title: cusR inducible 2

description: ChIP-Seq of inducible cusR with C-terminal FLAG tag

value: cusR

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol


title: 0.1mM THP-1 rep2

status: Public on Mar 17 2025

type: SRA

city: Tokyo

first: Gaku

last: Ichihara

address: 6-3-1 Niijuku, Katsushika-ku

country: Japan

institute: Tokyo University of Science

library_source: transcriptomic

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Cutadpat-v2.10.
The filtered reads were mapped to reference RNA (GRCh38 release-101) using Bowtie2-2.4.2 (parameters: -p 2 -L 16 --very-sensitive-local -N 1 -nofw -seed 656565 -reorder) and read number of each gene were counted.
Between-sample normalization was performed against raw count data by using R 3.5.1. (https://cran.r-project.org/) and TCC package (EEE-E method).
Assembly: GRCh38 release 101
Supplementary files format and content: Text file (.txt) of raw count matrix for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: monocytes

growth_protocol:
MMNK-1 cells (JCRB, Osaka, Japan) were maintained in low-glucose DMEM (Wako, Osaka, Japan), supplemented with 5% heat inactivated FBS (Biowest, Riverside, MO) at 37°C under 5% CO2 atmosphere. The cells were detached with Accutase (Innovative Cell Technologies, San Diego, CA) and passaged every 2-3 days.
THP-1 cells (ATCC, Rockville, MD) were maintained in RPMI1640 (Wako, Japan) and supplemented with 10% heat inactivated FBS, penicillin, streptomycin, L-glutamine (Gibco, Thermo Fisher, Waltham, MA), and 2-mercapethanol (0.05 mM, Sigma Aldrich, St. Louis, MO), at 37°C in an atmosphere of 5% CO2. The cells were subcultured every 3-4 days.

extract_protocol:
PolyA RNAs were isolated from the cell lysates, using Dynabeads M-270 Streptavidin (Thermo Fisher Scientific, MA) conjugated with biotin-3’ WTA-EcoP-dT25 and amplified according to the previous report with some modifications (GSE110711). 100 ng of the whole-transcriptome library was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs Inc., Tokyo, Japan) with some modifications.
Standard illumina protocols were followed to generate RNA libraries.

treatment_protocol: 1,2-DCP was diluted in complete medium for co-cultures of MMNK-1 and differentiated THP-1 cells. The DMSO concentration was adjusted to 0.1%. The seeded cells were exposed to 1,2-DCP concentrations of 0, 0.1 and 0.4 mM, for 24 hours and then incubated at 37°C, sealed in a Tedlar polyvinyl fluoride (PVF) gas sampling bags

tag: tissue

value: Blood

tag: cell type

value: human macrophages differentiated by PMA

tag: cell line

tag: treatment

value: 0.1 mM 1,2-DCP for 24 hrs


title: SYOI, sgPCGF3, R2

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University of Edinburgh

description: Library name: SYOI_sgPCGF3_R2

data_processing:
FPKM were obtained using featurecounts and bigwig using Bowtie alignment to T2T and bamcoverage
FPKM and bigwig
Assembly: hg19 for FPKM, T2T for bigwigs
Supplementary files format and content: FKPM in xls, RNA profiles in bigwig

source_name: SYO-I

growth_protocol: DMEM, 10% fetal bovine serum and cultured at 37C at 5% CO2.

extract_protocol:
RNA was prepared using RNeasy mini kit (QIAGEN) according to the manufacturer’s protocoland including the DNaseI (QIAGEN) treatment.
RNA-Seq library preparation and sequencing were performed at the High Throughput Sequencing Unit of the Genomics & Proteomics core facility of DKFZ using TruSeq Stranded Total RNA Library Prep kit (Illumina) and HiSeq 2000 v4 single-read 50bp sequencing system.

treatment_protocol: Stable HSSY-II cells expressing Cas9 were first generated and subsequently infected with the corresponding sgRNA

value: SYO-I

value: Human synovial sarcoma cells

tag: genotype

value: Stable Cas9 expression

value: Cas9, PCGF3 knockout


title: 0.1mM THP-1 rep1


title: WT_CD4SP_1

city: Toronto

first: Shaofeng

last: Liu

state: <None>

address: 8th floor, Dr. Tak Mak lab, Princess Margaret Cancer Centre

country: Canada

institute: UHN

description: SMARTer Mouse TCR a/b Profiling Kit

library_source: other

data_processing:
Data were analyzed using MiXCR and VDJtools. Statistical analyses were performed using Prism 5.0 (GraphPad), with the two-tailed paired t-test employed for comparison of repertoire properties.
Assembly: mm10
Supplementary files format and content: TSV files (MiXCR processed files)
Library strategy: TCR-Seq

molecule: other

organism: Mus musculus

source_name: thymus

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Micro Kit (50) (#74034).
TCR libraries were prepared using SMARTer Mouse TCR a/b Profiling Kit
Libraries were  sequenced using the MiSeq platform (Illumina)

treatment_protocol: Single cell suspensions were prepared from mouse thymus, thymocytes were stained with BV605-CD8 and BV711-CD4. CD4SP and CD8SP thymocytes were sorted by FACS (BD Aira Fusion)

value: thymus

value: thymocytes

value: wild type


title: ONPRC006_B

city: Los Angeles

first: Jonathan

last: DiRusso

state: California

address: 615 Charles E. Young Drive

department: Molecular, Cell and Developmental Biology

country: USA

institute: University of California Los Angeles

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw GEX libraries were mapped to the Ensemble rhesus macaque reference genome (Macaca_mulatta.Mmul_10 release 109) using cellranger count (version 6.1.1) from 10x genomics. The aligned data was filtered using SoupX default parameters and quality assessment and filtering of UMIs and individual cells performed using the scater R package with experiment specific thresholds. Data set merging and normalization were performed using the Seurat R package (version 4.0) with default settings.
Assembly: Macaca_mulatta.Mmul_10 Release 109
Supplementary files format and content: Raw matrix files from CellRanger version 6.1.1 using Macaca_mulatta.Mmul_10 release 109.

molecule: polyA RNA

organism: Macaca mulatta

source_name: Ovary

extract_protocol:
Gonads were dissociated using a enzymatic mix (collagenase and dispase in FBS), washed and immdiately proceeded to GEM encapsulation.
Libraries for 10X genomics were produced according to manufacturer's instructions.

value: Ovary

tag: embryonic day/stage


title: cpxR native 1

city: Boston

first: James

last: Galagan

state: Massachusetts

address: 36 Cummington Mall

department: Biomedical Engineering

institute: Boston University

description: ChIP-Seq of native cpxR with C-terminal SPA tag

library_source: genomic

data_processing:
For ChIP-Seq: Adapters were trimmed from reads using Cutadapt version 2.6
For ChIP-Seq: Reads were aligned to GenBank ID U00096.3 using Bowtie2 versioni 2.3.4.1
For ChIP-Seq: Peak calling was done using SPAT
For ChIP-Seq: Peaks with low shift (<45 bases) between forward and reverse coverage were filtered
For ChIP-Seq: Peaks with low enrichment compared to WT controls were filtered
For ChIP-Seq: Peaks from SPA-tagged TFs that matched NagC artifacts were filtered
For ChIP-Seq: Peaks with low overall enrichment (<4.75-fold over genomic average coverage) were filtered
For ChIP-Seq: Peaks mapped to strong tag-independent artifacts (described in manuscript) were filtered
For ChIP-Seq: Peaks mapped to weak tag-independent artifacts were filtered (described in manuscript)
For ChIP-Seq: Peaks adjacent to inducible watermarks were re-added (described in manuscript)
For Library-ChIP: Inserted sequences were counted from raw reads by identifying the anchor sequence (from the flank of the insertion site) "GGACGGATCCTCGAGCATGC", and taking the following 37 nucleotides after the anchor.
For Library-ChIP: Low abundance hits were dropped out (< 0.1% of preIP reads)
For Library-ChIP: Counts were normalized within-sample for sequencing depth by dividing counts by average counts for each insertion sequence
For Library-ChIP: Enrichment was determined as the ratio of normalized postIP:preIP counts
Assembly: U00096.3
Supplementary files format and content: ChIP-Seq: GFF file containing peak calls that passed all filtering steps
Supplementary files format and content: Library-ChIP: TSV file where first column is the inserted sequence identified in processing step 1, columns 2 and 3 are the number of times sequence was identified in R1 and R2 reads, column 4 is the identifier of the sequence from the designed insertion pool, and column 5 is the sum of R1 and R2 reads

molecule: genomic DNA

organism: Escherichia coli K-12

growth_protocol: Cells were grown in indicated media at 30°C with shaking in vented flasks

extract_protocol:
TF-DNA complexes were fixed with formaldehyde and glycine.  For in vivo ChIP-Seq, cells were sheared via sonication; for in vitro ChIP-Seq, DNA was sheared via sonication prior to TF-DNA binding.  Sheared DNA was immunoprecipitated (IP) using anti-FLAG, anti-V5, or anti-6xHis mAb (indicated in metadata).  DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).  For Library-ChIP, preIP samples used sheared DNA purified via ProteinaseK digestion and Qiaquick PCR purification kit prior to addition of anti-tag antibody; postIP samples used sheared DNA that was immunoprecipitated, washed, purified, and extracted in the same way as ChIP-Seq.
ChIP-DNA was converted into NGS libraries compatible with the Illumina platform using the NEBNext Ultra DNA (NEB Cat. No. E7465).  For Library-ChIP, libraries were constructed similarly to Illumina's 16S metagenomic library prep (Illumina Ref #15044223 Rev. B).  Briefly, an initial PCR was performed on DNA with a universal primer pair targeting flanks of the insertion site on the pAMD plasmid where designed sequences were inserted.  These primers contained overhangs that could be targeted by Illumina Nextera XT Index Kit v2 (Illumina Cat. No. FC-131-2001) primers.  First PCR was cleaned up with Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).  Second PCR used a unique pair of primers from the Illumina Nextera kit for each sample, and were cleaned up with AMPureXP beads (Fisher Scientific Cat. No. NC9933872).

treatment_protocol: Inducible strains were treated with arabinose prior to crosslinking, some native strains were treated with GlcNac for 5 minutes prior to crosslinking (treatments indicated in metadata).

tag: strain

tag: transcription factor

value: cpxR

tag: chip antibody

value: anti-FLAG mAb

tag: antibody vendor/catalog#

tag: media

tag: time

value: Log-Phase

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: ONPRC007_A

description: 10X Genomics


title: cbl inducible 2

description: ChIP-Seq of inducible cbl with C-terminal FLAG tag

value: cbl

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: SYOI, sgPCGF1, R1

description: Library name: SYOI_sgPCGF1_R1

value: Cas9, PCGF1 knockout


title: SYOI, sgPCGF1, R2

description: Library name: SYOI_sgPCGF1_R2


title: 0mM THP-1 rep2

value: Blood

value: human macrophages differentiated by PMA

value: 0 mM 1,2-DCP for 24 hrs


title: ONPRC001_B

description: 10X Genomics


title: SYOI, Empty Vector, R2

description: Library name: SYOI_EV_R2

value: SYO-I

value: Human synovial sarcoma cells

value: Stable Cas9 expression

value: Cas9, empty vector


title: 0mM THP-1 rep3


title: 0mM THP-1 rep1


title: betI inducible 2

description: ChIP-Seq of inducible betI with C-terminal FLAG tag

value: betI

value: M9 Minimal with 0.4% glycerol


title: SYOI, Empty Vector, R1

description: Library name: SYOI_EV_R1


title: ONPRC001_A

description: 10X Genomics

value: Ovary


title: basR inducible 2

description: ChIP-Seq of inducible basR with C-terminal FLAG tag

value: basR

value: anti-FLAG mAb


title: SYOI, sgPCGF3, R1

description: Library name: SYOI_sgPCGF3_R1

value: Cas9, PCGF3 knockout


title: 0.4mM MMNK-1 rep3

source_name: cholangiocytes

value: fetal liver

value: immortalized human cholangiocytes

value: 0.4 mM 1,2-DCP for 24 hrs


title: Pou4f3(+/+) P3 cochlear,rep3

city: Nanjing

first: Guoqiang

last: Wan

state: Jiangsu

address: Xuefu Road 12

department: Medical School

country: China

institute: Nanjing University

data_processing:
Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
The sequences were processed and analyzed by GENEWIZ. Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. The estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were set < 0.05 to detect differential expressed ones.
Assembly: mm8
Supplementary files format and content: speadsheet files include FPKM values for each Sample

source_name: cochlear

extract_protocol:
Total RNA of cochleae from P3 wildtype and Pou4f3(Δ/+) mice was extracted using RNAiso plus kit (TaKaRa, Japan). Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), NanoDrop (Thermo Fisher Scientific, USA) and 1% agarose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified doublestranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptorligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using a Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, CA, USA). Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).

