title: IC3635X, REP3

city: San Antonio

first: Hanzhou

last: Wang

address: 8403 Floyd Curl Drive, MSC 7784

institute: UT Health at San Antonio

description: Library name: 1666

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg38) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
Gene count measurements were obtained using HTSeq-count
Assembly: hg38
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count. Merged HTSeq file is similar to individual HTSeq file, first column is gene symbol, and first row is sample name, and each column with read counts from each sample.

source_name: PDX, X-radiation therapy resistant

extract_protocol:
Tumors were collected when tumor volume was 0.3~0.6 cm3.Tumor bearing mice were euthanized with CO2, tumor tissue was collected from three mice and put in 2ml cryogenic vial and flash frozen in liquid nitrogen. Tumor tissue was ground to a fine powder under liquid nitrogen in a cooled mortar and pestle. Tissue powder was transferred to dry ice-cooled cryogenic tube. Twenty to ~50mg tissue powder was measured and transferred to a precooled 1.5ml eppendorf tube, and RNA isolated by adding 1ml Trizol solution (ThermoFisher), and mixing immediately.  300l chloroform was added to the lysate mixture, and vortexed vigorously for 1min, and then left at room temperature for 5 minutes. The following procedure was performed as instructed in the manual of RNeasy Kit (QIAGEN).
The quality of total RNAs was checked by Agilent Fragment Analyzer (Agilent Technologies, Santa Clara, CA), and only samples with RQN >7 were used for subsequent mRNA-seq library preparation and sequencing. Approximately 500ng total RNA was used for stranded mRNA-seq library preparation by following the NEB Directional mRNA-seq sample preparation guide (New England Biolabs, Ipswich, MA). The first step in the workflow involved purifying poly-A containing mRNA using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched by PCR amplification to create the final RNA-seq library. RNA-seq libraries were subjected to quantification process and subsequent 100bp paired read sequencing run with Illumina NovaSeq 6000 platform at 100 bp paired-end module (Greehey Children’s Cancer Research Institute’s Genome Sequencing Facility at UTHSCSA).

value: PDX, X-radiation therapy resistant


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_early_stg12_stamens, 8w/10w/23d (rep. 2)

status: Public on Sep 17 2025

type: SRA

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

library_source: transcriptomic

data_processing:
Paired-end sequencing reads, were adapter- and quality trimmed by cutadapt (version 1.10) and sickle (version 1.33) with parameters pe -t sanger -q 20 -l 50
RNA-seq reads were aligned to the respective reference genome using the RNA-Seq aligner STAR (version 2.7.1a) with the parameters --alignIntronMin 20 --alignIntronMax 10000 --bamRemoveDuplicatesType UniqueIdenticalNotMulti --chimSegmentMin 10 --chimOutType Junctions WithinBAM --outFilterMismatchNmax 3 --outFilterMultimapNmax 1 --outSAMattributes NH HI NM MD AS nM jM jI XS ch --outSAMprimaryFlag AllBestScore --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Gene expression values were quantified as estimated counts by salmon (0.14.1).
Assembly: Genomic reference sequences and annotations for the genome-guided transcriptome assembly and subsequent annotation procedures were obtained from Ensembl, release 34 (for A. thaliana), Phytozome, version 12 (for A. lyrata, C. rubella, E. salsugineum, M. truncatula, and B. distachyon), and RefSeq (for T. hassleriana).
Supplementary files format and content: gene transfer format files contain updated gene and transcript structure information for each organism
Supplementary files format and content: semicolon-separated text files contain estimated raw counts for each sample

molecule: total RNA

organism: Arabidopsis lyrata

source_name: stamens

growth_protocol: All plants were grown on soil, except those used for the collection of early-stage root samples, which were grown on 0.8% plant agar plates, pH 5.8, containing ½ MS and vitamins (Duchefa M0222).

extract_protocol:
Dissected organs were homogenised and total RNA was isolated using RNeasy Plant Mini Kit (QIAGEN 74904), following the manufacturer's instructions. RNA integrity was measured using an Agilent 2200 TapeStation.
Strand-specific total RNA-Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit according to the manufacturer’s specifications (Illumina 20020610). ERCC RNA Spike-In Control Mix (Ambion 4456740) was added at the beginning of the library preparation before the ribosomal RNA (rRNA) depletion step to allow sample-specific estimation of the lower detection limit. All RNA-Seq libraries were sequenced as paired-end 75bp reads.

tag: cultivar

value: Arabidopsis lyrata (MN47)

tag: tissue

value: stamens


title: IC3635X, REP2

state: TX

country: USA

description: Library name: 1565

organism: Homo sapiens


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_early_stg12_stamens, 8w/10w/23d (rep. 1)


title: Cerv-DMSO-3

city: Lyon

first: Pierre-Olivier

last: Vidalain

address: 21 Avenue Tony Garnier

country: France

institute: CIRI

description: Library name: S03

data_processing:
The produced paired-end reads which passed Illumina’s chastity filter were subject to de-multiplexing and trimming of Illumina adaptor residuals using Illumina’s bcl2fastq software version 2.20.0.422 (no further refinement or selection).
Quality of the reads in fastq format was checked with the software FastQC (version 0.11.8; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Raw reads having average Q-values below 24 or incorporating uncalled ‘N’ bases or being smaller than 25 bases after trimming were filtered using the BBTools software suite (version 38.86; https://sourceforge.net/projects/bbmap/). The splice aware RNA mapping software STAR (version 2.7.10a; PMID: 23104886) was used to map the surviving reads to the GCF_017639785.1 reference genome provided by NCBI.
To count the uniquely mapped reads to annotated genes, the software htseq-count (HTSeq version 0.13.5) was used.
Normalization of the raw counts and differential gene expression analysis was carried out with help of the R software package DESeq2 (version 1.26.0).
Assembly: GCF_017639785.1
Supplementary files format and content: Text files (.couts) containing genes counts (raw values)

organism: Mesocricetus auratus

source_name: Cerebellum

growth_protocol: Hamster cerebellum slices were cultured on inserts at the air-liquid interface (37°C; 5% CO2) with Minimal Essential Medium GlutaMAX (ThermoFisher Scientific) supplemented with 25% heat-inactivated horse serum (Gibco), D-glucose (5 g/L; Sigma-Aldrich) and human recombinant insulin (0.02 mg/mL; Sigma-Aldrich).

extract_protocol:
Hamster cerebellum slices were collected in 350 µL of TRI reagent (Euromedex) with two stainless steel beads and lysed using a TissueLyserII (Qiagen) at Vmax for 10 min. RNA was extracted using Direct-zol RNA Miniprep Kits (Zymo Research).
DNA library construction, sequencing and data analysis described in these sections were performed by Microsynth AG (Balgach, Switzerland). Total RNA was quantified using Quant-iT RiboGreen (Thermofisher) and integrity was checked on Fragment analyzer (Agilent) with a kit suitable for RNA. Library Preparation was done using the Illumina® Stranded mRNA Prep, Ligation and 60 ng total RNA input. Final libraries were quantified using pico488 (Lumiprobe) and library size was checked on Fragment analyzer (Agilent). Samples were pooled equimolar prior to sequencing. Subsequently the Illumina NovaSeq platform and an SP, 300 cycles kit were used to sequence the libraries in paired-end fashion.

treatment_protocol: Cultures were treated with DMSO alone or Molidustat at 25 microM for 24 h.

value: Cerebellum

tag: treatment

value: treated for 24h with DMSO alone


title: IC3635X, REP1

description: Library name: 1564


title: Cerv-DMSO-2

description: Library name: S02


title: CD19_CART_R_1

city: chengdu

first: pei

last: shu

address: guoxue lane

country: China

institute: west chia hospital, sichuan university

description:
Library name: CD19_CART_R_1.fq.gz
CD19 CAR-T in vitro pretreated with raji

data_processing:
Sequencing by Synthesis
Assembly: HISAT2 v2.0.5
Supplementary files format and content: processed data in vivo.xls

source_name: blood

extract_protocol:
RNA was harvested Rneasy mini plus kit (Qiagen).
RNA libraties for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit (Illumina).

value: blood

tag: cell type

value: T cells

tag: genotype

value: CAR-T cells

tag: batch

value: same batch


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_mid_stg12_stamens, 8w/10w/24d (rep. 3)


title: Cerv-DMSO-1

description: Library name: S01


title: CD19_CART_2

description:
Library name: CD19_CART_2.fq.gz
CD19 CAR-T in vitro repeated

value: CD19 CAR-T in vitro repeated


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_stg11_stamens, 8w/10w/25d (rep. 3)


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_stg11_stamens, 8w/10w/25d (rep. 2)


title: IC3635,  REP3

description: Library name: 1578

source_name: PDX, primary

value: PDX, primary


title: IC3635, REP2

description: Library name: 1577


title: Pt 'AML4', unenriched BMA, day 163 post-alloHCT, HLA transcripts captured from cell-barcoded RNA, MAS-seq augmented

city: Seattle

first: Sami

middle: B

last: Kanaan

address: 1100 FAIRVIEW AVE N

department: TST

institute: FRED HUTCHINSON CANCER CENTER

description:
Library name: AML4_d163_BM
AML4_d163_merged_Seurat_QCed_HLAMAS_matrix.mtx.gz
AML4_d163_merged_Seurat_QCed_HLAMAS_features.tsv.gz

data_processing:
Library strategy: scrHLA-typing
Circular Consensus Sequencing (CCS) reads conversion to "HiFi" read BAM files onboard Sequel IIe (Pacific Biosciences of California, Inc.)
hifi.BAM to segmented.BAM (`skera` version 1.2.0)
segmented.BAM to 5p--3p.BAM (`Lima` version 2.7.1)
5p--3p.BAM to tagged.BAM via `tag` program (`isoseq` version 3.8.2)
tagged.BAM to refined.BAM via `refine` program (`isoseq` version 3.8.2)
refined.BAM to corrected.BAM via `correct` program (`isoseq` version 3.8.2)
Add barcode stats to corrected.BAM via `bcstats` program (`isoseq` version 3.8.2)
Align corrected.BAM to IMGT/HLA database (version: 3.51.0 – 2023-01) using `scrHLAtag` (version 0.1.5)
molecule_info_gene.txt.gz and molecule_info_mRNA.txt.gz files (output from scrHLAtag) are read into the `Top_HLA_List()` function to predict most likely alleles (`scrHLAmatrix` version 0.16.6 in `R` version 4.2.0). The output is written into a .CSV list.
Realign corrected.BAM to IMGT/HLA database (version: 3.51.0 – 2023-01) using `scrHLAtag` (version 0.1.5) and adding the .CSV list of HLA candidate alleles as an argument.
Newly generated molecule_info_gene.txt.gz and molecule_info_mRNA.txt.gz files (output from scrHLAtag) are once again read into the `Top_HLA_List()` function to predict most likely alleles (`scrHLAmatrix` version 0.16.6 in `R` version 4.2.0). The output is written into a .CSV list. The scrHLAtag--scrHLAmatrix steps are repeated a few more times until the list of HLA candidate alleles converges to the putative genotypes of the cells in the sample.
Final molecule_info_gene.txt.gz and molecule_info_mRNA.txt.gz files (output from scrHLAtag) are read into the `HLA_Matrix()` function to filter errors, remove PCR duplicates, and summarize HLA counts (`scrHLAmatrix` version 0.16.6 in `R` version 4.2.0). The output is a Seurat-compatible object of class ‘Assay’.
Assembly: IMGT/HLA (version: 3.51.0 – 2023-01)
Supplementary files format and content: <…>_features.tsv.gz  A tab-separated file with feature (HLA) information, including HLA allele names.
Supplementary files format and content: <…>_matrix.mtx.gz  A compressed Matrix Market file containing the assay data (HLA allele expression matrix).

