title: Mouse intestinal organoid cultured in matrigel or type I collagen (hashtag library)

city: Tokyo

first: Shiro

last: Yui

address: 1-5-45, Yushima, Bunkyo-ku

department: Center for stem cell and Regenerative medicine

country: Japan

institute: Institute of Science Tokyo

description:
Library name: Mouse_Hashtag library
hashtag index A952: collagen organoid Day4 hashtag index A953:matrigel organoid Day4

data_processing:
Paired-end FASTQ files (R1: cell barcodes, R2: RNA reads) were processed as follows: adapter trimming, quality filtering, and phase-shift base removal were performed using Cutadapt v4.1. Filtered reads were annotated and mapped to the GRCm39 (release 107) mouse reference genome using STARsolo (v2.7.10a) with known BD Rhapsody barcode whitelist and the following parameters: --clipAdapterType CellRanger4, --outSAMmultNmax 1, --outFilterScoreMinOverLread 0, --outFilterMatchNminOverLread 0, --outFilterMultimapScoreRange 0, --seedSearchStartLmax 30, --soloType CB_UMI_Complex, --soloUMIdedup NoDedup, --soloMultiMappers Rescue, --soloFeatures Gene GeneFull, --soloCBmatchWLtype EditDist_2, --soloUMIlen 8, --soloAdapterSequence NNNNNNNNNGTGANNNNNNNNNGACA, --soloCBposition 2_0_2_8 2_13_2_21 3_1_3_9, --soloUMIposition 3_10_3_17. UMI compression was not performed, as the BD Rhapsody UMI length (8 bases, directly attached to polyT) is insufficient to avoid UMI collisions (minimum 10 bases required; Perukhov et al., Genome Biol., 2018). The resulting non-UMI count matrix was converted to a genes × cells matrix. Inflection threshold from the barcode rank plot was determined using the DropletUtils package in R (v4.2.1), and cell barcodes within the range of inflection × 0.9 to inflection × 1.1 were separated using the Dropkick package (Heiser et al., Genome Biol., 2022).
For assignment of each tag to each cell barcode, read counts of each tag in each valid cell barcode, which defined by the cDNA matrix, were extracted from tag/cell barcode expression matrix. Unassigned cell barcodes were labeled as “not-detected” cells. Then, sum of the total read counts of each tags were normalized to 10M reads, and log2 fold-change between first most counted tags and second most counted tags within each cell barcode. Doublet cells (double-positive cells of any pair of Tags (identified by flowDensity package) and log2 fold-change between first and second most counted tags < 0.07856 were identified as doublets. Finally, remained cell barcodes were assigned to the first most counted tags.
For DBEC correction (mRNA leak-derived backgroud subtraction of gene expression), genes of which log2(x+1)-transformed maximum expression over 8 were selected, and biexponential transformation was performed by using FlowTrans package in R version 4.2.1 (2022-06-23). Next, normal mixture components (model E) was detected by using mclust package in R version 4.2.1 (2022-06-23), average expression of each component were calculated, and genes of which the maximum average expression over 5.5 were selected for background subtration. Then, if the components of which difference of the maximum average expression against maximal average expression under 5 were detected, the expression value of the components set as 0 for background subtracion.
Assembly: GRCm39 release-107
Supplementary files format and content: tab-separated values file

