title: C038_2_HTO

description: Library name: Capture 2_HTO

data_processing:
For data processing, reads from each capture were processed via 10X Genomics Cell Ranger software (v7.0.0). First, ‘cellranger mkfastq’ and bcl2fastq (v2.19.1) were used to convert and demultiplex the Illumina sequencer’s BCL files into FASTQ files for each of the gene expression (GEX), antibody-derived tag (ADT), and hashtag oligo (HTO) libraries. Second, ‘cellranger multi’ was used with default settings to generate count matrices. The GEX data were mapped and quantified to the GRCh38 human reference genome, and the transcriptome and feature barcoding (ADT and HTO) data were quantified against a ‘feature.csv’ file containing the barcode sequences provided by BioLegend. Finally, the DropletUtils R/Bioconductor package (v1.18.1) was then used to load the Cell Ranger output files into R (v4.2.1) and to identify nonempty droplets via the ‘emptyDrops’ method with default settings (Lun et al. 2019). For demultiplexing, the ‘demuxmix’ method from the demuxmix (v1.0.0) R/Bioconductor package (Klein et al. 2023) was applied to the HTO data, with the ‘naive’ model and default parameters, to multiplex nonempty droplets to their sample of origin. This process was performed separately for each capture. A droplet was assigned to a sample if the best demuxmix assignment matched the corresponding HTO combination of a sample or was otherwise assigned as a ‘multiplet,’ ‘negative,’ or ‘uncertain’ sample.
Assembly: GRCh38 human reference genome
Supplementary files format and content: features.tsv.gz is a compressed text file storing the information about the genes (features) measured in the experiment, typically including their gene names and corresponding identifiers (e.g. Ensembl IDs).
Supplementary files format and content: matrix.mtx.gz is a compressed tab-separated value file containing the gene expression count matrix, where each row represents a gene and each column represents a single cell.
Supplementary files format and content: barcodes.tsv.gz is a compressed text file containing the unique cell barcodes associated with each column in the gene expression matrix,  identifying each individual cell analyzed in the single-cell RNA seq experiment

molecule: protein

source_name: Tonsils

extract_protocol:
The cryopreserved mononuclear cell suspensions from the tonsil samples were thawed and processed to form single-cell suspensions. The samples were stained for surface antigen expression via the indicated antibodies and TotalSeq HashTags (BioLegend) for 30 min at 4°C, followed by viability dye staining for 15 min at 4°C. Sample suspensions were sorted via a BD FACSAria Fusion Flow Cytometer (BD Biosciences) to isolate CD3+CD4+CD45RA-CD45RO+CXCR5+CD27+ TFH cells.
Equal numbers of sorted cells from each tonsil sample were pooled and stained with TotalSeq-A Human Universal Cocktail in accordance with the manufacturer’s protocols. Sequence tags of DNA-barcoded mAbs for CITE-seq were incorporated into existing scRNA-seq methods to enable simultaneous quantification of protein and gene expression by single cells. A total of 40,000 cells from the stained TFH pool were subjected to 3’-tag capture via the 10X Genomics Chromium Controller. Library preparation was conducted for sequencing according to the manufacturer’s protocols. Next-generation sequencing was performed using the Illumina NovaSeq 6000 System.

treatment_protocol: Healthy donor tonsils

value: Tonsils

value: T follicular helper cell

value: Healthy donor (no treatment)


title: C038_1_HTO

status: Public on Aug 25 2025

type: SRA

city: Parkville

first: Joanna

last: Groom

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

description: Library name: Capture 1_HTO

library_source: other

organism: Homo sapiens

tag: tissue

tag: cell type

tag: treatment


title: Mouse skin, radiated, Week 2, Rep 3

city: Bronx

first: Kosaku

last: Shinoda

state: New York

address: 1301 Morris Park Ave

department: Medicine

country: USA

institute: Albert Einstein College of   Medicine/Montefiore Medical Center

description:
Library name: Sample 16
W2-3

library_source: transcriptomic

data_processing:
Fastq files were trimmed for  adaptor and low quality sequence using Trim Galore v0.6.7
Transcript-level counts were estimated by Kallisto v0.46.2
Outputs from Kallisto were imported into R using the Bioconductor package tximport (v1.28.0), and the expression levels of each gene were estimated.
Assembly: mm10
Supplementary files format and content: comma-separated text file including gene-level raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Skin

extract_protocol:
Samples were extracted for total RNA using the RNeasy mini-kit (Qiagen) protocol.
Samples were sent to Azenta (GENEWIZ) for RNA sequencing, and bioinformatic analysis was performed using Kallisto and DESeq2 software.

treatment_protocol: Radiation conducted for the four groups of mice at initial time point. Output was delivered over 420 seconds at a dose rate of 3.6 Gy/min for a total of 25 Gy. After radiation, treated skin was shaved over the left flank with an electric razor. Skin biopsies were taken at each time point from the radiated site, stored in RNAlater, and frozen at -80 degrees Celsius.

value: Skin


title: C038_2_ADT

description: Library name: Capture 2_ADT


title: R7_trp3 hESC H9 cells, graft, Month6

city: Milan

first: Elena

last: Cattaneo

address: Via Celoria, 26

department: Bioscience

country: Italy

institute: University of Milan

description: Library name: R7_trp3

data_processing:
nf-core scrnaseq pipeline v2.5.1
Assembly: GRCh38
Supplementary files format and content: Features_matrix_grafts.mtx Matrix file includes raw counts of grafted cells
Supplementary files format and content: Features_matrix_vitro.mtx Matrix file includes raw counts of in-vitro cells
Supplementary files format and content: Features_processed_grafts.tsv tab-delimited text file includes gene names of grafted cells
Supplementary files format and content: Features_processed_vitro.tsv tab-delimited text file includes gene names of in-vitro cells
Supplementary files format and content: MetaData_processed_grafts.tsv tab-delimited text file includes processed dataset metadeta of grafted cells
Supplementary files format and content: MetaData_processed_vitro.tsv tab-delimited text file includes processed dataset metadeta of in-vitro cells

molecule: polyA RNA

source_name: Brain graft

extract_protocol:
Nuclei were thawed in ice and transferred in a glass douncer with 1mL of nuclei lysis buffer till complete homogenization.The nuclei suspension was centrifuged at 500 g for 5 min at 4 °C, and resuspended in cold resuspension buffer. The resuspended nuclei were then filtered through a 30 μm nylon mesh into pre-coated 1.5ml eppendorfs. DRAQ7 was added immediately before fluorescence-activated nuclear sorting. Intact nuclei were identified based on DRAQ7 and side scatter (SSC) signals and sorted with the BD FACSAria III Cell Sorter using a 100 μm nozzle into collection tubes coated with D-PBS supplemented with 2% BSA.
10,000 to 12,000 nuclei per sample (in up to 45 μl total volume) were collected for the library preparation. Single nuclei were captured using the Chromium Single Cell 3´ Chips (10X Genomics, cat. no. PN-120233, v3.1) loaded with master mix and barcoded beads. After pooling and amplification, the quality of the resulting libraries was checked by a Bioanalyzer (DNA HS kit, Agilent) and sequencing was performed on an Illumina NovaSeq 6000 in 100 bp paired-end mode.

value: Brain graft

tag: cell line

value: hESC H9

value: hESC differentiated into MSN enriched culture


title: C038_1_ADT

description: Library name: Capture 1_ADT


title: Mouse skin, radiated, Week 3, Rep 3

description:
Library name: Sample 24
W3-3


title: C038_2_GEX

description: Library name: Capture 2_GEX

library_source: transcriptomic single cell


title: Mouse skin, radiated, Week 2, Rep 2

description:
Library name: Sample 14
W2-2


title: Mouse skin, control, Week 2, Rep 2

description:
Library name: Sample 15
W2-2C


title: C038_1_GEX

description: Library name: Capture 1_GEX


title: R2_trp3 hESC H9 cells, graft, Month6

description: Library name: R2_trp3


title: CON-ASPC-3_IgG

city: Shanghai

first: Hongrui

last: Chen

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

country: China

institute: Shanghai ninth people's hospital

description: Library name: Sample12

library_source: genomic

data_processing:
CUT&Tag reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: adipose

extract_protocol:
CUT&Tag analysis was performed using the Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) as described by the manufacturers with some modifications. Briefly, nuclei were extracted from the 10,000 fresh cells, and added the ConA beads incubating at room temperature for 10 min. The mixed complexes were the incubated with antibodies with IgG antibody as a control, and the next day, followed by the secondary antibody. A diluted pA-Tn5 adapter complex was then added to the above system and incubated at room temperature for 1 h. After extensive washing, system were subsequently sheared by adding 5 × TTBL. Subsequent proteinase K and DNA extract beads were used for obtaining eluted DNA.
Finally, the sequencing libraries were established after 12 cycles of PCR amplification and sequenced using Illumina Novaseq 6000 with paired-end 2x150 as the sequencing mode.

value: adipose

value: adipose stem and progenitor cells

tag: antibody


title: Mouse skin, radiated, Week 2, Rep 1

description:
Library name: Sample 12
W2-1


title: Mouse skin, control, Week 2, Rep 1

description:
Library name: Sample 13
W2-1C


title: Mouse skin, control, Week 1, Rep 4

description:
Library name: Sample 11
W1-4C


title: CON-ASPC-3

description: Library name: Sample11


title: Mouse skin, radiated, Week 1, Rep 4

description:
Library name: Sample 10
W1-4


title: CON-ASPC-2

description: Library name: Sample9


title: Mouse skin, radiated, Week 1, Rep 3

description:
Library name: Sample 8
W1-3


title: Mouse skin, control, Week 1, Rep 3

description:
Library name: Sample 9
W1-3C


title: CON-ASPC-1

description: Library name: Sample7


title: Mouse skin, radiated, Week 2, Rep 4

description:
Library name: Sample 18
W2-4


title: CON-ASPC-1_IgG

description: Library name: Sample8


title: FIL-ASPC-3_IgG

description: Library name: Sample6


title: FIL-ASPC-3

description: Library name: Sample5


title: Mouse skin, control, Week 1, Rep 1

description:
Library name: Sample 5
W1-1C


title: FIL-ASPC-2_IgG

description: Library name: Sample4


title: Mouse skin, radiated, Week 1, Rep 1

description:
Library name: Sample 4
W1-1


title: Mouse skin, sham, Rep 3

description:
Library name: Sample 3
Sham-4


title: FIL-ASPC-1_IgG

description: Library name: Sample2


title: Mouse skin, sham, Rep 1

description:
Library name: Sample 1
Sham-2


title: FIL-ASPC-1

description: Library name: Sample1


title: PANC-1, ESRP1

city: Seoul

first: Taehong

last: Min

address: 369, Sangdo-ro, Dongjak-gu, Seoul, Republic of Korea

department: School of Systems Biomedical Science

country: South Korea

institute: Soongsil University

data_processing:
We quantified transcript-level and gene-level abundances using Salmon with Refseq annotation for GRCh38 genome.
The quantified transcript levels were normalized by Transcript Per Million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

growth_protocol: MIA-PaCa2 and PANC-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was isolated with easy-BLUE Total RNA extraction kit (Promega, 17061). 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq mRNA Sample Prep Kit according to the manufacturer’s instructions.