value: cochlear


title: asnC native 2

description: ChIP-Seq of native asnC with C-terminal SPA tag

value: asnC

value: Sigma/Cat. No. F1804

value: Log-Phase


title: 0.4mM MMNK-1 rep2


title: HSSY, sgSSX, R1

description: Library name: HSSY_sgSSX_R1

source_name: HS-SY-II

value: HS-SY-II

value: Cas9, SS18-SSX knockout


title: 0.4mM MMNK-1 rep1


title: HSSY, sgSSX, R2

description: Library name: HSSY_sgSSX_R2

value: Human synovial sarcoma cells

value: Stable Cas9 expression


title: Pou4f3(+/+) P3 cochlear,rep1


title: arsR native 2

description: ChIP-Seq of native arsR with C-terminal V5 tag

value: arsR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: Pou4f3(+/+) P3 cochlear,rep2


title: cadC inducible 3

description: ChIP-Seq of inducible cadC with C-terminal FLAG tag

value: cadC

value: M9 Minimal with 0.4% glycerol

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: HSSY, sgPCGF3, R1

description: Library name: HSSY_sgPCGF3_R1

value: Cas9, PCGF3 knockout


title: allS inducible 2

description: ChIP-Seq of inducible allS with C-terminal FLAG tag

value: allS

value: anti-FLAG mAb


title: ONPRC006_A

description: 10X Genomics

value: Ovary


title: 0.1mM MMNK-1 rep2

value: fetal liver

value: immortalized human cholangiocytes

value: 0.1 mM 1,2-DCP for 24 hrs


title: 0.1mM MMNK-1 rep3


title: Pou4f3(Δ/Δ) P3 cochlear,rep3

value: cochlear


title: allR native 14

description: ChIP-Seq of native allR with C-terminal V5 tag

value: allR

value: Log-Phase

value: 40mM glyoxylate


title: HSSY, sgPCGF1, R2

description: Library name: HSSY_sgPCGF1_R2

value: HS-SY-II

value: Human synovial sarcoma cells

value: Stable Cas9 expression

value: Cas9, PCGF1 knockout


title: Chrna9KO_CD4SP_2

description: SMARTer Mouse TCR a/b Profiling Kit

value: thymus

value: thymocytes

value: Chrna9 KO


title: 0.4mM THP-1 rep3

value: Blood

value: human macrophages differentiated by PMA

value: 0.4 mM 1,2-DCP for 24 hrs


title: Pou4f3(Δ/Δ) P3 cochlear,rep1


title: HSSY, sgPCGF1, R1

description: Library name: HSSY_sgPCGF1_R1


title: 0.1mM MMNK-1 rep1

value: fetal liver


title: Pou4f3(Δ/Δ) P3 cochlear,rep2


title: 0mM MMNK-1 rep3

value: immortalized human cholangiocytes

value: 0 mM 1,2-DCP for 24 hrs


title: HSSY, Empty Vector, R2

description: Library name: HSSY_EV_R2

value: Cas9, empty vector


title: Pou4f3(Δ/+) P3 cochlear,rep3

value: cochlear


title: allR native 13

value: allR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: allR native 12

value: M9 Minimal lacking NH4Cl with 0.4% glycerol

value: 40mM allantoin


title: HSSY, sgPCGF3, R2

description: Library name: HSSY_sgPCGF3_R2

value: HS-SY-II

value: Human synovial sarcoma cells

value: Stable Cas9 expression

value: Cas9, PCGF3 knockout


title: 0mM MMNK-1 rep2


title: aaeR inducible 2

description: ChIP-Seq of inducible aaeR with C-terminal FLAG tag

value: aaeR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: allR native 15


title: Pou4f3(Δ/+) P3 cochlear,rep1


title: 0mM MMNK-1 rep1

value: fetal liver

value: immortalized human cholangiocytes

value: 0 mM 1,2-DCP for 24 hrs


title: HSSY, Empty Vector, R1

description: Library name: HSSY_EV_R1

value: Cas9, empty vector


title: Pou4f3(Δ/+) P3 cochlear,rep2

value: cochlear


title: lung, bleomycin, INPUT-eCLIP, rep 1

status: Public on Mar 16 2025

city: Houston

first: Maria

middle: Elisa

last: Ruiz Echartea

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: 3_eCLIP_input
library strategy is AGO2-eCLIP

data_processing:
The umi_tools (v1.1.1) tool was used to prune Unique molecular identifier (UMIs) from reads.  Cutadapt (v3.2) was used for trimming 3’ adapters. Repetitive elements and rRNA sequences were removed and non-repeat mapped reads mapped genome using STAR (v2.7.7a). PCR duplicates were removed with umi_tools (v1.1.1). miRbase (v22.1) miRNAs were reverse mapped to reads with bowtie (v1.2.3) and miRNA portion of each read trimmed. STAR (v2.7.7a) was used to map the miRNA portion of each read to the genome. PCR duplicates were trimmed, and miRNA target cluster peaks were identified with CLIPper (v2.1.0). Individual clusters were annotated with corresponding miRNAs names and peaks annotated to transcripts GENCODE release M25 (GRCm38.p6). Peaks present in both biological samples were selected for downstream analysis. Data peaks were visualized with the UCSC genome browser.
Assembly: GRCm38
Supplementary files format and content: bigWig, peak files with quantitative data of AGO2 binding for each chromosome strand
Supplementary files format and content: bigWig, peak files with quantitative data for miRNA binding for each chromosome strand

source_name: lung

extract_protocol:
Lung AG02-eCLIP+let-7-seq was performed as described in the associated paper from approximately 20x106 cells after UV crosslinking. A primary mouse monoclonal AGO2/EIF2C2 antibody (sc-53521, Santa Cruz Biotechnology) was added to the lung homogenized lysate for immunoprecipitation (IP) at 4°C prior to isolation of AGO2-RNA complexes. The libraries were enriched for binding to let-7 with 5’ biotinylated ssDNA probes antisense to let-7a-5p, let-7b-5p, let-7d-5p, let-7f-5p.
Eluted RNA was purified using an RNA Clean and Concentrator-5 Kit (Zymo Research, cat. #R1015/R1016) and taken through reverse transcription, DNA adapter ligation, and PCR amplification to generate sequencing libraries.

treatment_protocol: Eight week old male mice were treated with 4U/kg of bleomycin intratracheally, then lungs were harvested on day-6 for AG02-eCLIP+let7.

value: lung

value: wild-type

value: bleomycin


title: lung, bleomycin, INPUT-eCLIP, rep 2

description:
Library name: 4_eCLIP_input
library strategy is AGO2-eCLIP


title: lung, bleomycin, AGO2-eCLIP, rep 2

description:
Library name: 2_eCLIP_bleo
library strategy is AGO2-eCLIP

value: AGO2 antibody (Santa Cruz Biotechnology, sc-53521)


title: lung, bleomycin, AGO2-eCLIP, rep 1

description:
Library name: 1_eCLIP_bleo
library strategy is AGO2-eCLIP


title: LDR6_Biorep2

city: Cold Spring Harbor

first: Lucas

last: Cheadle

address: 1 Bungtown Road

institute: Cold Spring Harbor Lab

data_processing:
The raw FASTQ files were processed using Cell Ranger (v7.1.0) and aligned to the mm10 reference genome. Loom files for cell dynamics analysis were generated using Velocyto (v0.17.17) by mapping BAM files to the gene annotation GTF file (refdata-gex-mm10-2020-A).
Assembly: mm10
Supplementary files format and content: Unfiltered cellranger output files, raw_feature_bc_matrix

molecule: nuclear RNA

growth_protocol: All experiments were performed in compliance with protocols approved by the Institutional Animal Care and Use Committee at Cold Spring Harbor Laboratory. C57Bl/6J mice were acquired from JAX (cat. 000664) and housed in normal 12-h light:12-h dark cycles at average temperatures of 68–70 °F, 54–58% humidity and food and water ad libitum

extract_protocol:
The V1 tissue was transferred to a 1 mL dounce containing 300 µL of ice-cold supplemented Homogenization Buffer (0.25M Sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, 5mM DTT, 0.75mM Spermine, 2.5mM Spermidine, 0.05X Protease Inhibitor Cocktail, 1U/µL of Rnase Inhibitor and 0.15% IGEPAL CA-630). The tissue was homogenized with a loose and tight pestle about 10-15 times, respectively. The samples were filtered using 20µm filter and sent to the Single Cell Facility for 10X Genomics processing, library preparation and next-generation sequencing.
Single-cell gene expression libraries were prepared using the Single Cell 3′ Gene Expression kit v3.1 (10× Genomics, #1000268) according to manufacturer’s instructions.

treatment_protocol: After the experimental procedure, the whole brain was dissected and kept in 1X ice-cold Hank's Balanced Salt Solution (HBSS) supplemented with Mg and Ca. The V1 brain region was located using a zoom stereo microscope and both V1 hemisphere were dissected with the assistance of a circular blade punch and micro needle blade. The tissue was immediately processed for single nucleus RNA sequencing.

value: sensory stimulated


title: LDR4_Biorep3


title: LDR4_Biorep2


title: LDR6_Biorep3


title: LDR4_Biorep1


title: LDR6_Biorep1


title: LDR2_Biorep1


title: LDR2_Biorep3


title: LDR2_Biorep2


title: LDR30_Biorep2


title: LDR30_Biorep3


title: LDR30_Biorep1


title: LDR0_Biorep3

value: sensory deprived


title: LDR0_Biorep1


title: LDR0_Biorep2


title: P27_Biorep6

value: normally reared


title: P27_Biorep5


title: P27_Biorep2


title: P27_Biorep3


title: P27_Biorep4


title: P27_Biorep1


title: FXS 2 scRNA-seq

city: Leeds

first: Marine

last: Krzisch

state: West Yorkshire

address: Woodhouse Lane

department: School of Biomedical Sciences

institute: University of Leeds

description: FXS_SW iPSC were acquired from the group of Steven Warren and differentiated into neural precursor cells (NPC). The NPC were labeled with tdTomato using a lentiviral approach.

data_processing:
Fastq files were obtained using "cellranger mkfastq" (Cell Ranger v3 from 10x Genomics).
Sequencing data was mapped to reference genome composed of human hg38, mouse mm10, GFP and Tdtomato sequences with cellranger (v3.0.2) according to 10x genomics pipeline. We use Ensemble version 97 gene annotation to assign UMI to genes.
Genome_build: hg38
Supplementary_files_format_and_content: filtered_gene_bc_matrices text output files from Cell Ranger count.

source_name: tdTomato+ cells from chimeric mouse brain

growth_protocol: Neural precursor cells were generated using pluripotent stem cells (PSC) neural induction medium from Thermofisher and the associated protocol. The cells were then sorted for PSA-NCAM expression via MACS sorting using anti-PSA-NCAM microbeads (Miltenyi Biotech) to obtain NPC directed towards a neuronal fate.

extract_protocol:
Brains were extracted using the Adult mouse and rat brain dissociation kit and the gentleMACS Octo dissociator from Miltenyi biotech.
Single-cell RNA-Seq libraries were generated from each time point using the 10X Genomics Chromium Controller Instrument (10X Genomics, Pleasanton, CA) and ChromiumTM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, 16 rxns PN-1000075, according to manufacturer’s instructions. Reverse transcription and sample indexing was performed using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Briefly, the suspended cells were loaded on a Chromium controller Single-Cell Instrument to first generate single-cell Gel Bead-In-Emulsions (GEMs). After breaking the GEMs, the barcoded cDNA was then purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed and ligated with adaptors. Finally, PCR amplification was performed to enable sample indexing and enrichment of the 3’ RNA-Seq libraries. The final libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay kit (Q32851) and the fragment size distribution of the libraries were determined using the Agilent 2100 BioAnalyzer High Sensitivity DNA kit (5067-4626). Pooled libraries were then sequenced using Illumina Sequencing By Synthesis (SBS) chemistry.