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
scrHLA-typing's starting material is unfragmented cell-barcoded (CB) whole transcriptome cDNA from single-cell RNA-seq libraries (e.g., those generated by 10x Genomics). Briefly, cDNA is incubated with custom-designed 5-prime biotinylated DNA oligonucleotides HLA-specific (HLA hybridization probes) and blocking oligos to prevent PCR artifacts. After incubation, the biotinylated probes are bound to streptavidin magnetic beads, allowing for the enrichment of HLA target sequences. These molecules are then PCR-amplified and interlinked together following steps in the ‘multiplexed arrays isoform sequencing’ (MAS-seq) protocol as described in the PacBio Procedure & Checklist for MAS-seq library prep (PacBio #102-678-600 REV03 MAR2023). Libraries are sequenced on a PacBio Sequel IIe with 2 hours pre-extension time and 30 hours movie time.
scrHLA-typing

value: Bone marrow

value: mononuclear cells


title: CD19_CART_1

description:
Library name: CD19_CART_1.fq.gz
CD19 CAR-T in vitro

value: CD19 CAR-T in vitro


title: NT_S_2

description:
Library name: NT_S_2.fq.gz
CD19 CAR-T in vitro in SDF-1 repeated

value: CD19 CAR-T in vitro in SDF-1 repeated


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_stg11_stamens, 8w/10w/25d (rep. 1)


title: Cerv-Moli-1

description: Library name: S05

value: treated for 24h with Molidustat at 25 microM


title: IC3635, REP1

description: Library name: 1576


title: Pt 'AML4', CD34-enriched BMA, day 163 post-alloHCT, HLA transcripts captured from cell-barcoded RNA, MAS-seq augmented

description:
Library name: AML4_d163_34
AML4_d163_merged_Seurat_QCed_HLAMAS_matrix.mtx.gz
AML4_d163_merged_Seurat_QCed_HLAMAS_features.tsv.gz


title: Pt 'AML4', unenriched BMA, day 90 post-alloHCT, HLA transcripts captured from cell-barcoded RNA, MAS-seq augmented

description:
Library name: AML4_d90_BM
AML4_d90_merged_Seurat_QCed_HLAMAS_matrix.mtx.gz
AML4_d90_merged_Seurat_QCed_HLAMAS_features.tsv.gz


title: ChrRNA_ETOP_R2

city: Seville

first: Silvia

last: Jimeno-González

address: Avda. Américo Vespucio 24

department: Genética

country: Spain

institute: Universidad de Sevilla

data_processing:
NovaSeq Control Software v1.8 was used for basecalling
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQ Generation based on bcl2fastq with default parameters. Mapping and subsequent analysis of the data were done using Europe Galaxy Server. Reads were mapped to December 2013 human genome assembly (GRCh38/hg38) using HISAT2 (v.2.2.1+galaxy1) using default parameters but specifying --rna-strandness RF and paired.end parameters --fr.
BAM files from the two independent replicates were merged with 'Merge BAM Files' (v.1.2.0).
Genome Coverage was calculated using bamCoverage (v. 3.5.1.0.0) from deepTools with default parameters but dividing genome in 1 bp bin size and normalizing mapped reads in Counts Per Million (CPM).
Assembly: hg38
Supplementary files format and content: Bedgraph files include CPM values for each sample
Library strategy: ChrRNA-seq

source_name: hTert RPE-1

growth_protocol: RPE-1 cells were grown in Dubelcco’s Modified Eagle’s Medium (DMEM) F-12 supplemented with 50 units ml-1 penicillin, 50 units ml-1 streptomycin and 10% Fetal Bovine Serum (FBS). Cells were cultured at 37ºC in 5% CO2 atmosphere.

extract_protocol:
Cytoplasmic, nucleoplasmic and chromatin-associated RNA fractions were extracted. Two independent replicates were performed.  For that, cell pellets were lysed in 400 μl of cold cytoplasmic lysis buffer (0.15% NP-40, 10 mM Tris pH 7.5, 150 mM NaCl) and incubated on ice for 5 min. The lysates were layered onto 1 ml cold sucrose buffer (10 mM Tris pH 7.5, 150 mM NaCl, 24% sucrose w/v), and centrifuged at 3500 g for 10 min. Supernatant from lysates was centrifuged again at 14,000 x g for 1 min and its supernatant frozen as cytoplasmatic RNA fraction. Nuclear pellets from lysates were resuspended into 250 μl cold glycerol buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol). Then, 250 μl of cold nuclei lysis buffer (20 mM HEPES pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40, 1 mM DTT) was added to the samples, followed by a pulsed vortexing and incubated on ice for 2 min. Samples were then centrifuged for 2 min at 13,000 × g. The supernatant was frozen as nucleoplasmic RNA fraction and the pellet, representing the chromatin-associated RNA fraction, was rinsed with 1 ml of cold PBS and resuspended in 50 μl of PBS-EDTA. All buffer were suplemented with RNase inhibitors (RNasinPlus, Promega). Finally, only chromatin-associated RNA was extracted using TRIZOL and 5 μg of RNA was treated with TURBO DNA-free kit for DNA removal according to manufacturer’s instructions.
Libraries preparation of chromatin-associated RNA were realized using Illumina Stranded Total RNA prep ligation with Ribo-Zero plus kit, according to its reference guide.

treatment_protocol: For ChrRNAseq, RPE-1 cells were serum starved by 48h incubation in the same medium, but with reduced 0.1% FBS content. Then, cells were treated with 50µM etoposide for 30 minutes.

tag: cell line

value: hTert RPE-1

value: Immortalized retinal pigment epithelial cells

tag: cell cycle

tag: etoposide treatment

value: Yes


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_early_stg12_carpels, 8w/10w/17d (rep. 2)

source_name: carpels

value: Arabidopsis lyrata (MN47)

value: carpels


title: NT_S_1

description:
Library name: NT_S_1.fq.gz
CD19 CAR-T in vitro in SDF-1

value: CD19 CAR-T in vitro in SDF-1


title: ChrRNA_DMSO_R2

value: No


title: ChrRNA_ETOP_R1


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_early_stg12_carpels, 8w/10w/17d (rep. 1)


title: Tcell donors, nuclei prep for multiome, HLA transcripts captured from cell-barcoded whole RNA (3-prime)

description: Library name: MO_nuclei_prep_3p

data_processing:
Library strategy: scrHLA-typing
Circular Consensus Sequencing (CCS) reads conversion to "HiFi" read BAM files onboard Sequel IIe (Pacific Biosciences of California, Inc.)
hifi.BAM to 5p--3p.BAM (`Lima` version 2.7.1)
5p--3p.BAM to tagged.BAM via `tag` program (`isoseq` version 3.8.2)
tagged.BAM to refined.BAM via `refine` program (`isoseq` version 3.8.2)
refined.BAM to corrected.BAM via `correct` program (`isoseq` version 3.8.2)
Add barcode stats to corrected.BAM via `bcstats` program (`isoseq` version 3.8.2)
Align corrected.BAM to IMGT/HLA database (version: 3.51.0 – 2023-01) using `scrHLAtag` (version 0.1.5)
molecule_info_gene.txt.gz and molecule_info_mRNA.txt.gz files (output from scrHLAtag) are read into the `Top_HLA_List()` function to predict most likely alleles (`scrHLAmatrix` version 0.16.6 in `R` version 4.2.0). The output is written into a .CSV list.
Realign corrected.BAM to IMGT/HLA database (version: 3.51.0 – 2023-01) using `scrHLAtag` (version 0.1.5) and adding the .CSV list of HLA candidate alleles as an argument.
Newly generated molecule_info_gene.txt.gz and molecule_info_mRNA.txt.gz files (output from scrHLAtag) are once again read into the `Top_HLA_List()` function to predict most likely alleles (`scrHLAmatrix` version 0.16.6 in `R` version 4.2.0). The output is written into a .CSV list. The scrHLAtag--scrHLAmatrix steps are repeated a few more times until the list of HLA candidate alleles converges to the putative genotypes of the cells in the sample.
Final molecule_info_gene.txt.gz and molecule_info_mRNA.txt.gz files (output from scrHLAtag) are read into the `HLA_Matrix()` function to filter errors, remove PCR duplicates, and summarize HLA counts (`scrHLAmatrix` version 0.16.6 in `R` version 4.2.0). The output is a Seurat-compatible object of class ‘Assay’.
Assembly: IMGT/HLA (version: 3.51.0 – 2023-01)
Supplementary files format and content: <…>_features.tsv.gz  A tab-separated file with feature (HLA) information, including HLA allele names.
Supplementary files format and content: <…>_matrix.mtx.gz  A compressed Matrix Market file containing the assay data (HLA allele expression matrix).

source_name: T cells

extract_protocol:
scrHLA-typing's starting material is unfragmented cell-barcoded (CB) whole transcriptome cDNA from single-cell RNA-seq libraries (e.g., those generated by 10x Genomics). Briefly, cDNA is incubated with custom-designed 5-prime biotinylated DNA oligonucleotides HLA-specific (HLA hybridization probes) and blocking oligos to prevent PCR artifacts. After incubation, the biotinylated probes are bound to streptavidin magnetic beads, allowing for the enrichment of HLA target sequences. These molecules are then PCR-amplified and long-read sequenced. Long-read sequencing involves constructing PacBio SMRTbells using PacBio SMRTbell Prep kit 3.0 (PacBio #102-141-700), as per manufacturer’s protocol (PacBio Procedure & Checklist #102-359-000 REV03 DEC2023). Libraries are sequenced on a PacBio Sequel IIe with 2 hours pre-extension time and 30 hours movie time.
scrHLA-typing

value: T cells


title: NT_RS_1

description:
Library name: NT_RS_1.fq.gz
CD19 CAR-T in vitro pretreated with raji in sdf-1

value: blood

value: CAR-T cells


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_mature_pollen, 8w/10w/25d (rep. 3)

source_name: pollen

value: pollen


title: NT_R_2

description:
Library name: NT_R_2.fq.gz
CD19 CAR-T in vitro pretreated with raji repeated

value: same batch


title: Pt 'AML8', CD34-enriched BMA, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML8_34

value: Bone marrow


title: NT_R_1

description:
Library name: NT_R_1.fq.gz
CD19 CAR-T in vitro pretreated with raji


title: NT_2

description:
Library name: NT_2.fq.gz
CD19 CAR-T in vitro repeated

value: CD19 CAR-T in vitro repeated


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_mature_pollen, 8w/10w/25d (rep. 2)


title: DU145 cells,Knockdown1,PD-L1

city: Dalian

first: lin

last: zhong

state: Liaoning

address: West Section Lvshun South Road

institute: Dalian Medical University

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Assembly: human NCBI genome build 38
Supplementary files format and content: Txt file includes raw counts for each Sample
Supplementary files format and content: Txt file includes FPKM values for each Sample

source_name: prostate

growth_protocol: DU145 cells were maintained at standard culture conditions (37°C, 5% CO2) in DMEM medium with 10% FBS.