value: pancreatic cancer

tag: genotype

value: ESRP1 overexpression


title: PANC-1, ESRP2

value: ESRP2 overexpression


title: Mouse skin, sham, Rep 2

description:
Library name: Sample 2
Sham-3


title: H3K27ac antibody, Esrrg LKO B6, high-fat diet, ZT10,rep2

city: Houston

first: Dongyin

last: Guan

state: TX

address: 1 Baylor Plaza, ABBR

institute: Baylor College of Medicine

description: Library name: H3k27ac.B6_Esrrg-LKO_Rep2

data_processing:
ChIA-PETdata was processed by ChIA-PET Tool V3(https://github.com/GuoliangLi-HZAU/ChIA-PET_Tool_V3) for long reads. ChIA-PET Tools do linker filters and paired-end reads were mapped to mm10 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideratio and removed duplicates generated by PCR amplification. Next, the non-redundant uniquely-mapped reads from 3 categories were merged and used for peak calling. ChIA-PET further clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) and others.Interaction data or loops with significant PETs >= 3 and PET distance > 8 kb are used for downstream analyses. ChIA-PET can be visualized on Juicebox as 2D contact maps by using Juicer software (Durand et al., 2016) version 1.6.2 to create .hic file format. The selected unique-mapped reads were used to make tagdirectory and peak calling was performed with HOMER.
Assembly: mm10
Supplementary files format and content: tab-delimited bedpe text files include clusters for each sample
Supplementary files format and content: .hic include 2D contact map

source_name: Liver

extract_protocol:
ChIA-PET experiments were performed as described (Zhu et al. 2023) with minor changes. In briefly, mouse livers were harvested and cross-linked in 1% formaldehyde for 20min, followed by quenching with 1/20 volume of 2.5M glycine solution for 5 min, and two washes with 1×PBS. Nuclear extracts were prepared by Dounce homogenization. 30 ml AluI enzyme were used to digested genome of dual-crosslinked liver nuclei at 37℃ O/N. Exposed ends of genomic DNA were dA-tailed and ligated with dT-overhang biotinylated bridge linker at 16℃ O/N. The ligated chromatin was sheared by sonication and pull-down by H3K27ac antibody. Immunoprecipied DNA was subjected to Tn5 tagmentation,
M280 Dynabeads streptavidin pull-down and PCR amplification. PCR products were subjected to size-selection and pairend sequencing on Illumina Hiseq or Novaseq platform.

value: Liver

tag: time

tag: strain

tag: diet

value: High-fat Diet

tag: Sex

value: male


title: PANC-1, LPCX

value: LPCX control


title: CON-ASPC-2_IgG

description: Library name: Sample10


title: MIA-PaCa2, ESRP2


title: H3K27ac antibody, Esrrg WT B6, high-fat diet, ZT10,rep2

description: Library name: H3k27ac.B6_EsrrgGFP_Rep2


title: H3K27ac antibody, Esrrg WT B6, high-fat diet, ZT10, rep1

description: Library name: H3k27ac.B6_EsrrgGFP_Rep1


title: ChIP_SKP1A KO ESC_H2Aub1_lot2

city: Yokohama

first: Shinsuke

last: Ito

state: Kanagawa

address: 1-7-22 Suehirocho

department: IMS

country: Japan

institute: RIKEN

description: Library name: Sample 69

data_processing:
Reads were aligned to UCSC mm9 or UCSC mm10 using bowtie2. The SAM files were converted to the BAM format using Samtools. The PCR duplicates were removed by Picardtools. The BAM files were converted to bigwig files by deepTools2 for visualization. The bigwig files were normalized to reads per million mapped sequence reads (RPKM).
Assembly: mm9
Supplementary files format and content: bigwig

source_name: mouse embryonic stem cells

growth_protocol: Embryonic stem cells were cultured in DMEM supplemented with 20% fetal bovine serum, GlutaMax, MEM nonessential amino acids, 2-mercaptoethanol, GlutaMax and LIF on MEF feeder layers at 37°C in a 5% CO2 incubator.

extract_protocol:
For mESCs, 10^6-10^7 cells were cross-linking by 1% formaldehyde for 10 min at room temperature. Cross-linked cells were washed once with PBS, added swelling buffer (0.1% NP-40, 1 mM DTT in PBS) and chilled on ice for 10 minutes. After centrifuge, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1mM EDTA, 140 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), and then were sonicated by using a BioRuptor sonicator (Diagenode).  On the other hand, protein A/G beads were prepared as washed twice with beads blocking buffer and suspended with beads blocking buffer with approximately 5 µg of antibody and incubated at 4ºC for more than 2 hours. Then, antibody attached beads were washed twice with beads blocking buffer and the chromatin samples were added to those antibody-attached-beads. After overnight incubation at 4ºC, chromatin samples bound beads were washed with RIPA for 2 times, RIPA high salt buffer(10 mM Tris-HCl pH8.0, 1mM EDTA, 500 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) twice, LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) twice and TE twice. The chromatins were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1 % SDS) overnight at 65ºC and treated with RNase for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA samples were purified and used for further  ChIP-seq.
ChIP-seq libraries were prepared by using NEBNext Ultra II FS DNA prep kit (NEB E7805) following manufacturer’s instruction.

treatment_protocol: For induction of conditional KO ESCs, 800 nM (final concentration) 4-OH Tamoxifen (SIGMA) dissolved in ethanol was added into the culture medium.  To inhibit the proteasome activity, 10 µM MG132 was added to ES medium for 3 hours.

value: mouse embryonic stem cells

value: Tamoxifen+

value: SKP1A KO

tag: chip antibody


title: MIA-PaCa2, LPCX


title: Mouse skin, control, Week 1, Rep 2

description:
Library name: Sample 7
W1-2C


title: MIA-PaCa2, ESRP1


title: ChIP_SKP1A KO ESC_H2Aub1_lot1

description: Library name: Sample 68


title: H3K27ac antibody, Esrrg LKO B6, high-fat diet, ZT10,rep1

description: Library name: H3k27ac.B6_Esrrg-LKO_Rep1


title: Trisomic Day 20 hiPSC-CM, Replicate 2, scATACseq

city: San Francisco

first: Angelo

last: Pelonero

state: CA

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

description: 10X Genomics

library_source: genomic single cell

data_processing:
Reads were demultiplexed and aligned with 10X Genomics Cellranger pipelines for initial data processing. Detailed methods are provided in Ranade et al. manuscript.
Assembly: Hg38
Supplementary files format and content: 10x genomics fragments files and associaed index files

source_name: iPSC Cardiac Differentiation

growth_protocol: Trisomic DS1 (UWWC1-DS1) and isogenic control disomic DS2U (UWWC1-DS2U) hiPSC lines were obtained through WiCell (Madison, WI). Both cell lines were transitioned from mTeSR1 media (Stemcell Technologies, 85850) to E8 media (ThermoFisher Scientific, A1517001) and grown on hESC-Qualified Matrigel (Millipore, CLS354277). Cells were passaged by enzymatic dissociation using Accutase (ThermoFisher Scientific, 00-4555-56) when 70-80% confluent in E8 media containing Y-27632 for the first day of passaging (Stemcell Technologies, 72308).

extract_protocol: All library construction steps were performed according to manufacturer's protocols.

treatment_protocol: hiPSCs were extracted using Accutase, which was neutralized by dilution with PBS. Day 20 cardiomyocytes were extracted using 0.25% Trypsin and neutralized with PBS+1% FBS

value: iPSC Cardiac Differentiation

value: Trisomic


title: ChIP_SKP1A fl/fl ESC_H2Aub1_lot2

description: Library name: Sample 67

value: Tamoxifen-

value: WT


title: Trisomic Day 20 hiPSC-CM, Replicate 1, scATACseq

description: 10X Genomics


title: Disomic Day 20 hiPSC-CM, Replicate 2, scATACseq

description: 10X Genomics

value: Disomic


title: ChIP_SKP1A fl/fl ESC_H2Aub1_lot1

description: Library name: Sample 66


title: FIL-ASPC-2

description: Library name: Sample3

value: adipose


title: Disomic Day 20 hiPSC-CM, Replicate 1, scATACseq

description: 10X Genomics


title: Disomic dCas9-VPR DONSON sgRNA infected Day 20 CM, scRNAseq

description: 10X Genomics

data_processing:
Reads were demultiplexed and aligned with 10X Genomics Cellranger pipelines for initial data processing. Detailed methods are provided in Ranade et al. manuscript.
Some samples were prepared using single index library prep and some were prepared with dual index preparation. All samples for scRNAseq were prepared using NEXTGem V3.1 reagents.
Assembly: Hg38
Supplementary files format and content: 10x genomics  scRNA counts matrices

extract_protocol:
hiPSCs were extracted using Accutase, which was neutralized by dilution with PBS. Day 20 cardiomyocytes were extracted using 0.25% Trypsin and neutralized with PBS+1% FBS
All library construction steps were performed according to manufacturer's protocols. Samples were uniformly treated with 9 PCR cycles at cDNA step and 9 PCR cycles at library amplification steps.

treatment_protocol: For CROP-seq and sgRNA treatments, lentivirus infection of hiPSCs was performed. Lentivirus was generated in 293T cells and purified using Lenti-X concentrator.

value: sgRNA infected


title: No ASC control Replicate 3

city: West Lafayette

first: Marxa

middle: Leao

last: Figueiredo

state: IN

address: 625 Harrison St

department: Basic Medical Sciences

institute: Purdue University

description: Library name: LPS_3

data_processing:
Data was checked for QC using FastQC, adapters were trimmed with Cutadapt
Clean data was then aligned to the reference genome with HISAT, and transcripts were assembled with StringTie
Differential expression analyses was performed using DESeq2
Assembly: GRCm38, ensembl release 101
Supplementary files format and content: text file, gene counts

source_name: Lung

extract_protocol:
RNA was preserved in RNALater (Invitrogen) at 4°C overnight, or for up to one week, according to the manufacturer’s protocol, to ensure RNA quality was not compromised. The lung tissues were then removed from RNAlater™ and stored at -80°C. Total RNA was isolated from 15 – 18 mg of these lung tissues. The lung tissues were then added to 600 µL of RLT buffer, supplemented with 10uL of β-Mercaptoethanol (MP Biomedicals, Santa Ana, CA), and homogenized using a PRO200 homogenizer (MidSci, ValleyPark, MO) in three pulses of 10-15 s each at mid-power (setting 3). For cell pellets collected from in vitro experiments, 350 µL of RLT buffer was added to each sample and homogenized by passing the cells through a 27G tuberculin syringe three times. Lysates collected fromin vivo experiments were processed using the Qiagen RNeasy kit (Qiagen, Germantown, MD) and eluted in 50 μL of Ultrapure DNAse/RNase-free distilled water (Invitrogen).
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip.

value: Lung

value: no vector


title: No ASC control Replicate 4

description: Library name: LPS_4


title: No ASC control Replicate 2

description: Library name: LPS_2


title: Disomic dCas9-VPR CXADR sgRNA infected Day 20 CM, scRNAseq

description: 10X Genomics


title: No ASC control Replicate 1

description: Library name: LPS_1


title: Disomic dCas9-VPR Control sgRNA infected Day 20 CM, scRNAseq

description: 10X Genomics


title: ASC bearing IL27 vector Replicate 4

description: Library name: IL27ASC_4

value: received IL27 vector by NEON electroporation


title: Mouse skin, radiated, Week 1, Rep 2

description:
Library name: Sample 6
W1-2

value: Skin


title: Trisomic dCas9-KRAB Control sgRNA infected Day 20 CM, scRNAseq

description: 10X Genomics


title: Disomic dCas9-VPR HMGN1 sgRNA infected Day 20 CM, scRNAseq

description: 10X Genomics


title: ASC bearing IL27 vector Replicate 1

description: Library name: IL27ASC_1


title: Disomic dCas9-VPR ETS2 sgRNA infected Day 20 CM, scRNAseq

description: 10X Genomics


title: ASC bearing empty vector Replicate 3

description: Library name: ASC_3

value: received Empty vector by NEON electroporation


title: ASC bearing empty vector Replicate 4

description: Library name: ASC_4


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 2, Amplicon Library_10, scRNAseq

description: 10X Genomics

value: CROPseq library


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 2, Amplicon Library_9, scRNAseq

description: 10X Genomics


title: ASC bearing empty vector Replicate 2

description: Library name: ASC_2


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 2, Amplicon Library_7, scRNAseq

description: 10X Genomics


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate21, Amplicon Library_8, scRNAseq

description: 10X Genomics


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 2, Amplicon Library_6, scRNAseq

description: 10X Genomics


title: Esrrg antibody, 129, High-fat Diet fed, ZT22

data_processing:
*library strategy: ChIA-PET
ChIA-PETdata was processed by ChIA-PET Tool V3(https://github.com/GuoliangLi-HZAU/ChIA-PET_Tool_V3) for long reads. ChIA-PET Tools do linker filters and paired-end reads were mapped to mm10 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideratio and removed duplicates generated by PCR amplification. Next, the non-redundant uniquely-mapped reads from 3 categories were merged and used for peak calling. ChIA-PET further clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) and others.Interaction data or loops with significant PETs >= 3 and PET distance > 8 kb are used for downstream analyses.  ChIA-PET can be visualized on Juicebox as 2D contact maps by using Juicer software (Durand et al., 2016) version 1.6.2 to create .hic file format. The selected unique-mapped reads were used to make tagdirectory and peak calling was performed with HOMER.
Assembly: mm10
Supplementary files format and content: tab-delimited bedpe text files include clusters for each sample
Supplementary files format and content: .hic include 2D contact map

extract_protocol:
ChIA-PET experiments were performed as described (Zhu et al. 2023) with minor changes. In briefly,  mouse livers were harvested and cross-linked in 1% formaldehyde for 20min, followed by quenching with 1/20 volume of 2.5M glycine solution for 5 min, and two washes with 1×PBS. Nuclear extracts were prepared by Dounce homogenization. 30 ml AluI enzyme were used to digested genome of dual-crosslinked liver nuclei at 37℃ O/N. Exposed ends of genomic DNA were dA-tailed and ligated with dT-overhang biotinylated bridge linker at 16℃ O/N. The ligated chromatin was sheared by sonication and pull-down by H3K27ac antibody. Immunoprecipied DNA was subjected to Tn5 tagmentation,
M280 Dynabeads streptavidin pull-down and PCR amplification. PCR products were subjected to size-selection and pairend sequencing on Illumina Hiseq or Novaseq platform.