source_name: small intestine

growth_protocol: Mouse small intestinal organoids were established and maintained as previously described (Yui et al., Cell Stem Cell, 2018). Briefly, small intestines from C57BL/6 wild-type mice were harvested, flushed with cold phosphate-buffered saline (PBS; Nacalai Tesque, 14249-24), and opened longitudinally. The tissues were cut into 2–5 mm fragments and incubated in 2 mM ethylenediaminetetraacetic acid (EDTA; Invitrogen, #AM9260G) in PBS at 4 °C for 30 minutes in a 50 mL conical tube (VIOLAMO, 1-3500-22) to dissociate the epithelial layer. The epithelial fractions were collected by vigorous shaking, filtered through a 70 μm cell strainer (Falcon, #352350), and centrifuged at 500 × g for 3 minutes in a 15 mL conical tube (Falcon, #188271-013). The resulting crypts were resuspended in either Matrigel (Corning, 356231) or collagen type I (Cellmatrix Type I-A; Nitta Gelatin, 631-00651) and plated as 30 μL domes in pre-warmed 24-well plates (Corning, 3524). After polymerization at 37 °C for 30 minutes, Matrigel-embedded domes were overlaid with 500 μL of ENR medium [Advanced DMEM/F12 (Gibco, #12634-010) supplemented with 1% (v/v) penicillin/streptomycin (Nacalai Tesque, #26253-84), 1% (v/v) GlutaMAX (Gibco, #35050-061), 1X B27 supplement (Gibco, #17504-044), 1X N2 supplement (Gibco, #17502-048), recombinant murine EGF (50 ng/mL; PeproTech, #315-09), recombinant murine Noggin (100 ng/mL; PeproTech, #1967-NG), and recombinant murine R-spondin1 (400 ng/mL; Qkine, QK006)]. For collagen-embedded organoids, domes were overlaid with 500 μL of ENRW medium, which consists of ENR medium supplemented with recombinant murine Wnt3a (100 ng/mL; Abcam, #ab81484), nicotinamide (10 mM; Sigma-Aldrich, #72340), and 1% (v/v) bovine serum albumin (BSA; Sigma-Aldrich, #A9576).

extract_protocol:
Four days after the start of culture, single-cell suspensions were obtained from each type of organoid. For Matrigel-embedded organoids, Cell Recovery Solution (Corning, #354253) was used, while collagen-embedded organoids were digested with collagenase solution (0.5 mg/mL in PBS; Sigma-Aldrich, #C7657). The collected organoids were then incubated in TrypLE Express (Thermo Fisher) for 15–30 minutes. Mechanical dissociation was performed using pipetting or a 5 mL syringe to obtain single-cell suspensions. The resulting cells were filtered through a 40 μm cell strainer (Falcon, #352340) to remove debris and aggregates. Isolated cells were incubated with biotinylated anti-mouse EpCAM antibodies, followed by staining with TotalSeq PE-conjugated streptavidin (BioLegend).
Library construction was conducted by ImmunoGeneTeqs, Inc. Briefy, obtained single-cell suspensions were subjected to a BD Rhapsody system according to the manufacturer’s protocol. The reverse-transcribed, exonuclease-I treated BD Rhapsody beads were subjected to TAS-Seq protocol (Shichino et al. Commun Biol. 2022) for cDNA and hashtag library amplification. Whole-transcriptome library was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs). Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer (Illumina).

value: small intestine

value: intestinal epithelial cells

value: C57BL/6 WT

value: Intestinal epithelium isolated from mouse proximal small intestine were cultured in matrigel-ENR or collagen-ENRW.


title: shACSL5+PA-2

status: Public on Jan 09 2026

type: SRA

city: Chongqing

first: Shaojie

last: Cheng

state: -- None selected --

address: No.1, Yi-Xue-Yuan Road, Yu-Zhong District

country: China

institute: Chongqing Medical University

description: Library name: Sample 11

library_source: transcriptomic

data_processing:
Raw reads were firstly processed using fastp (v0.22.0) and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2 (v2.1.0). FPKM of each gene was calculated and the read counts of each gene were obtained by featureCounts.
Assembly: GRCh38
Supplementary files format and content: File include Count values for each sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium (Gibco, USA) with 10% FBS and 1% penicillin/streptomycin. All cells were cultured in a 5% CO2 incubator at 37 °C.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's instructions. 1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: To investigate the role of ACSL5 mediate lung-tropic metastasis of breast tumors, Cancer cells were treated with or without palmitic acid. All cells were cultured in a 5% CO2 incubator at 37 °C.