extract_protocol:
RNA was harvested using TRIzol and cleaned using RNAeasy Kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate

value: prostatic cancer cells


title: DU145 cells,Knockdown2,PD-L1


title: Pt 'AML6', unenriched BMA, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML6_BM

value: mononuclear cells


title: Pt 'AML8', unenriched BMA, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML8_BM


title: Pt 'AML6', CD34-enriched BMA, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML6_34


title: RNA-Seq of Arabidopsis lyrata (MN47): flower_stg12, 8w/10w/15d (rep. 2)

source_name: flowers

value: flowers


title: RNA-Seq of Arabidopsis lyrata (MN47): flower_stg12, 8w/10w/15d (rep. 3)


title: nPOD_6505_snATAC_MM_547

city: La Jolla

first: Rebecca

last: Melton

address: 9500 Gilman Dr

institute: University of California, San Diego

library_source: genomic

data_processing:
Cellranger atac (v1.1.0) was used to demultiplex, barcode processing, and feature counting. Hg38 genome assembly was used.
Assembly: hg38
Supplementary files format and content: raw_peak_bc_matrix.h5 contains barcode level peak counts for all detected UMIs

molecule: genomic DNA

source_name: pancreas

extract_protocol:
Roughly 40 mg of ground tissue was resuspended in 1 ml of nuclei permeabilization buffer. Nuclei suspension was filtered with a 30-µm filter. Nuclei were counted using a hemocytometer, and 15,360 nuclei were used for tagmentation.
snATAC-seq libraries were generated using the Chromium Single Cell ATAC Library & Gel Bead Kit v1.1 (10x Genomics, 1000175), Chromium Chip H Single Cell ATAC Kit (10x Genomics, 1000161) and indexes (Single Index Kit N Set A, 1000212) following manufacturer instructions. Final libraries were quantified using a Qubit fluorometer (Life Technologies), and the nucleosomal pattern was verified using a TapeStation (High Sensitivity D1000, Agilent). NovaSeq 6000 sequencers (Illumina) with the following read lengths (Read1 + Index1 + Index2 + Read2): 50 + 8 + 16 + 50.

value: pancreas


title: NT_1

description:
Library name: NT_1.fq.gz
CD19 CAR-T in vitro

value: CD19 CAR-T in vitro


title: CD19_C_CART_1

description:
Library name: CD19_C_CART_1.fq.gz
in vitro

value: in vitro


title: RNA-Seq of Arabidopsis lyrata (MN47): flower_stg12, 8w/10w/15d (rep. 1)

value: Arabidopsis lyrata (MN47)


title: DU145 cells,Knockdown,Control


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_early_stg12_carpels, 8w/10w/17d (rep. 3)

value: carpels


title: Pt 'AML15', unenriched BMA, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML15_BM


title: nPOD_6512_snATAC_MM_546


title: Pt 'AML4', CD34-enriched BMA, day 90 post-alloHCT, HLA transcripts captured from cell-barcoded RNA, MAS-seq augmented

description:
Library name: AML4_d90_34
AML4_d90_merged_Seurat_QCed_HLAMAS_matrix.mtx.gz
AML4_d90_merged_Seurat_QCed_HLAMAS_features.tsv.gz


title: NT_RS_2

description:
Library name: NT_RS_2.fq.gz
CD19 CAR-T in vitro pretreated with raji in sdf-1 repeated


title: ChrRNA_DMSO_R1

value: hTert RPE-1

value: Immortalized retinal pigment epithelial cells

value: No


title: CE2MS2M_3

city: Shanghai

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome
Assembly: hg38
Supplementary files format and content: Processed_TPM_CE_RPE.xls

growth_protocol: The ARPE19 cells were cultured in normal rat plasma, cigarette exposed rat plasma, or stop exposed rat plasma.

extract_protocol:
Total RNA was isolated from the samples and RNA integrity was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: CE2MS2M_2


title: nPOD_6393_snATAC_MM_545


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_mature_pollen, 8w/10w/25d (rep. 1)


title: Pt 'AML4', unenriched BMA, day 163 post-alloHCT, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML4_d163_BM


title: CE2MS2M_1


title: RNA-Seq of Arabidopsis lyrata (MN47): apex_inflorescence, 8w/10w/13d (rep. 1)

source_name: inflorescence apex

value: inflorescence apex


title: nPOD_6521_snATAC_MM_544


title: nPOD_6429_snATAC_MM_543


title: Pt 'AML4', unenriched BMA, day 140 post-alloHCT, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML4_d140_BM


title: CE2M_3


title: RNA-Seq of Arabidopsis lyrata (MN47): apex_vegetative, 11d (rep. 3)

source_name: vegetative apex

value: vegetative apex


title: RNA-Seq of Arabidopsis lyrata (MN47): apex_vegetative, 11d (rep. 2)


title: CE2M_2


title: CE2M_1


title: nPOD_6282_snATAC_lib2_MM_536


title: nPOD_6520_snATAC_MM_537


title: nPOD_6424_snATAC_MM_535


title: Pt 'AML4', CD34-enriched BMA, day 90 post-alloHCT, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML4_d90_34


title: nPOD_6236_snATAC_MM_460


title: RNA-Seq of Arabidopsis lyrata (MN47): leaf_1+2, 10d (rep. 3)

source_name: leaf

value: leaf


title: RNA-Seq of Arabidopsis lyrata (MN47): apex_inflorescence, 8w/10w/13d (rep. 3)


title: Con2M_2


title: Pt 'AML15', CD117-enriched BMA, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML15_117

value: Bone marrow


title: Pt 'AML1', unenriched BMA, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML1_BM


title: Con2M_1


title: RNA-Seq of Arabidopsis lyrata (MN47): apex_inflorescence, 8w/10w/13d (rep. 2)


title: nPOD_6278_snATAC_MM_396


title: Pt 'AML4', CD34-enriched BMA, day 163 post-alloHCT, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML4_d163_34


title: Pt 'AML1', CD34-enriched BMA, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML1_34


title: RNA-Seq of Arabidopsis lyrata (MN47): leaf_1+2, 10d (rep. 1)


title: Pt 'AML4', CD34-enriched BMA, day 140 post-alloHCT, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML4_d140_34


title: RNA-Seq of Arabidopsis lyrata (MN47): hypocotyl, 12d (rep. 3)

source_name: hypocotyl

value: hypocotyl


title: CE1MS1M_2


title: CE1MS1M_3


title: nPOD_6234_snATAC_MM_395


title: Pt 'AML1', CD34-enriched BMA, HLA transcripts captured from cell-barcoded whole RNA (3-prime)

description: Library name: AML1_34_3p


title: Pt 'AML4', unenriched BMA, day 90 post-alloHCT, HLA transcripts captured from cell-barcoded whole RNA

description: Library name: AML4_d90_BM


title: Con2M_3


title: RNA-Seq of Arabidopsis lyrata (MN47): apex_vegetative, 11d (rep. 1)


title: RNA-Seq of Arabidopsis lyrata (MN47): hypocotyl, 12d (rep. 2)


title: nPOD_6479_snATAC_lib2_MM_392


title: CE1M_3


title: Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-SMAD4 ab, biol. rep2

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

description:
Library name: MuSC CUTTag vehicle SMAD4 biol rep 2
HCl_SMAD4_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates

data_processing:
Paired-end sequencing reads were subsampled to equal total depth per condition and sample to match read counts between replicates. Reads were then aligned to the mouse reference genome (GRCm39) using Bowtie2 version 2.5.4 with the following parameters: --very-sensitive --no-mixed --no-discordant. Aligned reads were subsequently filtered using samtools version 1.21 with options -b -h -f 2 -F 256 -F 2048 -F 1024 -q 30 to retain only properly paired reads (mapping quality ≥30) aligned to autosomes and sex chromosomes, while excluding reads mapped to ENCODE blacklisted regions. The filtered BAM files were converted to BED format using BEDTools version 2.31.1.
Peak calling was performed independently for each biological replicate using JAMM version 1.0.7.6 with the -r window parameter.
To establish consensus peak sets, per-replicate peaks were subjected to Irreproducible Discovery Rate (IDR) analysis using the IDR package version 2.0.3 with parameters --rank signal.value --idr-threshold 0.05. IDR was run on filtered peaks output from JAMM for transcription factors and on all peaks output for the H3K27ac modification. Only peaks meeting the IDR threshold of 0.05 were retained, generating consensus peak lists for each experimental condition.
Assembly: GENCODE M32 (GRCm39)
Supplementary files format and content: *_subsampled.bw => BigWig files to display the data in a genome browser
Supplementary files format and content: *.narrowPeak.bed => consensus peaks per condition and sample that passed the IDR threshold
Library strategy: CUT&Tag

organism: Mus musculus

source_name: skeletal muscle

growth_protocol: Mononucleated cells were isolated from forelimb, hindlimb, dorsal, and breast muscles of female 9-week-old mice and cultured in DMEM (Gibco, 41966029), 15% FBS (Gibco), 2.5 ng/mL basic FGF (Sigma, F3133), 10 ng/mL leukemia inhibitory factor (Sigma, ESG1106), and 1% Pen/Strep (Gibco) in Matrigel® (Corning, 356231)-coated dishes at 3% O2 and 5% CO2 at 37 °C for one day. After one day, the cells were detached, FACSed for GFP (PAX7-GFP reporter) to enrich for muscle stem cells, and cultured for another two days as before in medium additionally containing 1x B27 without vitamin A (Gibco, 12587010). In order to eliminate the effect of BMPs in the culture medium (e.g. from serum supplements), cells were then cultured in serum-free medium containing soluble BMP receptor (recombinant mouse BMPR-1A-Fc Chimera, R&D Systems, 437-MR) at a concentration of 200 ng/mL for 6 h.

extract_protocol:
Cells were washed, trypsinized, centrifuged, and resuspended in serum-free growth medium before fixing them in 0.1% formaldehyde for 2 minutes and subsequent quenching with glycine at twice the molar concentration of formaldehyde for 5 minutes. The cells were centrifuged at 4 °C for 4 minutes at 1,300 x g and the pellet was resuspended in CUT&Tag wash buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl (Sigma-Aldrich, 71386), 500 µM Spermidine (Sigma-Aldrich, S0266), 1x Complete protease inhibitor EDTA-free (Roche, 5056489001)) prior to slowly freezing the cells with 10% DMSO.
CUT&Tag was performed on 100,000 fixed frozen cells per condition as described by Kaya-Okur et al. 2019 and 2020. Briefly, cells were bound to concanavalin A-coated magnetic beads (Bangs Laboratories, 86057) and incubated with primary antibody overnight, followed by incubation with secondary antibody and later the CUTANA pAG-Tn5 enzyme (EpiCypher, 15-1017). Subsequently, the cleavage was induced and then the DNA was released, purified, and barcoded by amplification with barcoded primers for 13 cycles. Lastly, the libraries were purified and pooled.

treatment_protocol: Cells were stimulated with 100 ng/mL BMP4 or BMP6 or with vehicle (4 mM HCl containing 0.1% BSA) for 1 h.

