates were treated by 4C-64C medium minus 8Br-cAMP for 1 day.


title: S2-8Bira rep1

description:
Library name: Sample 29
column name in counts.txt: S2-Bira-1

value: WT

value: S1 cell aggeregates were treated by 4C-64C medium minus Birabresib for 1 day.


title: SMARCA5 KOBMDM, 1h IFN 100U/ml, replicate1 (ATAC-seq)

description: Library name: ATAC_KO_1hIFN_R4

data_processing:
All samples were analysed following the Nextflow pipeline that can be freely downloaded from https://github.com/fgualdr/mmatac. Briefly:
FASTQ files were filtered and trimmed using FASTP (v0.23.2)
Reads were aligned to the mouse genome (mm39; GCA_000001635.9) using STAR (v2.7.9a) with parameters: --runMode alignReads, --alignIntronMax 1, --alignMatesGapMax 100000, --alignEndsType EndToEnd, --outSAMtype BAM Unsorted, and --outSAMattributes All.
Duplicate reads were identified and marked using PICARD (v2.27.4).
Multi-mapped reads were assigned using a custom Bayesian EM algorithm (https://github.com/fgualdr/mmatac).
Peaks were called using MACS2 (v2.2.7.1) with parameters: --nomodel --keep-dup all and the narrowPeak setting enabled.
Reference peak set (n=140,383) was created by selecting peaks with q-value ≤ 10⁻³ and ≥ 40% overlap between replicates.
Bigwig files were generated using deeptools (v3.5.1).
Normalization was performed using invariant peaks with GeneralNormalizer (https://github.com/fgualdr/GeneralNormalizer).
Unsupervised clustering was done using PCA (FactoMineR, v2.11), UMAP (uwot, v0.1.16), k-nearest neighbor (FNN, v1.1.4.1), and Louvain clustering (igraph, v1.4.2).
Heatmaps were generated using ComplexHeatmap (v2.14.0).
Assembly: mm39
Supplementary files format and content: bigWig

extract_protocol:
Cells (5 × 10⁴) were lysed in 50 µL lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM MgCl₂; 0.1% Igepal CA-630) by pipetting. Nuclei were pelleted (500 × g, 10 min, 4°C), resuspended in reaction buffer (containing Tn5 transposase), and tagmented at 37°C for 60 minutes with gentle shaking. Reactions were stopped by adding cleanup buffer (900 mM NaCl, 30 mM EDTA, 2 µL 5% SDS, and 20 µg/µL Proteinase K) and incubating at 40°C for 30 minutes. Tagmented DNA was purified using 2× Agencourt AMPure XP beads.
Purified DNA was PCR-amplified using HotStart KAPA HiFi enzyme. Fragments smaller than 600 bp were selected using 0.65× Agencourt AMPure XP beads, followed by 1.8× AMPure XP purification. Libraries were sequenced as paired-end 51 bp reads on an Illumina NovaSeq 6000 platform.

treatment_protocol: Individual ATAC were performed on mouse primary BMDMs derived from wild-type or SMARCA5-deleted cells under untreated, LPS-stimulated, or IFNβ-stimulated conditions for 1 and 2 hours.

value: BMDM

value: 1h IFNb 100 U/ml


title: IP_LHP1_FLAG_rep1

description: Library name: Sample 32


title: Input_LHP1_FLAG

description: Library name: Sample 31


title: FAP22 Before diet (T0) RNA-Seq

description:
Library name: FAP22_PRE-T0
FAP22 Before diet (T0) RNA-Seq


title: S2-8Br rep1

description:
Library name: Sample 27
column name in counts.txt: S2-8Br-1


title: SMARCA5 KOBMDM, 1h IFN 100U/ml, replicate2 (ATAC-seq)

description: Library name: ATAC_KO_1hIFN_R5


title: H3K27ac Chip-seq in SMARCA5 KOBMDM, 1h IFN 100U/ml, replicate2

description: Library name: H3K27Ac_1hIFN_KO_R2

value: H3K27ac:Abcam, Cat# ab47290


title: wt, 12 day-old, nr 12

city: Poznan

first: Andrzej

last: Pacak

address: Uniwersytetu Poznanskiego 6

country: Poland

institute: Adam Mickiewicz University, Poznan

description:
2 x 150 bp
study vs. control5_9_11vs6_10_12.xls

data_processing:
Adapters were trimmed using Skewer (version 0.2.2) software (Jiang H, Lei R, Ding SW, Zhu S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182.).
Sequences received from  CeGaT GmbH were analysed using CLC Genomics Workbench 21.0.5 (QIAGEN Aarhus A/S).
The first nine nucleotides were removed from 5’ end of the reads.
Then adapter and quality trimming was performed with the following parameters: automatic removal of read-through adapter sequences, removal of low quality sequence (limit = 0.05), removal of 5’ and 3’ adapters, removal of sequences on length: minimum length 50 nt.
Expression level was calculated using TPM expression value (for particular RNA-Seq library) and differential expression in two groups methods (Statistical analysis for RNA-Seq data in two groups using global TMM - Trimmed Mean of M values, normalization). Bonferroni and FDR p-value correction were applied in the analyses.
Assembly: Arabidopsis thaliana TAIR10.51
Supplementary files format and content: File extensions .xlsx. CLC Genomics Workbench analyses was performed for paired-end RNA libraries. Annotation to Arabidopsis thaliana TAIR10.51 database.
Supplementary files format and content: File study vs. control1_3_7vs2_4_8.xls. CLC Genomics Workbench statistical analysis for RNA-Seq data in two groups: mutants (S3846Nr1 (1), S3846Nr3 (3), S3846Nr7 (7)) and wt (S3846Nr2 (2), S3846Nr4 (4), S3846Nr8 (8)), 5-day-old.
Supplementary files format and content: File study vs. control5_9_11vs6_10_12.xls. CLC Genomics Workbench statistical analysis for RNA-Seq data in two groups: mutants (S3846Nr5 (5), S3846Nr9 (9), S3846Nr11 (11)) and wt (S3846Nr6 (6), S3846Nr10 (10), S3846Nr12 (12)), 12-day-old.

source_name: Whole plants

growth_protocol: The seedlings were cultured in vitro on B5 medium/1% sucrose solidified with 0.7% agar. The seeds were surface sterilized using sterile water with a drop of Tween 20 for 5 min, then 70% ethanol for 5 min, then 50% commercial bleach for 5 min, rinsed three times in distilled, sterile water. Seeds were sown on the medium, stratified in a cold room for 2 days and cultured in a plant growth chamber with the following parameters (23°C, 10hL/14hD photoperiod, at 60–70 µmol·m−2·s−1 supplied by Sanyo FL40SS.W/37 lamps).

extract_protocol:
100 mg of the ground material was used to isolate total RNA. Spectrum Plant Total RNA Kit (Sigma-Aldrich) was used to isolate the RNA with on a column DNA digestion step according to the manufacturer’s protocol (Sigma-Aldrich).
lRNA libraries were constructed using mRNA-Seq Library Prep kit v2 (Lexogen) according to the manufacturer’s protocol. The libraries insert length was adjusted for 150 read paired-end sequencing (2 x 150 bp). Libraries quality control was performed using 2100 Bioanalyzer (Agilent Technologies Inc.). Six libraries with specific six nucleotides i7 indexes were pooled together and sequenced on one lane. Twelve libraries, on two lanes, were sequenced by CeGaT GmbH, Tübingen, Germany. Paired-end sequencing was performed using NovaSeq 6000.

treatment_protocol: The whole 5 day-old or 12 day-old Arabidopsis wt and geralt mutant plants were grown in vitro. The seedlings were harvested approximately 4h after turn on the light in the plant growth chamber.

value: Whole plants

value: WT Col (N6000)

tag: age

value: 12 day-old


title: FAP21 6 months of diet (T2) RNA-Seq

description:
Library name: FAP21_6mo-T2
FAP21 6 months of diet (T2) RNA-Seq

value: PBMC


title: phr2, 12 day-old, nr 11

value: SALK_116579 (geralt)


title: SMARCA5 KOBMDM, 1h LPS 10ng/ml, replicate1 (ATAC-seq)

description: Library name: ATAC_KO_1hLPS_R4

value: 1h LPS 10 ng/ml


title: FAP21 3 months of diet (T1) RNA-Seq

description:
Library name: FAP21_3mo-T1
FAP21 3 months of diet (T1) RNA-Seq

value: FAP

value: 3 months of diet


title: S2 rep1

description:
Library name: Sample 25
column name in counts.txt: S2-1

value: S1 cell aggeregates were treated by 4C-64C medium for 1 day.