tag: cell line

tag: cell type

value: breast cancer cell

tag: treatment

value: ACSL5-knockdown, palmitic acid treated breast cancer cells derived from lung metastases


title: B cell, untreated, Replicate 1

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description: Library name: B cell wild type 1

library_source: genomic

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated using a copy number aware UMI deduplicator. Pipeline available at https://github.com/laurabiggins/TrAEL-seq Samples were imported into Seqmonk v1.49.1, truncated to a single base, then quantified either as total read count or as strand bias (R-F)/(R+F) equivalent to RFD. Assembly: GRCm38
Assembly: GRCm38
Supplementary files format and content: Replication Fork Direction and Read Count data in 50KB windows
Supplementary files format and content: b cell summaries.txt

molecule: genomic DNA

organism: Mus musculus

source_name: Splenic B cell

growth_protocol: Single cell suspensions from spleens were prepared by passing the spleens through 70μm cell strainers in ice-cold RPMI-1640 with 2% FBS. B cells were isolated from the peripheral lymph nodes of mice using the B cell isolation kit (Miltenyi Biotec) and cultured in Dutch-modified RPMI-1640 media supplemented with 10% FBS, 50µM 2-mercaptoethanol, 100units/ml penicillin and 100μg/ml streptomycin (both ThermoFisher Scientific).

extract_protocol:
2x106 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE. ½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl multiplexed TrAEL-seq adaptor 1 ([App]YYYYNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUAGCA/iBiodT/TGCUACACTCTTTCCCTACACGACGCTCTTCCG) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were pooled, equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added per plug. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl per plug β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol per plug and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

treatment_protocol: B-cells were cultured in 24-well plates at 0.8x106 cells per mL in Dutch-modified RPMI-1640 media supplemented with 10% FBS, 50µM 2-mercaptoethanol, 100units/ml penicillin and 100μg/ml streptomycin B- cell stimulation was achieved with 50μg/mL Lipopolysaccharide.

value: Splenic B cell

value: untreated


title: Mouse intestinal organoid cultured in matrigel or type I collagen (cDNA library)

description:
Library name: Mouse_cDNA library
hashtag index A952: collagen organoid Day4 hashtag index A953:matrigel organoid Day4

library_source: transcriptomic single cell

tag: tissue

tag: genotype

tag: batch


title: Lung cell, adult, uninfected, BCR

city: Kumamoto-city

first: Takushi

last: Nomura

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: Joint Research Center for Human Retrovirus Infection

institute: Kumamoto University

description:
Library name: G4-8_BCR
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2

data_processing:
Raw sequencing reads from the gene expression libraries were processed using Cell Ranger v7.1.0, aligning reads to the mm10 based build of the mouse genome. The resulting output file, which is a gene-cell barcode matrix, was imported into R (v4.4.1) and analyzed using Seurat (v4.4.0). We created Seurat object with “CreateSeuratObject” function (min.cells = 3, min.features = 200).
Assembly: The raw sequence reads were processed by assembling them with mm10, supplemented with the SARS-CoV-2 and Timer protein messenger RNA sequences. However, since these additional genes were not detected, the results were equivalent to those obtained from assembly with the original mm10.
Supplementary files format and content: Processed data files are composed of h5 format (filtered_feature_bc_matrix.h5), matrix format (matrix.mtx.gz), feature format (features.tsv.gz) and barcode format (barcodes.tsv.gz)

molecule: total RNA

source_name: Lung

extract_protocol:
Cells obtained from the left lung were processed by a Dead cell removal kit (Miltenyi) and positive selection using CD45+ microbeads (Miltenyi). The harvested cells were filtered and were processed using Chromium Controller (10x Genomics), following the manufacturer’s protocols.
Single-cell suspensions were processed using the Chromium Next GEM Single Cell 5′ Reagent Kits v2 (10x Genomics). Gene expression libraries were prepared according to the manufacturer’s protocol. cDNA libraries were sequenced on the NextSeq500 platform (Illumina) to reach a minimum depth of 50,000 reads/cell.  Enrichment of V(D)J segments and construction of the single-cell TCR library were performed using the Chromium Single Cell Mouse TCR Amplification Kit (10x Genomics). Similarly, the single-cell BCR library was constructed using the Chromium Single Cell Mouse BCR Amplification Kit (10x Genomics).