value: Liver

value: Esrrg

value: High-fat Diet

value: male


title: ASC bearing empty vector Replicate 1

description: Library name: ASC_1


title: Esrrg antibody, B6, High-fat Diet fed, ZT10


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 2, Amplicon Library_5, scRNAseq

description: 10X Genomics

value: iPSC Cardiac Differentiation


title: H3K27ac antibody, 129, High-fat Diet fed, ZT22


title: H3K27ac antibody, 129, High-fat Diet fed, ZT10


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 2, Amplicon Library_3, scRNAseq

description: 10X Genomics


title: ASC bearing IL27 vector Replicate 3

description: Library name: IL27ASC_3


title: H3K27ac antibody, 129, Normal  chow fed, ZT22

value: Normal Chow


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 2, Amplicon Library_2, scRNAseq

description: 10X Genomics


title: ASC bearing IL27 vector Replicate 2

description: Library name: IL27ASC_2


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 2, Amplicon Library_1, scRNAseq

description: 10X Genomics


title: Disomic dCas9-VPR BACH1 sgRNA infected Day 20 CM, scRNAseq

description: 10X Genomics


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 1, Amplicon Library_10, scRNAseq

description: 10X Genomics


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 1, Amplicon Library_9, scRNAseq

description: 10X Genomics


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 1, Amplicon Library_8, scRNAseq

description: 10X Genomics


title: H3K27ac antibody, 129, Normal  chow fed, ZT10


title: H3K27ac antibody, B6, Normal  chow fed, ZT22


title: H3K27ac antibody, B6, High-fat Diet fed, ZT10


title: H3K27ac antibody, B6, Normal  chow fed, ZT10


title: S129,liver,DIO,rep3

description: Library name: Sv129_DIO_Rep3

data_processing:
For each sample, adapters were trimmed with fastp and aligned to the mouse genome mm10 with Bowtie2. The aligned bam files of biological replicates were then merged and subjected to peak calling of open chromatin regions. The tag directories were established, and normalized read counts were measured using Homer.
Assembly: mm10
Supplementary files format and content: Processed data file format is .bed file contained all DIO samples merged peaks
Supplementary files format and content: UCSC genome browser tracks (bigwig files) for each samples.

extract_protocol:
ATAC-seq experiments were performed as described (Guan et al. 2018) with minor changes. In brief, 50,000 isolated LMs were resuspended in 50 μL transposase mixture (25 μL 2× TD buffer, 2.5 μL tagment DNA enzyme (TDE1) (Illumina, 15027865), 0.5 μL 1% digitonin, and 22 μL nuclease-free water) (Illumina, catalog 15027865). Transposition reactions were incubated at 37°C for 30 minutes in an Eppendorf Thermo Mixer with agitation at 300 rpm. Transposed DNA was purified using the QIAGEN MinElute Reaction Cleanup kit (catalog 28204), and purified DNA was eluted in 10 μL elution buffer (10 mM Tris-HCl, pH 8). Transposed fragments were amplified and purified as described previously.
Libraries were quantified using KAPA Library Quantification Kits (Roche, KK4873). All fast-ATAC libraries were sequenced using paired-end, dual-index sequencing on an Illumina NextSeq 500 instrument.

value: wild type


title: S129,liver,DIO,rep2

description: Library name: Sv129_DIO_Rep2


title: B6, Liver,DIO,rep2

description: Library name: B6_DIO_Rep2


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 1, Amplicon Library_7, scRNAseq

description: 10X Genomics


title: B6, Liver,DIO,rep3

description: Library name: B6_DIO_Rep3


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 1, Amplicon Library_6, scRNAseq

description: 10X Genomics


title: S129,liver,DIO,rep1

description: Library name: Sv129_DIO_Rep1


title: B6, Liver,DIO,rep1

description: Library name: B6_DIO_Rep1


title: Errg-Cre, HFD, 129, ZT22, Rep3

description:
ErrgCreHFD.129.ZT22.Rep3
Esrrg.GFPandCre.quantileNormalized.txt

data_processing:
RNA-seq reads were aligned to mm10 using STAR. The tag directories were established and quantile normalized counts were measured with RefSeq genes using Homer.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include quantile normalized tag counts for each Sample .

extract_protocol:
Total RNA was extracted from liver tissue or isolated endothelial cells and kupffer cells using Trizol reagent followed by RNeasy Mini Kit (#74104).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Errg-Cre

value: high fat and sucrose diet, D12492i


title: Errg-Cre, HFD, 129, ZT22, Rep2

description:
ErrgCreHFD.129.ZT22.Rep2
Esrrg.GFPandCre.quantileNormalized.txt


title: Esrrg-LKO, Diet-induced obesity, B6, ZT22, Rep3

description:
Library name: EsrrgLKO.DIO.B6.ZT22.Rep3
B6.Esrrg-LKO.quantileNormalized.txt

value: Esrrg LKO


title: Esrrg-LKO, Diet-induced obesity, B6, ZT22, Rep2

description:
Library name: EsrrgLKO.DIO.B6.ZT22.Rep2
B6.Esrrg-LKO.quantileNormalized.txt


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 2, Amplicon Library_4, scRNAseq

description: 10X Genomics

value: Disomic


title: Errg-Cre, HFD, 129, ZT22, Rep1

description:
ErrgCreHFD.129.ZT22.Rep1
Esrrg.GFPandCre.quantileNormalized.txt


title: Esrrg-LKO, Diet-induced obesity, B6, ZT22, Rep1

description:
Library name: EsrrgLKO.DIO.B6.ZT22.Rep1
B6.Esrrg-LKO.quantileNormalized.txt


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 1, Amplicon Library_5, scRNAseq

description: 10X Genomics


title: H3K27ac antibody, B6, High-fat Diet fed, ZT22


title: Esrrg-LKO, Diet-induced obesity, B6, ZT18, Rep2

description:
Library name: EsrrgLKO.DIO.B6.ZT18.Rep2
B6.Esrrg-LKO.quantileNormalized.txt


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 1, Amplicon Library_4, scRNAseq

description: 10X Genomics


title: Errg-Cre, HFD, 129, ZT18, Rep3

description:
ErrgCreHFD.129.ZT18.Rep3
Esrrg.GFPandCre.quantileNormalized.txt


title: Esrrg-LKO, Diet-induced obesity, B6, ZT18, Rep1

description:
Library name: EsrrgLKO.DIO.B6.ZT18.Rep1
B6.Esrrg-LKO.quantileNormalized.txt


title: Esrrg-LKO, Diet-induced obesity, B6, ZT18, Rep3

description:
Library name: EsrrgLKO.DIO.B6.ZT18.Rep3
B6.Esrrg-LKO.quantileNormalized.txt


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 1, Amplicon Library_3, scRNAseq

description: 10X Genomics


title: Esrrg-LKO, Diet-induced obesity, B6, ZT14, Rep3

description:
Library name: EsrrgLKO.DIO.B6.ZT14.Rep3
B6.Esrrg-LKO.quantileNormalized.txt


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 1, Amplicon Library_2, scRNAseq

description: 10X Genomics


title: Esrrg-LKO, Diet-induced obesity, B6, ZT14, Rep2

description:
Library name: EsrrgLKO.DIO.B6.ZT14.Rep2
B6.Esrrg-LKO.quantileNormalized.txt


title: Errg-Cre, HFD, 129, ZT18, Rep1

description:
ErrgCreHFD.129.ZT18.Rep1
Esrrg.GFPandCre.quantileNormalized.txt


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 1, Amplicon Library_1, scRNAseq

description: 10X Genomics


title: Esrrg-LKO, Diet-induced obesity, B6, ZT14, Rep1

description:
Library name: EsrrgLKO.DIO.B6.ZT14.Rep1
B6.Esrrg-LKO.quantileNormalized.txt


title: Esrrg-LKO, Diet-induced obesity, B6, ZT10, Rep3

description:
Library name: EsrrgLKO.DIO.B6.ZT10.Rep3
B6.Esrrg-LKO.quantileNormalized.txt


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 12, Endogenous Library, scRNAseq

description: 10X Genomics


title: Esrrg-LKO, Diet-induced obesity, B6, ZT10, Rep1

description:
Library name: EsrrgLKO.DIO.B6.ZT10.Rep1
B6.Esrrg-LKO.quantileNormalized.txt


title: Esrrg-LKO, Diet-induced obesity, B6, ZT10, Rep2

description:
Library name: EsrrgLKO.DIO.B6.ZT10.Rep2
B6.Esrrg-LKO.quantileNormalized.txt


title: Esrrg-LKO, Diet-induced obesity, B6, ZT6, Rep3

description:
Library name: EsrrgLKO.DIO.B6.ZT6.Rep3
B6.Esrrg-LKO.quantileNormalized.txt


title: Errg-Cre, HFD, 129, ZT14, Rep2

description:
ErrgCreHFD.129.ZT14.Rep2
Esrrg.GFPandCre.quantileNormalized.txt


title: Esrrg-LKO, Diet-induced obesity, B6, ZT6, Rep2

description:
Library name: EsrrgLKO.DIO.B6.ZT6.Rep2
B6.Esrrg-LKO.quantileNormalized.txt


title: Errg-Cre, HFD, 129, ZT14, Rep1

description:
ErrgCreHFD.129.ZT14.Rep1
Esrrg.GFPandCre.quantileNormalized.txt


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 10, Endogenous Library, scRNAseq

description: 10X Genomics


title: Esrrg-LKO, Diet-induced obesity, B6, ZT2, Rep3

description:
Library name: EsrrgLKO.DIO.B6.ZT2.Rep3
B6.Esrrg-LKO.quantileNormalized.txt


title: Esrrg-LKO, Diet-induced obesity, B6, ZT6, Rep1

description:
Library name: EsrrgLKO.DIO.B6.ZT6.Rep1
B6.Esrrg-LKO.quantileNormalized.txt