title: S2-8Bira rep2

description:
Library name: Sample 30
column name in counts.txt: S2-Bira-2


title: FAP22 3 months of diet (T1) RNA-Seq

description:
Library name: FAP22_3mo-T1
FAP22 3 months of diet (T1) RNA-Seq


title: CTCF Chip-seq in SMARCA5 KOBMDM, untreated, replicate2

description: Library name: CTCF_KO_R2

value: CTCF:Upstate, Cat# 07-729


title: SMARCA5 KOBMDM, 1h LPS 10ng/ml, replicate2 (ATAC-seq)

description: Library name: ATAC_KO_1hLPS_R5


title: wt, 12 day-old, nr 10


title: phr2, 12 day-old, nr 9


title: FAP21 Before diet (T0) RNA-Seq

description:
Library name: FAP21_PRE-T0
FAP21 Before diet (T0) RNA-Seq

value: Before diet


title: wt, 5 day-old, nr 8

description:
2 x 150 bp
study vs. control1_3_7vs2_4_8.xls

value: 5 day-old


title: S1-P25 rep2

description:
Library name: Sample 22
column name in counts.txt: S1P25-2

value: WT

value: Mouse EPSCs were treated by totipotency medium for 25 passages.


title: FAP20 6 months of diet (T2) RNA-Seq

description:
Library name: FAP20_6mo-T2
FAP20 6 months of diet (T2) RNA-Seq

value: 6 months of diet


title: SMARCA5 KOBMDM, 2h IFN 100U/ml, replicate2 (ATAC-seq)

description: Library name: ATAC_KO_2hIFN_R5

value: BMDM

value: 2h IFNb 100 U/ml


title: FAP20 3 months of diet (T1) RNA-Seq

description:
Library name: FAP20_3mo-T1
FAP20 3 months of diet (T1) RNA-Seq


title: FAP20 Before diet (T0) RNA-Seq

description:
Library name: FAP20_PRE-T0
FAP20 Before diet (T0) RNA-Seq


title: SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate2 (ATAC-seq)

description: Library name: ATAC_KO_2hLPS_R5

value: 2h LPS 10 ng/ml


title: SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate1 (ATAC-seq)

description: Library name: ATAC_KO_2hLPS_R4


title: phr2, 5 day-old, nr 7

value: Whole plants


title: S2 rep2

description:
Library name: Sample 26
column name in counts.txt: S2-2


title: S1-P25 rep1

description:
Library name: Sample 21
column name in counts.txt: S1P25-1


title: FAP19 6 months of diet (T2) RNA-Seq

description:
Library name: FAP19_6mo-T2
FAP19 6 months of diet (T2) RNA-Seq


title: EPS rep4

description:
Library name: Sample 18
column name in counts.txt: EPS-2

value: Mouse EPSCs were cultured in LCDM medium.


title: wt, 12 day-old, nr 6

value: WT Col (N6000)

value: 12 day-old


title: SMARCA5 KOBMDM, untreated, replicate1 (ATAC-seq)

description: Library name: ATAC_KO_UT_R4


title: phr2, 12 day-old, nr 5

value: SALK_116579 (geralt)


title: EPS rep3

description:
Library name: Sample 17
column name in counts.txt: EPS-1


title: FAP19 3 months of diet (T1) RNA-Seq

description:
Library name: FAP19_3mo-T1
FAP19 3 months of diet (T1) RNA-Seq

value: PBMC

value: FAP


title: SMARCA5 KOBMDM, untreated, replicate2 (ATAC-seq)

description: Library name: ATAC_KO_UT_R5


title: S1-P38 rep2

description:
Library name: Sample 24
column name in counts.txt: S1P38-2

value: Mouse EPSCs were treated by totipotency medium for 38 passages.


title: wt, 5 day-old, nr 4


title: S1-P38 rep1

description:
Library name: Sample 23
column name in counts.txt: S1P38-1


title: mESC-S1 rep2

description:
Library name: Sample 16
column name in counts.txt: ESS1-2

value: Mouse ESCs were treated by totipotency medium for 2 days.


title: FAP19 Before diet (T0) RNA-Seq

description:
Library name: FAP19_PRE-T0
FAP19 Before diet (T0) RNA-Seq

value: Before diet


title: CTCF Chip-seq in WT BMDM, untreated, replicate2

description: Library name: CTCF_WT_R2

value: wild type

value: CTCF:Upstate, Cat# 07-729


title: WT BMDM, 1h IFN 100U/ml, replicate1 (ATAC-seq)

description: Library name: ATAC_WT_1hIFN_R4

value: 1h IFNb 100 U/ml


title: SMARCA5 KOBMDM, 2h IFN 100U/ml, replicate1 (ATAC-seq)

description: Library name: ATAC_KO_2hIFN_R4


title: phr2, 5 day-old, nr 3

value: 5 day-old


title: FAP18 6 months of diet (T2) RNA-Seq

description:
Library name: FAP18_6mo-T2
FAP18 6 months of diet (T2) RNA-Seq

value: 6 months of diet


title: mESC-S1 rep1

description:
Library name: Sample 15
column name in counts.txt: ESS1-1

value: WT


title: FAP18 3 months of diet (T1) RNA-Seq

description:
Library name: FAP18_3mo-T1
FAP18 3 months of diet (T1) RNA-Seq

value: 3 months of diet


title: WT BMDM, 1h LPS 10ng/ml, replicate1 (ATAC-seq)

description: Library name: ATAC_WT_1hLPS_R4

value: BMDM

value: 1h LPS 10 ng/ml


title: wt, 5 day-old, nr 2

description:
2 x 150 bp
study vs. control1_3_7vs2_4_8.xls

value: Whole plants

value: WT Col (N6000)


title: mESC rep2

description:
Library name: Sample 14
column name in counts.txt: ES-2

value: Mouse ESCs were cultured in 2i/L medium.


title: WT BMDM, 1h LPS 10ng/ml, replicate2 (ATAC-seq)

description: Library name: ATAC_WT_1hLPS_R5


title: mESC rep1

description:
Library name: Sample 13
column name in counts.txt: ES-1


title: FAP17 6 months of diet (T2) RNA-Seq

description:
Library name: FAP17_6mo-T2
FAP17 6 months of diet (T2) RNA-Seq

value: PBMC


title: P7Ascl1_cKO single cell Tomato-

city: New York

first: Stefanie

middle: G

last: Wohl

state: NY

address: 33w 42nd Street

department: Biological and Vision Sciences

institute: SUNY Optometry

description:
Library name: sample 18
P7-Ascl-cKO-Tom neg

library_source: transcriptomic single cell

data_processing:
Cutadapt (v5.0) (Martin, 2011) was used to cut the adaptors from the small RNA-seq data. Sequencing reads from both small and large RNA-Seq projects were mapped to the reference genome (mm10) using the STAR aligner (v2.5.0c) (Dobin et al., 2013). Alignments were guided by a Gene Transfer Format (GTF) file. The mean read insert sizes and their standard deviations were calculated using Picard tools (v.1.126) (http://broadinstitute.github.io/picard). The read count tables were generated using HTSeq (v0.6.0) (Anders et al., 2015), normalized based on their library size factors using DEseq2 (Love et al., 2014), and differential expression analysis was performed. The Read Per Million (RPM) normalized BigWig files were generated using BEDTools (v2.17.0) (Quinlan and Hall, 2010) and bedGraphToBigWig tool (v4). Gene set enrichment analysis was performed using GSEA tool (PMID: 16199517). To compare the level of similarity among the samples and their replicates, we used two methods: principal-component analysis and Euclidean distance-based sample clustering. All the downstream statistical analyses and generating heatmaps and plots were performed in R environment (v3.1.1) (https://www.r-project.org/). Because of the possibility of a global effect in mature miRNA levels in our Dicer1 knockout (cKO) model, we made count tables for all genes and used the none miRNA genes as our spike-in factor. Spike-in normalization is generally used when gene expression is affected globally. We then used Geometric Library Size Factor (GLSF) normalization as described in DESeq R package for our spike-in factors and applied it to normalize the miRNA genes. Raw files (fastq) and RPM-normalized BigWig files were used to visualize genomic data in interactive genomic browsers (IGV).
scRNA-seq FASTQ files were preprocessed using PIP Seeker, a comprehensive analysis solution that performs barcode matching, quality control, mapping with the STAR aligner40, deduplication, transcript counting, cell calling, clustering, differential expression, and cell type annotation. The resulting matrices from PIPseeker were imported into Monocle3 (Cao et al., 2019, Qiu et al., 2017, Trapnell et al., 2014) for downstream analysis. Matrices were aggregated and first-pass filtering for cell quality was performed, keeping cells with < 25% reads coming from mitochondrial transcripts and displaying total transcript numbers between 500 and 10,000 transcripts per cell. Dimension reduction was performed using the top 3234 transcripts displaying high variance across the data using UMAP dimension reduction (McInnes et al., 2020) on the top 17 PCAs (umap.min_dist = 0.1, umap.n.neighbors = 15,umap.metric = “euclidean”). Cells were clustered within the reduced dimension space using the cluster_cells function (reduction_method = “UMAP”, cluster_method = “louvain”, num_iter = 5, partition_qval = 0.01). Cell type calls were performed based on enrichment of transcripts within individual clusters using established markers (Clark et al., 2019). Similar analyses were utilized to determine major amacrine cell subtypes after sub-setting of amacrine cells from the total datasets.
Assembly: mm10
Supplementary files format and content: Excel file include normalized counts for long RNA or short RNA samples
Supplementary files format and content: sc files include barcodes, features, matrix obtained from PIP Seeker