treatment_protocol: The NPC were labeled via infection with a lentivirus carrying the expression cassette of a fluorescent protein (GFP or tdTomato). The NPC were then purified by FACS sorting to obtain a population of highly fluorescent cells.

tag: source detailed

value: From NSG chimeric mice

value: FXS_SW tdT iPS cell line


title: FXS 1 scRNA-seq


title: Control 2 scRNA-seq

description: C1.2_SW iPSC were acquired from the group of Steven Warren and differentiated into neural precursor cells (NPC). The NPC were labeled with GFP using a lentiviral approach.

source_name: GFP+ cells from chimeric mouse brain

value: C1.2_SW-GFP iPS cell line


title: WT, Seedlings, Spd, rep3

city: Waterloo

first: Benjamin

middle: Jean-Marie

last: Tremblay

state: Ontario

address: 200 University Ave W

department: Department of Biology

institute: University of Waterloo

description: Library name: sdl_wt_spd_3

data_processing:
Reads were quality filtered and adapter-trimmed using Trim Galore! with default parameters.
Trimmed reads were mapped onto the TAIR10 genome using STAR with default parameters.
Gene-level quantification based on the Araport11 annotations were obtained using StringTie with default parameters.
Assembly: TAIR10
Supplementary files format and content: CSV files include raw counts or TPM values for all samples and detected genes.

organism: Arabidopsis thaliana

source_name: 14 day-old seedlings

growth_protocol: Arabidopsis thaliana (Col-0) seeds were surface sterilized using chlorine gas and stratified in the dark at 4 ˚C for 72 h before sowing on half-strength MS medium with 0.8% agarose and 1% (w/v) sucrose. Seedlings were grown in a tissue culture chamber at 22 ˚C with continuous 100 µmol m-2 s-1 photosynthetically active radiation (PAR) for 14 d. Plants to be grown to maturity were transplanted to soil in individual pots and moved to a growth chamber with 150 µmol m-2 s-1 PAR in long day conditions.

extract_protocol:
RNA was extracted from approximately 50 mg samples of pooled frozen ground 14 d seedling or unopened bud tissue using the RNeasy mini Kit (Qiagen).
Libraries were prepared using a polyA-enrichment strategy by Novogene (Beijing, China) or Sickkids (Toronto, Canada).

treatment_protocol: Spermidine treatments were performed by supplementing MS medium with 100 µM spermidine.

value: 14 day-old seedlings

value: 100 µM Spermidine


title: WT, Seedlings, MS, rep2

description: Library name: sdl_wt_ms_2

value: mock


title: Control 1 scRNA-seq


title: WT, Seedlings, Spd, rep2

description: Library name: sdl_wt_spd_2


title: WT, Seedlings, MS, rep3

description: Library name: sdl_wt_ms_3


title: WT, Seedlings, MS, rep1

description: Library name: sdl_wt_ms_1


title: WT, Seedlings, Spd, rep1

description: Library name: sdl_wt_spd_1


title: mtn1-1mtn2-5, Seedlings, Spd, rep3

description: Library name: sdl_mtn11mtn25_spd_3


title: mtn1-1mtn2-5, Seedlings, MS, rep3

description: Library name: sdl_mtn11mtn25_ms_3


title: mtn1-1mtn2-5, Seedlings, MS, rep2

description: Library name: sdl_mtn11mtn25_ms_2


title: mtn1-1mtn2-5, Seedlings, Spd, rep1

description: Library name: sdl_mtn11mtn25_spd_1


title: FXS replicate 2

data_processing:
To remove the mouse contamination, the Illumina pair-end reads were first mapped to mouse reference (Ensembl GRCm38.97) with STAR 15 (version 2.5.1b). The un-mapped reads were re-aligned to the human reference, which STAR indexed files were created with the gene annotation including Ensembl GRCh38.97, GFP and tdTomato with --alignIntronMax  6000000 and --sjdbOverhang 50 options.
The genes counts were obtained using featureCounts function from Subread package with unstranded option.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include numberb of reads assigned to each gene for each Sample

source_name: FX2 dCdT

extract_protocol:
Miltenyi Adult mouse and rat Brain Dissociation Kit and the gentleMACS Octo Dissociator (Miltenyi Biotec 130-107-677).
Up to 10 ng of sample was prepared using Takara’s SMART-Seq v4 Ultra Low Input RNA protocol per manufacturer’s guidelines. Briefly, RNA underwent reverse transcription via template switching and amplification, resulting in double stranded cDNA. The amount of cDNA between 100-3000 bp was calculated by Fragment Analyzer and Qubit. 150pg of the sample in range was then added to Illumina’s Nextera XT and processed according to manufacturer’s guidelines. Briefly, the cDNA underwent tagmentation, using Nextera XT’s transposase, and unique dual indexes were added by PCR amplification. Final libraries went through QC with the Fragment Analyzer and qPCR on a Roche Light Cycler 480 II. All libraries were then pooled and sequenced at paired end 51 base-pair using the Illumina NovSeq 6000. Demultiplexed sequencing data was used for analysis.

value: FX2 dCdT

value: Induced pluripotent stem cell line

value: FXS

value: 1 month after injection


title: mtn1-1mtn2-5, Seedlings, MS, rep1

description: Library name: sdl_mtn11mtn25_ms_1


title: mtn1-1mtn2-1, Seedlings, Spd, rep3

description: Library name: sdl_mtn11mtn21_spd_3


title: isogenic control (demethylation) replicate 1

source_name: FX2 dCT

value: FX2 dCT

value: isogenic control


title: mtn1-1mtn2-1, Seedlings, Spd, rep2

description: Library name: sdl_mtn11mtn21_spd_2


title: FXS replicate 1


title: mtn1-1mtn2-1, Seedlings, Spd, rep1

description: Library name: sdl_mtn11mtn21_spd_1


title: S6p_3

city: Changsha

first: danfeng

last: cao

state: Hunan

address: Xiangya International Academy of Translational Medicine, Central South University, No. 172, Tongzipo Road, Yuelu District, Changsha City, Hunan Province

institute: central south university

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were processed using Trimmomatic software and the low quality reads were removed to obtain the clean reads.
Hisat2 software was used to sequence clean reads with the reference genome to obtain the location information on the reference genome or genes and the sequence characteristic information of the sequenced samples
Htseq-count software was used to obtain the number of reads in each sample, which matched to protein-coding genes.
CuffLinks software was used to calculate the FPKM value of protein-coding genes.
Assembly: human genome (GRCh38)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Human tumor cell lines

growth_protocol: NCI-H1299 cells were cultured in RPMI-1640 medium, supplemented with 10% FBS, 1% L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin at 37℃ in a humidifier incubator with 5% CO2.

extract_protocol:
RNA Isolation and Library Preparation Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NCI-H1299 cells were treated with vehicle (0.1% DMSO) or 25 μM 6p for 48 h. Three independent samples were analyzed for each group.

value: Tumor cell line

value: treated with 6p for 48 hours


title: mtn1-1mtn2-1, Seedlings, MS, rep3

description: Library name: sdl_mtn11mtn21_ms_3


title: mtn1-1mtn2-1, Seedlings, MS, rep2

description: Library name: sdl_mtn11mtn21_ms_2


title: S6p_2


title: S6p_1


title: mtn1-1mtn2-1, Seedlings, MS, rep1

description: Library name: sdl_mtn11mtn21_ms_1


title: con_3

value: untreated


title: con_2


title: SWAT_MALE_HFD_2

city: New Haven

first: Matthew

middle: S

last: Rodeheffer

state: Connecticut

address: 316 Cedar St.

department: Comparative Medicine

institute: Yale University

data_processing:
Reads were aligned to reference genome mm9 with TopHat discarding alignments with more than 2 mismatches and not specifying library type as this sets the default library type.
The python module HTSeq was used specifying for an unstranded RNA analysis with preset parameters to quantify gene expression.
Assembly: mm9
Supplementary files format and content: tab-delimited text file matrix includes unnormalized reads per gene

source_name: C57Bl6/J Male mice

growth_protocol: All animals were kept in temperature and humidity-controlled rooms on a 12-hour:12-hour light:dark cycle, with lights on from 7:00 a.m. to 7:00 p.m.

extract_protocol:
RNA was isolated using Direct-zol RNA Miniprep Kit (Zymo Research).
mRNA was purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg2+  (Roche Kapa mRNA Hyper Prep Cat# KR1352).  Following first-strand synthesis with random primers, second strand synthesis and A-tailing was performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs were ligated to library insert fragments.  Library amplification amplified fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP were not amplified. Indexed libraries were quantified by qRT-PCR using a commercially available kit (Roche KAPA Biosystems Cat# KK4854) and insert size distribution determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp were used for sequencing.  For flow cell preparation and sequencing, sample concentrations were normalized to 15 pM and loaded onto an Illumina HiSeq 2500 V4 flow cell at a concentration that yields 25 million passing filter clusters per sample. Samples were sequenced using 75 bp single-end sequencing according to Illumina protocols. The 6 bp index is read during additional sequencing reads that automatically follow the completion of read 1.  Data generated during sequencing runs are simultaneously transferred to the YCGA high-performance computing cluster. A positive control (prepared bacteriophage Phi X library) provided by Illumina was spiked into every lane at a concentration of 0.3% to monitor sequencing quality in real time. Signal intensities were converted to individual base calls during a run using the system's Real Time Analysis (RTA) software.  Base calls were transferred from the machine's dedicated personal computer to the Yale High Performance Computing cluster via a 1 Gigabit network mount for downstream analysis.  Primary analysis - sample de-multiplexing and alignment to the mouse genome - was performed using Illumina's CASAVA 1.8.2 software suite. Only samples with an error rate less than 2 % and with a distribution of reads per sample in a lane within reasonable tolerance were further processed.

treatment_protocol: Male C57Bl6/J mice 6-8 weeks old were kept on standard diet (SD- Harlan Laboratories 2018S) or fed 60% lard high-fat diet (HFD- Research Diets D12492) for 3 days before perigonadal (VWAT) and inguinal subcutaneous (SWAT) tissue collection. Each sample is pooled from tissues from 3 male mice. APCs were isolated via FACS as lineage negative (CD45-/CD31-), CD29+, CD34+, Sca1+, and CD24 -/+.

value: inguinal WAT (SWAT)

tag: Sex

value: male

value: Adipocyte precursor cells

tag: diet

value: 60% lard high-fat diet (HFD)

value: Day 3


title: SWAT_MALE_HFD_3


title: con_1


title: mtn1-1mtn2-5, Seedlings, Spd, rep2

description: Library name: sdl_mtn11mtn25_spd_2

value: 14 day-old seedlings


title: SWAT_MALE_HFD_1


title: isogenic control (demethylation) replicate 2


title: SWAT_MALE_SD_1

value: Standard diet (SD)

value: Day 0


title: VWAT_MALE_SD_2

value: perigonadal WAT (VWAT)


title: SWAT_MALE_SD_2


title: VWAT_MALE_HFD_1


title: VWAT_MALE_SD_1


title: SWAT_MALE_SD_3


title: VWAT_MALE_SD_3


title: NR4A2KO CAR T cells- Tumor Stimulated stim 2 rep 3

city: Melbourne

first: Kevin

middle: C

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: Sample33
CD8-NR4A2KO-day-2-OVCAR-stim-3_sorted.bam

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (hg19)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: hg19
Supplementary files format and content: count file generated by featureCounts

source_name: CD8+ T cells

extract_protocol:
Total RNA extracted from cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.