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 9, Endogenous Library, scRNAseq

description: 10X Genomics


title: Esrrg-LKO, Diet-induced obesity, B6, ZT2, Rep2

description:
Library name: EsrrgLKO.DIO.B6.ZT2.Rep2
B6.Esrrg-LKO.quantileNormalized.txt


title: Esrrg-LKO, Diet-induced obesity, B6, ZT2, Rep1

description:
Library name: EsrrgLKO.DIO.B6.ZT2.Rep1
B6.Esrrg-LKO.quantileNormalized.txt


title: Errg-Cre, HFD, 129, ZT10, Rep2

description:
ErrgCreHFD.129.ZT10.Rep2
Esrrg.GFPandCre.quantileNormalized.txt


title: Errg-Cre, HFD, 129, ZT10, Rep3

description:
ErrgCreHFD.129.ZT10.Rep3
Esrrg.GFPandCre.quantileNormalized.txt


title: ChIP_WT ESC_PSMC5_lot2

description: Library name: Sample 65

value: mouse embryonic stem cells

value: Tamoxifen-

value: WT

value: anti-PSMC5(Enzo, BML-PW8895)


title: Errg-Cre, HFD, 129, ZT18, Rep2

description:
ErrgCreHFD.129.ZT18.Rep2
Esrrg.GFPandCre.quantileNormalized.txt


title: ChIP_WT ESC_PSMC5_lot1

description: Library name: Sample 64


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 8, Endogenous Library, scRNAseq

description: 10X Genomics


title: Errg-Cre, HFD, 129, ZT14, Rep3

description:
ErrgCreHFD.129.ZT14.Rep3
Esrrg.GFPandCre.quantileNormalized.txt


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 7, Endogenous Library, scRNAseq

description: 10X Genomics


title: Errg-Cre, HFD, 129, ZT10, Rep1

description:
ErrgCreHFD.129.ZT10.Rep1
Esrrg.GFPandCre.quantileNormalized.txt


title: ChIP_WT ESC_PCGF2_lot1

description: Library name: Sample 62

value: anti-PCGF2 (in-house)


title: ChIP_WT ESC_PCGF2_lot2

description: Library name: Sample 63


title: Errg-Cre, HFD, 129, ZT6, Rep3

description:
ErrgCreHFD.129.ZT6.Rep3
Esrrg.GFPandCre.quantileNormalized.txt


title: ChIP_WT ESC_KDM2B_lot1

description: Library name: Sample 59

value: anti-KDM2B (in-house)


title: Errg-Cre, HFD, 129, ZT6, Rep2

description:
ErrgCreHFD.129.ZT6.Rep2
Esrrg.GFPandCre.quantileNormalized.txt

value: Liver


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 11, Endogenous Library, scRNAseq

description: 10X Genomics

value: CROPseq library


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 6, Endogenous Library, scRNAseq

description: 10X Genomics


title: ChIP_WT ESC_H3K27me3_lot2

description: Library name: Sample 58

value: anti-H3K27ac (CST,9733)


title: Errg-Cre, HFD, 129, ZT6, Rep1

description:
ErrgCreHFD.129.ZT6.Rep1
Esrrg.GFPandCre.quantileNormalized.txt

value: male


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 5, Endogenous Library, scRNAseq

description: 10X Genomics

value: iPSC Cardiac Differentiation


title: ChIP_SKP1A KO EBd2_H3K27ac_lot2

description: Library name: Sample 56

value: Tamoxifen+

value: SKP1A KO

value: anti-H3K27ac (CST,8173)


title: ChIP_WT ESC_H3K27me3_lot1

description: Library name: Sample 57


title: ChIP_SKP1A KO EBd2_H3K27ac_lot1

description: Library name: Sample 55


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 4, Endogenous Library, scRNAseq

description: 10X Genomics


title: Errg-Cre, HFD, 129, ZT2, Rep3

description:
ErrgCreHFD.129.ZT2.Rep3
Esrrg.GFPandCre.quantileNormalized.txt

value: Errg-Cre

value: high fat and sucrose diet, D12492i


title: ChIP_SKP1A KO ESC_H3K27ac_lot2

description: Library name: Sample 54


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 3, Endogenous Library, scRNAseq

description: 10X Genomics

value: Disomic


title: Errg-Cre, HFD, 129, ZT2, Rep2

description:
ErrgCreHFD.129.ZT2.Rep2
Esrrg.GFPandCre.quantileNormalized.txt


title: ChIP_SKP1A KO ESC_H3K27ac_lot1

description: Library name: Sample 53

value: mouse embryonic stem cells


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 2, Endogenous Library, scRNAseq

description: 10X Genomics


title: ChIP_SKP1A fl/fl EBd2_H3K27ac_lot1

description: Library name: Sample 51

value: Tamoxifen-


title: Errg-Cre, HFD, 129, ZT2, Rep1

description:
ErrgCreHFD.129.ZT2.Rep1
Esrrg.GFPandCre.quantileNormalized.txt


title: ChIP_SKP1A fl/fl EBd2_H3K27ac_lot2

description: Library name: Sample 52

value: WT


title: Disomic dCas9-VPR CROPseq infected Day 20 Screen, Replicate 1, Endogenous Library, scRNAseq

description: 10X Genomics


title: ChIP_SKP1A fl/fl ESC_H3K27ac_lot2

description: Library name: Sample 50


title: ChIP_WT ESC_KDM2B_lot2

description: Library name: Sample 60


title: ChIP_SKP1A fl/fl ESC_H3K27ac_lot1

description: Library name: Sample 49


title: ChIP_SKP1A KO EBd2_RING1B_lot2

description: Library name: Sample 48

value: anti-RING1B (#3, in house)


title: Disomic dCas9-VPR CROPseq infected, Amplicon Library, scRNAseq

description: 10X Genomics

source_name: iPSC

value: iPSC


title: ChIP_SKP1A fl/fl EBd2_RING1B_lot2

description: Library name: Sample 46


title: ChIP_SKP1A KO ESC_RING1B_lot4

description: Library name: Sample 47


title: Disomic dCas9-VPR CROPseq infected, Endogenous Library, scRNAseq

description: 10X Genomics


title: ChIP_SKP1A fl/fl ESC_RING1B_lot4

description: Library name: Sample 45


title: Trisomic Day 20 hiPSC-CM, Replicate 2, scRNAseq

description: 10X Genomics

value: Trisomic


title: ChIP_SKP1A KO EBd2_RING1B_lot1

description: Library name: Sample 44


title: ChIP_SKP1A KO ESC_RING1B_lot3

description: Library name: Sample 43


title: ChIP_SKP1A fl/fl EBd2_RING1B_lot1

description: Library name: Sample 42


title: Trisomic Day 20 hiPSC-CM, Replicate 1, scRNAseq

description: 10X Genomics


title: ChIP_SKP1A fl/fl ESC_RING1B_lot3

description: Library name: Sample 41


title: ChIP_SKP1A fl/fl+MG132 ESC_RING1B_lot2

description: Library name: Sample 38


title: Disomic Day 20 hiPSC-CM, Replicate 1, scRNAseq

description: 10X Genomics


title: ChIP_SKP1A fl/fl+MG132 ESC_RING1B_lot1

description: Library name: Sample 37


title: Disomic Day 20 hiPSC-CM, Replicate 2, scRNAseq

description: 10X Genomics


title: ChIP_SKP1A KO ESC_RING1B_lot2

description: Library name: Sample 36


title: Trisomic Day 10 hiPSC-CM, Replicate 2, scRNAseq

description: 10X Genomics


title: ChIP_SKP1A fl/fl ESC_RING1B_lot2

description: Library name: Sample 34


title: Trisomic Day 10 hiPSC-CM, Replicate 1, scRNAseq

description: 10X Genomics


title: Disomic Day 10 hiPSC-CM, Replicate 2, scRNAseq

description: 10X Genomics


title: ChIP_SKP1A fl/fl+MG132 ESC_FK1_lot2

description: Library name: Sample 30

value: anti-polyUb (MBL, FK1)


title: Disomic Day 10 hiPSC-CM, Replicate 1, scRNAseq

description: 10X Genomics


title: ChIP_SKP1A KO+MG132 ESC_FK1_lot1

description: Library name: Sample 31


title: ChIP_SKP1A fl/fl+MG132 ESC_FK1_lot1

description: Library name: Sample 29


title: ChIP_SKP1A KO+MG132 ESC_FK1_lot2

description: Library name: Sample 32


title: ChIP_SKP1A fl/fl ESC_RING1B_lot1

description: Library name: Sample 33


title: 1833TR-p94 x MBE1.5

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

data_processing:
The library pools were denatured and sequenced on Illumina NovaSeq 6000 using the S Prime flowcells as pair-end 65 nt reads according to the manufacturer’s protocol.  Raw sequencing reads were filtered by Illumina NovaSeq Control Software, only the Pass-Filter (PF) reads were de-multiplexed allowing 1 mismatch and used for further analysis.
Demultiplexed raw sequence file (FASTQ) were analyzed using Partek® Flow® software package. Raw reads were aligned using STAR 2.7.8a, followed by quantification to annotation model hg38 – Ensembl Transcripts release 110. After noise filtering, counts were normalized as FPKM+1.
Assembly: hg38 – Ensembl Transcripts release 110.
Supplementary files format and content: Tab-Delimited text file with (FPKM+1) value for each sample

growth_protocol: HCC1937 and SUM159-M1a were grown in Ham’s F12 media supplemented with 10% FBS, 10 g/mL Insulin and 20 ng/mL EGF as well as pen/strep.  MDA-MB-468 and MDA-MB-231 subline 1833TR were cultured in DMEM + 10% FBS + Pen/strep. Cells were grown in 10 cm plates to 50% confluence and media was changed one day before treatment. All cells were cultured in 37C incubator with 5% CO2.

extract_protocol:
Total RNA were extracted using Qiagen RNAeasy kit.
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Pico chip (Agilent Technologies, CA).  Messenger RNA was enriched from these samples using QIAseq FastSelect - rRNA HMR Kit (Qiagen, CA), fragmented and converted to cDNA and Illumina sequencing library using the PrepX RNA-seq library preparation protocol on the Apollo 324TM NGS Library Prep System (Takara Bio, CA).

treatment_protocol: 1uM MBE1.5 or 0.1% DMSO control was added to cells and rocked. Cells were treated for 9 hours before lysis to to collect total RNA sample

value: Human breast cancer

tag: aldh1a3 activity


title: ChIP_SKP1A KO ESC_FK1_lot2

description: Library name: Sample 28


title: ChIP_SKP1A fl/fl ESC_FK1_lot2

description: Library name: Sample 26


title: ChIP_SKP1A fl/fl ESC_FK1_lot1

description: Library name: Sample 25


title: ChIP_SKP1A KO ESC_FK1_lot1

description: Library name: Sample 27


title: ChIP_SKP1A KO+MG132 ESC_RING1B_lot1

description: Library name: Sample 39


title: ChIP_SKP1A KO+MG132 ESC_RING1B_lot2

description: Library name: Sample 40


title: 1833TR-p94 x DMSO


title: ChIP_SKP1A KO EBd2_EED_lot2

description: Library name: Sample 24

value: anti-EED (CST,85322)


title: ChIP_SKP1A fl/fl EBd2_EED_lot2

description: Library name: Sample 22


title: MDA-468 x MBE1.5


title: ChIP_SKP1A KO ESC_EED_lot4

description: Library name: Sample 23


title: MDA-468 x DMSO


title: SUM159-M1a-p44 x MBE1.5


title: ChIP_SKP1A fl/fl ESC_EED_lot4

description: Library name: Sample 21


title: ChIP_SKP1A KO EBd2_EED_lot1

description: Library name: Sample 20


title: ChIP_SKP1A KO ESC_EED_lot3

description: Library name: Sample 19


title: ChIP_SKP1A KO ESC_RING1B_lot1

description: Library name: Sample 35


title: ChIP_SKP1A fl/fl ESC_EED_lot3

description: Library name: Sample 17


title: SUM159-M1a-p44 x DMSO


title: ChIP_SKP1A fl/fl EBd2_EED_lot1

description: Library name: Sample 18


title: HCC1937 x MBE1.5


title: ChIP_SKP1A fl/fl+MG132 ESC_EED_lot2

description: Library name: Sample 15


title: HCC1937 x DMSO


title: ChIP_SKP1A fl/fl ESC_EED_lot2

description: Library name: Sample 13


title: ChIP_SKP1A KO ESC_EED_lot2

description: Library name: Sample 14


title: ChIP_SKP1A KO+MG132 ESC_EED_lot1

description: Library name: Sample 12


title: ChIP_SKP1A fl/fl+MG132 ESC_EED_lot1

description: Library name: Sample 11


title: Caudal lung cells, Ctsl treated, biol rep 3

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 W Watertown Plank Rd

institute: MCW

description:
Library name: D31-06
10X Genomics

data_processing:
Samples were mapped by CellRanger count (10XGenomics) with Chemistry parameter SC3Pv4, based on MesAur2.0 reference.
Cells, after filtering, were subjected to Louvain clustering based on the UMAP, with resolution set to 1.
Trajectory inference was performed using Slingshot, and trajectory-based genes were detected using tradeSeq.
Assembly: MesAur2.0
Supplementary files format and content: The raw_feature_bc_matrix.h5 files produced by CellRanger count of 10X Genomics that contain the feature barcode matrix