value: Lung

value: CD45 positive cells

tag: Sex

value: male

tag: time

value: 5 days post infection

tag: library type

value: mRNA


title: ZT18 Vehicle Rep1

city: Manchester

first: Robert

last: Maidstone

address: Michael Smith Building, Oxford Road

institute: University of Manchester

library_source: other

data_processing:
Reads were aligned to the mm10 genome using bowtie (v1.1.0)
sorted and indexed using Samtools (v1.2)
Peaks were called across ZT6 (from Array Express E-MTAB-10224)  and these ZT18 samples, separately for dexamethasone- and vehicle-treated , using MACS (v2.1.1),
Assembly: mm10
Supplementary files format and content: Peak list and reads for 4 samples deposited here, plus 4 samples previous deposited on Array Express E-MTAB-10224). Excel, 1 sheet per sample

molecule: protein

source_name: Liver

growth_protocol: Hnf4afl/flAlbCre+/- mice (aged 6-8 weeks), generated as described (Hayhurst et al., 2001). Male mice were used throughout. All animals had ad libitum access to standard laboratory chow and water, and were group-housed at room temperature (22°C) on 12hr:12hr light-dark cycles. Experimental mice (i.e. Cre transgene carriers) and floxed littermate controls were housed together, randomly assigned to cages at weaning, and then randomly assigned to treatment groups.

extract_protocol:
Tissue was collected after 1 hour. Chromatin was prepared from flash-frozen liver tissue using the Active Motif ChIP-IT High Sensitivity kit (Active Motif). 25μg of chromatin was incubated overnight at 4C with a GR antibody cocktail (ProteinTech 24050-1-A (lot 00044414) and Cell Signaling D8H2 (lot 2)). To permit direct comparison between samples, and to control for technical variation between ChIP reactions, a spike-in ChIP normalisation strategy was employed, with 30ng spike-in chromatin (53083, Active Motif) and 2μg spike-in antibody (61686, Active Motif (lot 34216004)) being included in each IP reaction. To obtain sufficient DNA for next-generation sequencing, three IP reactions were carried out for each sample, and then pooled for the pull-down step. Antibody was pulled down using washed magnetic protein G agarose beads (ReSyn Biosciences). Beads were washed five times with AM1 Wash Buffer (Active Motif) then DNA eluted as per ChIP-IT kit instructions. ChIP-seq DNA was purified with the MinElute PCR Purification kit (Qiagen).
Illumina TruSeq ChIP Library Preparation Kit, according to the manufacturer’s protocol
Sequenced paired end 76bp on HISEQ4000 at the Genomic Technologies Core Facility University of Manchester

treatment_protocol: Dexamethasone and vehicle treatment was carried out at the National Cancer Institute as previously described (Caratti et al., 2018). For acute treatment with dexamethasone, mice were injected by the intraperitoneal route with water-soluble dexamethasone (D2915 - Sigma-Aldrich) at a dose of 1mg/kg, dissolved in water for injection to a final dexamethasone concentration of 0.2mg/ml. Corresponding vehicle treatment was an equivalent mass of (2-hydroxypropyl)-beta-cyclodextrin (H107 - Sigma-Aldrich) dissolved in water for injection.