value: CD8+ T cells

value: NR4A2KO CAR

value: Tumor stimulated stim 2


title: NR4A2KO CAR T cells- Tumor Stimulated stim 3 rep 1

description:
Library name: Sample34
CD8-NR4A2KO-day-3-OVCAR-stim-1_sorted.bam

value: Tumor stimulated stim 3


title: NR4A2KO CAR T cells- Tumor Stimulated stim 2 rep 2

description:
Library name: Sample32
CD8-NR4A2KO-day-2-OVCAR-stim-2_sorted.bam


title: NR4A2KO CAR T cells- Tumor Stimulated stim 3 rep 2

description:
Library name: Sample35
CD8-NR4A2KO-day-3-OVCAR-stim-2_sorted.bam


title: NR4A2KO CAR T cells- Tumor Stimulated stim 3 rep 3

description:
Library name: Sample36
CD8-NR4A2KO-day-3-OVCAR-stim-3_sorted.bam


title: NR4A2KO CAR T cells- Tumor Stimulated stim 2 rep 1

description:
Library name: Sample31
CD8-NR4A2KO-day-2-OVCAR-stim-1_sorted.bam


title: NR4A2KO CAR T cells- Tumor Stimulated stim 1 rep 3

description:
Library name: Sample30
CD8-NR4A2KO-day-1-OVCAR-stim-3_sorted.bam

value: Tumor stimulated stim 1


title: NR4A2KO CAR T cells- Tumor Stimulated stim 1 rep 2

description:
Library name: Sample29
CD8-NR4A2KO-day-1-OVCAR-stim-2_sorted.bam


title: AGFP_S1_L001_R1_001

city: Oslo

first: Tor Erik

last: Rusten

address: Ullernschaussen 70

department: Molecular Cell Biology

country: Norway

institute: University of Oslo

description: Library name: Sample 2 RasV12, scrib-/- tumor GFP+

data_processing:
Sequencing was performed on an Illumina MiSeq system. Raw data were analyzed with the Tuxedo suite (RRID:SCR_013194) and reads were mapped to Drosophila genome release 5.2. Expression was recorded as FPKM: fragments per kilo-base per million reads.
Assembly: reads were mapped to Drosophila genome release 5.2
Supplementary files format and content: Expression was recorded as FPKM: fragments per kilo-base per million reads
Supplementary files format and content: Processed_RNAseq_FKPMDillardEtAl.xlsx

organism: Drosophila melanogaster

source_name: eye antennal disc

growth_protocol: Eye antennal discs were harvested from day 6 wandering larvae

extract_protocol:
50 Eye antennal discs were dissected from wL3 larvae
total RNA was extracted from using Trizol (Life Sciences) according to manufacturer’s protocol.TruSeq RNA Library Prep Kit (Illumina) was used to prepare libraries,

treatment_protocol: No treatment

value: eye antennal disc

value: y,w,ey-flp/y,w;UAS-RasV12/Act>y+>Gal4, UAS-GFP; Frt82B scrib2/Frt82B, tubGal80

tag: batch


title: NR4A2KO CAR T cells- unstimulated rep 2

description:
Library name: Sample26
CD8-NR4A2KO-day-1-IL2-only-2_sorted.bam

value: Unstimulated


title: NR4A2KO CAR T cells- Tumor Stimulated stim 1 rep 1

description:
Library name: Sample28
CD8-NR4A2KO-day-1-OVCAR-stim-1_sorted.bam


title: A_S2_L001_R1_001

description: Library name: Sample 3 RasV12, scrib-/- tumor microenvironment (TME) GFP-


title: NR4A2KO CAR T cells- unstimulated rep 3

description:
Library name: Sample27
CD8-NR4A2KO-day-1-IL2-only-3_sorted.bam


title: VWAT_MALE_HFD_3


title: VWAT_MALE_HFD_2


title: GMRGFP_S7_L001_R1_001

description: Library name: Sample 1 control

value: GMRGFP


title: NR4A2KO CAR T cells- unstimulated rep 1

description:
Library name: Sample25
CD8-NR4A2KO-day-1-IL2-only-1_sorted.bam


title: AT2 cells, knockout, RNA-seq, rep 3

description: Library name: 6_AT2_knockout

data_processing:
The FASTQ files underwent quality control metrics (trimming), read mapping, and gene annotation with default parameters with the RNA-seq Alignment v2.0.2 pipeline (BaseSpace, Illumina).
The RNA-Seq Differential Expression v1.0.1 workflow (BaseSpace, Illumina) was used with default parameters to extract gene counts and to obtain differentially expressed genes with an adjusted p value (FDR) < 0.05 between control and knockout samples.
Assembly: GRCm38
Supplementary files format and content: csv files contain TPM values for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Approximately 800 ng of total RNA was used for construction of sequencing libraries.
Nonstrand-specific, polyA+ -selected RNA-seq libraries were generated using the Illumina TruSeq protocol.

treatment_protocol: Treatment protocol is as described in associated paper.

value: lung

value: let7afd-/-;Sftpc-CreER/+; R26-tdT/+

value: tamoxifen


title: NR4A2/A1R CAR T cells- Tumor Stimulated stim 3 rep 3

description:
Library name: Sample24
CD8-NR4A2-hA1R-day-3-OVCAR-stim-3_sorted.bam

value: NR4A2/A1R CAR


title: P1779_F1_rep1

city: BETHESDA

first: Cihan

last: Oguz

state: MD

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

institute: NIH

description: Library name: SCAF3642

data_processing:
Raw scRNA-Seq data derived from 10x Genomics Single Cell Chromium 3' v3 mRNA libraries were processed using Cell Ranger v6.0.0 run with default parameter settings and the GRCh38-2020-A transcriptome reference to generate the counts in the filtered_feature_bc_matrix.h5 files.
Assembly: hg38 (Cell Ranger GRCh38-2020-A reference). Human GRCh38 (GENCODE v32/Ensembl98): https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-reference-release-notes)
Supplementary files format and content: Cell Ranger scRNA-seq count matrices are in the h5 data format (one h5 file per sample).

source_name: liver tumor

growth_protocol: liver cancer tumor biopsy isolation

extract_protocol:
RNA was extracted from fresh-frozen needle biopsy tumor samples at baseline and post-treatment, whereas RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of Bioanalyzer 2100 system (Agilent Technologies, California, USA).
10x Genomics Single Cell Chromium 3' mRNA libraries were prepared as instructed by the 10x Genomics user guides (https://www.10xgenomics.com/resources/user-guides/).

treatment_protocol: Tremilimumab + Durvalumab + Bevacuzumab

value: liver tumor

value: liver cells

value: Immunotherapy


title: P1779_F1_rep2

description: Library name: SCAF3659


title: NR4A2/A1R CAR T cells- Tumor Stimulated stim 3 rep 2

description:
Library name: Sample23
CD8-NR4A2-hA1R-day-3-OVCAR-stim-2_sorted.bam


title: AT2 cells, knockout, RNA-seq, rep 1

description: Library name: 4_AT2_knockout


title: NR4A2/A1R CAR T cells- Tumor Stimulated stim 3 rep 1

description:
Library name: Sample22
CD8-NR4A2-hA1R-day-3-OVCAR-stim-1_sorted.bam


title: AT2 cells, knockout, IgG CUT&RUN, rep 1

description: Library name: 11_IgG_knockout

data_processing:
CUT&RUN sequencing data was trimmed for low quality reads and Illumina adapters using the trim galore package (https://github.com/FelixKrueger/TrimGalore). Data was mapped using bowtie2 against the mouse genome UCSC build GRCm38/mm10. Peaks were called using MACS2 with IgG serving as control in each sample. Differential peaks between control and knockout samples were determined using DiffReps. H3K27ac peaks significance was achieved with an FDR adjusted q value < 0.05, and fold change exceeding 1.5x. H3K27me3 differential peaks made use of FDR < 0.10, and fold change exceeding 1.5x. Signal tracks were generated using DeepTools v2.1.0 https://deeptools.readthedocs.io/en/2.1.0/index.html) and BEDTOOLS v2.31.0 suite (https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html) for annotation of differential peaks overlapping genes +/-10kb from its genebody. Enriched motifs were derived using the findMotifsGenome.pl HOMER tool. Data peaks were visualized with the UCSC genome browser.
Assembly: GRCm38
Supplementary files format and content: bigWig, peak files with quantitative data
Library strategy: CUT&Run

extract_protocol:
AT2 cell CUT&RUN-seq was performed as described in the associated paper. CUT&RUN was carried on isolated chromatin from sorted cells (~100,000 from pools of two mice per sample) isolated by flow cytometry based on AT2 cell specific Sftpc-CreER reporter recombination.
The KAPA HyperPrep kit (Roche, Basel, Switzerland) was used for library preparation. Assessment of library quality and quantity was done with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA).

treatment_protocol: Eight week old mice were treated with 160 mg/kg of tamoxifen every other day four times, then cells were harvested on day-6 following last treatment.


title: AT2 cells, control, RNA-seq, rep 3

description: Library name: 3_AT2_control

value: Sftpc-CreER/+; R26-tdT/+


title: P1779_rep1

description: Library name: SCAF3645

value: Untreated


title: AT2 cells, knockout, IgG CUT&RUN, rep 2

description: Library name: 12_IgG_knockout


title: P1700_F1_rep1

description: Library name: SCAF3646


title: AT2 cells, control, RNA-seq, rep 2

description: Library name: 2_AT2_control


title: P1700_rep1

description: Library name: SCAF3644


title: AT2 cells, control, IgG CUT&RUN, rep 1

description: Library name: 9_IgG_control


title: NR4A2/A1R CAR T cells- Tumor Stimulated stim 2 rep 3

description:
Library name: Sample21
CD8-NR4A2-hA1R-day-2-OVCAR-stim-3_sorted.bam

value: CD8+ T cells


title: NR4A2/A1R CAR T cells- Tumor Stimulated stim 2 rep 2

description:
Library name: Sample20
CD8-NR4A2-hA1R-day-2-OVCAR-stim-2_sorted.bam

value: Tumor stimulated stim 2


title: P1699_F1_rep1

description: Library name: SCAF2223


title: AT2 cells, knockout, H3K27me3 CUT&RUN, rep 2

description: Library name: 8_H3k27me3_knockout


title: P1699_rep1

description: Library name: SCAF2132


title: AT2 cells, knockout, RNA-seq, rep 2

description: Library name: 5_AT2_knockout


title: NR4A2/A1R CAR T cells- Tumor Stimulated stim 2 rep 1

description:
Library name: Sample19
CD8-NR4A2-hA1R-day-2-OVCAR-stim-1_sorted.bam


title: HeLa Chol-Dep-SREBP2

city: Shanghai

first: Wei

last: Qi

state: Shanghai

address: B514, L Building

department: School of Life Science and Technology

institute: ShanghaiTech University

description: Library name: LPPS-IP_FKR0240286764-2A

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim-galore (version 0.4.4_dev) and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Bowtie2 (version v1.3.0).
ChIP-seq sample depleted repeat sequences by Picard (version 2.23.6) and normalized by drosophila histone modification.
These reads were used to generate binding site with MACS2 (version 2.2.7.1).
Assembly: hg38
Supplementary files format and content: bigwig files were generated using deeptools (version 3.4.3).

source_name: HeLa

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% LPDS (cholesterol-depletion) and 100 units/ml penicillin and 100 μg/ml and streptomycin sulfate with 5% CO2 at 37 °C.

extract_protocol:
ChIP-seq was performed according to the manufacturer’s instructions of ChIP assay kit. HeLa cells were fixed with 0.8% formaldehyde for crosslinking for 7 minutes. After lysis and sonication, the chromatin DNA was purified using SREBP2 antibody and purified DNA was used for sequencing.
The ChIP-Seq library preparation was proceeded as follows: (1) The DNA fragments were end-repaired and A-tailed. (2) The DNA fragments with A tail were ligated with sequencing adaptors. (3) The final DNA library was obtained after size selection and PCR amplification. Libraries were analyzed for size distribution by Agilent 5400 system (Agilent, USA) and quantified by QPCR (1.5 nM).

treatment_protocol: HeLa cells were treated with cholesterol-depleted medium.

value: HeLa

value: Wild type

value: Cholesterol depletion

tag: antibody


title: AT2 cells, control, H3K27me3 CUT&RUN, rep 2

description: Library name: 6_H3k27me3_control

tag: tissue


title: NR4A2/A1R CAR T cells- Tumor Stimulated stim 1 rep 1

description:
Library name: Sample16
CD8-NR4A2-hA1R-day-1-OVCAR-stim-1_sorted.bam

tag: cell type

value: Tumor stimulated stim 1


title: NR4A2/A1R CAR T cells- Tumor Stimulated stim 1 rep 2

description:
Library name: Sample17
CD8-NR4A2-hA1R-day-1-OVCAR-stim-2_sorted.bam


title: Hela Chol-Dep-H3K27ac

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim-galore (version 0.4.4_dev) and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Bowtie2(version v1.3.0).
ChIP-seq sample depleted repeat sequences by Picard (version 2.23.6) and normalized by drosophila histone modification.
These reads were used to generate binding site with MACS2 (version 2.2.7.1).
Assembly: hg38
Supplementary files format and content: bigwig files were generated using deeptools(version 3.4.3).