organism: Mesocricetus auratus

source_name: caudal lung

extract_protocol:
The caudal lung lobe was excised and preserved in a storage medium containing 1% BSA and 2 μg/mL Actinomycin D (ThermoFisher) in 1xPBS until further processing. The tissue was then transferred to a digestion medium supplemented with 2 μg/mL Actinomycin D, 750 Mandl units/mL Collagenase CLS II (Sigma), and 1 mg/mL DNase I (Millipore Sigma) in 2 mL Dispase medium (Corning). Mechanical dissociation was performed using tweezers for 2 minutes, followed by incubation at 37°C with 5% CO2 for 30 minutes. After digestion, the cell suspensions were filtered through 70 μm syringe strainers (pluriSelect). Red blood cells were lysed using a lysis buffer (BioLegend), and the remaining cells were washed with 0.04% BSA in 1xPBS, resuspended in the same buffer, and filtered through a 40 μm cell strainer (Fisher Scientific) to remove cell clumps before cryopreservation. Upon thawing, cells were filtered again using a 40 μm Flowmi cell strainer (SP Bel-Art). Dead cells were removed with a dead cell removal kit (Miltenyi Biotec), and cell viability was assessed using Acridine Orange/Propidium Iodide (AOPI) staining.
The library was prepared using Chromium GEM-X Single Cell 3’ Reagent Kits V4, following the manufacturer’s instructions.

value: caudal lung


title: Caudal lung cells, Ctsl treated, biol rep 2

description:
Library name: D31-05
10X Genomics


title: ChIP_SKP1A fl/fl ESC_EED_lot1

description: Library name: Sample 9


title: ChIP_SKP1A KO ESC_EED_lot1

description: Library name: Sample 10


title: ChIP_EED KO+FLAG-EED 106-S KR ESC_FLAG_lot2

description: Library name: Sample 8

value: EED KO


title: Caudal lung cells, control, biol rep 3

description:
Library name: D31-03
10X Genomics


title: ChIP_EED KO+FLAG-EED 106-S KR ESC_FLAG_lot1

description: Library name: Sample 7

value: Tamoxifen+

value: anti-FLAG (Sigma, F7425)


title: Caudal lung cells, Ctsl treated, biol rep 1

description:
Library name: D31-04
10X Genomics


title: ChIP_EED KO+FLAG-EED 1-106KR ESC_FLAG_lot2

description: Library name: Sample 6


title: ChIP_EED KO+FLAG-EED WT ESC_FLAG_lot2

description: Library name: Sample 4


title: ChIP_EED KO ESC_FLAG_lot2

description: Library name: Sample 2


title: Caudal lung cells, control, biol rep 1

description:
Library name: D31-01
10X Genomics


title: ChIP_EED KO ESC_FLAG_lot1

description: Library name: Sample 1


title: EED KO+N-KR EED EB day2_RNA-seq_rep1

description:
Library name: Sample 23
DK22001_81_24

data_processing:
Reads were mapped onto UCSC mm9 from and counted the reads on exon using STAR (version 2.5.2b: --outSAMtype BAM SortedByCoordinate), and the counted reads are normalized to TPM(Transcripts Per Million). Each gene reads on exon were normalized by DESeq2 for fold change and p-value calculation.
Assembly: mm9
Supplementary files format and content: bigwig

extract_protocol:
Total RNAs from mESCs and Embryoid bodies (EBs) were isolated using  Rneasy Mini Colums (Qiagen).
RNA-sequencing libraries were prepared with  NEBNext Ultra II RNA prep kit (NEB E7775) and NEBNext poly(A) mRNA magnetic isolation module following manufacturer’s instruction.


title: ChIP_SKP1A KO+MG132 ESC_EED_lot2

description: Library name: Sample 16

value: SKP1A KO


title: ChIP_EED KO+FLAG-EED WT ESC_FLAG_lot1

description: Library name: Sample 3


title: EED KO+N-KREED EB day1_RNA-seq_rep1

description:
Library name: Sample 21
DK22001_81_23


title: EED KO+N-KR EED EB day2_RNA-seq_rep2

description:
Library name: Sample 24
DK24001_30_12


title: EED KO+N-KR EED+3i_RNA-seq_rep2

description:
Library name: Sample 20
DK24001_30_10


title: siACTL6A biol rep 3 SCC1 cells ATAC-seq data

city: Palo Alto

first: Andrey

last: Finegersh

address: 900 Blake Wilbur Dr, 3rd Floor

institute: Stanford University

description: Library name: SIACTL6A3 ATAC

data_processing:
RNA-seq: Data analysis was done using nf-core RNA sequencing analysis pipeline (nf-core/rnaseq: version 3.14.0). Differential gene expression analysis was done using DESeq2.
ATAC-seq: Analysis was done using nf-core ATAC-seq pipeline (nf-core/atacseq:  2.1.2). In brief, alignment to human reference genome (GRCh38) was done using Bowtie2 aligner (2.4.4). Narrow peaks were called by MACS2 (2.2.7.1) and differential accessibility analysis was conducted with DESeq2 (1.28.0).  Foot printing analysis was performed using TOBIAS 0.13.3.
Assembly: GRCh38
Supplementary files format and content: RNA-seq: tab delimited file of transcripts per million (TPM) for each sample
Supplementary files format and content: ATAC-seq: BigWig files with reads annotated to the human reference genome (GRCh38)

growth_protocol: UM-SCC1 (SCC070) cell line was purchased from and Sigma-Aldrich. It was grown in DMEM-F12 supplemented with L-glutamine, HEPES, 10% FBS, and 100 IU/ml penicillin 100µg/ml streptomycin and incubated at 37°c in a 5% CO2 incubator. Cell line authentication was done by ATCC cell authentication service using STR profiling. Cells were tested frequently for the presence of Mycoplasma using Bulldog Bio Inc E-MYCO mycoplasma PCR kit.

extract_protocol:
RNA-seq: Total RNA extraction was done using Trizol/chloroform method. SCC1 cells were collected following transient ACTLA6 knockdown in 1.5 ml microcentrifuge tubes. 500 µl Trizol (Invitrogen, Cat. No: 15596026) was added to the cell pellets then phase separation was done by adding 100 µl Chloroform to each tube. The mixture was incubated for 5 minutes at RT followed by centrifugation at 12000g for 15 minutes at 4°C. Top phase was transferred carefully to a new tube and 500 µl Isopropanol was added to precipitate RNA. After 10 minutes incubation at RT, the samples were centrifuged at 12000g for 20 minutes at 4°c. Next, the supernatant was discarded and washing was done with 75 % ice-cold Ethanol twice. RNA was dried at Rt for 10 minutes and suspended with Nuclease free ultrapure water.
ATAC-seq: 100,000 SCC1 cells were collected after 72 hours siRNA transfection. Nuclei preparation, tagmentation reaction and purification, PCR amplification of tagmented DNA were done according to manufacturer’s protocol.
RNA-seq: Libraries were made using Illumina® Stranded mRNA Prep kit (20040534)
ATAC-seq: Library preparation was performed using an ATAC-seq Kit (Active Motif, Cat. No: 53150). Size distribution was analyzed using Agilent 2100 bioanalyzer.

treatment_protocol: Reverse transient knockdown was done using ON-TARGET plus human ACTL6A SMART pool siRNAs (l-008243-00-0005, Dharmacon). Briefly, either ACTL6A or non-targeting control siRNA (ON-TARGET plus Non-targeting Pool, D-0001810-10-05, Dharmacon) was added at 100 nM concentration to 150 µl serum free OPTIMEM medium. Next, 10 µl transfection reagent (X-tremeGENE™ 360, Sigmaaldrich) was mixed with OPTIMEM medium and incubated at RT for 30 minutes. Then the mixture was added dropwise to a 6 well plate contained 1.5 ml growth OPTIMEM with 10% FBS. Next, SCC1 cells were transferred to the wells at density of 200,000 cells/well. After 72 hours the cells were collected for downstream experiments and analysis.

value: Squamous cell carcinoma

value: ACTL6A KD


title: siACTL6A biol rep 1 SCC1 cells ATAC-seq data

description: Library name: SIACTL6A1 ATAC


title: siACTL6A biol rep 2 SCC1 cells ATAC-seq data

description: Library name: SIACTL6A2 ATAC


title: Control biol rep 3 SCC1 cells ATAC-seq data

description: Library name: NTC3 ATAC

value: Non-targeting siRNA


title: EED KO+WT EED EB day2_RNA-seq_rep2

description:
Library name: Sample 18
DK24001_30_09

value: mouse embryonic stem cells


title: EED KO+WT EED EB day2_RNA-seq_rep1

description:
Library name: Sample 17
DK22001_81_21


title: EED KO+WT EED EB day1_RNA-seq_rep2

description:
Library name: Sample 16
DK24001_30_08


title: EED KO+N-KR EED+3i_RNA-seq_rep1

description:
Library name: Sample 19
DK22001_81_22


title: EED KO+WT EED EB day1_RNA-seq_rep1

description:
Library name: Sample 15
DK22001_81_20


title: ChIP_EED KO+FLAG-EED 1-106KR ESC_FLAG_lot1

description: Library name: Sample 5


title: Control biol rep 2 SCC1 cells ATAC-seq data

description: Library name: NTC2 ATAC


title: Caudal lung cells, control, biol rep 2

description:
Library name: D31-02
10X Genomics


title: EED KO+WT EED+3i_RNA-seq_rep1

description:
Library name: Sample 13
DK22001_81_19


title: Control biol rep 1 SCC1 cells ATAC-seq data

description: Library name: NTC1 ATAC


title: EED KO+N-KR EED EB day1_RNA-seq_rep2

description:
Library name: Sample 22
DK24001_30_11


title: siACTL6A biol rep 3 SCC1 cells RNA-seq data

description:
Library name: SIACTL6A 3 RNA
raw_counts_all_samples.txt


title: EED KO EB day2_RNA-seq_rep2

description:
Library name: Sample 12
DK24001_30_06


title: EED KO EB day1_RNA-seq_rep1

description:
Library name: Sample 9
DK22001_81_17


title: EED KO EB day2_RNA-seq_rep1

description:
Library name: Sample 11
DK22001_81_18


title: siACTL6A biol rep 2 SCC1 cells RNA-seq data

description:
Library name: SIACTL6A2 RNA
raw_counts_all_samples.txt


title: EED KO+3i_RNA-seq_rep2

description:
Library name: Sample 8
DK24001_30_04


title: EED KO EB day1_RNA-seq_rep2

description:
Library name: Sample 10
DK24001_30_05


title: siACTL6A biol rep 1 SCC1 cells RNA-seq data

description:
Library name: SIACTL6A1 RNA
raw_counts_all_samples.txt


title: Control biol rep 3 SCC1 cells RNA-seq data

description:
Library name: NTC3 RNA
raw_counts_all_samples.txt


title: EED KO+3i_RNA-seq_rep1

description:
Library name: Sample 7
DK22001_81_16


title: EED f/f EB day2_RNA-seq_rep1

description:
Library name: Sample 5
DK22001_81_15

value: Tamoxifen-

value: wild type


title: EED f/f EB day2_RNA-seq_rep2

description:
Library name: Sample 6
DK24001_30_03


title: EED f/f EB day1_RNA-seq_rep2

description:
Library name: Sample 4
DK24001_30_02


title: Control biol rep 2 SCC1 cells RNA-seq data

description:
Library name: NTC2 RNA
raw_counts_all_samples.txt

value: WT


title: EED f/f+3i_RNA-seq_rep2

description:
Library name: Sample 2
DK24001_30_01


title: Control biol rep 1 SCC1 cells RNA-seq data

description:
Library name: NTC1 RNA
raw_counts_all_samples.txt


title: EED f/f EB day1_RNA-seq_rep1

description:
Library name: Sample 3
DK22001_81_14


title: mCre-MP-rep2

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

data_processing:
Mapper.pl in miRDeep2 was used for preprocessing and adapter removal (-d -e -h -k TGGAATTCTCGGGTGCCAAGG -l 18 -m -v). Quantifier.pl in miRDeep2 was used to map sequencing reads to miRNAs (-t mmu -d -e 0 -W). Sequences of precursors and mature miRNAs in mouse were downloaded from miRbase v22.
Assembly: mm10
Supplementary files format and content: Text file includes raw counts for each sample