value: skeletal muscle

value: muscle stem cells

value: vehicle

tag: antibody

value: SMAD4 (Cell Signalling, #38454)

value: biol rep 2


title: RNA-Seq of Arabidopsis lyrata (MN47): root_whole_root, 6d (rep. 3)

source_name: root

value: root


title: Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-pSMAD1/5/9 ab, biol. rep2

description:
Library name: MuSC CUTTag vehicle pSMAD1/5/9 biol rep 2
HCl_pSMAD1_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates

value: pSMAD1/5/9 (Cell Signalling, #13820)


title: RNA-Seq of Arabidopsis lyrata (MN47): leaf_1+2, 10d (rep. 2)

value: Arabidopsis lyrata (MN47)


title: Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-H3K27ac ab, biol. rep2

description:
Library name: MuSC CUTTag vehicle H3K27ac biol rep 2
HCl_H3K27ac_on_all.narrowPeak: includes high confidence peaks that agree between the replicates

value: H3K27ac (Abcam, ab4729)


title: nPOD_6267_snATAC_MM_390

value: pancreas


title: CE1MS1M_1


title: RNA-Seq of Arabidopsis lyrata (MN47): hypocotyl, 12d (rep. 1)


title: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-pSMAD1/5/9 ab, biol. rep2

description:
Library name: MuSC CUTTag BMP6 pSMAD1/5/9 biol rep 2
BMP6_pSMAD1_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates


title: nPOD_6405_snATAC_MM_388


title: CE1M_2


title: RNA-Seq of Arabidopsis lyrata (MN47): root_whole_root, 6d (rep. 2)


title: CE1M_1


title: RNA-Seq of Arabidopsis lyrata (MN47): root_whole_root, 6d (rep. 1)


title: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-SMAD4 ab, biol. rep2

description:
Library name: MuSC CUTTag BMP6 SMAD4 biol rep 2
BMP6_SMAD4_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates


title: nPOD_6401_snATAC_MM_394


title: Con1M_3


title: nPOD_6456_snATAC_MM_387


title: nPOD_6229_snATAC_MM_386


title: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-H3K27ac ab, biol. rep2

description:
Library name: MuSC CUTTag BMP6 H3K27ac biol rep 2
BMP6_H3K27ac_on_all.narrowPeak: includes high confidence peaks that agree between the replicates


title: Con1M_2


title: Bactrocera_tryoni_eggs_sRNA_rep2

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description:
Library name: Bactrocera_tryoni_eggs_sRNA_rep2
Small RNA sequencing from Bactrocera tryoni eggs replicate 2

library_source: other

data_processing:
Reads in the fastq files were adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' clipped using fastx_clipper (fastx_toolkit, Hannon Lab) using the default setting. The first and the last four bases were trimmed (both adapters contain four random nucleotides at their respective termini) and reads of >17nt and <41nt were kept for the analyses. Trimmed reads were first mapped to infrastructural RNAs including ribosomal RNA, small nuclear RNA, small nucleolar RNA, microRNA, and transfer RNA, which are annotated in their respetive genomes or genomes from closely related species using bowtie v1.2.3 allowing up to one mismatch. Reads that did not map to these infrastructural RNAs were subsequently mapped to the corresponding species' genomes. The sam file was further processed to the bam file, then to the bed file using samtools/1.19 and bedtools/2.28.0. The coverage of uniquely mappable reads on 0.5kb genomic tiles was measured using bedtools intersect.
Assembly: GCA_905231855.2_idEriTena2.2 for Eristalis tenax GCF_016617805.1_CSIRO_BtryS06_freeze2 for Bactrocera tryoni GCF_002204515.2_AaegL5.0 for Aedes aegypti GCF_013141755.1_UCI_ANSTEP_V1.0 for Anopheles stephensi GCA_032399595.1_TetCarb_2.0 for Tetragonula carbonaria GCA_031308135.1_ado_dt_MfTpo_fix for Acheta domesticus GCA_964035755.1_iqTelOcea1 for Teleogryllus oceanicus
Supplementary files format and content: *_genomic-tile-coverage.txt: coverage of uniquely mappable piRNA (>22nt) reads on individual 0.5kb genomic tiles <tile position with genomic coodinate and strand> <coverage per 1 million piRNA reads>

molecule: other

organism: Bactrocera tryoni

source_name: eggs

growth_protocol: Insects were kept at standard conditions at room temperature.

extract_protocol:
Small RNA sequencing was performed on ovaries and eggs collected from a variety of insects. About 10 pairs of ovaries from 1 week to up to 3 months old females and eggs within up to 8 hours of egg laying have been collected per replicate. Total RNA was extracted by TRIZOL (Thermo Fisher) and the genomic DNA was removed by DNase I (Thermo Fisher).
Small RNAs were first size-selected from the total RNA by 12% w/v UREA-PAGE using radio-labelled 19mer (5′-CGUACGCGGGUUUAAACGA) and 35mer (5'-CUCAUCUUGGUCGUACGCGGAAUAGUUUAAACUGU) spikes, and oxidised using sodium periodate. The oxidised small RNAs were further size-selected by PAGE. The size-selected oxidised small RNAs were ligated to the 3' adapter 5rApp/NNNNAGATCGGAAGAGCACACGTCT/3ddC, and then to the 5' adapter ACACUCUUUCCCUACACGACGCUCUUCCGAUCUNNNN where Ns are randomised. The first strand cDNA synthesis was performed using SuperScript II (Thermo Fisher) and the RT primer GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT. The library was amplified using KAPA LongRange DNA polymerase (Sigma) with a universal TruSeq forward primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and a barcode-containing TruSeq reverse primer (e.g. CAAGCAGAAGACGGCATACGAGATxxxxxxGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT where xxxxxx were the barcode).

value: eggs

tag: Sex

value: mixed

tag: strain

value: wild type

value: oxidized

tag: age

value: 0 - 2 hour old


title: nPOD_6310_snATAC_MM_385


title: nPOD_6228_snATAC_MM_391


title: Bactrocera_tryoni_eggs_sRNA_rep1

description:
Library name: Bactrocera_tryoni_eggs_sRNA_rep1
Small RNA sequencing from Bactrocera tryoni eggs replicate 1


title: Con1M_1


title: Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-pSMAD1/5/9 ab, biol. rep1

description:
Library name: MuSC CUTTag vehicle pSMAD1/5/9 biol rep 1
HCl_pSMAD1_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates

value: biol rep 1


title: nPOD_6362_snATAC_MM_383


title: Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag without primary ab, biol. rep1

description: Library name: MuSC CUTTag vehicle negative control biol rep 1


title: PPARG-KQ_1_PPARg

city: Wynnewood

first: Xuanmao

last: Jiao

state: PA

address: 100 E Lancaster Ave, LIMR R234

department: Pennsylvania Cancer and Regenerative Medicine Research Center

institute: Baruch S. Blumberg Institute

description:
PPARg_KQ-mutant_pooled.bigWig
PPARg_KQ-mutant_pooled_peaks.narrowPeak

data_processing:
Raw ChIP-seq reads were aligned to the hg38 reference genome using the Bowtie v.2 algorithm. Only uniquely aligned reads were retained for subsequent analyses.
Peak calling of individual ChIP-seq replicates was performed with MACS2 with default parameters. Consensus peaks were identified by intersecting MACS2 peaks obtained from each sample using bedtools intersect (v.2.25.0) with min. overlap > 0.6.
MCF10A PPARg WT and PPARg K154/155Q consensus peaks were than intersected with bedtools intersect (-v) to obtain a list of uniquely-bound peaks in PPARg WT and PPARg K154/155Q. Merged bigwig tracks for visualization were created from merged bam files from all replicates using the bamCoverage function with scaling factor normalization and heatmaps and average profiles were plotted with deepTools2
The gene annotations of the peaks were ascribed using ChIP-enrich. The HOMER motif discovery suite (v.4.10) was used for motif analysis, using random, matched regions as background.
For CEBP sites enriched at KQ mutant only peak we used the Homer motif CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer. Motifs were ranked by log P value from hypergeometric enrichment calculations (or binomial) to determine motif enrichment. Observed/ expected fold change enrichment analyses were performed using GAT.
Assembly: hg38
Supplementary files format and content: Bigwig

source_name: Breast

growth_protocol: The MCF10A-NeuT cells were infected with retrovirus expressing PPARg Wt, PPARg K154/155Q or PPARg K77R. The retrovirus were generated from pMSCV-IRES-GFP transfected HEK-293T cells. The infected MCF10A-NeuT cells which stably express PPARg WT, PPARg K154/155Q or PPARg K77R were maintained in Dulbecco's Modification of Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 100 U/mL of each penicillin and streptomycin.

extract_protocol:
Cell lysis and chromatin fragmentation on cross-linked whole-cells was prepared in ChIP buffer (50 mM Tris-HCL pH 7.5, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC, 0.1% SDS) with protease inhibitors (1 mM PMSF and Complete protease inhibitor tablet from Roche) by probe sonication (Fisher Scientific F60 Sonic Dismembrator). Samples were sonicated at low power (level 4) for three pulses of 10 seconds each and at a higher power (level 6) for two pulses of 10 seconds each. Proteins were bound at 4°C overnight with 10 μg anti-PPARγ (sc-7196, Santa Cruz Biotechnologies) in ChIP buffer with protease inhibitors and then immunoprecipitated with Protein A Sepharose Beads (GE Healthcare). Beads were washed for 5 minutes each with the following buffers: ChIP Buffer, mixed Micelle buffer (150 mM NaCl, 20 mM Tris-HCl pH 8.0, 5 mM EDTA, 5.2% Sucrose, 1% Triton X-100, 0.2% SDS), Buffer 500 (250 mM NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 25 mM HEPES, 0.5% Triton X-100, 0.05% NaDOC), LiCl/Detergent Buffer (250 mM LiCl, 10 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5% IGEPAL CA-630, 0.5% NaDOC), and Tris-EDTA pH 8.0. Cross-linking was reversed at 65°C overnight in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) and DNA was isolated using phenol/chloroform extraction and NaCl/EtOH precipitation with 20 μg glycogen carriers.
Approximately 10 ng of ChIP DNA (quantified by Qubit 2.0 Fluorometer, Invitrogen) was prepared for sequencing according to the amplification protocol from Illumina using enzymes from New England Biolabs and PCR purification (#28104) and MinElute (#28004) kits from Qiagen. Deep sequencing was performed by the Functional Genomics Core (J. Schugg and K. Kaestner) of the Penn Diabetes Research Center using Illumina HiSeq 2000 and aligned sequences were obtained using the Solexa Analysis Pipeline.

value: Breast

value: Transformed human mammary epithelial cells

value: PPARg-KQ

tag: chip antibody

value: PPARg


title: nPOD_6450_snATAC_MM_371


title: Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-SMAD4 ab, biol. rep1

description:
Library name: MuSC CUTTag vehicle SMAD4 biol rep 1
HCl_SMAD4_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates

value: skeletal muscle

value: muscle stem cells

value: vehicle

value: SMAD4 (Cell Signalling, #38454)


title: Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, CUT&Tag with anti-H3K27ac ab, biol. rep1

description:
Library name: MuSC CUTTag vehicle H3K27ac biol rep 1
HCl_H3K27ac_on_all.narrowPeak: includes high confidence peaks that agree between the replicates


title: PPARG-KQ_2_PPARg


title: Bactrocera_tryoni_ovaries_sRNA_rep1

description:
Library name: Bactrocera_tryoni_ovaries_sRNA_rep1
Small RNA sequencing from Bactrocera tryoni ovaries replicate 1

source_name: ovaries

value: ovaries

value: female

value: 1 week old


title: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag without primary ab, biol. rep1

description: Library name: MuSC CUTTag BMP6 negative control biol rep 1


title: nPOD_6479_snATAC_lib1_MM_367

value: pancreas


title: SOL_OMA_MRSAVAP_12hr_2

city: Nagasaki

first: Naoki

last: Iwanaga

address: Sakamoto, 1-7-1

country: Japan

institute: Nagasaki University

description: Library name: SOL.OMA.12hr.2

data_processing:
RNA-seq libraries were sequenced using paired end reads (150nt of read1 and read2) on a DNBSEQ-G400RS instrument (MGI Tech).
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software.
Trimmed reads were then mapped to the human GRCh38 genome using STAR (version 2.7.2b). Reads on annotated genes were counted using featureCounts (version 1.6.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: lung tissue

extract_protocol:
RNA was harvested using Rneasy miini plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit (Clontech, 634442) and MGIEasy Universal Library Conversion Kit (App-A) (MGI, 1000004155) according to the manufacturer’s instruction..