extract_protocol:
long and small RNA: Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). The SMART-Seq HT Kit (Takara) was utilized to generate complementary DNA (cDNA) from 1 ng of total RNA input. The synthesis process included 13 PCR cycles. Single-cell RNA sequencing was performed using pre-templated instant partitions (PIP) sequencing (PIPseq, (Lee et al., 2024)).
single cell RNA-seq: The T20 kit (≤ 20,000 cells output, FBS-SCR-T20-4-V4.05, Fluent Biosciences) was used according to the manufacturer's instructions. In brief, tubes containing template beads were thawed on ice, and the required number of input cells was added per tube (i.e., approximately 25,000–30,000 live cells fora split T20 kit, 2x "T10"). The suspension was mixed gently by pipetting and processed further according to the manufacturer’s instructions. After the cDNA synthesis, purification, and library preparation, the concentration, integrity, and quality were assessed using the Agilent 2100 Bioanalyzer System and the high-sensitivity DNA kit (Agilent Technologies, Santa Clara, CA, USA).
For bulk long RNA library preparation, cDNA was quantified using the Invitrogen Quant-iT system and subsequently diluted to a concentration of 0.3 ng/μL for library preparation. Libraries were prepared using the Nextera XT DNA Library Preparation Kit, employing a total of 12 PCR cycles to amplify and uniquely barcode the samples. Small RNA libraries were prepared from 10 ng of purified miRNA using the SMARTer® smRNA-Seq Kit for Illumina (Takara Bio), following the manufacturer’s protocol. The kit utilizes a ligation-free method based on SMART (Switching Mechanism at the 5′ end of RNA Template) technology to generate high-quality libraries from low-input small RNA. After adapter ligation and cDNA synthesis, libraries were amplified using PCR and purified using AMPure XP beads according to the protocol specifications. The quality and size distribution of the final libraries were assessed using the Agilent High Sensitivity D1000 ScreenTape on the TapeStation 4200 system (Agilent Technologies) to confirm the presence of expected small RNA insert sizes (~140–150 bp for miRNA). Library concentrations were measured using the Quant-iT™ dsDNA High Sensitivity Assay Kit (Invitrogen) to ensure accurate quantification. Libraries were normalized to equimolar concentrations based on fluorometric measurements and pooled accordingly. Sequencing was performed on the Illumina NovaSeq X+ platform using paired-end 100-cycle reads, providing high-depth coverage suitable for small RNA transcriptome analysis.
Small RNA libraries were prepared from 10 ng of purified miRNA using the SMARTer® smRNA-Seq Kit for Illumina (Takara Bio), following the manufacturer’s protocol. The kit utilizes a ligation-free method based on SMART (Switching Mechanism at the 5′ end of RNA Template) technology to generate high-quality libraries from low-input small RNA. After adapter ligation and cDNA synthesis, libraries were amplified using PCR and purified using AMPure XP beads according to the protocol specifications. The quality and size distribution of the final libraries were assessed using the Agilent High Sensitivity D1000 ScreenTape on the TapeStation 4200 system (Agilent Technologies) to confirm the presence of expected small RNA insert sizes (~140–150 bp for miRNA). Library concentrations were measured using the Quant-iT™ dsDNA High Sensitivity Assay Kit (Invitrogen) to ensure accurate quantification. Libraries were normalized to equimolar concentrations based on fluorometric measurements and pooled accordingly. Sequencing was performed on the Illumina NovaSeq X+ platform using paired-end 100-cycle reads, providing high-depth coverage suitable for small RNA transcriptome analysis.  For scRNA-seq, after the cDNA synthesis, purification, and library preparation, the concentration, integrity, and quality were assessed using the Agilent 2100 Bioanalyzer System and the high-sensitivity DNA kit (Agilent Technologies, Santa Clara, CA, USA).
For scRNA-seq, after the cDNA synthesis, purification, and library preparation were conducted following the manufacturer's instructions. The concentration, integrity, and quality were assessed using the Agilent 2100 Bioanalyzer System and the high-sensitivity DNA kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: animals were treated with Tamoxifen to induce Cre recombinase.

value: retina

value: tissue

value: various

value: Dicer-cKO

value: tamoxifen to induce Cre


title: phr2, 5 day-old, nr 1

value: SALK_116579 (geralt)


title: P28_Postnatal_ME

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

description: Library name: P28_PostnatalME

library_source: genomic single cell

data_processing:
Raw fastq files were processed using Cellranger ATAC v2.1.0 to generate the alinment bam files and the fragments files.
Assembly: mm10
Supplementary files format and content: fragments.tsv.gz for ATAC-seq fragments

source_name: Bone marrow

extract_protocol: 10x Genomics Chromium  Next GEM Single Cell ATAC Reagent Kit v2 User Guide

value: Bone marrow

value: Lin-Kit+ cells


title: WT BMDM, 2h IFN 100U/ml, replicate1 (ATAC-seq)

description: Library name: ATAC_WT_2hIFN_R4

value: wild type

value: 2h IFNb 100 U/ml


title: WT BMDM, 2h IFN 100U/ml, replicate2 (ATAC-seq)

description: Library name: ATAC_WT_2hIFN_R5


title: FAP17 3 months of diet (T1) RNA-Seq

description:
Library name: FAP17_3mo-T1
FAP17 3 months of diet (T1) RNA-Seq

value: FAP

value: 3 months of diet


title: P28_Fetal_ME

description: Library name: P28_FetalME


title: WT BMDM, 2h LPS 10ng/ml, replicate1 (ATAC-seq)

description: Library name: ATAC_WT_2hLPS_R4

value: BMDM

value: 2h LPS 10 ng/ml


title: P7Ascl1_cKO single cell Tomato+

description:
Library name: sample 16
P7-Ascl-cKO-Tomplus


title: P7Ascl1_wt single cell Tomato-

description:
Library name: sample 17
P7-Ascl-wt-Tom neg

value: wt


title: FAP17 Before diet (T0) RNA-Seq

description:
Library name: FAP17_PRE-T0
FAP17 Before diet (T0) RNA-Seq

value: Before diet


title: P28_WT

description: Library name: P28_WT


title: WT BMDM, 2h LPS 10ng/ml, replicate2 (ATAC-seq)

description: Library name: ATAC_WT_2hLPS_R5


title: P7Ascl1_wt single cell Tomato+

description:
Library name: sample 15
P7-Ascl-wt-Tomplus


title: WT BMDM, untreated, replicate1 (ATAC-seq)

description: Library name: ATAC_WT_UT_R4


title: FAP15 3 months of diet (T1) RNA-Seq

description:
Library name: FAP15_3mo-T1
FAP15 3 months of diet (T1) RNA-Seq

value: PBMC


title: E18_Fetal_ME

description: Library name: E18_FetalME

source_name: Liver

value: Liver


title: P7Ascl1_cKO microRNA-3

description:
Library name: sample 14
SR_P7_AcKO_pos_83_S42

value: retina

value: tissue


title: P7Ascl1_cKO microRNA-2

description:
Library name: sample 13
SR_P7_AcKO_pos_81_S41

value: various

value: Dicer-cKO


title: E18_WT

description: Library name: E18_WT


title: FAP15 6 months of diet (T2) RNA-Seq

description:
Library name: FAP15_6mo-T2
FAP15 6 months of diet (T2) RNA-Seq

value: 6 months of diet


title: FAP15 Before diet (T0) RNA-Seq

description:
Library name: FAP15_PRE-T0
FAP15 Before diet (T0) RNA-Seq


title: mouse extended pluripotent stem cell EPS rep2

description:
Library name: Sample 12
column name in counts.txt: E2

value: WT

value: Mouse  EPSCs were cultured in LCDM medium.