source_name: spleen

extract_protocol:
Adult or neonatal spleens were isolated in complete media and CD8+ T cells were positively selected for using magnetic microbead (Miltenyi) selection according to manufacturer’s instructions. Cells were then prepped for naive CD8 subset FACS sorting on the SONY by staining with CD8, CD4, CD44 and CD122 and Viability Dye (∼97% purity) and 200,000+ CD8+ cells sorted into PBS + 2% BSA + 2 mM EDTA. 10,000 FACS sorted cells were placed in Trizol and RNA was extracted according to manufacturer’s instructions, with the addition of a chloroform extraction, Glycoblue (ThermoFisher) carrier prior to precipitation (1 hour at 4°C), and a second wash of the pelleted RNA in 70% ethanol. RNA integrity was confirmed on a Fragment Analyzer (AATI).
Libraries were prepared with NEBNext Small RNA Library Prep Kit (New England Biolabs) using 40-50ng total RNA as input, size selected for insert sizes ~18-35bp.
small RNA-seq

value: spleen

value: CD8+ T cells


title: EED f/f+3i_RNA-seq_rep1

description:
Library name: Sample 1
DK22001_81_13


title: EED KO+WT EED+3i_RNA-seq_rep2

description:
Library name: Sample 14
DK24001_30_07


title: WT-MP-rep2


title: WT-TN-rep2


title: MCF10A, Tunicamycin, Replicate 1

city: Albany

first: Morgan

middle: A

last: Sammons

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

description:
Tun_5000bp.ibed
Tun_10000bp.ibed
Tun_20000bp.ibed

data_processing:
Cantata Bio (Dovetail) analysis pipeline https://dovetail-capture.readthedocs.io/en/latest/
Assembly: GRCh38.p12
Supplementary files format and content: Tab-delimited tables that contain significant (CHiCAGO score > 5) bait fragment and other end end fragment interactions generated using CHiCAGO tool at genome bin window sizes: 5kB, 10kB or 20kB. Files contain bait (promoter region) and other end genomic locations, bait name, number of reads and interaction score.
Library strategy: Micro-C with Promoter capture

growth_protocol: Human mammary epithelial cells, MCF10A, were cultured in 1:1 Dulbecco’s Modified Eagle’s Medium: Ham’s F-12 (Gibco, #11330-032) supplemented with 5% horse serum (Gibco, #16050-122), 20 ng/mL epidermal growth factor (Peprotech, #AF-100-15), 0.5 ng/mL hydrocortisone (Sigma, #H-0888), 100 ng/mL cholera toxin (Sigma, #C-8052), 10 mg/mL insulin (Sigma, #I[1]1882), and 1% penicillin-streptomycin (Gibco, #15240-062) on 10 cm plates until they reached ~70% confluency.

extract_protocol:
Cantata Bio Dovetail® Micro-C Assay
Cantata Bio Dovetail® Micro-C Assay with Dovetail® Targeted (Promoter) Enrichment Panel Service

treatment_protocol: Cells were treated with either 0.001% DMSO (control), 100 µM etoposide (Thermo Scientific, #J63651.MC) or 2 µM tunicamycin (Thermo Scientific, #J62217.MA) for 6h.

value: Epithelial

value: 2 µM Tunicamycin


title: mCre-MP-rep1


title: MCF10A, Etopopside, Replicate 2

description:
Etop_5000bp.ibed
Etop_10000bp.ibed
Etop_20000bp.ibed

value: 100 µM Etoposide


title: mCre-TN-rep1


title: MCF10A, Etopopside, Replicate 1


title: WT-MP-rep1


title: WT-TN-rep1


title: MCF10A, DMSO, Replicate 2

description:
DMSO_5000bp.ibed
DMSO_10000bp.ibed
DMSO_20000bp.ibed


title: Adult-CD8-4

extract_protocol:
Spleens from adult or neonatal mice were collected in RPMI+10% FBS and mashed through a 40µM cell strainer to create a single-cell suspension. Spleens underwent magnetic enrichment with CD8a and CD4 MicroBeads (Miltenyi Biotec; cat# 130-117-044; cat# 130-117-043), respectively, per the manufacturer’s instructions.
Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and glycoBlue as a carrier to improve recovery. Libraries were prepared with NEBNext Small RNA Library Prep Kit (New England Biolabs) using 20-100ng total RNA as input, size selected for insert sizes ~18-35bp.
small RNA-seq


title: Adult-CD8-3


title: Neo-CD8-2


title: Spleen-IAV-rec-3

city: Daejeon

first: Suhee

last: Hwang

address: 55, Expo-ro, Yuseong-gu

department: Korea Virus Research Institute

institute: Institue for Basic Science

description:
Library name: IAV-Spleen-3
10x Genomics

data_processing:
Cell Ranger (v7.2.0)
Assembly: GCF_943737965.1, SARS-CoV-2 delta variant (hCoV-19/South Korea/NMC-nCoV-11/2021; EPI_ISL_10189547) and H1N1 influenza A virus (maCA04/09)
Supplementary files format and content: matrix files

organism: Phodopus roborovskii

source_name: Spleen

extract_protocol:
Phodopus roborovskii hamsters were infected with either SARS-CoV-2 delta variant (10^5.5 TCID50/mL) or H1N1 influenza A virus maCA04/09 (10^7.0 TCID50/mL), and a control group received PBS. BALF, lung and spleen were collected from three hamsters per group at 30 days post-infection, using separate tools to avoid cross-contamination.
Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (PN-1000121; 10X Genomics)

value: Spleen


title: Neo-CD8-1


title: MCF10A, Tunicamycin, Replicate 2


title: Spleen-IAV-rec-2

description:
Library name: IAV-Spleen-2
10x Genomics


title: Sox10Dom/+ Murine Enteric Progenitors, Biological Replicate 2

city: Nashville

first: E Michelle

last: Southard-Smith

state: TN

address: 2215 Garland Ave,

department: Medicine, Genetic Medicine

institute: Vanderbilt University Medical Center

data_processing:
The sequencing output FASTQs were processed with CellRanger 5.0.0 and aligned to the reference transcriptome (exons)
Assembly: mm10
Supplementary files format and content: Matrix : Included are the raw matrix counts used in the manuscript
Supplementary files format and content: Features: Included is a list of the Ensembl IDs and gene symbols corresponding to the associated matrix file
Supplementary files format and content: Barcodes: Included is an ordered list of barcodes corresponding to the 10x matrix files

source_name: fetal intestine

extract_protocol:
Enteric neurons and glia were isolated from the fetal intestines of Phox2b-CFP, Sox10-YFP mice 15.5 days post-coitus using FACS.
10X libraries of entire lines were generated using version 3 Chromium Single Cell 3’ library reagents.  Libraries were sequenced using a Nova-seq 6000 or Nextseq 500 and a paired-end 50 bp sequencing

value: fetal intestine

value: Phox2b-CFP, Sox10-YFP,Sox10Dom/+


title: Adult-CD8-1


title: Sox10Dom/+ Murine Enteric Progenitors, Biological Replicate 1


title: mCre-TN-rep2


title: mCre-MP-2

data_processing:
Adaptors were trimmed from raw reads with trim_galore.
Reads were mapped to the mm10 genome with hisat2.
FeatureCounts was then used to counts mapped reads for genomic features using GENCODE mouse gene annotation v21 (-s 0 -Q 50).
Assembly: mm10
Supplementary files format and content: Text file includes raw counts for each sample

extract_protocol:
Adult or neonatal spleens were isolated in complete media and CD8+ T cells were positively selected for using magnetic microbead (Miltenyi) selection according to manufacturer’s instructions. Cells were then prepped for naive CD8 subset FACS sorting on the SONY by staining with CD8, CD4, CD44 and CD122 and Viability Dye (∼97% purity) and 200,000+ CD8+ cells sorted into PBS + 2% BSA + 2 mM EDTA. 20,000 FACS sorted cells were placed in Trizol and RNA was extracted according to manufacturer’s instructions, with the addition of a chloroform extraction, Glycoblue (ThermoFisher) carrier prior to precipitation (1 hour at 4°C), and a second wash of the pelleted RNA in 70% ethanol. RNA integrity was confirmed on a Fragment Analyzer (AATI).
The RNAseq libraries were prepared with Ultra II Directional RNA kit (NEB) using 40-50ng total RNA as input. Libraries were quantified using Qubit and checked for size distribution on the Fragment Analyzer prior to pooling and sequencing.


title: Spleen-IAV-rec-1

description:
Library name: IAV-Spleen-1
10x Genomics


title: mCre-TN-2


title: Adult-CD8-2


title: WT-MP-2


title: Lung-IAV-rec-3

description:
Library name: IAV-Lung-3
10x Genomics

value: Lung


title: WT-TN-2


title: Sox10+/+ Murine Enteric Progenitors, Biological Replicate 4

value: Phox2b-CFP, Sox10-YFP,Sox10+/+


title: Sox10+/+ Murine Enteric Progenitors, Biological Replicate 3


title: Neo-CD8-4


title: mCre-MP-1


title: mCre-TN-1


title: MCF10A, DMSO, Replicate 1


title: WT-MP-1


title: Neo-CD8-3


title: Lung-IAV-rec-1

description:
Library name: IAV-Lung-1
10x Genomics


title: WT-TN-1


title: Sox10Dom/+ Murine Enteric Progenitors, Biological Replicate 3


title: Sox10+/+ Murine Enteric Progenitors, Biological Replicate 1


title: BALF-IAV-rec-3

description:
Library name: IAV-BALF-3
10x Genomics

source_name: BALF

value: BALF


title: High-fat Diet, 129, ZT22, Rep3

description:
HFD.129.ZT22.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt

value: Liver

value: Wild Type

value: high fat and sucrose diet, D12492i

value: male


title: BALF-IAV-rec-2

description:
Library name: IAV-BALF-2
10x Genomics


title: subject 11, non-inf, 54W

city: Tokyo

first: Mayu

last: Suzuki

address: 2-1-1 Nihonbashi-Honcho, Chuo-ku

department: Japan Medical Office

institute: Takeda Pharmaceutical Co., Ltd.

description:
Library name: IonXpress_095
IonXpress_095

data_processing:
Torrent Suite 5.12.1
Assembly: hg19
Supplementary files format and content: spreadsheet file with the .xls extension includes raw counts for each sample

source_name: colonic mucosa

extract_protocol:
RNA samples were prepared using RNeasy Mini Kit (Qiagen).
AmpliSeq libraries were prepared using Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (Themo Fisher Scientific) with 10 ng of RNA.