source_name: Hela

growth_protocol: Hela cells were growth in DMEM supplemented with 10% LPDS (cholesterol-depletion) and 100 units/ml penicillin and 100 μg/ml and streptomycin sulfate with 5% CO2 at 37 °C .

extract_protocol:
ChIP-seq was performed according to the manufacturer’s instructions of ChIP assay kit. Hela cells were fixed with 0.8% formaldehyde for crosslinking for 7 minutes. After lysis and sonication, the chromatin DNA was purified using H3K27ac antibody and purified DNA was used for sequencing.
The ChIP-Seq library preparation was proceeded as follows: (1) The DNA fragments were end-repaired and A-tailed. (2) The DNA fragments with A tail were ligated with sequencing adaptors. (3) The final DNA library was obtained after size selection and PCR amplification. Libraries were analyzed for size distribution by Agilent 5400 system（Agilent, USA） and quantified by QPCR (1.5 nM).

treatment_protocol: Hela cells were treated with cholesterol-depleted medium.

tag: cell line

value: Hela


title: NR4A2/A1R CAR T cells- Tumor Stimulated stim 1 rep 3

description:
Library name: Sample18
CD8-NR4A2-hA1R-day-1-OVCAR-stim-3_sorted.bam

tag: treatment


title: AT2 cells, control, H3K27me3 CUT&RUN, rep 1

description: Library name: 5_H3k27me3_control

tag: genotype


title: HeLa FBS-SREBP2

description: Library name: FBS-IP_FKR0240286762-2A

value: FBS


title: NR4A2/A1R CAR T cells- unstimulated rep 2

description:
Library name: Sample14
CD8-NR4A2-hA1R-day-1-IL2-only-2_sorted.bam

value: Unstimulated


title: Hela Chol-Dep-input


title: AT2 cells, knockout, H3K27ac CUT&RUN, rep 2

description: Library name: 4_H3K27ac, knockout

value: lung

value: let7afd-/-;Sftpc-CreER/+; R26-tdT/+


title: AT2 cells, control, IgG CUT&RUN, rep 2

description: Library name: 10_IgG_control

value: tamoxifen


title: AT2 cells, control, RNA-seq, rep 1

description: Library name: 1_AT2_control


title: AT2 cells, knockout, H3K27ac CUT&RUN, rep 1

description: Library name: 3_H3K27ac, knockout


title: F167A-R-rep 3

data_processing:
Illumina PE150 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim-galore (version 0.4.4_dev) and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2(version 2.2.0).
The number of reads falling in the exons were calculated using featureCounts (version v1.5.3) and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38 and mm10
Supplementary files format and content: comma-delimited text files include FPKM values for each Sample

source_name: Liver

growth_protocol: HeLa cells were growth in DMEM supplemented with 10% FBS or 10% LPDS (cholesterol-depletion) and 100 units/ml penicillin and 100 μg/ml and streptomycin sulfate with 5% CO2 at 37 °C . WT and F167A mutation mice were growth in specific pathogen free (SPF) animal laboratory room.

extract_protocol:
RNA were harvested using Trizol reagent. 200 ng of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends ligated to prepare for was of DNA fragments, Adaptor with hairpin loop structure hybridization. In order to select cDNA fragments of preferentially 370 420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

treatment_protocol: HeLa cells were treated with FBS or cholesterol-depletion medium. WT and F167A mutation mice were treated with fasting and refeeding.

value: Liver

value: SREBP2 F167A/F167A

value: Refeeding


title: Hela SREBP1 KO-Chol-Dep-rep 2


title: Hela SREBP1 KO-Chol-Dep-rep 3


title: F167A-R-rep 2


title: AT2 cells, control, H3K27ac CUT&RUN, rep 1

description: Library name: 1_H3K27ac_control

value: Sftpc-CreER/+; R26-tdT/+


title: NR4A2/A1R CAR T cells- unstimulated rep 1

description:
Library name: Sample13
CD8-NR4A2-hA1R-day-1-IL2-only-1_sorted.bam

value: NR4A2/A1R CAR


title: Control CAR T cells- Tumor Stimulated stim 3 rep 3

description:
Library name: Sample12
CD8-MOCK-day-3-OVCAR-stim-3_sorted.bam

value: CD8+ T cells

value: Control CAR

value: Tumor stimulated stim 3


title: F167A-R-rep 1


title: Hela SREBP1 KO-Chol-Dep-rep 1


title: AT2 cells, knockout, H3K27me3 CUT&RUN, rep 1

description: Library name: 7_H3k27me3_knockout


title: Hela SREBP1 KO-FBS-rep 3


title: Control CAR T cells- Tumor Stimulated stim 3 rep 1

description:
Library name: Sample10
CD8-MOCK-day-3-OVCAR-stim-1_sorted.bam


title: Control CAR T cells- Tumor Stimulated stim 3 rep 2

description:
Library name: Sample11
CD8-MOCK-day-3-OVCAR-stim-2_sorted.bam


title: F167A-F-rep 3

value: Fasting


title: Hela SREBP1 KO-FBS-rep 2


title: NR4A2/A1R CAR T cells- unstimulated rep 3

description:
Library name: Sample15
CD8-NR4A2-hA1R-day-1-IL2-only-3_sorted.bam


title: AT2 cells, control, H3K27ac CUT&RUN, rep 2

description: Library name: 2_H3K27ac_control


title: Hela SREBP1 KO-FBS-rep 1


title: F167A-F-rep 2


title: F167A-F-rep 1


title: Control CAR T cells- Tumor Stimulated stim 2 rep 3

description:
Library name: Sample9
CD8-MOCK-day-2-OVCAR-stim-3_sorted.bam

value: Tumor stimulated stim 2


title: WT-R-rep 3

value: Wild type


title: Hela SREBP2 KO-Chol-Dep-rep 3

value: Hela

value: Cholesterol depletion


title: Control CAR T cells- Tumor Stimulated stim 2 rep 2

description:
Library name: Sample8
CD8-MOCK-day-2-OVCAR-stim-2_sorted.bam


title: WT-R-rep 2


title: Control CAR T cells- Tumor Stimulated stim 1 rep 3

description:
Library name: Sample6
CD8-MOCK-day-1-OVCAR-stim-3_sorted.bam

value: Tumor stimulated stim 1


title: Hela SREBP2 KO-Chol-Dep-rep 2


title: Hela SREBP2 KO-Chol-Dep-rep 1


title: WT-R-rep 1


title: Control CAR T cells- Tumor Stimulated stim 1 rep 2

description:
Library name: Sample5
CD8-MOCK-day-1-OVCAR-stim-2_sorted.bam


title: Control CAR T cells- Tumor Stimulated stim 2 rep 1

description:
Library name: Sample7
CD8-MOCK-day-2-OVCAR-stim-1_sorted.bam


title: Hela SREBP2 KO-FBS-rep 3

value: FBS


title: WT, Buds, Spd, rep4

description: Library name: bud_wt_spd_4

source_name: Unopened flower buds

value: Unopened flower buds

value: wild-type

value: 100 µM Spermidine


title: Control CAR T cells- Tumor Stimulated stim 1 rep 1

description:
Library name: Sample4
CD8-MOCK-day-1-OVCAR-stim-1_sorted.bam


title: WT-F-rep 3

value: Liver


title: Hela SREBP2 KO-FBS-rep 2


title: Control CAR T cells- unstimulated rep 3

description:
Library name: Sample3
CD8-MOCK-day-1-IL2-only-3_sorted.bam

value: Unstimulated


title: Hela SREBP2 KO-FBS-rep 1


title: WT, Buds, Spd, rep3

description: Library name: bud_wt_spd_3


title: Control CAR T cells- unstimulated rep 2

description:
Library name: Sample2
CD8-MOCK-day-1-IL2-only-2_sorted.bam


title: WT, Buds, Spd, rep2

description: Library name: bud_wt_spd_2


title: Hela WT-Chol-Dep-rep 3


title: WT-F-rep 1


title: MMTV-NIC-Ube2iflfl, 6-week-old, replicate 1, scRNA-seq

city: Iowa City

first: Zhijie

last: Li

state: IA

address: 285 Newton Road

institute: University of Iowa

description: 10x Genomics

data_processing:
The scRNA-seq reads were then mapped to custom mm10 reference genome using Cell Ranger v.5.0.1 (cellranger count function), and Seurat was used for further analysis. Cells with unique RNA feature counts less than 200 and more than 5% mitochondrial contamination were removed from further processing. UMAP was generated using Seurat RunUMAP function with default settings by PCA reduction with dims 1:20, followed by FindNeighbors with dims 1:30 and FindClusters with a resolution of 0.4. Differential gene expression was then calculated by FindMarkers and FindAllMarkers with thresholds for percentage of cells between conditions. Adjusted p-value < 0.05 was used as the threshold for statistically significant difference.
Assembly: A custom reference genome including NeuIRESCre transgene was constructed using Cell Ranger (cellranger mkref function). Custome genome information included in mm10_NIC.tar on series record.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mammary tissue

extract_protocol:
mammary glands were harvested from 6-week-old MMTV-NIC and MMTV-NIC/Ube2ifl/fl  mice, and 10-week-old FVB, MMTV-NIC and MMTV-NIC/Ube2ifl/fl  mice (all in FVB background). Basal and luminal epithelial cells were mixed at a 1:1 ratio, and prepared according to 10X Genomics cell preparation guidelines. Approximately, 10,000 cells were loaded per channel to generate single-cell gel beads-in-emulsion (GEMs).
Single-cell RNA-Seq libraries were prepared with Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (#1000128, 10X Genomics), Chromium Next GEM Chip G Single Cell Kit (#1000127, 10X Genomics), and Chromium i7 Multiplex Kit (#120262, 10X Genomics). Libraries were sequenced on an Illumina HiSeq 4000 with 150 bp paired-end reads in the genomics core at University of Iowa (Iowa City, IA).

value: Mammary tissue

value: basal and luminal epithelial cells

value: FVB

tag: age

value: 6 weeks old


title: Hela WT-Chol-Dep-rep 2


title: MMTV-NIC, 6-week-old, replicate 1, scRNA-seq

description: 10x Genomics

tag: strain


title: WT, Buds, Spd, rep1

description: Library name: bud_wt_spd_1


title: A2ARKO + NR4A2/A1R CAR T cells - Tumor Stimulated + NECA(10uM) rep 3

description:
Library name: Sample24
TC-24_sorted.bam

source_name: T cells

value: T cells

value: A2ARKO+ NR4A2/A1R CAR

value: Tumor stimulated + NECA(10uM)


title: Hela WT-Chol-Dep-rep 1

value: Wild type


title: Control CAR T cells- unstimulated rep 1

description:
Library name: Sample1
CD8-MOCK-day-1-IL2-only-1_sorted.bam

value: CD8+ T cells

value: Control CAR


title: A2ARKO + NR4A2/A1R CAR T cells - Tumor Stimulated + NECA(10uM) rep 2

description:
Library name: Sample23
TC-23_sorted.bam


title: WT, Buds, MS, rep4

description: Library name: bud_wt_ms_4

value: mock


title: Hela WT-FBS-rep 3

value: Hela

value: FBS


title: MMTV-NIC-Ube2iflfl, 10-week-old, replicate 2, scRNA-seq

description: 10x Genomics

value: 10 weeks old


title: MMTV-NIC-Ube2iflfl, 10-week-old, replicate 1, scRNA-seq

description: 10x Genomics


title: WT, Buds, MS, rep2

description: Library name: bud_wt_ms_2

value: Unopened flower buds

value: wild-type


title: A2ARKO + NR4A2/A1R CAR T cells - Tumor Stimulated + NECA(10uM) rep 1

description:
Library name: Sample22
TC-22_sorted.bam


title: WT, Buds, MS, rep3

description: Library name: bud_wt_ms_3


title: WT-F-rep 2

value: Liver

value: Fasting


title: Hela WT-FBS-rep 2


title: Hela WT-FBS-rep 1


title: A2ARKO + NR4A2/A1R CAR T cells - Tumor Stimulated rep 2

description:
Library name: Sample20
TC-20_sorted.bam

value: Tumor stimulated


title: WT, Buds, MS, rep1

description: Library name: bud_wt_ms_1


title: MMTV-NIC, 10-week-old, replicate 1, scRNA-seq

description: 10x Genomics

value: Mammary tissue

value: basal and luminal epithelial cells

value: FVB


title: A2ARKO + NR4A2/A1R CAR T cells - Tumor Stimulated rep 3

description:
Library name: Sample21
TC-21_sorted.bam

value: T cells

value: A2ARKO+ NR4A2/A1R CAR


title: CD4_CD3xCLL1_64H_D5776

city: South San Francisco

first: Ittai

middle: Ethan

last: Eres

state: CA

address: 750 Gateway Boulevard

department: CRADI

institute: Amgen

data_processing:
Omicsoft ArrayStudio + In-House Software
RNA sequencing reads were aligned to human reference gnome hg38 and fragments per kilobase per million sequenced (FPKM) values were determined with ArraySuite software (Omicsoft, Cary, NC) and in-house software.
Genes with average FPKM values >=1 in at least one cell type and treatment group were considered "expressed" and subjected to downstream differential analysis with DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Blood