value: lung tissue


title: PPARG-KQ_1_input


title: SOL_OMA_MRSAVAP_12hr_1

description: Library name: SOL.OMA.12hr.1


title: nPOD_6220_snATAC_MM_384


title: Bactrocera_tryoni_ovaries_sRNA_rep2

description:
Library name: Bactrocera_tryoni_ovaries_sRNA_rep2
Small RNA sequencing from Bactrocera tryoni ovaries replicate 2

value: wild type


title: SOL_OMA_MRSAVAP_12hr_3

description: Library name: SOL.OMA.12hr.3


title: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-pSMAD1/5/9 ab, biol. rep1

description:
Library name: MuSC CUTTag BMP6 pSMAD1/5/9 biol rep 1
BMP6_pSMAD1_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates

value: pSMAD1/5/9 (Cell Signalling, #13820)


title: nPOD_6431_snATAC_MM_366


title: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-SMAD4 ab, biol. rep1

description:
Library name: MuSC CUTTag BMP6 SMAD4 biol rep 1
BMP6_SMAD4_on_filt.narrowPeak: includes high confidence peaks that agree between the replicates


title: OMA_MRSAVAP_12hr_3

description: Library name: OMA.12hr.3

value: OMA


title: PPARG-WT_1_PPARg

description:
PPARg_PPARG_WT_pooled.bigWig
PPARg_PPARG_WT_pooled_peaks.narrowPeak

value: PPARg-WT


title: nPOD_6264_snATAC_MM_365


title: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, CUT&Tag with anti-H3K27ac ab, biol. rep1

description:
Library name: MuSC CUTTag BMP6 H3K27ac biol rep 1
BMP6_H3K27ac_on_all.narrowPeak: includes high confidence peaks that agree between the replicates

value: H3K27ac (Abcam, ab4729)

value: biol rep 1


title: OMA_MRSAVAP_12hr_2

description: Library name: OMA.12hr.2


title: PPARG-WT_2_input

value: Breast

value: Transformed human mammary epithelial cells


title: PPARG-WT_2_PPARg

value: PPARg


title: nPOD_6282_snATAC_lib1_MM_345


title: Trim66_KO_homo_HiC_rep_3

first: Yalei

last: Kong

address: No. 280, Chongqing South Road

institute: Shanghai Jiao Tong University

description:
Library name: sample 14
HiC_homo_3

data_processing:
CUT&Tag: Reads were mapped to the mouse reference genome (mm10) using Bowtie 2 (version 2.5.1) with the “--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700” parameters. The olfactory enhancer peaks were visualized in a multi-region track using the UCSC genome browser and deeptools (version 3.5.5).
Hi-C: The In situ Hi-C data were processed following the 4DN Hi-C data processing pipeline (https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline). Briefly, sequencing reads were aligned to the mm10 reference genome with BWA (version 0.7.17). Valid Hi-C contacts were extracted by removing PCR duplicates and short cis contacts within 1 kb using pairtools (version 1.0.1) . Hi-C contact matrices were then generated by binning the genome at multiple resolutions and normalized using matrix balancing implemented in cooler (version 0.9.2). To account for variations in sequencing depth and alignment efficiency, contact frequencies were normalized by dividing the binned interaction counts by the total number of Hi-C contacts at the specified resolution. Contact matrices were visualized using Python libraries including pandas, seaborn, and matplotlib. Aggregate pileup analyses were conducted using the pileup function from the coolpuppy package (version 1.1.0). A/B compartment profiles were derived from ICE-normalized intrachromosomal contact maps at 500 kb resolution by converting them into observed-over-expected (O/E) matrices. Principal component analysis (PCA) was performed, and PC1 values were interpreted based on GC content. Regions with positive PC1 scores, typically gene-rich, were assigned as compartment A, while regions with negative PC1 scores were assigned  as compartment B. Compartment strength was assessed and visualized by saddle plots in cooltools (version 0.5.4). TADs were identified by calculating insulation scores via the diamond insulation algorithm implemented in cooltools, with a window size of 125 kb and a bin size of 25 kb.
Assembly: mm10
Supplementary files format and content: CUT&Tag: bigWig files
Supplementary files format and content: Hi-C: mcool files

source_name: Main Olfactory Epithelium (MOE)

extract_protocol:
CUT&Tag: The MOE from Olfr1507-ires-tdTomato; Trim66 -/- or Olfr1507-ires-tdTomato; Trim66 +/- mice was dissected and dissociated. Then more than 10,000 tdTomato-positive cells were sorted by flow cytometry
CUT&Tag: Libraries were prepared with the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903).
Hi-C: The MOE from Trim66 -/- or Trim66 +/- mice was dissected and dissociated.
Hi-C: The live cells were fixed with 1% formaldehyde for 10 min and quenched with 0.2 M glycine for 5 min at room temperature. The cells were then washed twice with 100 μL HBSS containing 0.1% BSA. The pelleted cells were resuspended in 100 μL of ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630, and protease inhibitors) and incubated on ice for 30 min. After centrifugation at 3,000 g for 5 min at 4 °C, the pelleted nuclei were washed once with 100 μL of ice-cold 1 NEB Buffer 3.1. Chromatin was solubilized in 20 μL of 0.3% SDS and incubated at 65 °C for 10 min, followed by quenching with 5 μL of 10% Triton X-100 and incubation at 37 °C for 10 min. The nuclei were digested with 50 U DpnII in a total volume of 50 μL at 37 °C for 3 h in a Thermomixer with interval shaking. DpnII was then inactivated by incubation at 65 °C for 20 min. For biotin labeling, 3 μL of 1 mM biotin-14-dATP, 0.3 μL of 10 mM dGTP, 0.3 μL of 10 mM dTTP, 0.3 μL of 10 mM dCTP, and 10 U Klenow were added. The reaction was performed at 37 °C for 1.5 h in a Thermomixer. Subsequently, 60 μL of ligation mixture (33.6 μL water, 12 μL 10 NEB T4 DNA ligase buffer, 12 μL 10% Triton X-100, 1.2 μL 10 mg/mL BSA, and 1.2 μL 2,000 U/μL T4 DNA ligase) was added, and the reaction was incubated at 25 °C for 4 h in a Thermomixer. Crosslinks were reversed and DNA was purified. The purified DNA was sheared to 300–500 bp using a Covaris M220. End repair, dA-tailing, and adaptor ligation were then performed using the Rapid Plus DNA Lib Prep Kit V2 (ABclonal). Biotin-labeled DNA fragments were enriched using 50 μL of Dynabeads MyOne Streptavidin C1 (Invitrogen). Sequencing libraries were prepared on beads, followed by 6–8 cycles of PCR amplification. Fragments ranging from 300 bp to 1,000 bp were size-selected. All libraries were sequenced on a NovaSeq X Plus platform following the manufacturer’s instructions.

value: Main Olfactory Epithelium (MOE)


title: PPARG-KQ_2_input

value: PPARg-KQ


title: OMA_MRSAVAP_12hr_1

description: Library name: OMA.12hr.1


title: nPOD_6375_snATAC_MM_344


title: Trim66_KO_homo_HiC_rep_2

description:
Library name: sample 13
HiC_homo_2


title: nPOD_6380_snATAC_MM_343


title: PPARG-WT_1_input


title: GAM_MRSAVAP_12hr_3

description: Library name: GAM.12hr.3


title: Control_2_PPARg

value: Vector Control


title: nPOD_6339_snATAC_MM_341


title: Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, biol. rep2

description:
Library name: MuSC RNA-seq 2 vehicle biol rep 2
TPM_joined.tab/.xlsx: TPM_HCL_TX_REP2
FPKM_joined.tab/.xlsx: FPKM_HCL_TX_REP2

data_processing:
FASTQ files were aligned to the human genome (GENCODE GRCm39) using STAR v2.7.11a with the following settings: --runThreadN 20 --outReadsUnmapped Fastx --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --seedSearchStartLmax 50 --outFilterMatchNmin 150 --alignSoftClipAtReferenceEnds No --outSAMattrIHstart 0 --alignEndsType EndToEnd --twopassMode Basic. The resulting *.bam file was sorted and indexed using samtools v1.17.
The sorted *.bam file was passed to StringTie v2.2.1 with the following settings: -u -p 36. The resulting *.gtf files were merged using stringtie merge and normalized read counts (TPM and FPKM) were generated using stringtie ballgown. The read counts of all experimental samples were then concatenated into two tables: output.tpm.csv and output.fpkm.csv.
Assembly: GENCODE M32 (GRCm39)
Supplementary files format and content: Stringtie ballgown output files: *.cov.refs.ballgown.gtf => contains details of the transcripts that StringTie assembles from RNA-seq data in the GTF format; *.gene_abund.ballgown.tab => contains gene abundance counts as normalized FPKM and TPM values as a table; *.out.ballgown.gtf => This is a file listing all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described above. Each line of the GTF is corresponds to a gene or transcript in the reference annotation.
Supplementary files format and content: FPKM_joined.tab, FPKM_joined.xlsx, TPM_joined.tab, TPM_joined.xlsx => fused tables with all the samples of the experiment in TAB and XLSX format provided as TPM and FPKM values; transcript_count.csv => fused table with fragment counts mapped to transcript; gene_count.csv => fused table with fragment counts mapped to genes

extract_protocol:
Cells were washed, trypsinized, centrifuged, and frozen at -80 °C for later RNA extraction. RNA was extracted using the NucleoSpin RNA XS kit (Macherey-Nagel, 740902) and residual DNA was removed using RNase-Free DNase from the NucleoSpin Mini RNA kit (Macherey-Nagel, 740955). RNA quantity and quality were assessed using a NanoDrop® 2000c spectrophotometer (Thermo Fisher Scientific)
Unstranded libraries were prepared by following the Smart-seq 2 protocol until the PCR amplification step and continued with the Nextera XT DNA library prep kit (Illumina, FC-131-1096) using the MGI universal and index primers for PCR amplification.

treatment_protocol: Cells were stimulated with 100 ng/mL BMP6 or with vehicle (4 mM HCl containing 0.1% BSA) for 1 h.

value: skeletal muscle

value: muscle stem cells

value: vehicle

value: biol rep 2


title: nPOD_6197_snATAC_MM_342

value: pancreas


title: Control_2_input


title: Trim66_KO_homo_HiC_rep_1

description:
Library name: sample 12
HiC_homo_1


title: GAM_MRSAVAP_12hr_1

description: Library name: GAM.12hr.1

value: lung tissue


title: Trim66_KO_het_HiC_rep_2

description:
Library name: sample 10
HiC_het_2


title: Trim66_KO_het_HiC_rep_3

description:
Library name: sample 11
HiC_het_3


title: Control_1_PPARg


title: nPOD_6247_snATAC_MM_339


title: Trim66_KO_het_HiC_rep_1

description:
Library name: sample 9
HiC_het_1


title: nPOD_6418_snATAC_MM_340


title: Sample3

city: Changsha, Hunan

first: Yufan

last: Yang

state: China

address: No. 86 Ziyuan Road

institute: Hunan Children's Hospital

description:
Library name: Sample3
one sample from murine kidney tissue

library_source: transcriptomic single cell

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

source_name: murine kidney tissue

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

value: murine kidney tissue

value: macrophage


title: Control_1_input


title: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, biol. rep2

description:
Library name: MuSC RNA-seq 2 BMP6 biol rep 2
TPM_joined.tab/.xlsx: TPM_BMP_TX_REP2
FPKM_joined.tab/.xlsx: FPKM_BMP_TX_REP2


title: Cultured adult mouse MuSC, serum starved, vehicle-stimulated for 1h, biol. rep1

description:
Library name: MuSC RNA-seq 2 vehicle biol rep 1
TPM_joined.tab/.xlsx: TPM_HCL_TX_REP1
FPKM_joined.tab/.xlsx: FPKM_HCL_TX_REP1


title: nPOD_6366_snRNA_MM_561

data_processing:
Cellranger (v6.0.1) was used to demultiplex, barcode processing, and gene counting. Hg38 genome assembly was used.
Assembly: hg38
Supplementary files format and content: raw_feature_bc_matrix.h5 contains barcode level counts for all detected UMIs

molecule: nuclear RNA

extract_protocol:
Roughly 40 mg ground pancreas tissue was suspended in 500 µL of nuclei buffer. Sample was incubated on a rotator for 5 min at 4 °C and then pelleted with a swinging bucket centrifuge (500× g, 5 min, 4 °C; 5920 R, Eppendorf). Supernatant was removed and pellet was resuspended in 400 μl of sort buffer and stained with DRAQ7 (1:100; Cell Signaling Technology, 7406). 75,000 nuclei were sorted using an SH800 sorter (Sony) into 50 μl of collection buffer. Sorted nuclei were then centrifuged at 1000g for 15 min (Eppendorf, 5920R; 4°C, ramp speed of 3/3), and supernatant was removed. Nuclei were resuspended in 18 to 25 μl of reaction buffer [RNase inhibitor (0.2 U/μl) and 1% BSA (Sigma-Aldrich, SRE0036) in PBS] and counted using a hemocytometer. 16,500 nuclei were loaded onto a Chromium controller (10x Genomics).
Libraries were generated using the 10x Genomics, Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, 1000121), Chromium Next GEM Chip G Single Cell Kit (10x Genomics, 1000120) and indexes (Single Index Kit T Set A, 10x Genomics, 1000213 or Dual Index Kit TT Set A, 10x Genomics, 1000215) according to the manufacturer specifications. Complementary DNA was amplified for 12 PCR cycles. SPRISelect reagent (Beckman Coulter) was used for size selection and cleanup steps. Final library concentration was assessed by the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), and fragment size was checked using a TapeStation (High Sensitivity D1000, Agilent). Libraries were sequenced using a Novaseq6000 (Illumina) with the following read lengths (Read1 + Index1 + Index2 + Read2): 28 + 8 + 0 + 90 (single index) or 28 + 10 + 10 + 90 (dual index).