title: FAP18 Before diet (T0) RNA-Seq

description:
Library name: FAP18_PRE-T0
FAP18 Before diet (T0) RNA-Seq


title: FAP14 6 months of diet (T2) RNA-Seq

description:
Library name: FAP14_6mo-T2
FAP14 6 months of diet (T2) RNA-Seq


title: mouse extended pluripotent stem cell EPS rep1

description:
Library name: Sample 11
column name in counts.txt: E1


title: P7Ascl1_cKO microRNA-1

description:
Library name: sample 12
SR_P7_AcKO_pos_79_S40

value: tamoxifen to induce Cre


title: FAP14 3 months of diet (T1) RNA-Seq

description:
Library name: FAP14_3mo-T1
FAP14 3 months of diet (T1) RNA-Seq


title: s5

description:
Library name: Sample 5
10x Genomics

data_processing:
The clean single-cell RNA-seq reads were mapped to mouse reference genome mm10 using Cell Ranger v5.0.1.
Assembly: mm10
Supplementary files format and content: gz archives contain Cell Ranger output (barcodes.tsv, features.tsv, matrix.mtx).

source_name: synthetic-embryo

extract_protocol:
S1-S8 embryoids were digested by 0.05% trypsin/TripLE into single cells, then washed and resuspended in 1X PBS (calcium and magnesium free) containing 2% FBS.  Cell suspensions were filtered through a 40 μm cell strainer.Cell viability was determined by Count Star, and the density of living cells were adjusted to 300-600 living cells per microliter. Cell suspension was loaded onto the Chromium single cell controller (10x Genomics). Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics) and Chromium Single Cell B Chip Kit (10x Genomics) were used to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cells were recovered (about 3,000 cells). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°Cfor 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200.
Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 according to the manufacture’s introduction. The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy.

value: synthetic-embryo

value: S4 on day 1 were treated by peri-implantation medium for 3 days on Aggrewell.


title: P7Ascl1_wt microRNA-3

description:
Library name: sample 11
SR_P7_Awt_pos_91_S45


title: mouse extended pluripotent stem cell EPS +CHIR-99021 +PD0325901 rep2

description:
Library name: Sample 10
column name in counts.txt: CP2

value: Mouse  EPSCs were treated by  CHIR-99021 and PD0325901 for 2 days.


title: P7Ascl1_wt microRNA-2

description:
Library name: sample 10
SR_P7_Awt_pos_89_S44


title: FAP14 Before diet (T0) RNA-Seq

description:
Library name: FAP14_PRE-T0
FAP14 Before diet (T0) RNA-Seq

value: FAP


title: s4

description:
Library name: Sample 4
10x Genomics

value: S3 cell aggregates were treated by blastiod medium for 3 days on Aggrewell.


title: mouse extended pluripotent stem cell EPS +CHIR-99021 +PD0325901 rep1

description:
Library name: Sample 9
column name in counts.txt: CP1


title: FAP13 6 months of diet (T2) RNA-Seq

description:
Library name: FAP13_6mo-T2
FAP13 6 months of diet (T2) RNA-Seq


title: mouse extended pluripotent stem cell EPS +CHIR-99021 +Elvitegravir rep2

description:
Library name: Sample 8
column name in counts.txt: CE2

value: Mouse  EPSCs were treated by  CHIR-99021 and Elvitegravir for 2 days.


title: s2

description:
Library name: Sample 2
10x Genomics

value: S1 cell aggregates were treated by 4C-64C medium for 1 day on Aggrewell.


title: WT BMDM, untreated, replicate2 (ATAC-seq)

description: Library name: ATAC_WT_UT_R5

value: BMDM

value: wild type


title: P7Ascl1_cKO mRNA-3

description:
Library name: sample 7
P7AcKOpos_81_S50

value: retina


title: mouse extended pluripotent stem cell EPS +CHIR-99021 +Elvitegravir rep1

description:
Library name: Sample 7
column name in counts.txt: CE1


title: mouse extended pluripotent stem cell EPS +CHIR-99021 +CD1530 rep2

description:
Library name: Sample 6
column name in counts.txt: CCD2_2

value: Mouse  EPSCs were treated by  CHIR-99021 and CD1530 for 2 days.


title: s7

description:
Library name: Sample 6
10x Genomics

value: S5 early egg cylinder-like embryoids were treated by post-implantation medium for 2 days on 6-well cell suspension non adherent culture plate


title: s1

description:
Library name: Sample 1
10x Genomics

value: Mouse EPSCc were treated by totipotency medium 2 days on Aggrewells


title: P7Ascl1_cKO mRNA-4

description:
Library name: sample 8
P7AcKOpos_83_S51

value: tissue

value: various

value: Dicer-cKO


title: FAP13 3 months of diet (T1) RNA-Seq

description:
Library name: FAP13_3mo-T1
FAP13 3 months of diet (T1) RNA-Seq

value: PBMC

value: 3 months of diet


title: FAP12 6 months of diet (T2) RNA-Seq

description:
Library name: FAP12_6mo-T2
FAP12 6 months of diet (T2) RNA-Seq

value: 6 months of diet


title: P7Ascl1_cKO mRNA-2

description:
Library name: sample 6
P7AcKOpos_79_S49

value: tamoxifen to induce Cre


title: FAP13 Before diet (T0) RNA-Seq

description:
Library name: FAP13_PRE-T0
FAP13 Before diet (T0) RNA-Seq

value: FAP

value: Before diet


title: WT BMDM, untreated, replicate2 (MNase-seq)

description: Library name: MNAse_WT_UT_R2

data_processing:
Workflow is available at https://github.com/fgualdr/mmchipseq
FASTQ files were filtered and trimmed using FASTP (v0.23.2)
Reads were aligned to the mouse genome (mm39; GCA_000001635.9) using STAR (v2.7.9a) with parameters: --runMode alignReads, --alignIntronMax 1, --alignMatesGapMax 100000, --alignEndsType EndToEnd, --outSAMtype BAM Unsorted, and --outSAMattributes All.
Duplicate reads were identified and marked using PICARD (v2.27.4).
Multi-mapped reads were assigned using a custom Bayesian EM algorithm (https://github.com/fgualdr/mmatac).
Genome-wide nucleosome occupancy signals were normalized using deeptools bamCoverage (v3.5.1) with parameters: --MNase --normalizeUsing CPM.
Bigwig files were generated using deeptools (v3.5.1) for visualization of nucleosome occupancy.
Assembly: mm39
Supplementary files format and content: bigWig

extract_protocol:
Cells were resuspended in a lysis buffer containing 15 mM NaCl, 15 mM Tris-HCl (pH 7.6), 60 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.3 M sucrose, 0.5 mM PMSF, 1 mM DTT, 0.2 mM spermine, and 1 mM spermidine. Lysis was achieved by adding 0.4% NP-40, and nuclei were collected and washed to remove detergent traces. MNase digestion was performed in a buffer containing 20 mM Tris-HCl (pH 7.6) and 5 mM CaCl₂ using 1.3 U MNase (Roche Cat# 10107921001) per sample. The reaction was incubated at 37°C for 100 minutes with gentle shaking, and digestion was stopped with 50 mM EDTA. Mononucleosomal DNA was isolated using gel electrophoresis on a 1% agarose gel, excised, and purified using the Millipore DNA Gel Extraction Kit (Millipore Cat# LSKGEL050). DNA was further purified with QIAquick PCR Purification Columns (Qiagen Cat# 28106).
Libraries were prepared from purified mononucleosomal DNA following the protocol in (Gualdrini et al., 2022). Sequencing was performed as 51-bp paired-end reads at high depth using an Illumina platform.

treatment_protocol: Individual MNaseseq were performed on mouse primary BMDMs derived from wild-type or SMARCA5-deleted cells under untreated or LPS-stimulated conditions.