growth_protocol: PBMC isolation & cell type purification via STEMCELL negative selection kit

extract_protocol:
Total RNA was harvested using Qiagen Rneasy Mini Kit (Qiagen #74004) with on-column DNase treatment following manufacturer's instructions
RNA libraries from 5ng of total RNA were prepared using the SMART-seq v4 Ultra-low input RNA kit (Takara #634890)

treatment_protocol: Cells were co-cultured in the presence of both tumor cells and the tested tool effector molecules

value: Blood

tag: donor


title: A2ARKO + NR4A2/A1R CAR T cells - Tumor Stimulated rep 1

description:
Library name: Sample19
TC-19_sorted.bam


title: FVB background, scRNA-seq

description: 10x Genomics


title: Ube2iF/F 5xKR-S1 Replicate 3

description:
Ube2iF_F 5xKR vs 5xKR-S1 RNAseq Counts.xlsx
Ube2iF_F 5xKR vs 5xKR-S1 RNAseq Differential test.xlsx

data_processing:
All the raw sequencing data were assessed by FastQC for quality control, and reads were mapped with STAR to mouse reference genome mm10 with default parameters. FeatureCounts were used to calculate read counts for each gene from STAR output bam files. Differential gene expression analysis was performed using DEseq2. Adjusted p-value < 0.05 was used as the threshold for statistically significant difference.
Assembly: mm10
Supplementary files format and content: Counts for each sample
Supplementary files format and content: Differentially expressed features for each sample

growth_protocol: Ube2iF/F cells were maintained at 37 ℃ and 5% CO2 in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin.

extract_protocol:
RNA (100-200 ng/ul) was isolated using the RNeasy Plus Mini Kit, knockdown confirmed with RT-PCR and protein Western blot.
RNA (~20 ug) was submitted to the sequencing core at University of Nebraska Medical Center for library construction and RNA sequencing with 75 bp paired-end reads on Novaseq6000 platform.

treatment_protocol: For adneovirus treatment, Ube2iF/F cells were seeded 1 day before adenovirus transduction at about 50% confluency. Ad5CMVeGFP or Ad5CMVCre-eGFP was diluted with serum-free Opti-MEM before adding into cells. Multiplicity of infection (MOI) was calculated based on PFU/ml. Virus solutions were incubated overnight and replaced with complete culture medium. Small interfering (si) RNAs for the specific knockdown were delivered using Lipofectamine RNAiMAX (Invitrogen) following the manufacturer’s instruction. Cells were harvested and analyzed 96 hours after transfection.

value: 5xKR-S1 with UBE2I knockout


title: mtn1-1mtn2-1, Buds, Spd, rep3

description: Library name: bud_mtn11mtn21_spd_3

value: 100 µM Spermidine


title: mtn1-1mtn2-1, Buds, Spd, rep4

description: Library name: bud_mtn11mtn21_spd_4


title: A2ARKO CAR T cells - Tumor Stimulated + NECA(10uM) rep 3

description:
Library name: Sample18
TC-18_sorted.bam

value: A2ARKO CAR

value: Tumor stimulated + NECA(10uM)


title: CD8_CD3xCLL1_64H_D5097


title: CD4_CD3xCLL1_64H_D5097


title: mtn1-1mtn2-1, Buds, Spd, rep1

description: Library name: bud_mtn11mtn21_spd_1


title: mtn1-1mtn2-1, Buds, Spd, rep2

description: Library name: bud_mtn11mtn21_spd_2


title: MMTV-NIC, 10-week-old, replicate 2, scRNA-seq

description: 10x Genomics


title: NK_NKCE-III_64H_D5097

value: NK

value: NKCE-III


title: NK_NKCE-IV_64H_D5097

value: NKCE-IV


title: Ube2iF/F 5xKR-S1 Replicate 2


title: A2ARKO CAR T cells - Tumor Stimulated + NECA(10uM) rep 2

description:
Library name: Sample17
TC-17_sorted.bam


title: mtn1-1mtn2-1, Buds, MS, rep4

description: Library name: bud_mtn11mtn21_ms_4

value: Unopened flower buds

value: mock


title: A2ARKO CAR T cells - Tumor Stimulated rep 2

description:
Library name: Sample14
TC-14_sorted.bam


title: A2ARKO CAR T cells - Tumor Stimulated rep 3

description:
Library name: Sample15
TC-15_sorted.bam


title: mtn1-1mtn2-1, Buds, MS, rep3

description: Library name: bud_mtn11mtn21_ms_3


title: Ube2iF/F 5xKR Replicate 2

value: 5xKR with UBE2I knockout


title: NK_NKCE-II_64H_D5097

value: NKCE-II


title: mtn1-1mtn2-1, Buds, MS, rep2

description: Library name: bud_mtn11mtn21_ms_2


title: NK_NKCE-I+IL2_64H_D5097


title: mtn1-1mtn2-1, Buds, MS, rep1

description: Library name: bud_mtn11mtn21_ms_1


title: Ube2iF/F siEtv1_2 Replicate 2

description:
Ube2iF_F siEtv1 vs siNT RNAseq Counts.xlsx
Ube2iF_F siEtv1 vs siNT RNAseq Differential test.xlsx

value: ETV1 knockdown


title: Ube2iF/F 5xKR Replicate 1

value: basal and luminal epithelial cells


title: NR4A2/A1R CAR T cells- Tumor Stimulated + NECA(10uM) rep 3

description:
Library name: Sample12
TC-12_sorted.bam

value: NR4A2/A1R CAR


title: CD8_CD3xCLL1_64H_D5922


title: G3, Buds, Spd, rep4

description: Library name: bud_g3_spd_4


title: A2ARKO CAR T cells - Tumor Stimulated + NECA(10uM) rep 1

description:
Library name: Sample16
TC-16_sorted.bam

value: T cells


title: Ube2iF/F 5xKR-S1 Replicate 1


title: NR4A2/A1R CAR T cells- Tumor Stimulated + NECA(10uM) rep 2

description:
Library name: Sample11
TC-11_sorted.bam


title: NK_NKCE-IV_64H_D5922


title: G3, Buds, Spd, rep3

description: Library name: bud_g3_spd_3


title: Ube2iF/F siEtv1_1 Replicate 2


title: Ube2iF/F 5xKR Replicate 3


title: NR4A2/A1R CAR T cells- Tumor Stimulated + NECA(10uM) rep 1

description:
Library name: Sample10
TC-10_sorted.bam


title: NK_NKCE-III_64H_D5922


title: NK_NKCE-I+IL2_64H_D5922


title: Ube2iF/F siEtv1_1 Replicate 1


title: G3, Buds, Spd, rep2

description: Library name: bud_g3_spd_2


title: G3, Buds, Spd, rep1

description: Library name: bud_g3_spd_1


title: NR4A2/A1R CAR T cells- Tumor Stimulated rep 2

description:
Library name: Sample8
TC-8_sorted.bam

value: Tumor stimulated


title: Ube2iF/F siNT Replicate 2

value: WT


title: NK_NKCE-II_64H_D5922

value: Blood


title: CD4_CD3xCLL1_64H_D5922


title: G3, Buds, MS, rep4

description: Library name: bud_g3_ms_4


title: A2ARKO CAR T cells - Tumor Stimulated rep 1

description:
Library name: Sample13
TC-13_sorted.bam


title: CD8_CD3xCLL1_64H_D0117


title: NR4A2KO CAR T cells- Tumor Stimulated + NECA(10uM)  rep 3

description:
Library name: Sample6
TC-6_sorted.bam

value: NR4A2KO CAR


title: G3, Buds, MS, rep2

description: Library name: bud_g3_ms_2


title: NK_NKCE-IV_64H_D0117


title: Ube2iF/F_Ad-mCherry Replicate 2

description:
Ube2iF_F mCherry vs Cre RNAseq Counts.xlsx
Ube2iF_F mCherry vs Cre RNAseq Differential test.xlsx


title: Ube2iF/F siEtv1_2 Replicate 1


title: NR4A2/A1R CAR T cells- Tumor Stimulated rep 3

description:
Library name: Sample9
TC-9_sorted.bam


title: Ube2iF/F_Ad-mCherry Replicate 1


title: G3, Buds, MS, rep1

description: Library name: bud_g3_ms_1


title: NR4A2KO CAR T cells- Tumor Stimulated + NECA(10uM)  rep 1

description:
Library name: Sample4
TC-4_sorted.bam


title: NK_NKCE-III_64H_D0117


title: NR4A2KO CAR T cells- Tumor Stimulated + NECA(10uM)  rep 2

description:
Library name: Sample5
TC-5_sorted.bam


title: NK_NKCE-I+IL2_64H_D0117


title: Vegetative nuclei, In vitro Pollen tube, Rep3

city: Lisbon

first: Jörg

middle: Dieter

last: Becker

address: ITQB NOVA Avenida da República

country: Portugal

institute: ITQB

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimgalore
Trimmed sequence reads were then mapped to an Arabidopsis reference genome using Hisat 2. The read counts were estimated using featureCounts.
Assembly: TAIR 10/ Araport 11
Supplementary files format and content: tab-delimited text files include Raw count values for each biological replicate of sperm cells and vegetative nuclei both from mature pollen grain and in vitro and semi in vivo grown pollen tubes

source_name: Vegetative nuclei

growth_protocol: Wild type (Col-0) plants and a transgenic marker line harbouringMGH3p::MGH3-GFPandACT11p::H2B-mRFPwere sown on soil in short-day conditions for 8 weeks in 8-h light at 21–23°C and then transferred to long-day conditions with 16-h light to induce flowering.

extract_protocol:
Fluorescence-activated Cell Sorting (FACS) based identification and purification of sperm cells and vegetative nuclei from mature pollen grain and growing pollen tubes both In Vitro and semi in vivo grown pollen tubes Fluorescence-activated Cell Sorting (FACS) based identification and purification of sperm cells and vegetative nuclei from mature pollen grain and growing pollen tubes both In Vitro and semi in vivo grown pollen tubes.
Smart-seq2 protocol was used to prepare RNA-seq libraries from FACS sorted sperm cells and vegetative nuclei both from mature pollen grain and in vitro and semi in vivo grown pollen tubes  (SIVPT).

treatment_protocol: Semi in vivo pollen tube growth assays were performed as described before. In short, Col-0 flowers were emasculated 16h before use, and were pollinated in vivo with the transgenic line for two hours. After two hours, the pistil was excised and cut at the junction of style and ovary and placed on liquid pollen germination medium containing 0.01% Boric acid, 5 mM CaCl2, 5 mM KCl, 1 mM MgSO4, 10% sucrose, final volume adjusted to pH 7.5). The pistil was incubated for another 4 hours at 22.5 oC , for the pollen tubes to emerge from the cut end of the pistil, resulting in a total of 6 hours of pollen tube growth.  For in vitro pollen tube growth assay, the flowers were collected and gently shaken in pollen germination medium for 3 minutes, followed by centrifugation at 1811 g for 3 minutes. The supernatant was removed gently and the pellet with released pollen was re-suspended in 1ml of pollen germination medium. The re-suspended pollen pellet in germination media was then spread on the cover slip of a round bottom dish as a thin layer. The dish was covered and incubated in the dark for 6h at 22.5 oC.