value: colonic mucosa


title: High-fat Diet, 129, ZT18, Rep3

description:
HFD.129.ZT18.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat Diet, 129, ZT22, Rep1

description:
HFD.129.ZT22.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: BALF-IAV-rec-1

description:
Library name: IAV-BALF-1
10x Genomics


title: subject 11, inf, 54W

description:
Library name: IonXpress_091
IonXpress_091


title: subject 11, non-inf, 14W

description:
Library name: IonXpress_087
IonXpress_087


title: High-fat Diet, 129, ZT18, Rep2

description:
HFD.129.ZT18.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat Diet, 129, ZT18, Rep1

description:
HFD.129.ZT18.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Spleen-SARS2-dec-3

description:
Library name: 40
10x Genomics


title: subject 11, inf, 14W

description:
Library name: IonXpress_083
IonXpress_083


title: Sox10+/+ Murine Enteric Progenitors, Biological Replicate 2


title: High-fat Diet, 129, ZT14, Rep1

description:
HFD.129.ZT14.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat Diet, 129, ZT10, Rep3

description:
HFD.129.ZT10.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat Diet, 129, ZT14, Rep2

description:
HFD.129.ZT14.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat Diet, 129, ZT10, Rep2

description:
HFD.129.ZT10.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat Diet, 129, ZT10, Rep1

description:
HFD.129.ZT10.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 11, non-inf, 0W

description:
Library name: IonXpress_079
IonXpress_079


title: Lung-IAV-rec-2

description:
Library name: IAV-Lung-2
10x Genomics


title: Spleen-SARS2-dec-2

description:
Library name: 39
10x Genomics


title: High-fat Diet, 129, ZT6, Rep2

description:
HFD.129.ZT6.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 11, inf, 0W

description:
Library name: IonXpress_075
IonXpress_075


title: Spleen-SARS2-dec-1

description:
Library name: 19
10x Genomics


title: subject 10, non-inf, 54W

description:
Library name: IonXpress_052
IonXpress_052


title: High-fat Diet, 129, ZT22, Rep2

description:
HFD.129.ZT22.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat Diet, 129, ZT6, Rep1

description:
HFD.129.ZT6.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Lung-SARS2-dec-2

description:
Library name: 20
10x Genomics


title: High-fat Diet, 129, ZT2, Rep2

description:
HFD.129.ZT2.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat Diet, 129, ZT2, Rep3

description:
HFD.129.ZT2.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 10, inf, 54W

description:
Library name: IonXpress_032
IonXpress_032


title: High-fat Diet, 129, ZT14, Rep3

description:
HFD.129.ZT14.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 10, non-inf, 14W

description:
Library name: IonXpress_028
IonXpress_028


title: Lung-SARS2-dec-1

description:
Library name: 17
10x Genomics


title: BALF-SARS2-dec-3

description:
Library name: 50
10x Genomics


title: Normal Chow, 129, ZT22, Rep3

description:
NC.129.ZT22.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt

value: Normal Chow


title: Normal Chow, 129, ZT22, Rep2

description:
NC.129.ZT22.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, 129, ZT22, Rep1

description:
NC.129.ZT22.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat Diet, 129, ZT6, Rep3

description:
HFD.129.ZT6.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 10, inf, 14W

description:
Library name: IonXpress_024
IonXpress_024


title: Normal Chow, 129, ZT18, Rep3

description:
NC.129.ZT18.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, 129, ZT14, Rep3

description:
NC.129.ZT14.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: BALF-SARS2-dec-2

description:
Library name: 48
10x Genomics


title: Normal Chow, 129, ZT18, Rep2

description:
NC.129.ZT18.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 9, non-inf, 54W

description:
Library name: IonXpress_012
IonXpress_012


title: subject 10, non-inf, 0W

description:
Library name: IonXpress_020
IonXpress_020


title: Normal Chow, 129, ZT14, Rep1

description:
NC.129.ZT14.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, 129, ZT18, Rep1

description:
NC.129.ZT18.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 10, inf, 0W

description:
Library name: IonXpress_016
IonXpress_016


title: BALF-SARS2-dec-1

description:
Library name: 8
10x Genomics


title: Spleen-SARS2-rec-3

description:
Library name: 29
10x Genomics


title: Lung-SARS2-dec-3

description:
Library name: 45
10x Genomics


title: Normal Chow, 129, ZT10, Rep3

description:
NC.129.ZT10.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Spleen-SARS2-rec-2

description:
Library name: 27
10x Genomics


title: Normal Chow, 129, ZT14, Rep2

description:
NC.129.ZT14.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 9, inf, 54W

description:
Library name: IonXpress_008
IonXpress_008


title: High-fat Diet, 129, ZT2, Rep1

description:
HFD.129.ZT2.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, 129, ZT10, Rep2

description:
NC.129.ZT10.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 9, non-inf, 14W

description:
Library name: IonXpress_004
IonXpress_004


title: Spleen-SARS2-rec-1

description:
Library name: 9
10x Genomics


title: Normal Chow, 129, ZT10, Rep1

description:
NC.129.ZT10.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, 129, ZT6, Rep3

description:
NC.129.ZT6.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Lung-SARS2-rec-3

description:
Library name: Delta-R-Lung-5
10x Genomics


title: subject 9, inf, 14W

description:
Library name: IonXpress_094
IonXpress_094


title: Normal Chow, 129, ZT6, Rep1

description:
NC.129.ZT6.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, 129, ZT2, Rep3

description:
NC.129.ZT2.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Lung-SARS2-rec-1

description:
Library name: Delta-R-Lung-1
10x Genomics


title: subject 9, non-inf, 0W

description:
Library name: IonXpress_090
IonXpress_090


title: Normal Chow, 129, ZT2, Rep2

description:
NC.129.ZT2.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 9, inf, 0W

description:
Library name: IonXpress_086
IonXpress_086


title: Normal Chow, 129, ZT2, Rep1

description:
NC.129.ZT2.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat diet, B6, ZT22, Rep3

description:
HFD.B6.ZT22.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: BALF-SARS2-rec-2

description:
Library name: 4
10x Genomics


title: BALF-SARS2-rec-3

description:
Library name: 34
10x Genomics


title: subject 8, non-inf, 0W

description:
Library name: IonXpress_082
IonXpress_082


title: High-fat diet, B6, ZT22, Rep2

description:
HFD.B6.ZT22.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat diet, B6, ZT18, Rep1

description:
HFD.B6.ZT18.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat diet, B6, ZT22, Rep1

description:
HFD.B6.ZT22.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 7, non-inf, 14W

description:
Library name: IonXpress_074
IonXpress_074


title: Spleen-ctrl-3

description:
Library name: Spleen-3
10x Genomics


title: BALF-SARS2-rec-1

description:
Library name: 1
10x Genomics


title: High-fat diet, B6, ZT18, Rep2

description:
HFD.B6.ZT18.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat diet, B6, ZT14, Rep3

description:
HFD.B6.ZT14.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat diet, B6, ZT14, Rep2

description:
HFD.B6.ZT14.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, 129, ZT6, Rep2

description:
NC.129.ZT6.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat diet, B6, ZT10, Rep3

description:
HFD.B6.ZT10.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 7, inf, 14W

description:
Library name: IonXpress_051
IonXpress_051


title: High-fat diet, B6, ZT10, Rep2

description:
HFD.B6.ZT10.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Spleen-ctrl-2

description:
Library name: Spleen-2
10x Genomics


title: Lung-SARS2-rec-2

description:
Library name: Delta-R-Lung-4
10x Genomics


title: Spleen-ctrl-1

description:
Library name: Spleen-1
10x Genomics


title: High-fat diet, B6, ZT18, Rep3

description:
HFD.B6.ZT18.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 7, inf, 0W

description:
Library name: IonXpress_027
IonXpress_027


title: High-fat diet, B6, ZT6, Rep2

description:
HFD.B6.ZT6.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat diet, B6, ZT10, Rep1

description:
HFD.B6.ZT10.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat diet, B6, ZT6, Rep3

description:
HFD.B6.ZT6.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Lung-ctrl-3

description:
Library name: Lung-3
10x Genomics


title: subject 8, inf, 0W

description:
Library name: IonXpress_078
IonXpress_078


title: subject 6, non-inf, 54W

description:
Library name: IonXpress_023
IonXpress_023


title: High-fat diet, B6, ZT2, Rep1

description:
HFD.B6.ZT2.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Lung-ctrl-2

description:
Library name: Lung-2
10x Genomics


title: High-fat diet, B6, ZT2, Rep3

description:
HFD.B6.ZT2.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Lung-ctrl-1

description:
Library name: Lung-1
10x Genomics


title: subject 6, inf, 54W

description:
Library name: IonXpress_019
IonXpress_019


title: High-fat diet, B6, ZT14, Rep1

description:
HFD.B6.ZT14.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 6, non-inf, 14W

description:
Library name: IonXpress_015
IonXpress_015


title: subject 7, non-inf, 0W

description:
Library name: IonXpress_031
IonXpress_031


title: subject 6, inf, 14W

description:
Library name: IonXpress_011
IonXpress_011


title: Normal Chow, B6, ZT22, Rep1

description:
NC.B6.ZT22.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: High-fat diet, B6, ZT2, Rep2

description:
HFD.B6.ZT2.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: BALF-ctrl-3

description:
Library name: BALF-3
10x Genomics


title: subject 6, non-inf, 0W

description:
Library name: IonXpress_007
IonXpress_007


title: Normal Chow, B6, ZT22, Rep2

description:
NC.B6.ZT22.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, B6, ZT22, Rep3

description:
NC.B6.ZT22.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: BALF-ctrl-2

description:
Library name: BALF-2
10x Genomics


title: Normal Chow, B6, ZT18, Rep3

description:
NC.B6.ZT18.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: BALF-ctrl-1

description:
Library name: BALF-1
10x Genomics


title: Normal Chow, B6, ZT18, Rep1

description:
NC.B6.ZT18.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, B6, ZT18, Rep2

description:
NC.B6.ZT18.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, B6, ZT14, Rep3

description:
NC.B6.ZT14.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: SL1344_T12_rep3

city: Hamilton

first: Marie-Ange

last: Massicotte

state: ON

address: MDCL 2108, 1200 Main St W, McMaster University

department: Biochemistry

country: Canada

institute: McMaster University

description:
Library name: Sample 12
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T12_rep3

data_processing:
Raw fastq files were  trimmed with Trimmomatic to remove Truseq adapter sequences.
Trimmed reads were aligned against the reference genome of S. Typhimurium SL1344 (NC_016810) using BWA(mem algorithm) with default settings.
Read counts were quantified using featureCounts.
DESeq2 was used for differential gene expression analysis.
Assembly: GCF_000210855.2
Supplementary files format and content: Fastq files contain raw unmapped reads for each sample, txt file contains read counts after alignment for all samples.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Intracellular bacteria

growth_protocol: Bone marrow-derived macrophages isolated from the femur and tibia of C57BL/6J mice were infected with Salmonella. At 0h, 4,h, 8h, and 12h post-infection, macrophages were lysed and intracellular bacteria were collected, pelleted, and washed to remove eukaryotic cell debris before RNA extraction.

extract_protocol:
RNA was extracted using a MasterPure RNA purification kit (Epicentre) and treated with DNase I (Invitrogen).
Purified total RNA was treated with RiboZero for rRNA depletion and strand-specific dUTP sequencing was performed on an Illumina NextSeq 2000 platform to obtain single-end reads.