title: P7Ascl1_cKO mRNA-1

description:
Library name: sample 5
cKO-S2_S2_L007


title: mouse extended pluripotent stem cell EPS +CHIR-99021 rep2

description:
Library name: Sample 4
column name in counts.txt: C2

value: WT

value: Mouse  EPSCs were treated by  CHIR-99021 for 2 days.


title: P7Ascl1_wt mRNA-4

description:
Library name: sample 4
P7Awtpos_91_S54

value: wt


title: FAP12 Before diet (T0) RNA-Seq

description:
Library name: FAP12_PRE-T0
FAP12 Before diet (T0) RNA-Seq


title: WT BMDM, 2h LPS 10ng/ml, replicate2 (MNase-seq)

description: Library name: MNAse_WT_2h_R2

value: BMDM

value: wild type

value: 2h LPS 10 ng/ml


title: WT BMDM, 2h LPS 10ng/ml, replicate1 (MNase-seq)

description: Library name: MNAse_WT_2h_R1


title: FAP11 6 months of diet (T2) RNA-Seq

description:
Library name: FAP11_6mo-T2
FAP11 6 months of diet (T2) RNA-Seq


title: P7Ascl1_wt mRNA-3

description:
Library name: sample 3
P7Awtpos_89_S53

value: retina


title: P7Ascl1_wt microRNA-1

description:
Library name: sample 9
SR_P7_Awt_pos__87_S43


title: WT BMDM, untreated, replicate1 (MNase-seq)

description: Library name: MNAse_WT_UT_R1


title: s3

description:
Library name: Sample 3
10x Genomics

value: synthetic-embryo

value: S2 cell aggregates were treated by 4C-64C medium for another day on Aggrewell.


title: P7Ascl1_wt mRNA-2

description:
Library name: sample 2
P7Awtpos_87_S52

value: tissue

value: various


title: mouse extended pluripotent stem cell EPS +CHIR-99021 rep1

description:
Library name: Sample 3
column name in counts.txt: C1


title: SMARCA5 KOBMDM, untreated, replicate2 (MNase-seq)

description: Library name: MNAse_KO_UT_R2


title: mouse extended totipotent stem cell rep2

description:
Library name: Sample 2
column name in counts.txt: all2

value: Mouse  EPSCs were treated by totipency medium for 2 days.


title: FAP11 3 months of diet (T1) RNA-Seq

description:
Library name: FAP11_3mo-T1
FAP11 3 months of diet (T1) RNA-Seq

value: PBMC

value: 3 months of diet


title: mouse extended totipotent stem cell rep1

description:
Library name: Sample 1
column name in counts.txt: all1

value: Mouse  EPSCs were treated by totipotency medium for 2 days.


title: FAP11 Before diet (T0) RNA-Seq

description:
Library name: FAP11_PRE-T0
FAP11 Before diet (T0) RNA-Seq

value: FAP


title: mouse extended pluripotent stem cell EPS +CHIR-99021 +CD1530 rep1

description:
Library name: Sample 5
column name in counts.txt: CCD2_1

value: Mouse  EPSCs were treated by  CHIR-99021 and CD1530 for 2 days.


title: SMARCA5 KOBMDM, untreated, replicate1 (MNase-seq)

description: Library name: MNAse_KO_UT_R1


title: P7Ascl1_wt mRNA-1

description:
Library name: sample 1
wt-S1_S1_L007

value: tamoxifen to induce Cre


title: submandibular gland,Sialadenitis, Day7, 5

city: chengdu

first: li

last: honglin

address: No.14, Section 3, Renmin South Road

institute: sichuan university

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: submandibular gland

growth_protocol: Female C57BL/6 mice (8-weeks, 16 – 18g) were housed in individually-ventilated cages (3 mice/cage) in a 12 h dark/light cycle at 18 – 24 °C.

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

treatment_protocol:
Female mice were given 1% sodium pentobarbital anesthesia, and fixed on a heating pad.
The submandibular skin incision was approximately 5 mm wide. The proximal and distal ends of the duct were ligated with 6-0 sutures after microscopic dissection of the right submandibular gland. The submandibular gland was relocated and the wound was sutured after the vascular bundle of the submandibular gland was confirmed to be intact and free of injury. In the sham-operated group, only skin incision and submandibular gland dissection were performed.

tag: strain

value: C57BL /6J

value: submandibular gland

tag: Sex

value: female

value: Ligation

value: Day 7


title: SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate2 (MNase-seq)

description: Library name: MNAse_KO_2h_R2

value: BMDM

value: 2h LPS 10 ng/ml


title: CCN1,rep2

city: La Jolla

first: Laura

last: Sancho

state: CA

address: 10010 N Torrey Pines

institute: Salk Institute for Biological Studies

description:
Library name: Sample4
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and alignment to the genome was performed with CellRanger Count v8.0.1. Intronic reads were included
The aggregation of samples per replicate were aggregated with CellRangerAggregate v8.0.1
vc_3.rds file is a compressed RDS object created from a Seurat object in R with all meta data used for analysis. Can be opened with readRDS in R
Assembly: mm10 2020-A
Supplementary files format and content: tar.gz compressed files containing matrix.mtx, barcodes.tsv, and features.tsv

molecule: nuclear RNA

source_name: visual cortex

extract_protocol:
Nuclei were isolated from frozen VC tissue. Tissue was manually homogenized using a two-step Dounce homogenizer (A and B) in NIMT buffer, containing (in mM: 250 sucrose, 25 KCl, 5 MgCl2, 10 Tris-Cl pH 8, 1 DTT; 1:100 dilution of Triton X100, Protease Inhibitor Cocktail; and 1:1000 dilution of RNaseOUT Recombinant Ribonuclease Inhibitor; SUPERase• In RNase Inhibitor [Thermo #AM2694]) on ice. Homogenized samples were mixed with 50% iodixanol (OptiPrep Density Gradient Medium;) and loaded onto 25% iodixanol cushion, and centrifuged at 10,000 g for 20 min at 4°C in a swinging bucket rotor. Pellets resuspended in ice-cold DPBS (HyClone) with 1:1000 dilution of RNaseOUT Recombinant Ribonuclease Inhibitor; SUPERase• In RNase Inhibitor. Nuclei were then incubated for 7 min on ice with Hoechst 33342 solution (20 mM)  (final concentration 0.5 µM), followed by centrifugation at 1000 g for 10 min at 4°C to pellet nuclei. Pellets were resuspended in blocking buffer containing DPBS with RNAse inhibitors, and 1:10 dilution of pure BSA, and blocked for 30 min on ice. Nuclei were purified using FACS
Library was performed accoding to the manufacturer's instructions (10x genomics- single cell 3' v3.1 HT). Briefly, 50k sorted nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the GEMs(gel bead-in-emulsion). The RNA from each bead was retrotranscripted to cDNA, which contains the Illumina R1 primer sequence, unique molecular identifier (UMI) and the 10x barcode. the pooled barcoded cDNAwas cleaned up, amplified, and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During library construction the Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: AAV-tdTomato or AAV-CCN1 was injected into the visual cortices (bilateral) of postnatal 14 wild-type B6 mice. Cortices were collected at P28

value: visual cortex

value: all cells

value: WT

value: AAV-CCN1 injection

tag: batch


title: submandibular gland,Sialadenitis, Day7, 4


title: SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate1 (MNase-seq)

description: Library name: MNAse_KO_2h_R1


title: FAP12 3 months of diet (T1) RNA-Seq

description:
Library name: FAP12_3mo-T1
FAP12 3 months of diet (T1) RNA-Seq

value: PBMC


title: FAP10 6 months of diet (T2) RNA-Seq

description:
Library name: FAP10_6mo-T2
FAP10 6 months of diet (T2) RNA-Seq

value: 6 months of diet


title: CCN1,rep1

description:
Library name: Sample2
10x Genomics


title: submandibular gland,Sialadenitis, Day7, 2


title: FAP10 Before diet (T0) RNA-Seq

description:
Library name: FAP10_PRE-T0
FAP10 Before diet (T0) RNA-Seq

value: Before diet


title: submandibular gland,Sialadenitis, Day7, 3


title: Pdgfrb_INTACT_WT2

city: Los Angeles

first: Jonathan

middle: William

last: Nelson

address: 1333 San Pablo St.