value: Vegetative nuclei


title: Ube2iF/F_Ad-Cre Replicate 3

value: UBE2I knockout


title: NR4A2/A1R CAR T cells- Tumor Stimulated rep 1

description:
Library name: Sample7
TC-7_sorted.bam


title: NR4A2KO CAR T cells- Tumor Stimulated rep 3

description:
Library name: Sample3
TC-3_sorted.bam


title: Ube2iF/F siNT Replicate 1


title: Vegetative nuclei, In vitro Pollen tube, Rep2


title: NK_NKCE-II_64H_D0117

value: NK


title: Ube2iF/F_Ad-mCherry Replicate 3


title: Vegetative nuclei, In vitro Pollen tube, Rep1


title: Ube2iF/F_Ad-Cre Replicate 2


title: G3, Buds, MS, rep3

description: Library name: bud_g3_ms_3


title: Ube2iF/F_Ad-Cre Replicate 1


title: NR4A2KO CAR T cells- Tumor Stimulated rep 1

description:
Library name: Sample1
TC-1_sorted.bam


title: CD4_CTRL_16H_D5922

value: CTRL


title: Sperm cells, Semi In Vivo Pollen tube, Rep3

source_name: Sperm cells

value: Sperm cells


title: Ube2iF/F Etv1_GFP_Replicate 3

data_processing:
ChIP DNA samples were submitted to the DNA facility at Iowa State University for library construction and sequencing with 100 bp paired-end reads on Novaseq6000 platform.
The sequencing reads were mapped with BWA-MEM to mouse reference genome mm10 with default parameters, and peak calling was performed by MACS2. Annotation of ChIP peaks was using GREAT (version 4, mouse) with a gene regulatory domain defined as nearest gene within 100kb. Heatmap and density plot were generated using DeepTools, and ChIP-seq tracks were visualized by Integrative Genomics Viewer (IGV) for co-alignment of ChIP peaks. Motif enrichment analysis was performed by HOMER Motif Analysis (-findMotifsGenome).
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
After one wash with ice cold PBS, 5x107 cells were resuspended farnham lysis buffer (5mM PIPES pH 8.0, 85mM KCl, 0.5% NP-40 and protease inhibitor). Nuclei pellets were collected by centrifugation at 2,000 rpm at 4℃ for 5 min, and resuspended in RIPA buffer  for sonication using sonic dismembrator at 4℃ with the following settings: 35% amplitude in 10-minute rounds of on/off for 30s for 4 cycles. The sonicated chromatin was centrifuged at 13,000 rpm for 15 min at 4℃.
50 ul of sonicated chromatin was prepared as input chromatin DNA. The rest of supernatant was added into antibody-coupled beads and then rotated together at 4℃ overnight. The next day, beads were washed 5 times with RIPA buffer  for 4 mins, 5 times with LiCl wash buffer (100mM Tris-HCl pH 7.5, 500mM LiCl, 1% NP-40, 1%SDS), and once with TE buffer. Immunoprecipitated chromatin was eluted in 200 ul IP elution buffer (1% SDS, 0.1m NaHCO3) by incubation at 65℃ for 1 hour and centrifuged at 13,000 rpm for 5 min at room temperature. Supernatant containing ChIP DNA was reverse crosslinked by 65℃ incubation overnight. 20 ul of proteinase K and 8 ul of RNase A were added to digest protein and RNA, then purified by using QIAquick PCR purification kit according to the manufacturer’s instructions.

treatment_protocol: Ube2iF/F cells were seeded 1 day before adenovirus transduction at about 50% confluency. Ad5CMVeGFP or Ad5CMVCre-eGFP was diluted with serum-free Opti-MEM before adding into cells. Multiplicity of infection (MOI) was calculated based on PFU/ml. Virus solutions were incubated overnight and replaced with complete culture medium.

tag: chip antibody

value: ETV1 (GTX129202, GeneTex)


title: Control CAR- Tumor Stimulated rep 3

description: Library name: Sample5

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were trimmed for adaptor sequence using Ngmerge, then mapped to the hg38 genome with bowtie2
Peaks were called with Macs2
Assembly: GRCh38
Supplementary files format and content: Peak files called with macs2

extract_protocol:
Sorted CD8+ CAR T cells were lysed using the ZYMO research DNA isolation kit. Tagmentation then purification was performed on DNA, and isolated chromatin was amplified.
Sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit.

value: Control CAR


title: Sperm cells, Semi In Vivo Pollen tube, Rep2


title: CD4_CD3xCLL1_16H_D5922


title: Ube2iF/F Etv1_GFP_Replicate 2


title: Control CAR- Tumor Stimulated rep 2

description: Library name: Sample4


title: Sperm cells, In vitro Pollen tube, Rep3


title: CD4_CD3xCLL1_16H_D5097


title: Control CAR- Tumor Stimulated rep 1

description: Library name: Sample3


title: Sperm cells, Semi In Vivo Pollen tube, Rep1


title: CD4_CTRL_16H_D5776


title: Ube2iF/F Etv1_GFP_Replicate 1


title: Ube2iF/F Etv1_CRE_Replicate 3


title: NR4A2/A1R CAR- Tumor stimulated rep 2

description: Library name: Sample2

value: hA1R transduced CAR


title: Sperm cells, In vitro Pollen tube, Rep2


title: Ube2iF/F Etv1_CRE_Replicate 2


title: NR4A2KO CAR T cells- Tumor Stimulated rep 2

description:
Library name: Sample2
TC-2_sorted.bam


title: CD4_CD3xCLL1_16H_D5776


title: CD8_CTRL_16H_D5922


title: Ube2iF/F Etv1_CRE_Replicate 1


title: NR4A2/A1R CAR- Tumor stimulated rep 1

description: Library name: Sample1


title: CD8_CD3xCLL1_16H_D5922


title: BM-NK cells, SIS3, rep3

city: Hong Kong

first: Guang-yu

last: Lian

address: Li Ka Shing Medical Sciences Building, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin

department: Medicine and Therapeutics

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Base calling was conducted by base-calling software implemented on the RNA-seq instruments.
The internal software SOAPnuke was used to filter reads, including the removal of adaptors, reads in which unknown bases(N) are more than 0.1% and low quality reads.
Then the clean reads were mapped to mouse reference genome GRCm38 (mm10) using HISAT2 (Version: v2.0.4) with parameters: --phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000. StringTie was used to reconstruct transcripts (Version: v1.0.4), followed by Cufflinks (Version: v2.2.1) for annotation. While Bowtie2 (Version: v2.2.5) and RSEM (Version: v1.2.12) were conducted to quantify transcript abundances. DEseq2 was performed for DEG analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file of raw count matrix for all samples.

source_name: BM-NK cells, SIS3

growth_protocol: Bone marrow cells were isolated from the femurs from C57BL/6 mice and cultured in MEM-α medium with 10% FPS supplemented with 1ng/mL IL-7, 10ng/mL Flt3L, 30ng/mL SCF, 50ng/mL IL-15 and 50mM β-mercaptoethanol for 4 days. Then the cells were transferred to MEM-α medium containing 10% FBS supplemented with 50ng/mL IL-15, 20ng/mL IL-2, and 50mM β-mercaptoethanol to induce the maturation of NK cells for another week.

extract_protocol:
Total 1μg RNA was isolated with Pure-Link RNA Mini Kit (Life Technologies) followed by DNase treatment.
Liraries were constructed according to the instructions of DNBseq platform. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo- attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform for the following data analysis study.

treatment_protocol: Pre-treated with 10μM SIS3 for 3 hours before stimulated with 5ng/ml TGF-β1 for 3 hours

value: Bone marrow

value: Bone marrow-derived NK cells


title: CD8_CTRL_16H_D5097


title: Ube2iF/F SUMO1_GFP_Replicate 3

value: basal and luminal epithelial cells

value: SUMO1 (ab32058, abcam)


title: CD4_CTRL_16H_D5097


title: Ube2iF/F SUMO1_GFP_Replicate 2


title: CD8_CD3xCLL1_16H_D5097


title: BM-NK cells, SIS3, rep1


title: hA1R CAR T cells- LeY negative tumor (Unstimulated) rep 1

description:
Library name: Sample9
KS-4_sorted.bam

value: T cells

value: Unstimulated


title: BM-NK cells, SIS3, rep2


title: Control CAR T cells- LeY negative tumor (Unstimulated) rep 1

description:
Library name: Sample7
KS-1_sorted.bam


title: CD8_CD3xCLL1_16H_D0117


title: hA1R CAR T cells- Tumor Stimulated rep 3

description:
Library name: Sample6
KS-12_sorted.bam

value: Tumor stimulated


title: Ube2iF/F SUMO1_CRE_Replicate 3


title: BM-NK cells, TGF-beta, rep2

source_name: BM-NK cells, TGF-beta

treatment_protocol: Treated with 5ng/ml TGF-β1 for 3 hours

value: TGF-beta


title: Ube2iF/F SUMO1_CRE_Replicate 2


title: BM-NK cells, TGF-beta, rep3


title: NK_CTRL_16H_D5922

value: Blood


title: CD8_CTRL_16H_D0117


title: hA1R CAR T cells- LeY negative tumor (Unstimulated) rep 2

description:
Library name: Sample10
KS-6_sorted.bam


title: Sperm cells, In vitro Pollen tube, Rep1

value: WT


title: hA1R CAR T cells- Tumor Stimulated rep 1

description:
Library name: Sample4
KS-10_sorted.bam


title: Ube2iF/F SUMO1_CRE_Replicate 1

value: UBE2I knockout


title: BM-NK cells, TGF-beta, rep1


title: NK_NKCE-IV_16H_D5922

value: NK

value: NKCE-IV


title: Control CAR T cells- LeY negative tumor (Unstimulated) rep 2

description:
Library name: Sample8
KS-2_sorted.bam


title: BM-NK cells, Ctrl, rep3

source_name: BM-NK cells, Ctrl

treatment_protocol: untreated

value: control


title: hA1R CAR T cells- Tumor Stimulated rep 2

description:
Library name: Sample5
KS-11_sorted.bam


title: NK_NKCE-III_16H_D5922

value: NKCE-III


title: Ube2iF/F SUMO1_GFP_Replicate 1


title: BM-NK cells, Ctrl, rep1


title: NK_NKCE-I+IL2_16H_D5922


title: Control CAR T cells- Tumor Stimulated rep 2

description:
Library name: Sample2
KS-8_sorted.bam

value: Control CAR


title: Control CAR T cells- Tumor Stimulated rep 1

description:
Library name: Sample1
KS-7_sorted.bam


title: BM-NK cells, Ctrl, rep2


title: NK_NKCE-II_16H_D5922

value: NKCE-II


title: yPB_2_rep1

city: Planegg

first: Priyanka

last: Bansal

state: Bavaria

address: Großhaderner Str. 9

department: Molecular Biology

country: Germany

institute: Biomedical Center

description: 60 bp

data_processing:
The data processing of the Mnase-seq data was done as described before in (Chacin, E., Reusswig, KU., Furtmeier, J. et al. 2023)
Assembly: SacCer3
Supplementary files format and content: bw (bigwig) files generated from cenome coverage files using rtracklayer (Lawrence et al. 2009)

organism: Saccharomyces cerevisiae

growth_protocol:
In vitro remodeling assay: The remodleing assay was performed as decribed before with modification (Oberbeckmann, E., Niebauer, V. et al., 2021; Oberbeckmann, E., Krietenstein, N. et al., 2021; Chacin et al. 2023) The chromatin factors were used in the following concentrations: 20 nM INO80 and INO80 mutants, 30 nM ORC. The replication reaction was started by addition of SGD chromatin, incubated for 2h at 30°C. The reaction was stopped by addition of apyrase (NEB) with 0.2U and incubated for 20 min at 30°C.
Nuclei isolation: The nuclei isolation was performed as previously described (Chacin et al. 2023)  a 500ml - 1L YPDA culture was incubated for 16-20h at 30°C till OD600 = 0.1-1.0 measured with a GENESYS 20 Visible Spectrophotometer (Thermo Fisher)). The cells were colleced by centrifugation and spheroblasts generated by incubation with zymolyase (MP Biomedicals zymolyase 100T) in 1 M sorbitol, washed and resuspended in a Ficoll solution (18 % Ficoll Type 400 (Sigma-Aldrich), 20mM KH2PO4, 1 mM MgCl2, 0.25 mM EGTA pH 8.0, 0.25 mM EDTA pH 8.0). The resuspended sample was aliquoted an dcentrifuged for 30 min at 22,500 g at 4°C. For storage the samples were frozen in dry ice/ethanol bath and stored at -80°C.