value: Liver

value: Vehicle

tag: timepoint


title: Lung cell, adult, SARS-CoV2-infected, BCR

description:
Library name: G3-9_BCR
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2


title: shControl+PA-1

description: Library name: Sample 7

value: Lung metastatic breast cancer cells treated with palmitic acid


title: Ribose, DRG SCI 3dpi, rep2

city: London

first: Yayue

last: Song

address: Burlington Danes, Hammersmith Hospital, Imperial College London

institute: Imperial College London

description: Library name: Sample 11

data_processing:
Sequences were demultiplexed and adapters trimmed with bcl2fastq-v2.20 (Illumina) and read quality controls carried out using FastQC-v 0.12.1, trimming reads less than Phred33 quality score 20 and removing remaining adapters with Trim Galore-v- 0.6.10.
Assembly: Mus_musculus.GRCm38.100
Supplementary files format and content: csv file include FPKM values for each sample

source_name: Sciatic DRG neurons

extract_protocol:
RNA was harvested using RNeasy Micro kit (Qiagen)
Libraries were generated at Source Bioscience (Nottingham, UK) using the Kit for Illumina, NEBNext Ultra II Directional RNA Library Prep according to the recommended manufacturer protocol.

value: Sciatic DRG neurons

tag: strain


title: Lung cell, aged, uninfected, BCR

description:
Library name: G2-1_BCR
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2


title: "NTC" NO TAMOXIFEN CONTROL F

data_processing:
Sequencing library preparation and sequencing was performed by the University of Manchester Genomic Technologies Core Facility.  Sample quality was determined using a 2200 TapeStation (Agilent Technologies).  Libraries were generated using the TruSeq Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol.  The multiplexed libraries were analysed by paired-end sequencing on a HiSeq 4000 instrument (76 + 76 cycles, plus indices), then demultiplexed and converted using bcl2fastq software (v2.17.1.14, Illumina).
Adaptors were removed and ends trimmed using Trimmomatic (v0.36), then reads were mapped against the mouse genome (mm10/GRCm38) using STAR (v2.5.3).
Reads were counted in R using the Rsubread (v1.28.1),
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

growth_protocol: The Nr3c1flox/floxAlbCreERT2 line was created by crossing mice with the Nr3c1tm2Gsc transgene and mice with the Albtm1(cre/ERT2)Mtz transgene, both on a C57BL/6 background.

extract_protocol:
Total RNA was extracted from flash-frozen liver tissue using the ReliaPrep™ RNA Tissue Miniprep System (Promega), as per manufacturer instructions.
Library preparation, and RNA-sequencing using the HiSeq 4000 platform (Illumina) was carried out by the University of Manchester Genomic Technologies Core Facility

treatment_protocol: Cre-mediated recombination was induced by injecting mice with 0.1mg tamoxifen i.p. (T5648, Sigma-Aldrich) each day for 5 days. 14 days after the first injection, at ZT0, all mice were transferred to light-tight cabinets, and maintained in constant darkness.

value: liver

value: HOM flox/HET cre

value: F

value: NO TAMOXIFEN CONTROL


title: shControl+PA-2

description: Library name: Sample 8

value: breast cancer cell


title: "NFC" NO FLOX CONTROL M

value: WT flox/HET cre

value: M

value: NO FLOX CONTROL


title: HET 48 M rep2


title: shACSL5-2

description: Library name: Sample 5

value: ACSL5-knockdown breast cancer cells derived from lung metastases


title: HET 46 F


title: Lung cell, aged, SARS-CoV2-infected, BCR

description:
Library name: G1-1_BCR
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2

value: Lung

value: CD45 positive cells


title: Vehicle, DRG SCI 3dpi, rep1

description: Library name: Sample 7


title: shACSL5-3

description: Library name: Sample 6


title: Ribose, DRG SCI 3dpi, rep1

description: Library name: Sample 10


title: Lung cell, adult, uninfected, TCR

description:
Library name: G4-8_TCR
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2