department: Medicine

institute: University of Southern California

description: 10x Genomics

data_processing:
Fastq files were prepared using bcl2fastq (Illumina) and then aligned to a reference genome using Cellranger v. 6.1.2 (10x Genomics). Reads were mapped to both exonic and intronic regions to include the pre-mRNA transcriptome.
Ambient RNA contamination was estimated and removed using SoupX v. 1.6.2
Cells with cleaned-up reads were then subjected to doublet removal using DoubletFinder v. 2.0.4
Mitochondrial features were manually removed by excluding all features starting with mt-
The normalized count matrix integration, batch effect correctiong, and cell clustering were performed using Seurat v. 4.4.0
Assembly: mm10-2020-A
Supplementary files format and content: Raw and filtered feature-barcode matrices from each replicate
Supplementary files format and content: Integrated seurat objects containing replicates

source_name: Kidney

extract_protocol:
Kidney was dissected out after PBS washout via aortic perfusion and snap-frozen in liquid nitrogen immediately after dissection. Frozen tissue was stored at -80 °C until subsequent tissue processing. Prepare the nuclei isolation buffer (NIB, includes 146 mM NaCl, 10 mM Tris-HCl, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween-20, 0.01% BSA, pH 7.5), and add 1 tablet of cOmplete ULTRA per 10 ml NIB. The samples were ground for 30 times in 2ml NIB1 (4mL NIB + 20µl RNasin Plus + 20µl SUPERaseIN) with a 2ml Dounce grinder and a loose pestle, then homogenate was passed through a 200 µm strainer. The homogenate was ground for 15 times with a tight pestle, then 2 ml NIB1 was added and the homogenate was incubated for 5 min on ice. The homogenate was passed through a 40 µm strainer, then centrifuged at 500g for 5 min at 4°C. The pellet was resuspended in 4 ml NIB2 (4mL NIB + 4µl RNasin Plus + 4µl SUPERaseIN) and the suspension was incubated on ice for 5 min, then centrifuged at 500g for 5 min at 4°C. The pellet was resuspended in 1.5 ml of nuclei resuspension buffer (NSB, 10mL DPBS + 10µl RNasin Plus), then centrifuged at 500g for 5 min at 4°C. Repeat this step, then the suspension was passed through a 5 µm strainer. The suspension was centrifuged at 500g for 5 min at 4°C, and the pellet was resuspended in 10 ml NSB. The nuclei suspension was mixed with 5µl Vybrant Ruby stain and incubated on ice for 15 min. The nuclei were sorted in 500 µl final resuspension buffer (FSB, 1ml DPBS with 1% BSA + 5 µl Protector RNase inhibitor) with a low flow rate and pressure to ensure high viability. Two main gates were used. A 561+683 emission for the ruby stain and a 488 530/40 emission for GFP. Low trigger pulse width was used as singlet discriminator. One hundred thousand nuclei were collected and centrifuged at 500g for 5 min at 4°C. The top supernatant was carefully removed, and 50 µl volume was left to resuspend the nuclei pellet.
Single nucleus RNA-seq was performed using a Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 (10x Genomics). Single nuclei were partitioned in droplets with single Gel Beads, which contained primers with cell-tagging indexes. Single nucleus suspensions with concentration of at least 300/µl were loaded targeting 10,000 nuclei per sample. The resulting cDNA was profiled on a Bioanalyzer NanoChip (Agilent), then used as a template for library preparation according to the reagent kit protocol. ( https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry )

value: Male

value: Kidney

value: Pdgfrb+Cells


title: submandibular gland,Sialadenitis, Day7, 1

value: C57BL /6J


title: tdTomato,rep1

description:
Library name: Sample1
10x Genomics

value: AAV-tdTomato injection


title: FAP9 6 months of diet (T2) RNA-Seq

description:
Library name: FAP9_6mo-T2
FAP9 6 months of diet (T2) RNA-Seq

value: FAP


title: Pdgfrb_INTACT_WT1

description: 10x Genomics


title: E14_ME

description: Library name: E14_ME

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via cellranger v6.0.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Assembly: mm10
Supplementary files format and content: barcodes.tsv, genes.tsv, matrix.mtx

extract_protocol: 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) with Feature Barcode User Guide

value: Liver

value: Lin-Kit+ cells


title: submandibular gland, Control, Day7, 5

value: submandibular gland

value: female

value: Sham

value: Day 7


title: LL_2

city: Shanghai

first: Ping

last: Yang

address: 800 Rd dong chuan

institute: Shanghai Jiao Tong University

description: 10X Genomics

data_processing:
The sequencing data were demultiplexed and mapped to the mm10 transcriptome using the Cell Ranger package (10X Genomics), and the sequencing depth of different conditions and batches was normalised using the ''cellranger aggr'' function.
Assembly: mm10
Supplementary files format and content: processed data is in mtx and tsv format, which contains single cell transcriptom data.
Supplementary files format and content: Tab-seperated values files and matrix files.

source_name: Hippocampi

extract_protocol:
Mice were deeply anaesthetised with 0.14 g/kg sodium pentobarbital 24 h after the second hit. Acute brain slices were prepared and hippocampi were dissected and dissociated using the papain dissociation system (Worthington, Lakewood, NJ, USA; Cat# LK003153). Cells were loaded onto a 10 X Genomics Chromium chip (10X Genomics, Pleasanton, CA, USA) according to the manufacturer's recommendations.
Reverse transcriptions and library preparation were performed using the 10X Genomics Single Cell v2 Kit (Chromium Single Cell 30 Library & Gel Bead Kit v2, 10x Genomics) according to the 10x Genomics protocol. Sequencing was performed on the Illumina NovaSeq 6000 (from Novogene, Beijing, China).

value: brain cells

value: Hippocampi

value: P3 LPS and P14 LPS


title: E14_WT

description: Library name: E14_WT


title: FAP9 Before diet (T0) RNA-Seq

description:
Library name: FAP9_PRE-T0
FAP9 Before diet (T0) RNA-Seq

value: PBMC


title: submandibular gland, Control, Day7, 4


title: tdTomato,rep2

description:
Library name: Sample3
10x Genomics

value: visual cortex

value: all cells

value: WT


title: FAP10 3 months of diet (T1) RNA-Seq

description:
Library name: FAP10_3mo-T1
FAP10 3 months of diet (T1) RNA-Seq

value: 3 months of diet


title: LS_2

description: 10X Genomics

value: P3 LPS and P14 saline


title: E18_ME

description: Library name: E18_ME


title: submandibular gland, Control, Day7, 3

value: C57BL /6J


title: LS_1

description: 10X Genomics


title: FAP8 3 months of diet (T1) RNA-Seq

description:
Library name: FAP8_3mo-T1
FAP8 3 months of diet (T1) RNA-Seq

value: FAP


title: FAP8 6 months of diet (T2) RNA-Seq

description:
Library name: FAP8_6mo-T2
FAP8 6 months of diet (T2) RNA-Seq

value: 6 months of diet


title: SL_3

description: 10X Genomics

value: P3 saline and P14 LPS


title: submandibular gland, Control, Day7, 2

value: submandibular gland


title: FAP8 Before diet (T0) RNA-Seq

description:
Library name: FAP8_PRE-T0
FAP8 Before diet (T0) RNA-Seq

value: Before diet


title: P0_Fetal-ME_Mll3KO

description: Library name: P0_Fetal-ME_Mll3KO

value: Liver

value: Lin-Kit+ cells


title: submandibular gland, Control, Day7, 1

value: female

value: Sham

value: Day 7


title: FAP35 3 months of diet (T1) RNA-Seq

description:
Library name: FAP35_3mo-T1
FAP35 3 months of diet (T1) RNA-Seq

value: PBMC


title: SL_2

description: 10X Genomics

value: brain cells

value: Hippocampi


title: P0_Fetal-ME

description: Library name: P0_Fetal-ME


title: E18_WT

description: Library name: E18_WT


title: N920

city: München

first: Salih

last: Demir

address: Lindwurmstr. 2a

country: Germany

institute: LMU kinderchirurgie

description: Library name: MUC3067

data_processing:
The STAR aligner (v 2.4.2a) (Dobin et al., 2013) with modified parameter settings (--twopassMode=Basic) was used for split-read alignment against the human genome assembly hg19 and UCSC knownGene annotation.
Quantification of the number of mapped reads of each gene was performed using htseq-counts (v0.6.0) (Anders et al., 2015)
Assembly: hg19
Supplementary files format and content: txt. File include raw gene counts for every gene (rows) and every sample (columns)
Supplementary files format and content: csv. Files include FPKMvalues for each sample

source_name: Normal liver

extract_protocol:
RNA was isolated from cryopreserved tissue using Trizol reagent
TruSeq_Stranded_mRNA