title: Sample2

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


title: GapmeR 4

city: Boston

first: Mark

middle: W

last: Feinberg

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

description:
Library name: Sample 4
G5

data_processing:
Sequence reads were trimmed to remove adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by Subread package v.1.5.2
The hit counts were summarized and reported using the gene_id feature in the annotation file
Assembly: mm10
Supplementary files format and content: raw_counts.csv

growth_protocol: Cells (ATCC, CRL-2299) were cultured in Dulbecco’s Modified Eagle Medi-um/F12(1:1) (DMEM; Gibco, 11320-033) supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-streptomycin (P/S).

extract_protocol:
We used miRNeasy Tissue/Cells Advanced Kits (217684, Qiagen) for isolation of total RNA from the cells, as per the manufacturer’s instruction.
RNA liberaries were prepared using Illumina's ultra low input RNA

treatment_protocol: Transfections were performed using Lipofectamine 2000 (Invitrogen) as described in the manufacturer’s protocol. For knockdown studies to Gm39822, custom antisense LNA GapmeRs targeted to Gm39822 (Qiagen, Cat. No. LG00798344-DDA, 100 nM) or a negative control antisense LNA GapmeR (Qiagen, Cat. No. LG00000002-EFA, 100 nM) were used.

value: brain endothelial cells

value: Gm39822 knockdown


title: Cultured adult mouse MuSC, serum starved, BMP6-stimulated for 1h, biol. rep1

description:
Library name: MuSC RNA-seq 2 BMP6 biol rep 1
TPM_joined.tab/.xlsx: TPM_BMP_TX_REP1
FPKM_joined.tab/.xlsx: FPKM_BMP_TX_REP1

value: biol rep 1


title: Negative Control 1

description:
Library name: Sample 5
N1

value: control


title: Sample1

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


title: Negative Control 2

description:
Library name: Sample 6
N2


title: GAM_MRSAVAP_12hr_2

description: Library name: GAM.12hr.2


title: nPOD_6505_snRNA_MM_560


title: GapmeR 3

description:
Library name: Sample 3
G4


title: Ezh2b, wild type, rep3

city: Shenzhen

first: Zhihua

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
The sequencing was conducted on a DNBSEQ-T7 platform using the PE150 strategy.
To enhance data quality, we utilized fastp (version 0.21.0) for filtering, resulting in high-quality sequences (Clean Data) suitable for further analysis.
Clean RNA-seq reads were aligned to the mouse genome (GRCm38/mm10) using HISAT2 (version 2.1.0) with default parameters.
Read counts for each gene were calculated using StringTie (version 2.1.5), providing raw expression values that were subsequently standardized using FPKM (Fragments Per Kilobase Million).
Differential gene expression analysis was performed with edgeR (version 4.2.1), applying the criteria of |log2FoldChange| ≥ log2(1.5) and adjusted p-value (padj) < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited xls file includes raw counts for each Sample

source_name: MEF

growth_protocol: The embryonic fibroblasts were cultured in  DMEM high-glucose medium. DMEM supplemented with 10% fetal bovine serum (FBS, Gibco, USA), 100 U/mL penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen Life Technologies). The quality and quantity of the total RNA were assessed using a NanoDrop spectrophotometer (Thermo Scientific) and Qubit 4.0 for purity and concentration evaluation, while RNA integrity was measured using the Agilent 2100/4200 system.
Library construction involved the purification of mRNA from three micrograms of total RNA using poly-T oligo-attached magnetic beads. Following fragmentation with divalent cations, the first strand of complementary DNA (cDNA) was synthesized using random hexamers, followed by second strand synthesis with buffer, dNTPs, RNase H, and DNA polymerase I. The double-stranded cDNA was repaired and adenylated at the 3' end. Subsequent purification and fragment selection were performed using Hieff NGS® DNA Selection Beads, and the library was amplified via PCR and quantified with Qubit. The target region library was denatured and processed to generate single-stranded circular DNA, which was amplified through rolling circle amplification (RCA) to produce DNA nano balls (DNB).

value: MEF

value: Ezh2b, wild type


title: nPOD_6512_snRNA_MM_559


title: Ezh2b, wild type, rep2


title: nPOD_6393_snRNA_MM_558


title: Tumor, murine control T cells, 5 days, rep4

city: Philadelphia

first: Evan

last: Cresswell-Clay

address: 3501 Civic Center Blvd

department: DBHi

institute: CHOP

description: Library name: Sample 30

data_processing:
Reads were mapped and analyzed with a bioinformatic pipeline utilizing STAR, RSEM, SAMTOOLS, and the R package DESeq2
Assembly: mm10
Supplementary files format and content: gene counts files -- csv
Supplementary files format and content: counts_gene.csv

source_name: murine neuroblastoma tumor from TH-MYCN allograft-bearing mice

extract_protocol:
Total RNA was extracted from tumor tissue by homogenization in TRIzol reagent, followed by separation using chloroform. RNA was purified using RNeasy columns (QIAGEN) and quantified by Nanodrop. Sample quality was evaluated using Agilent TapeStation.
RNA library preparation and sequencing was conducted at Azenta Life Sciences (South Plainfield, NJ, USA) as follows: Total RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. Converted the RNA molecules into complementary DNA (cDNA) and incorporated UMIs during reverse transcription. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

value: murine control T cells


title: Ezh2b, wild type, rep1

last: Wang


title: nPOD_6521_snRNA_MM_557


title: Tumor, murine GPC2 CAR T cells, 5 days, rep4

description: Library name: Sample 15

value: murine neuroblastoma tumor from TH-MYCN allograft-bearing mice

value: murine GPC2 CAR T cells


title: GapmeR 2

description:
Library name: Sample 2
G3


title: Ezh2b, mutation, rep3

value: Ezh2b, mutation


title: nPOD_6429_snRNA_MM_556


title: GapmeR 1

description:
Library name: Sample 1
G2


title: Tumor, murine GPC2 CAR T cells, 5 days, rep3

description: Library name: Sample 13


title: MR3

city: Shenyang

first: Rong

last: Fu

address: Beiling Street, Yuhong District, Shenyang City, Liaoning Province

institute: Shenyang Medical College

description: Library name: SAMPLE9

data_processing:
1. Raw Data QC: FastQC v0.11.9 for read quality assessment.
2. Adapter Trimming: Trim Galore! v0.6.7 (Cutadapt) to remove adapters (--paired --quality 20).
3. Alignment: HISAT2 v2.2.1 to mouse genome (GRCm39/mm39) with default parameters.
4. Quantification: FeatureCounts v2.0.3 (ENSEMBL annotation) for gene-level counts.
5. Differential Expression: DESeq2 v1.34.0 (R) with FDR-adjusted p < 0.05.
Assembly: Reference: GRCm39/mm39 (ENSEMBL release 105).
Supplementary files format and content: 1.Gene Count Matrix: Tab-delimited text file; rows = genes (ENSEMBL IDs), columns = samples; raw counts. 2.Normalized Expression: TPM/FPKM values (log2-transformed) in CSV format. 3.Differential Expression Results: CSV files with log2FC, p-value, FDR for each comparison (WT vs. DB, DB vs. DB+MR409).

source_name: kidney

growth_protocol: We established two mouse models of diabetes: leptin receptor-deficient DB/DB diabetic mice or STZ-induced diabetic mice. All animal procedures were carried out in accordance with the National Institutes of Health (NIH) guidelines for the Care and Use of Laboratory Animals and approved by the Ethics Committee of Shenyang Medical College (SYYXY2021032301). Ten-weeks-old male DB/DB mice and control DB/m littermates, on a C57BL/KsJ background were purchased from the Model Animal Research Center of Nanjing University (Nanjing, Jiangsu, China) and housed under specific pathogen-free conditions in the Laboratory Animal Center of Shenyang Medical College (Shenyang, Liaoning, China). After a two-week acclimatization period, DB/DB mice or DB/m mice were divided into three groups: a wild type control group (WT, n=10), a DB/DB diabetic group (DB/DB, n=10) and DB/DB mice treated with MR409 group (DB/DB+MR409, n=10). All group mice were fed a regular mouse diet.

extract_protocol:
Total RNA was isolated from mouse kidney tissues using the Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. RNA integrity and quality were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and verified by RNase-free agarose gel electrophoresis. Eukaryotic mRNA was subsequently enriched from the total RNA using Oligo (dT) magnetic beads, while prokaryotic rRNA was depleted using the Ribo-Zero™ Magnetic Kit (Epicentre, Madison, WI, USA). The enriched mRNA was fragmented into short segments using a fragmentation buffer and reverse-transcribed into first-strand cDNA using random primers. Second-strand cDNA synthesis was performed using DNA polymerase I, RNase H, dNTPs, and reaction buffer. The resulting cDNA fragments were purified using the QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), followed by end repair, poly(A) tailing, and ligation to Illumina sequencing adapters.
The adapter-ligated cDNA libraries were size-selected by agarose gel electrophoresis, amplified by PCR, and subjected to high-throughput sequencing on the Illumina HiSeq2500 platform (Illumina, San Diego, CA, USA) at Gene Denovo Biotechnology Co. (Guangzhou, China). Sequencing data were processed to quantify gene abundance, followed by pathway enrichment analysis and Gene Ontology (GO) functional enrichment analysis of differentially expressed genes. These analyses were conducted using established bioinformatics pipelines and software tools.

treatment_protocol: The mice on DB/DB+MR409 group received subcutaneous injection of MR409 at 15 mg/mouse every other day, with MR409 dissolved in a 10% of 1, 2-propanediol solution. The mice in WT group and DB/DB group were subcutaneously injected with an equivalent volume of vehicle solution.