value: Intracellular bacteria


title: Normal Chow, B6, ZT10, Rep3

description:
NC.B6.ZT10.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: SL1344_T12_rep2

description:
Library name: Sample 11
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T12_rep2


title: Normal Chow, B6, ZT14, Rep1

description:
NC.B6.ZT14.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 5, inf, 54W

description:
Library name: IonXpress_089
IonXpress_089


title: Normal Chow, B6, ZT10, Rep2

description:
NC.B6.ZT10.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: SL1344_T12_rep1

description:
Library name: Sample 10
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T12_rep1


title: Normal Chow, B6, ZT10, Rep1

description:
NC.B6.ZT10.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, B6, ZT6, Rep3

description:
NC.B6.ZT6.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 5, non-inf, 14W

description:
Library name: IonXpress_085
IonXpress_085


title: SL1344_T8_rep3

description:
Library name: Sample 9
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T8_rep3


title: subject 5, inf, 14W

description:
Library name: IonXpress_081
IonXpress_081


title: Normal Chow, B6, ZT6, Rep2

description:
NC.B6.ZT6.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, B6, ZT14, Rep2

description:
NC.B6.ZT14.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, B6, ZT2, Rep3

description:
NC.B6.ZT2.Rep3
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: Normal Chow, B6, ZT2, Rep2

description:
NC.B6.ZT2.Rep2
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 6, inf, 0W

description:
Library name: IonXpress_003
IonXpress_003


title: Normal Chow, B6, ZT2, Rep1

description:
NC.B6.ZT2.Rep1
RNA-seq.Diet.B6and129.quantileNormalized.txt


title: subject 5, non-inf, 0W

description:
Library name: IonXpress_077
IonXpress_077


title: Propofol_CD8T_biol_rep_2

city: Toon

first: Junpei

address: Shitukawa

department: Graduate School of Medicine

institute: Ehime University

data_processing:
CLC Genomics Workbench v22.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomics Workbench (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC Genomics Workbench (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC Genomics Workbench
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Splenic CD8 T cells

growth_protocol: naïve CD8 T (CD44lowCD62Lhigh) cells were prepared using a CD8+ T cell Isolation kit (BioLegend) with biotin anti-CD44 antibody (BioLegend).  Naïve CD8 T cells (0.75 × 10^6) were stimulated with immobilized anti-TCR-β mAb (3 μg/ml, BioLegend) and anti-CD28 mAb (1 μg/ml,BioLegend) for 2 days in the presence of IL-2 (10 ng/ml, BioLegend). Next, the cells were transferred to a new plate and further cultured in the presence of IL-2 (10 ng/ml) for three days.

extract_protocol:
RNA was extracted using RNeasy plus Micro plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuabtSeq 3'mRNA-Seq Library Prep Kit for illumina following manufacturer's protocols.

treatment_protocol: Propofol (2-6 diisopropylphenol) was purchased from Sigma-Aldrich (cat#D126608-5G; St. Louis, MO, USA). Naïve CD8 T cells were stimulated in the presence or absence of 50 μM propofol for two days. Next, the cells were further cultured in the presence or absence of 50 μM propofol for three days.

value: Splenic CD8 T cells

value: WT

value: Propofol


title: SL1344_T4_rep3

description:
Library name: Sample 6
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T4_rep3


title: subject 5, inf, 0W

description:
Library name: IonXpress_073
IonXpress_073


title: SL1344_T8_rep1

description:
Library name: Sample 7
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T8_rep1


title: Propofol_CD8T_biol_rep_1


title: subject 4, non-inf, 54W

description:
Library name: IonXpress_050
IonXpress_050


title: subject 5, non-inf, 54W

description:
Library name: IonXpress_093
IonXpress_093


title: Ctrl_CD8T_biol_rep_2

value: Control


title: SL1344_T4_rep2

description:
Library name: Sample 5
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T4_rep2


title: Ctrl_CD8T_biol_rep_1


title: IκB– recip, MPP4, rep3

city: Los Angeles

first: Jennifer

last: Chia

address: 570 Boyer Hall

institute: UCLA

data_processing:
Reads were trimmed of adapter sequences and low-quality reads (q<30), then mapped to mm10 genome with bowtie2. Aligned reads were filtered based on mapping score (MAPQ ≥ 30) by Samtools, and duplicated reads were removed using Picard MarkDuplicates. MACS2 version 2.1.0 to identify peaks for each sample using pooled input samples as control, FDR < 0.01. These peaks were merged to generate a single reference peak file, and the number of reads that fell into each peak was counted using deeptools multiBamSummary. Consensus peaks between biological replicates were identified using ChIP-R version 1.1.0.
Assembly: mm10
Supplementary files format and content: ATAC_rawcounts.csv  contains the complete counts matrix of all samples and biological replicates with consensus peak calls, not normalized

source_name: bone marrow

extract_protocol:
Bone marrow from the bilateral femur and tibia was collected; red blood cells were lysed and mature hematopoietic cells were depleted using magnetic bead-based lineage antibody cocktail.  Pre-selected cells were then flow sorted to collect donor HSPC subsets: LT-HSC (CD45.1+/Lin– /Sca1+ cKitHi/Flt3–/CD150– CD48–), MPP2 (CD45.1+/Lin– /Sca1+ cKitHi/Flt3–/CD150+ CD48+), MPP3 (CD45.1+/Lin– /Sca1+ cKitHi/Flt3–/CD150– CD48+) and MPP4 (CD45.1+/Lin– /Sca1+ cKitHi/Flt3+). Between 500-1500 cells were collected per sample and processed for ATAC-seq as described in Buenrostro et al, 2013 using Tn5 transposase from Illumina.
Libraries were prepared with ATAC-seq with Nextera DNA Library Preparation Kit (Illumina, FC-121) according to manufacturer's instructions.

value: bone marrow

value: WT CD45.1 donor cells, from IkB CD45.2 recipient


title: IκB– recip, MPP4, rep2


title: SL1344_T4_rep1

description:
Library name: Sample 4
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T4_rep1


title: IκB– recip, MPP4, rep1


title: subject 4, non-inf, 14W

description:
Library name: IonXpress_026
IonXpress_026


title: SL1344_T8_rep2

description:
Library name: Sample 8
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T8_rep2


title: IκB– recip, MPP3, rep2


title: SL1344_T0_rep3

description:
Library name: Sample 3
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T0_rep3


title: subject 4, inf, 14W

description:
Library name: IonXpress_022
IonXpress_022


title: SL1344_T0_rep2

description:
Library name: Sample 2
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T0_rep2


title: subject 4, non-inf, 0W

description:
Library name: IonXpress_096
IonXpress_096


title: IκB– recip, MPP3, rep1


title: IκB– recip, MPP3, rep3


title: IκB– recip, MPP2, rep3


title: IκB– recip, MPP2, rep2


title: SL1344_T0_rep1

description:
Library name: Sample 1
Column name in SL1344_all_timepoint_featurecounts.txt: SL1344_T0_rep1


title: IκB– recip, HSC, rep3

value: LT-HSC


title: IκB– recip, MPP2, rep1


title: Thalamus_Pcoat+MB+_17mg per kg_Replicate2

city: Singapore

first: Benoit

last: Malleret

address: 5 Science Drive 2, Level 5, MD4-05-03C

department: Microbiology and Immunology

country: Singapore

institute: National University of Singapore, Yong Loo Lin School of Medicine

data_processing:
The raw reads were aligned to the Refseq Macaca mulatta genome assembly (NCBI accession number: GCF_000772875.2_Mmul_8.0.1) using STAR aligner.
The reads were also quantified against transcript sequences obtained from the same Refseq assembly using Salmon in mapping-free (alignment-free) mode to quantify transcript abundance.
Transcript abundances were then summarized into gene abundances using the tximport R/Bioconductor package.
Normalized gene abundances were expressed in transcript per million (TPM) after trimmed mean of M values (TMM) normalization.
Assembly: GCF_000772875.2_Mmul_8.0.1
Supplementary files format and content: tab-delimited text file includes count, abundance, length, and counts from abundance for each sample

organism: Macaca mulatta

source_name: Thalamus

extract_protocol:
Brain, heart, kidney and liver tissues were collected immediately post-mortem in multiple repeats of 1 mm2 squares and preserved in RNAlater (Sigma-Aldrich). Total RNA was isolated by homogenizing in TRIzol (Thermo Fisher Scientific) and performing double extraction with guanidinium thiocyanate-phenol-chloroform followed by a Qiagen RNeasy Micro clean-up procedure. 500 ng of total RNA was subjected to Ribo-Zero (Illumina) ribosomal RNA depletion, and used for construction of sequencing libraries.
Lexogen SENSE Total RNA-seq libraries were prepared according to the manufacturer’s protocol.

value: Thalamus

tag: age

tag: disease state

value: Pcoat+MB+

value: 17mg/kg methylene blue


title: subject 4, inf, 0W

description:
Library name: IonXpress_014
IonXpress_014


title: subject 3, non-inf, 54W

description:
Library name: IonXpress_010
IonXpress_010


title: IκB– recip, HSC, rep2


title: Thalamus_Pcoat+MB+_17mg per kg_Replicate3


title: IκB– recip, HSC, rep1


title: WT recip, MPP4, rep3

value: WT CD45.1 donor cells, from WT CD45.2 recipient


title: subject 4, inf, 54W

description:
Library name: IonXpress_030
IonXpress_030


title: subject 3, inf, 54W

description:
Library name: IonXpress_006
IonXpress_006


title: Thalamus_Pcoat+MB+_17mg per kg_Replicate1


title: WT recip, MPP4, rep1


title: WT recip, MPP3, rep3


title: Thalamus_Pcoat+MB+_10mg per kg_Replicate3

value: 10mg/kg methylene blue


title: WT recip, MPP4, rep2


title: subject 3, inf, 14W

description:
Library name: IonXpress_092
IonXpress_092


title: WT recip, MPP3, rep2


title: Thalamus_Pcoat+MB+_10mg per kg_Replicate2


title: Thalamus_Pcoat+MB+_10mg per kg_Replicate1


title: WT recip, MPP2, rep3


title: WT recip, MPP2, rep1


title: Thalamus_Pcoat+MB+_6mg per kg_Replicate2

value: 6mg/kg methylene blue


title: WT recip, HSC, rep1


title: WT recip, HSC, rep2


title: subject 2, inf, 54W

description:
Library name: IonXpress_076
IonXpress_076


title: Thalamus_Pcoat+MB+_6mg per kg_Replicate3


title: WT recip, HSC, rep3


title: subject 2, non-inf, 54W

description:
Library name: IonXpress_080
IonXpress_080


title: subject 2, non-inf, 14W

description:
Library name: IonXpress_053
IonXpress_053


title: subject 3, non-inf, 0W

description:
Library name: IonXpress_088
IonXpress_088


title: subject 3, non-inf, 14W

description:
Library name: IonXpress_002
IonXpress_002


title: ThyVg4RNA_VDJ

city: Hannover

first: Sarina

last: Ravens

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

data_processing:
The demultiplexing, barcoded processing, annotation were made using the Cell Ranger 3.1 (10x Genomics)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scVDJseq

source_name: γδ T cells

extract_protocol:
After blocking and staining, sorting was performed by using the FACSAria Fusion (BD)
Thymic and pLNs Vg4 cells were directly subjected to 5 'Single Cell V(D)J sequencing (10x genomics) library construction using the Kits from 10xGenomics

value: γδ T cells

value: thymus

value: 8-12 weeks old

value: VDJ


title: Thalamus_Pcoat+MB+_6mg per kg_Replicate1


title: Thalamus_Pcoat+MB-_Replicate5

value: Pcoat+MB-


title: S3

city: Hefei

first: yinzhong

last: shang

address: No.96, JinZhai Road Baohe District

department: Division of Life Sciences and Medicine

institute: University of Science and Technology of China

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data. Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1). Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data. Differential expression analysis:Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate  data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Assembly: Homo_sapiens.GRCh38.
Supplementary files format and content: The format of processed data files is microsoft excel spreadsheet. It contains gene_id, Sample_count, Sample_FPKM and GeneSymbol for each sample.

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.). 1 μg total RNA 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 double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR andP5/ P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: FXR1 knockdown


title: S2


title: LNVg4RNA_VDJ

value: peripheral lymph nodes


title: WT recip, MPP3, rep1


title: subject 2, inf, 14W

description:
Library name: IonXpress_049
IonXpress_049

value: colonic mucosa


title: S1


title: Thalamus_Pcoat+MB-_Replicate4


title: C2

value: WT


title: WT recip, MPP2, rep2

value: bone marrow


title: C3


title: subject 2, non-inf, 0W

description:
Library name: IonXpress_029
IonXpress_029


title: Thalamus_Pcoat+MB-_Replicate3


title: C1


title: subject 2, inf, 0W

description:
Library name: IonXpress_025
IonXpress_025


title: subject 1, non-inf, 54W

description:
Library name: IonXpress_021
IonXpress_021


title: Thalamus_Pcoat+MB-_Replicate2