value: Normal liver

tag: age (months)

value: male


title: SL_1

description: 10X Genomics


title: N835

description: Library name: MUC3066


title: FAP35 Before diet (T0) RNA-Seq

description:
Library name: FAP35_PRE-T0
FAP35 Before diet (T0) RNA-Seq


title: FAP9 3 months of diet (T1) RNA-Seq

description:
Library name: FAP9_3mo-T1
FAP9 3 months of diet (T1) RNA-Seq

value: 3 months of diet


title: LL_1

description: 10X Genomics

value: P3 LPS and P14 LPS


title: SS_2

description: 10X Genomics

value: P3 saline and P14 saline


title: P28_Fetal-ME_Mll3KO

description: Library name: P28_Fetal_ME_Mll3KO

value: Bone marrow


title: FAP7 6 months of diet (T2) RNA-Seq

description:
Library name: FAP7_6mo-T2
FAP7 6 months of diet (T2) RNA-Seq

value: FAP

value: 6 months of diet


title: P28_Fetal-ME

description: Library name: P28_Fetal_ME


title: SS_1

description: 10X Genomics


title: FAP7 3 months of diet (T1) RNA-Seq

description:
Library name: FAP7_3mo-T1
FAP7 3 months of diet (T1) RNA-Seq


title: N629

description: Library name: MUC3063


title: P28_WT

description: Library name: P28_WT


title: P28_Postnatal-ME

description:
Library name: P28_P0_ME
MLL::ENL was induced at P0 and the CITE-seq was done at P28.


title: Tgfβr2 control, replicates 1 and 2, scRNAseq

city: Pittsburgh

first: Kun-Che

last: Chang

state: PA

address: 1622 Locust St

department: Department of Ophthalmology

institute: University of Pittsburgh School of Medicine

description: 10X Genomics

data_processing:
We applied fastp with the default parameters to filter the adaptor sequence and remove the low-quality reads to achieve clean data. Then the feature-barcode matrices were obtained by aligning reads to the mm10 genome using CellRanger v7.2.0.
Assembly: mm10
Supplementary files format and content: Barcodes and genes files (.tsv), and matrix files (.mtx).

source_name: Retina

extract_protocol:
Retinas from P0 mice were isolated and dissociated using papain (Sigma-Aldrich, P3125) for 30 min. After mixing with Lo-ovomucoid buffer (1.5% BSA, 1.5% trypsin inhibitor dissolved in DPBS, pH 7.4), retinas were centrifuged at 400xg for 5 min. Cell pellets were resuspended in PBS containing 0.04% bovine serum albumin and filtered through a 40μm cell strainer (Falcon, 352340) to remove cell clumps. Cell pellets were labeled with Cell Multiplexing Oligo (10X Genomics). 10,000 cells were then input into the 10X library construction. GEM generation, reverse transcription, cDNA amplification, and library construction steps were performed according to manufacturer’s instructions (Chromium Single Cell 3′v1/v2/v3 platform, 10X Genomics). Libraries were sequenced using a NovaSeq 6000 sequencer (Illumina) with paired-end 150 bp reads.
Library construction steps were performed according to manufacturer’s instructions (Chromium Single Cell 3’v1/v2/v3 platform (10X Genomics, Pleasanton, CA).

value: Retina

value: WT


title: N1152

description: Library name: MUC4028


title: FAP6 6 months of diet (T2) RNA-Seq

description:
Library name: FAP6_6mo-T2
FAP6 6 months of diet (T2) RNA-Seq

data_processing:
Sequencing reads were preprocessed with fastp v0.21.0 (Chen et al., 2018) in default settings to remove reads associated with a low quality (phred quality <Q15), shorter than 15 nt reads, or with more than 5 Ns.
Reads passing the filtering step were aligned to the human Gencode v36 transcriptome using Salmon v1.4.0 (Patro et al., 2017) with option --validateMappings, --seqBias, and --gcBias.
Gene expression levels were normalized using tximport v.1.18 while DESeq2 v1.30.1 was applied for the differential expression analysis.
Assembly: hg38
Supplementary files format and content: Table of gene expression levels as raw counts.

extract_protocol:
RNA was extracted from peripheral blood mononuclear cells (PBMCs) and formalin-fixed paraffin-embedded (FFPE) intestinal tissue, including both mucosa and polyps from FAP patients, using the RNeasy Kit (Qiagen, Germany).
RNA quality was assessed using an Agilent Bioanalyzer (Agilent, USA). cDNA library preparation was carried out using the Illumina Stranded Total RNA Prep following the manufacturer’s instructions.


title: P0_WT

description: Library name: P0_WT

value: Liver

value: Lin-Kit+ cells


title: Experiment02-4

city: Xiamen

first: Lijun

last: Cai

address: No. 668, Jinhu Road

department: Central Laboratory,

institute: Zhongshan Hospital (Xiamen), Fudan University

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Novel transcripts prediction After assembling a transcriptome from one or more samples, Cuffcompare, a tool of Cufflinks v2.2.1, compared assembly to known transcripts. Then, novel transcripts can be predicted via results of Cuffcompare.
Alternative splicing analysis rMATs v4.1.0 is a computational tool to detect differential alternative splicing events from RNA-Seq data. And resulting bam files of aligner HISAT2 had been used as input during the analysis. SNV analysis Samtools v0.1.19 with command mpileup and Bcftools v0.1.19 were used to do SNV calling. Differential exon usage By differential exon usage (DEU), we mean changes in the relative usage of exons caused by the experimental condition. The relative usage of an exon is defined as number of transcripts from the gene that contain this exonnumber of all transcripts from the gene The basic concept can be summarized as follows. For each exon (or part of an exon) and each sample, we count how many reads map to this exon and how many reads map to any of the other exons of the same gene. We consider the ratio of these two counts, and how it changes across conditions, to infer changes in the relative exon usage. In the case of an inner exon, a change in relative exon usage is typically due to a change in the rate with which this exon is spliced into transcripts (alternative splicing). Note, however, that DEU is a more general concept than alternative splicing, since it also includes changes in the usage of alternative transcript start sites and polyadenylation sites, which can cause differential usage of exons at the 5’ and 3’ boundary of transcripts. To analysis DEU, we used Bioconductor package DEXSeq (V 1.21.1).
Principal component analysis This is another way to visualize sample-to-sample distances. In this ordination method, the data points (here, the samples) are projected onto the 2D plane such that they spread out in the two directions that explain most of the differences. The x-axis is the direction that separates the data points the most. The values of the samples in this direction are written PC1. The y-axis is a direction (it must be orthogonal to the first direction) that separates the data the second most. The values of the samples in this direction are written PC2. The percent of the total variance that is contained in the direction is printed in the axis label. Note that these percentages do not add to 100%, because there are more dimensions that contain the remaining variance (although each of these remaining dimensions will explain less than the two that we see). This analysis has been dealt with R language with FPKM value as the input.
Assembly: GRCm39.107
Supplementary files format and content: Matrix table with raw gene counts and FPKM values for every gene and every cell

extract_protocol:
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers.
First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: hepatocyte

value: Primary liver cancer


title: FAP6 3 months of diet (T1) RNA-Seq

description:
Library name: FAP6_3mo-T1
FAP6 3 months of diet (T1) RNA-Seq

value: PBMC


title: Experiment02-3


title: FAP6 Before diet (T0) RNA-Seq

description:
Library name: FAP6_PRE-T0
FAP6 Before diet (T0) RNA-Seq

value: Before diet


title: P28_Postnatal_WT

description:
Library name: P28_P0_WT
MLL::ENL was induced at P0 and the CITE-seq was done at P28.