value: kidney


title: MR2

description: Library name: SAMPLE8


title: Tumor, murine GPC2 CAR T cells, 5 days, rep2

description: Library name: Sample 5


title: nPOD_6282_snRNA_lib2_MM_554


title: nPOD_6520_snRNA_MM_555


title: MR1

description: Library name: SAMPLE7


title: Ezh2b, mutation, rep1


title: Ezh2a, wild type, rep3

value: Ezh2a, wild type


title: nPOD_6424_snRNA_MM_553


title: nPOD_6278_snRNA_MM_426


title: DB2

description: Library name: SAMPLE5


title: Ezh2a, wild type, rep1


title: Tumor, murine control T cells, 5 days, rep1

description: Library name: Sample 1


title: nPOD_6267_snRNA_MM_408


title: Ezh2a, wild type, rep2


title: Tumor, murine control T cells, 5 days, rep3

description: Library name: Sample 14


title: nPOD_6401_snRNA_MM_407


title: WT3

description: Library name: SAMPLE3


title: DN1_scATAC-seq_Tcf1Lef1dKO

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

data_processing:
The CITE-seq data were first split into the RNA parts (gene expression) and ADT (antibody-derived tags, distinguishing cell genotypes) parts. The RNA parts (DN1_CITE_r*-01-01-*) were preprocessed using the 10x Genomics pipeline (Cell Ranger) v6.1.1 using the mm10 genome (e.g., cellranger count  --sample=DN1_CITE_r1-01-01-01,DN1_CITE_r1-01-01-02,DN1_CITE_r1-01-01-03,DN1_CITE_r1-01-01-04). The ADT parts (DN1_CITE_r*-01-02-*) were preprocessed using CITE-seq-Count (https://github.com/Hoohm/CITE-seq-Count) v1.4.5 (e.g., CITE-seq-Count -R1 DN1_CITE_r1-01-02-01_S6_L006_R1_001.fastq.gz,DN1_CITE_r1-01-02-02_S7_L006_R1_001.fastq.gz,DN1_CITE_r1-01-02-03_S8_L006_R1_001.fastq.gz,DN1_CITE_r1-01-02-04_S4_L006_R1_001.fastq.gz -R2 DN1_CITE_r1-01-02-01_S6_L006_R2_001.fastq.gz,DN1_CITE_r1-01-02-02_S7_L006_R2_001.fastq.gz,DN1_CITE_r1-01-02-03_S8_L006_R2_001.fastq.gz,DN1_CITE_r1-01-02-04_S4_L006_R2_001.fastq.gz -t ADTbarcode.csv -cbf 1 -cbl 16 -umif 17 -umil 26 -cells 10000 -o DN1_ADT -trim 10 -T 5). The ADTbarcode.csv was provided as processed data. Individual cells with high quality on both RNA and ADT parts were kept for downstream analysis (RNA: ≥1000 covered genes. ADT: ≥1000 reads, ≥90% reads mapped to known ADT barcodes, and major ADT barcodes contain ≥90% mapped reads).
The scATAC-seq data were preprocessed using the 10X Genomics pipeline (Cell Ranger ATAC) v1.2.0 using the mm10 genome and default parameters. Samples from various genotypes were processed separately, and individual cells with high quality (TSS enrichment ≥ 7, unique barcode number ≥ 10,000, and doublet ratio < 1.5) were retained for downstream analysis
Assembly: mm10
Supplementary files format and content: CellRanger output file for RNA and CITE-seq-Count output files for ADT (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for CITE-seq.
Supplementary files format and content: Barcoded and aligned fragment file (in tsv format) for scATAC-seq.

source_name: thymocytes

growth_protocol: Thymi from WT, Tcf1−/−, Tcf1−/−Lef1−/−, Runx1−/−Runx3+/–, Tle1+/–34–/– mice at 5-7 weeks of age, and Lin–TCRb–CD8–CD44hiCD25– DN1 cells were sort purified.

extract_protocol:
Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) was performed on sort-purified Lin–TCRb–CD8–CD44hiCD25– DN1 cells from WT, Tcf1−/−, Tcf1−/−Lef1−/−, Runx1−/−Runx3+/–, Tle1+/–34–/– mice. The cells were ‘stained’ with DNA-barcoded, TotalSeq-C0301 anti-mouse hashtag antibodies against H-2 MHC-I (M1/42) and CD45 (30-F11) (BioLegend). Excess hashtag antibodies were removed through two rounds of washing with PBS. The ‘hashtagged” cells of various genotypes were combined and loaded onto 10X Genomics Chromium Controller to generate single-cell Gel Beads in emulsion (GEM).
Construction of gene expression libraries and cell surface protein libraries was performed using the 10X Genomics Chromium Next GEM Single Cell 5’ library kit (PN-1000165), following the manufacturer's instructions. The resulting gene expression and cell surface protein libraries were combined at a molecular ratio of 9:1 and sequenced on Illumina’s NovaSeq X plus platform in paired-end read mode, with a read length of 150 nucleotides at Admera Health. scATAC-seq libraries were constructed with 10X Genomics Chromium Next GEM Single Cell ATAC library kit (PN-1000175).  Libraries were quantified using a KAPA Library Quantification Kit (KK4835), assessed for quality using an Agilent Tapestation, and then sequenced on Illumina’s NovaSeq X plus in paired-end read mode with the read length of 150 nucleotides at the Admera Health.

treatment_protocol: Sorted cells were used directly for downstream analyses without further treatment.

value: thymocytes

value: Tcf1Lef1KO DN1 cells


title: Ezh2a, mutation, rep3

value: Ezh2a, mutation


title: Ezh2a, mutation, rep2


title: Ezh2b, mutation, rep2


title: DB3

description: Library name: SAMPLE6


title: DN1_scATAC-seq_Tle34KO

value: Tle1het/34KO DN1 cells


title: Ezh2a, mutation, rep1


title: DB1

description: Library name: SAMPLE4


title: nPOD_6456_snRNA_MM_405

source_name: pancreas

value: pancreas


title: DN1_scATAC-seq_WT

value: WT DN1 cells


title: WT2

description: Library name: SAMPLE2


title: DN1_scATAC-seq_Runx1KO

value: Runx1KO/3het DN1 cells


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg18_seeds, 28d+ (rep. 3)

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Paired-end sequencing reads, were adapter- and quality trimmed by cutadapt (version 1.10) and sickle (version 1.33) with parameters pe -t sanger -q 20 -l 50
RNA-seq reads were aligned to the respective reference genome using the RNA-Seq aligner STAR (version 2.7.1a) with the parameters --alignIntronMin 20 --alignIntronMax 10000 --bamRemoveDuplicatesType UniqueIdenticalNotMulti --chimSegmentMin 10 --chimOutType Junctions WithinBAM --outFilterMismatchNmax 3 --outFilterMultimapNmax 1 --outSAMattributes NH HI NM MD AS nM jM jI XS ch --outSAMprimaryFlag AllBestScore --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Gene expression values were quantified as estimated counts by salmon (0.14.1).
Assembly: Genomic reference sequences and annotations for the genome-guided transcriptome assembly and subsequent annotation procedures were obtained from Ensembl, release 34 (for A. thaliana), Phytozome, version 12 (for A. lyrata, C. rubella, E. salsugineum, M. truncatula, and B. distachyon), and RefSeq (for T. hassleriana).
Supplementary files format and content: gene transfer format files contain updated gene and transcript structure information for each organism
Supplementary files format and content: semicolon-separated text files contain estimated raw counts for each sample

organism: Arabidopsis thaliana

source_name: fruit-seeds

extract_protocol:
Dissected organs were homogenised and total RNA was isolated using RNeasy Plant Mini Kit (QIAGEN 74904), following the manufacturer's instructions. RNA integrity was measured using an Agilent 2200 TapeStation.
Strand-specific total RNA-Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit according to the manufacturer’s specifications (Illumina 20020610). ERCC RNA Spike-In Control Mix (Ambion 4456740) was added at the beginning of the library preparation before the ribosomal RNA (rRNA) depletion step to allow sample-specific estimation of the lower detection limit. All RNA-Seq libraries were sequenced as paired-end 75bp reads.

value: Arabidopsis thaliana (Col-0)

value: fruit-seeds


title: Tumor, murine GPC2 CAR T cells, 5 days, rep1

description: Library name: Sample 4


title: nPOD_6405_snRNA_MM_406


title: Tumor, murine control T cells, 5 days, rep2

description: Library name: Sample 3


title: nPOD_6229_snRNA_MM_404


title: Fos,Input

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

institute: CSIC-Instituto de Neurociencias de Alicante

description: Library name: Input

data_processing:
Fastq files were trimmed using trim_galore (v0.6.4_dev), after which they were aligned to the mm10 genome using Bowtie2 (v2.3.4.3). Files were filtered for mapq 30 using Samtools3 (v1.9). Macs2 was used for peakcalling. For profile generation, bigwig files were created using deepTools (v3.5.0).
Assembly: mm10
Supplementary files format and content: bigwig, narrowPeak(except for Input file)

source_name: Hippocampus

extract_protocol:
A Dounce homogenizer was used to dissociate hippocampal tissue suspended in ice-cold hypotonic NEB fixing buffer containing 250 mM sucrose, 25 mM KCl, 5 mM MgCl₂, 20 mM Hepes-KOH (pH 7.8), 0.5% IGEPAL CA-630, 0.2 mM spermine, 0.5 mM spermidine, 1× protease inhibitor, and 1.1% PFA. The homogenate was incubated at room temperature for 15 min followed by 0.125 M glycine for 5 min to stop the fixation and washed in the centrifuge twice with ice-cold NEB buffer without PFA. The pellet of nuclei was suspended in 400 μL of RIPA lysis buffer (1% IGEPAL CA-630, 0.1 SDS, 0.5% sodium deoxycholate; PBS 1x; pH 8) prior to its sonication in a Sonifier digital SFX 250 Branson for 9 cycles of 15s on/30 s off. After 15 min of centrifugation at 17000 x g, the supernatant containing isolated chromatin was collected. Samples were diluted in 4000 μL of ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, 167 mM NaCl; pH 8) and incubated overnight at 4°C with the α-Fos monoclonal antibody (Thermo scientific T.142.5). The next day the chromatin was incubated 3 hours with 60 μL of slurry Dynabeads coated to Protein G (Invitrogen) at 4ºC. Beads were thoroughly rinsed at 4ºC as follows: two washes in RIPA-150 buffer, three washes in RIPA-500 buffer (50mM Tris-HCl, 500 mM NaCl, 1 mM, EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate; pH 8), two washes in RIPA LiCl buffer (50 mM Tris-HCl, 1 mM EDTA, 1% NP-40, 0.7%, sodium deosycholate, 500 mM LiCl2), and two final washes in TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA; pH 8.0), five minutes each. Samples were resuspended in 200 μl Elution buffer (1%SDS, 0.1M NaHCO3) and treated with 1 μl of 10 mg/mL RNase A (Fermentas) overnight at 65°C in agitation for crosslink reversion. Samples were treated with 2 μl of 20 mg/mL Proteinase K (Thermo Scientific) for 5 hours at 55°C in agitation. Last, DNA precipitation was performed by phenol-chloroform-isoamyl alcohol (Sigma-Aldrich).
Hiseq v4

value: Hippocampus

value: 2 months

value: none (input)

value: WT

value: Saline


title: DN1_CITE-seq_r2_ADT

data_processing:
The CITE-seq data were first split into the RNA parts (gene expression) and ADT (antibody-derived tags, distinguishing cell genotypes) parts. The RNA parts (DN1_CITE_r*-01-01-*) were preprocessed using the 10x Genomics pipeline (Cell Ranger) v6.1.1 using the mm10 genome (e.g., cellranger count  --sample=DN1_CITE_r1-01-01-01,DN1_CITE_r1-01-01-02,DN1_CITE_r1-01-01-03,DN1_CITE_r1-01-01-04). The ADT parts (DN1_CITE_r*-01-02-*) were preprocessed using CITE-seq-Count (https://github.com/Hoohm/CITE-seq-Count) v1.4.5 (e.g., CITE-seq-Count -R1 DN1_CITE_r1-01-02-01_S6_L006_R1_001.fastq.gz,DN1_CITE_r1-01-02-02_S7_L006_R1_001.fastq.gz,DN1_CITE_r1-01-02-03_S8_L006_R1_001.fastq.gz,DN1_CITE_r1-01-02-04_S4_L006_R1_001.fastq.gz -R2 DN1_CITE_r1-01-02-01_S6_L006_R2_001.fastq.gz,DN1_CITE_r1-01-02-02_S7_L006_R2_001.fastq.gz,DN1_CITE_r1-01-02-03_S8_L006_R2_001.fastq.gz,DN1_CITE_r1-01-02-04_S4_L006_R2_001.fastq.gz -t ADTbarcode.csv -cbf 1 -cbl 16 -umif 17 -umil 26 -cells 10000 -o DN1_ADT -trim 10 -T 5). The ADTbarcode.csv was provided as processed data. Individual cells with high quality on both RNA and ADT parts were kept for downstream analysis (RNA: ≥1000 covered genes. ADT: ≥1000 reads, ≥90% reads mapped to known ADT barcodes, and major ADT barcodes contain ≥90% mapped reads).
The scATAC-seq data were preprocessed using the 10X Genomics pipeline (Cell Ranger ATAC) v1.2.0 using the mm10 genome and default parameters. Samples from various genotypes were processed separately, and individual cells with high quality (TSS enrichment ≥ 7, unique barcode number ≥ 10,000, and doublet ratio < 1.5) were retained for downstream analysis
Assembly: mm10
Supplementary files format and content: CellRanger output file for RNA and CITE-seq-Count output files for ADT (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for CITE-seq.
Supplementary files format and content: Barcoded and aligned fragment file (in tsv format) for scATAC-seq.
Library strategy: CITE-seq