extract_protocol:
Nuclei Mnase digest: The nuclei isolation was performed upon digestion with 16-64 U Mnase in Mnase buffer (150 mM Tris-HCl pH 7.5, 500 mM NaCl, 14 mM CaCl2, 2 mM EDTA, 2 mM EGTA and 50 mM β-mercaptoethanol) to achive an 80 % to 20 % ratio of mono- / di-nucleosome distribution. The reaction was stopped by addition of 45 mM Tris pH 8.5, 10 mM EDTA and  0.5 % SDS. A proteinase K step followed by phenol-chlorofoem extraction, ethanol prectipitation, RNase A digestion an disoprpanaol preciptitaion was performed. To isolat the mononucleosomal DNA a 1.5 % agarose gel was run for 1.5h at 120 V in 1X TAE. The mononucleosomal DNA was cut out and purified using  PureLink Quick Gel Extraction kit (Invitrogen). The exact DNA amount was determined using the Qubit 3.0 Fluorometer (life technologies)
The sequencing libraries were prepared using 10 ng mononucleosomal DNA. The samples were diluted to 10 nM, pooled according to the sequencing reads required (~5 million reads per sample), and quantified via BioAnalyzer. The pool was sequenced with an Illumina NextSeq 1000 in 60 bp paired-end mode (Laboratory for Functional Genome Analysis, Ludwig-Maximilians-Universität Munich). The MNase-seq data was analysed as previously described (Chacin et al., 2023).

tag: chromatin

value: in vivo chromatin

tag: histone type

value: in vivo

tag: orc

tag: remodeler

value: MAT alpha, his3delta1 leu2delta0 lys2delta0 ura3delta0 ARP8::ARP8-S65A, S233A


title: Mata_2_rep1

description: 60 bp

value: MAT alpha, his3delta1 leu2delta0 lys2delta0 ura3delta0


title: yPB_3_rep1

description: 60 bp


title: Sample from human 3D skin model in the SPCM+V8 protease-treated group, replicate3

city: Odawara

first: Masafumi

last: Yokota

state: Kanagawa

address: 5-3-28 Kotobukicho

institute: Kao corporation

data_processing:
The AmpliSeq RNA plugin of the Ion Torrent Suite Software Plugins (Thermo Fisher Scientific) was used for the primary analysis of the sequencing data.
Assembly: hg19
Supplementary files format and content: csv files: RPM values for each sample

source_name: Normal Human Epidermal Keratinocytes (NHEK)

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen). Libraries were prepared from 10 ng of total RNA.
RNA libraries for RNA-seq were prepared using Ion AmpliSeq Transcriptome Human Gene Expression kit following manufacture's protocols.

value: topical treatment of 1% (w/v) V8 protease solution after SLE cream application

tag: time

value: 3 hr


title: AT2 organoids, knockout, RNA-seq, rep 2

description: Library name: 4_organoid_knockout

source_name: lung

value: lung

value: cultured AT2 organoids

value: let7afd-/-;Sftpc-CreER/+; R26-tdT/+

value: tamoxifen


title: Sample from human 3D skin model in the SPCM+V8 protease-treated group, replicate2

value: Normal Human Epidermal Keratinocytes (NHEK)


title: NK_CTRL_16H_D5097

value: Blood

value: NK

value: CTRL


title: INO80EE_ORC_dephos_rep1

description: 60 bp

value: in vitro reconstituted chromatin

value: Drosophila melanogaster embryos

value: ORC

value: Lamda phosphatase treated


title: NK_NKCE-IV_16H_D5097

value: NKCE-IV


title: AT2 organoids, knockout, RNA-seq, rep 1

description: Library name: 3_organoid_knockout


title: Mata_1_rep1

description: 60 bp

value: in vivo chromatin

value: in vivo


title: Control CAR T cells- Tumor Stimulated rep 3

description:
Library name: Sample3
KS-9_sorted.bam

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (hg19)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: hg19
Supplementary files format and content: count file generated by featureCounts

extract_protocol:
Total RNA extracted from cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.

value: T cells

value: Control CAR

value: Tumor stimulated


title: Sample from human 3D skin model in the SPCM+V8 protease-treated group, replicate1

value: topical treatment of 1% (w/v) V8 protease solution after SLE cream application

value: 3 hr


title: AT2 organoids, control, RNA-seq, rep 2

description: Library name: 2_organoid_control

value: lung

value: cultured AT2 organoids

value: Sftpc-CreER/+; R26-tdT/+

value: tamoxifen


title: Sample from human 3D skin model in the V8 protase-treated group, replicate3

value: Normal Human Epidermal Keratinocytes (NHEK)

value: topical treatment of 1% (w/v) V8 protease solution


title: arp8_ORC_dephos_rep1

description: 60 bp

value: in vitro reconstituted chromatin

value: Drosophila melanogaster embryos


title: NK_NKCE-III_16H_D5097

value: Blood

value: NK

value: NKCE-III


title: arp8_ORC_DDK_rep1

description: 60 bp

value: ORC

value: DDK Phosphorylated


title: AT2 organoids, control, RNA-seq, rep 1

description: Library name: 1_organoid_control


title: NK_NKCE-I+IL2_16H_D5097


title: Sample from human 3D skin model in the V8 protase-treated group, replicate2


title: 6month lung, knockout, RNA-seq, rep 4

description: Library name: 8_6m_knockout

value: whole lung

value: let7afd-/-;Sftpc-CreER/+; R26-tdT/+


title: NK_NKCE-II_16H_D5097

value: NKCE-II


title: Sample from human 3D skin model in the V8 protase-treated group, replicate1

value: 3 hr


title: NK_CTRL_16H_D0117

value: CTRL


title: SDINO80_ORC_rep1

description: 60 bp


title: arp8_mut3_ORC_rep1_

description: 60 bp


title: Sample from human 3D skin model in the non-treatment group, replicate3

value: topical treatment of PBS


title: 6month lung, knockout, RNA-seq, rep 3

description: Library name: 7_6m_knockout

value: lung


title: NK_NKCE-IV_16H_D0117

value: NKCE-IV


title: INO80EE_ORC_DDK_rep1

description: 60 bp


title: 6month lung, knockout, RNA-seq, rep 2

description: Library name: 6_6m_knockout

value: tamoxifen


title: Sample from human 3D skin model in the non-treatment group, replicate2

value: Normal Human Epidermal Keratinocytes (NHEK)


title: yPB_1_rep2

description: 60 bp

value: in vivo chromatin

value: in vivo

value: MAT alpha, his3delta1 leu2delta0 lys2delta0 ura3delta0 ARP8::ARP8-S65A, S233A


title: NK_NKCE-III_16H_D0117

value: Blood

value: NK


title: Sample from human 3D skin model in the non-treatment group, replicate1


title: 6month lung, knockout, RNA-seq, rep 1

description: Library name: 5_6m_knockout


title: yPB_1_rep1

description: 60 bp


title: 6month lung, control, RNA-seq, rep 4

description: Library name: 4_6m_control

value: Sftpc-CreER/+; R26-tdT/+


title: NK_NKCE-I+IL2_16H_D0117


title: WT, Buds, Spd, rep3

description: Library name: ws3_FRDM190670914-1a_HLKMYDSXX

data_processing:
Reads were quality filtered and adapter-trimmed using Trim Galore! with default parameters.
Reads were mapped onto the TAIR10 genome assembly, deduplicated, and cytosine methylation calls performed using Bismark with default parameters.
Assembly: TAIR10
Supplementary files format and content: bedGraph files include fraction of methylated cytosines in CG, CHG or CHH contexts.

extract_protocol:
DNA was extracted from approximately 50 mg samples of pooled frozen ground unopened bud tissue using the DNeasy Plant Mini Kit (Qiagen).
Whole-genome bisulfite treatment and library preparation were performed by Novogene (Beijing, China).

treatment_protocol: Spermidine treatments were performed by supplementing MS medium with 100 µM spermidine.

value: Unopened flower buds

value: wild-type

value: 100 µM Spermidine


title: Mata_3_rep2

description: 60 bp

value: MAT alpha, his3delta1 leu2delta0 lys2delta0 ura3delta0


title: 6month lung, control, RNA-seq, rep 3

description: Library name: 3_6m_control

data_processing:
The FASTQ files underwent quality control metrics (trimming), read mapping, and gene annotation with default parameters with the RNA-seq Alignment v2.0.2 pipeline (BaseSpace, Illumina).
The RNA-Seq Differential Expression v1.0.1 workflow (BaseSpace, Illumina) was used with default parameters to extract gene counts and to obtain differentially expressed genes with an adjusted p value (FDR) < 0.05 between control and knockout samples.
Assembly: GRCm38
Supplementary files format and content: csv files contain TPM values for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Approximately 800 ng of total RNA was used for construction of sequencing libraries.
Nonstrand-specific, polyA+ -selected RNA-seq libraries were generated using the Illumina TruSeq protocol.

value: whole lung


title: Mata_3_rep1

description: 60 bp


title: NK_NKCE-II_16H_D0117

value: NKCE-II


title: 6month lung, control, RNA-seq, rep 2

description: Library name: 2_6m_control


title: WT, Buds, Spd, rep2

description: Library name: ws2_FRDM190670913-1a_HLKMYDSXX


title: 6month lung, control, RNA-seq, rep 1

description: Library name: 1_6m_control


title: Ube2iF/F HA_CRE

data_processing:
Libraries were pooled to equimolar concentrations and sequenced with paired-end 150 bp reads on a NovoSeq HiSeq X instrument.
The sequencing reads were mapped with BWA-MEM to mouse reference genome mm10 with default parameters, and peak calling was performed by MACS2. Annotation of CUT&RUN peaks was using GREAT (version 4, mouse) with a gene regulatory domain defined as nearest gene within 100kb. Heatmap and density plot were generated using DeepTools, and CUT&RUN tracks were visualized by Integrative Genomics Viewer (IGV) for co-alignment of peaks. Motif enrichment analysis was performed by HOMER Motif Analysis (-findMotifsGenome).
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&RUN

growth_protocol: Ube2iF/F cells with exogenous expression of HA-tagged Etv1 were maintained at 37 ℃ and 5% CO2 in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin.

extract_protocol:
Cells in log-phase culture (60-80% confluent) were harvested by cell scraping, centrifuged at 300 g and washed twice in calcium-free wash-buffer ((20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM spermidine and protease inhibitor cocktail, cOmplete Mini, EDTA-free Roche). Cells were counted and 500,000 cells per antibody per condition were used for CUT&RUN. Preactivated Concanavalin A-coated magnetic beads (Bangs Laboratories Inc) were added to cell suspension and incubated at 4°C for 10 minutes. Antibody buffer (wash buffer with 2mM EDTA and 0.025% digitonin) containing anti-HA-tag (#3724, Cell Signaling Technology) was added and cells were incubated overnight at 4°C on nutator. The following day, cells were washed in dig-wash buffer (wash buffer containing 0.03% digitonin) and pAG-MNase was added at a concentration of 500 μg/mL. The pAG-MNase reactions were quenched with 2X Stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 100 μg/mL RNAse A, 50 μg/mL Glycogen, and 2 pg/mL sonicated yeast spike-in control). Released DNA fragments were Phosphatase K (1 μL/mL, Thermo Fisher Scientific) treated for 1 hr at 50°C and purified by phenol/chloroform-extracted and ethanol-precipitated. CUT&RUN experiments were performed in parallel as positive control and fragment sizes analyzed using an 2100 Bioanalyzer (Agilent).
CUT&RUN libraries were prepared using the KAPA Hyper Prep Kit (Roche). Quality control post-library amplification was conducted using the 2100 Bioanalyzer for fragment analysis.

treatment_protocol: Ube2iF/F cells with exogenous expression of HA-tagged Etv1 were seeded 1 day before adenovirus transduction at about 50% confluency. Ad5CMVeGFP or Ad5CMVCre-eGFP was diluted with serum-free Opti-MEM before adding into cells. Multiplicity of infection (MOI) was calculated based on PFU/ml. Virus solutions were incubated overnight and replaced with complete culture medium.

value: basal and luminal epithelial cells

value: UBE2I knockout