title: Experiment02-2


title: N1100

description: Library name: MUC3048


title: FAP4 6 months of diet (T2) RNA-Seq

description:
Library name: FAP4_6mo-T2
FAP4 6 months of diet (T2) RNA-Seq


title: Young_male.4h.C

city: Liverpool

first: Ufuk

last: Ersoy

address: William Henry Duncan Building

country: United Kingdom

institute: University of Liverpool

description:
Library name: Sample 13
Young male replicate C
Young_male_vs_young_female_RNA_kinetics.csv

data_processing:
The raw FASTQ files are trimmed to remove Illumina adapter sequences with Cutadapt version 4.5.
Reads shorter than 15 bp were discarded after trimming. Only read pairs were retained; if one read of a pair was removed, its mate was also discarded.
Reads were aligned to the Equus caballus EquCab3.0 primary assembly (Ensembl release 114) using STAR (version 2.5.3) with the following parameters: --outFilterMismatchNmax 40, --outFilterScoreMinOverLread 0.2, --outFilterMatchNminOverLread 0.2, --alignEndsType Extend5pOfReads12, and --outSAMattributes nM MD NH.
GEDI toolkit was utilised to merge and convert bam files into a CIT file (22) and then processed using GRAND-SLAM (version 2.0.7) to generate new-to-total RNA values (NTR) and read counts.
RNA synthesis rates and half-lives were estimated with the grandR using binomial distributions for reads from labelled and unlabelled RNAs.
Assembly: Equus caballus EquCab3.0 primary assembly (Ensembl release 114)
Supplementary files format and content: csv files containing RNA half-life and synthesis rate

organism: Equus caballus

source_name: Cartilage

growth_protocol: Chondrocytes were isolated from cartilage and cultured in complete DMEM for 2 days in a humidified atmosphere containing 5% CO₂ at 37°C.

extract_protocol:
RNA was extracted using TRIzol and chloroform, then alkylated with iodoacetamide (IAA) for 15 minutes at 50°C.
RNA libraries from submitted equine total RNA samples were performed using the NEBNext polyA selection and Ultra II Directional RNA library prep kits, (New England Biolabs, UK, #E7760S).

treatment_protocol: Cells were treated with 4sU for 4 hours

value: Cartilage

value: chondrocyte

value: young

value: 4-thiouridine (4sU) treated


title: N692

description: Library name: MUC3065

value: Normal liver

value: male


title: FAP4 3 months of diet (T1) RNA-Seq

description:
Library name: FAP4_3mo-T1
FAP4 3 months of diet (T1) RNA-Seq

source_name: PBMC

value: 3 months of diet


title: P28_Fetal_ME

description:
Library name: P28_E105_ME
MLL::ENL was induced at E10.5 and the CITE-seq was done at P28.

value: Bone marrow


title: T1152

description: Library name: MUC4029

source_name: Transitional liver cell tumor

value: Transitional liver cell tumor

value: female

tag: ctnnb1 genotype

tag: pretext


title: T1120

description: Library name: MUC3057

source_name: Hepatoblastoma

value: Hepatoblastoma


title: Experiment02-1

value: Liver

value: WT


title: Control02-4

value: hepatocyte

value: Control


title: FAP7 Before diet (T0) RNA-Seq

description:
Library name: FAP7_PRE-T0
FAP7 Before diet (T0) RNA-Seq

value: PBMC

value: FAP


title: Tgfβr2 KO, replicates 1 and 2, scRNAseq

description: 10X Genomics

value: Retina

value: TgfBr2 knockout


title: Young_male.4h.B

description:
Library name: Sample 12
Young male replicate B
Young_male_vs_young_female_RNA_kinetics.csv

value: Cartilage

value: chondrocyte

value: young


title: FAP4 Before diet (T0) RNA-Seq

description:
Library name: FAP4_PRE-T0
FAP4 Before diet (T0) RNA-Seq

value: Before diet


title: T1100

description: Library name: MUC3053

value: male


title: Control02-3

value: Primary liver cancer


title: Young_male.4h.A

description:
Library name: Sample 11
Young male replicate A
Young_male_vs_young_female_RNA_kinetics.csv

value: 4-thiouridine (4sU) treated


title: FAP3 3 months of diet (T1) RNA-Seq

description:
Library name: FAP3_3mo-T1
FAP3 3 months of diet (T1) RNA-Seq

value: 3 months of diet


title: N1006

description: Library name: MUC3070

value: Normal liver


title: T1006

description: Library name: MUC3083

value: Hepatoblastoma


title: Control02-2

value: Liver

value: WT


title: N1004

description: Library name: MUC3069

value: female


title: Young_female.4h.E

description:
Library name: Sample 10
Young female replicate E
old_vs_young_RNA_kinetics.csv
Young_male_vs_young_female_RNA_kinetics.csv


title: FAP3 Before diet (T0) RNA-Seq

description:
Library name: FAP3_PRE-T0
FAP3 Before diet (T0) RNA-Seq

value: PBMC


title: Young_female.4h.D

description:
Library name: Sample 9
Young female replicate D
old_vs_young_RNA_kinetics.csv
Young_male_vs_young_female_RNA_kinetics.csv


title: Experiment01-4

value: hepatocyte


title: Control02-1

value: Control


title: FAP2 6 months of diet (T2) RNA-Seq

description:
Library name: FAP2_6mo-T2
FAP2 6 months of diet (T2) RNA-Seq

value: FAP

value: 6 months of diet


title: FAP2 3 months of diet (T1) RNA-Seq

description:
Library name: FAP2_3mo-T1
FAP2 3 months of diet (T1) RNA-Seq


title: P28_Fetal_WT

description:
Library name: P28_E105_WT
MLL::ENL was induced at E10.5 and the CITE-seq was done at P28.

value: Bone marrow

value: Lin-Kit+ cells


title: T920

description: Library name: MUC3080


title: Experiment01-3


title: Young_female.4h.B

description:
Library name: Sample 7
Young female replicate B
old_vs_young_RNA_kinetics.csv
Young_male_vs_young_female_RNA_kinetics.csv

value: Cartilage

value: chondrocyte

value: young


title: FAP2 Before diet (T0) RNA-Seq

description:
Library name: FAP2_PRE-T0
FAP2 Before diet (T0) RNA-Seq

value: Before diet


title: Experiment01-2

value: Primary liver cancer


title: Young_female.4h.A

description:
Library name: Sample 6
Young female replicate A
old_vs_young_RNA_kinetics.csv
Young_male_vs_young_female_RNA_kinetics.csv

value: 4-thiouridine (4sU) treated


title: T692

description: Library name: MUC3078

value: Hepatoblastoma

value: male


title: T835

description: Library name: MUC3079

source_name: Pediatric hepatocellular carcinoma

value: Pediatric hepatocellular carcinoma

value: wildtype


title: T1004

description: Library name: MUC3082

value: female


title: Old.4h.E

description:
Library name: Sample 5
Old replicate E
old_vs_young_RNA_kinetics.csv

value: old

value: WT


title: T629

description: Library name: MUC3076


title: Experiment01-1

value: Liver

value: hepatocyte


title: T577

description: Library name: MUC3074


title: B003 first branch, early flowering stage, rep2

city: Nanchang

first: Xinjie

last: Yuan

state: Jiangxi

address: No. 602, Nanlian Road

department: Institute of Vegetables and Flowers

institute: Jiangxi Academy of Agricultural Sciences

description: Library name: B003 rep 2

data_processing:
Index of the reference genome was built and paired-end clean reads were aligned to the reference genome using using HISAT2. StringTie was used to count the reads numbers mapped to each gene.
Assembly: PRJNA788020
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

organism: Capsicum annuum

source_name: first branch

extract_protocol:
RNA was harvested using RNAprep Pure Plant Plus Kit (TIANGEN), 1.0 μg of total RNA was used for the construction of secuencing libraries
RNA libraries for RNA-seq were prepared using VAHTS Universal V10 RNA-seq Library Prep Kit (vazyme) following manufacturer's protocols

value: first branch


title: Control01-4

value: Control


title: B003 first branch, early flowering stage, rep3

description: Library name: B003 rep 3


title: Old.4h.D

description:
Library name: Sample 4
Old replicate D
old_vs_young_RNA_kinetics.csv

value: Cartilage


title: B003 first branch, early flowering stage, rep1

description: Library name: B003 rep 1


title: B010 first branch, early flowering stage, rep3

description: Library name: B010 rep 3


title: Old.4h.C

description:
Library name: Sample 3
Old replicate C
old_vs_young_RNA_kinetics.csv

value: chondrocyte


title: T291

description: Library name: MUC3072

value: Transitional liver cell tumor


title: Young_female.4h.C

description:
Library name: Sample 8
Young female replicate C
old_vs_young_RNA_kinetics.csv
Young_male_vs_young_female_RNA_kinetics.csv

value: young


title: Control01-3

value: Primary liver cancer


title: Control01-2


title: T365

description: Library name: MUC3073


title: Old.4h.B

description:
Library name: Sample 2
Old replicate B
old_vs_young_RNA_kinetics.csv

value: 4-thiouridine (4sU) treated


title: B010 first branch, early flowering stage, rep1

description: Library name: B010 rep 1


title: T6

description: Library name: MUC8468

value: Hepatoblastoma


title: Control01-1