value: DN1 cells from WT, Tcf1KO, Tcf1/Lef1KO, Runx1KO/3het, Tle1/het34KO mice


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg18_seeds, 28d+ (rep. 2)


title: nPOD_6310_snRNA_MM_403


title: Fos_KA_3,ChIP

description: Library name: 6_Fos_KA

value: anti-fos

value: Kainic Acid


title: nPOD_6220_snRNA_MM_402


title: DN1_CITE-seq_r1_ADT

value: thymocytes


title: Fos_KA_2,ChIP

description: Library name: 5_Fos_KA


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg18_seeds, 28d+ (rep. 1)


title: DN1_CITE-seq_r2_RNA


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg17a_seeds, 28d+ (rep. 3)


title: nPOD_6362_snRNA_MM_401


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg17a_seeds, 28d+ (rep. 2)


title: nPOD_6234_snRNA_MM_400


title: WT1

description: Library name: SAMPLE1

value: kidney


title: DN1_CITE-seq_r1_RNA


title: Liver tumor, 8 weeks post AAV8-TTR-Cre injection, mouse 12

city: Hamilton

first: Gregory

last: Steinberg

state: Ontario

address: 1280 Main Street

country: Canada

institute: McMaster University

description: Library name: ACLY KO 12

data_processing:
Sequence quality was assessed using FastQC followed by the removal of low-quality reads and adapter sequences using Cutadapt. Genome alignment was performed using HISAT2 and the Mus musculus mm10 reference genome. Quantification of reads was performed using featureCounts. Differential gene expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: All processed data files are in the format of a two column table with Entrez ID and featureCounts output.

source_name: Liver Tumor

growth_protocol: At 2 wks. of age, C57BL-6/ Aclyf/f mice, obtained from JAX were injected with diethyl nitrosamine (DEN) at 25 mg/kg body weight. After weaning mice were housed with littermates and fed a normal chow diet (Teklad 8640 22/5). At 10 weeks of age, mice were switched to a high fat and high fructose diet (Western Diet (WD): 40 kcal% fat (mostly palm oil), 20 kcal% fructose and 0.02% cholesterol) (Research Diets, Inc., Code: D19101102). When the mice reached 7.5 months, mice were bled from the tail vein, and plasma alpha-fetoprotein (AFP) levels were determined.

extract_protocol:
After 4 (early time point) or 8 (late time point) weeks following AAV injection mice were anesthetized using ketamine/xylazine and liver tumor tissues were collected, flash frozen in liquid nitrogen, and stored for molecular analysis. For RNA-sequencing, frozen tumor tissue (~30 mg) was homogenized with Buffer RLT (RNeasy Mini Kit, Qiagen # 74106), and RNA isolation was performed using RNeasy kit (Qiagen, ID: 74106) following the manufacturer’s instructions. Sample quality was assessed using the Agilent 2100 Bioanalyzer G2938C with the Aligent RNA 6000 Nano Kit (Agilent; Santa Clara, CA, USA).
Only samples passing the RNA integrity number threshold of 7.0 were used for sequencing. mRNA was enriched using NEBNext Poly(A) mRNA Isolation Module (NEB, Ipswich, MA, USA) followed by library preparation using NEBNext® Ultra™ II Directional RNA library kit (NEB, Ipswich, MA, USA). Next-generation sequencing was conducted at the McMaster Genomics Facility, Farncombe Institute, McMaster University, using Illumina HiSeq 1500 (Illumina; San Diego, CA, USA). Samples were randomly distributed across lanes of a HiSeq Rapid v2 flow cell to eliminate lane-specific effects and single-end 50 bp reads were generated at 12.5 million clusters per sample.

treatment_protocol: Animals were grouped based on their AFP levels so there were no differences between groups and were then injected with AAV intravenously (AAV8-YFP or AAV8-TTR-Cre).

value: Liver Tumor

tag: genetic modification

value: Acly tm1.1Welk

tag: timepoint

value: 8 weeks


title: nPOD_6450_snRNA_MM_399

value: pancreas


title: Fos_SAL_2,ChIP

description: Library name: 2_Fos_Sal


title: Liver tumor, 8 weeks post AAV8-TTR-Cre injection, mouse 11

description: Library name: ACLY KO 11


title: Fos_SAL_3,ChIP

description: Library name: 3_Fos_Sal


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg17a_seeds, 28d+ (rep. 1)


title: Fos_SAL_1,ChIP

description: Library name: 1_Fos_Sal


title: nPOD_6459_snRNA_MM_398


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg16_seeds, 28d+ (rep. 2)


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg16_seeds, 28d+ (rep. 1)


title: Liver tumor, 8 weeks post AAV8-TTR-Cre injection, mouse 9

description: Library name: ACLY KO 9


title: nPOD_6479_snRNA_MM_382


title: YY1_WT_ChIP_seq

data_processing:
Data were mapped to the mouse reference genome mm10 with bwa 0.7.15 (mem with default parameters), samtools 1.3.1, and sambamba 0.6.3.
ChIP-Seq peaks were called with macs2 2.1.0.20140616 with “-B” to generate read pileups
Overlaps between peaks were identified with bedtools 2.26.0
DNA motifs were identified (findMotifsGenome.pl: “-size 200 -mask”) and visualized (motif2Logo.pl: “-pdf -ns 1000 -bit”) with homer 4.8.3
GO analysis was conducted with ClusterProfiler 4.8.1 (after removing peaks that are not on reference chromosomes).
Assembly: mm10
Supplementary files format and content: bigWig files

extract_protocol: Libraries were prepared with an NEBNext Ultra DNA Library Prep Kit (New England Biolabs) and 11–18 cycles of PCR amplification, and then sized-selected with PCRClean DX magnetic beads (Aline Biosciences) (0.55´ to remove long fragments, and 0.9´ to remove short fragments). Libraries were quantified by a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and a High Sensitivity DNA Analysis Kit on a Bioanalyzer 2100 (Agilent)

value: Main Olfactory Epithelium (MOE)


title: Liver tumor, 8 weeks post AAV8-TTR-Cre injection, mouse 10

description: Library name: ACLY KO 10


title: nPOD_6236_snRNA_MM_397


title: EZH2_WT_Input


title: nPOD_6431_snRNA_MM_381


title: EZH2_WT_ChIP_seq


title: Fos_KA_1,ChIP

description: Library name: 4_Fos_KA


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg17a_siliques, 28d+ (rep. 3)

value: Arabidopsis thaliana (Col-0)


title: Liver tumor, 4 weeks post AAV8-TTR-Cre injection, mouse 7

description: Library name: ACLY KO 7

value: 4 weeks


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg17a_siliques, 28d+ (rep. 2)

value: fruit-seeds


title: Input_control_for_ATF5


title: nPOD_6264_snRNA_MM_380


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg16_seeds, 28d+ (rep. 3)


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg17a_siliques, 28d+ (rep. 1)


title: Liver tumor, 4 weeks post AAV8-TTR-Cre injection, mouse 6

description: Library name: ACLY KO 6


title: nPOD_6228_snRNA_MM_361


title: TRIM66_WT_Input


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg16_siliques, 28d+ (rep. 3)


title: nPOD_6282_snRNA_lib1_MM_360


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg16_siliques, 28d+ (rep. 2)


title: Liver tumor, 4 weeks post AAV8-TTR-Cre injection, mouse 5

description: Library name: ACLY KO 5


title: Liver tumor, 4 weeks post AAV8-TTR-Cre injection, mouse 4

description: Library name: ACLY KO 4


title: TRIM66_WT_ChIP_seq_rep_2


title: Liver tumor, 4 weeks post AAV8-TTR-Cre injection, mouse 3

description: Library name: ACLY KO 3


title: RNA-Seq of Arabidopsis thaliana (Col-0): fruit_stg16_siliques, 28d+ (rep. 1)


title: ATF5_WT_Input_rep_3


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_carpels, 21d+ (rep. 3)

source_name: carpels

value: carpels


title: Liver tumor, 4 weeks post AAV8-TTR-Cre injection, mouse 2

description: Library name: ACLY KO 2


title: Liver tumor, 8 weeks post AAV8-TTR-Cre injection, mouse 8

description: Library name: ACLY KO 8


title: nPOD_6380_snRNA_MM_358


title: nPOD_6197_snRNA_MM_357


title: Liver tumor, 4 weeks post AAV8-TTR-Cre injection, mouse 1

description: Library name: ACLY KO 1


title: ATF5_WT_Input_rep_2


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_carpels, 21d+ (rep. 2)


title: nPOD_6339_snRNA_MM_356


title: Liver tumor, 8 weeks post AAV8-YFP injection, mouse 9

description: Library name: ACLY WT 9


title: ATF5_WT_Input_rep_1


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_carpels, 21d+ (rep. 1)


title: ATF5_WT_ChIP_seq_rep_4


title: nPOD_6418_snRNA_MM_355


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_late_stg12_carpels, 21d+ (rep. 3)


title: nPOD_6247_snRNA_MM_354


title: Liver tumor, 8 weeks post AAV8-YFP injection, mouse 8

description: Library name: ACLY WT 8


title: nPOD_6375_snRNA_MM_359


title: ATF5_WT_ChIP_seq_rep_3


title: Liver tumor, 8 weeks post AAV8-YFP injection, mouse 7

description: Library name: ACLY WT 7


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_late_stg12_carpels, 21d+ (rep. 2)


title: TRIM66_WT_ChIP_seq_rep_1


title: ATF5_WT_ChIP_seq_rep_2

extract_protocol:
Dissected MOE was dissociated by the Papain Dissociation System (Worthington) at 37 °C for 15 min and trituration for 5-15 times with a cut P1000 pipette tip. Cells were filtered by a 40-μm strainer (Falcon). After spinning at 400 g for 2 min, cells were resuspended in DMEM (Gibco). ChIP-Seq was performed on dissociated MOE cells with a ChIP-IT High Sensitivity Kit (Active Motif) and an S2 focused-ultrasonicator (Covaris) (settings: frequency sweeping, intensity = 3, duty cycle = 2%, cycles per burst = 200, 15 cycles of 1 min on and 1 min off). Final DNA product was eluted into ~60 mL.
Libraries were prepared with an NEBNext Ultra DNA Library Prep Kit (New England Biolabs) and 11–18 cycles of PCR amplification, and then sized-selected with PCRClean DX magnetic beads (Aline Biosciences) (0.55´ to remove long fragments, and 0.9´ to remove short fragments). Libraries were quantified by a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and a High Sensitivity DNA Analysis Kit on a Bioanalyzer 2100 (Agilent)


title: Liver tumor, 8 weeks post AAV8-YFP injection, mouse 6

description: Library name: ACLY WT 6


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_late_stg12_carpels, 21d+ (rep. 1)