value: male

value: 5 days post infection


title: AAV-TKT, DRG SCI 3dpi, rep3

description: Library name: Sample 6


title: HET 48 M rep1


title: shControl+PA-3

description: Library name: Sample 9


title: shACSL5-1

description: Library name: Sample 4


title: Vehicle, DRG SCI 3dpi, rep3

description: Library name: Sample 9


title: Lung cell, adult, SARS-CoV2-infected, TCR

description:
Library name: G3-9_TCR
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2

value: mRNA


title: HET 44 M


title: Lung cell, aged, uninfected, TCR

description:
Library name: G2-1_TCR
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2


title: Vehicle, DRG SCI 3dpi, rep2

description: Library name: Sample 8


title: Lung cell, aged, SARS-CoV2-infected, TCR

description:
Library name: G1-1_TCR
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2


title: Lung cell, adult, SARS-CoV2-infected, GEX

description:
Library name: G3-9_GEX
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2


title: Lung cell, adult, uninfected, GEX

description:
Library name: G4-8_GEX
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2


title: AAV-TKT, DRG SCI 3dpi, rep2

description: Library name: Sample 5


title: WT 46 M

value: HOM flox/WT cre


title: shControl-2

description: Library name: Sample 2

value: Lung metastatic breast cancer cells


title: AAV-GFP, DRG SCI 3dpi, rep3

description: Library name: Sample 3

value: Sciatic DRG neurons


title: shControl-3

description: Library name: Sample 3


title: HET 42 F

value: liver


title: WT 44 M


title: HET 40 M

value: HOM flox/HET cre


title: Lung cell, aged, SARS-CoV2-infected, GEX

description:
Library name: G1-1_GEX
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2


title: 231-LT1T2-3

description: Library name: Sample 15

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters. HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count/FPKM values for each sample

growth_protocol: HCC1806 cells were cultured in RPMI 1640 medium (Gibco, USA) with 10% fetal bovine serum (FBS) (HyClone) and 1% penicillin/streptomycin (Beyotime, Shanghai, China). MDA-MB-231 cells were cultured in DMEM medium (Gibco, USA) with 10% FBS and 1% penicillin/streptomycin. All cell lines were cultured in a 5% CO2 incubator at 37 °C.

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
PolyA RNA library: A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.
Total RNA library: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations.

treatment_protocol: Fresh lung tissues and primary tumors were harvested and washed twice with DPBS. The tissues were chopped into pieces and dissociated using a Tumor Dissociation Kit (Miltenyi Biotec, Germany). Cell suspensions were filtered through 70 μm and 40 μm cell strainers (Biosharp, China), lysed with Red Blood Cell Lysis Solution (Biosharp, China), and washed with DPBS containing 2% FBS. GFP+ tumor cells were sorted using fluorescence-activated cell sorting (FACS).

value: cluster T1T2 from lung metastatic breast cancer cells


title: AAV-TKT, DRG SCI 3dpi, rep1

description: Library name: Sample 4


title: shControl-1

description: Library name: Sample 1


title: WT 42 M


title: AAV-GFP, DRG SCI 3dpi, rep2

description: Library name: Sample 2


title: 231-LT1T2-1

description: Library name: Sample 13


title: Multiplexed, B6 spleen/blood, naive CD4+ T cells, host/recipient, HTO

city: Lebanon

first: J. Louise

last: Lines

state: NH

address: DHMC

country: USA

institute: Dartmouth College

description:
Library name: tissue_transfer_HTO
Hashtag-derived oligonucleotide (HTO)
tissue_transfer_matrix.mtx.gz
tissue_transfer_barcodes.tsv.gz
tissue_transfer_features.tsv.gz

data_processing:
The CellRanger Single-Cell Software Suite (10x Genomics) versions v2.1.1 to v7.1.0 were used to perform barcode processing and transcript counting after alignment to the mm10 reference genome with default parameters. Sample barcode hashtags were matched to cells using the HTODemux function of the Seurat package. Droplets containing reads from multiple hashtags were deemed doublets or triplets and filtered out. Hashtags associated with low numbers of reads, likely suggestive of free-floating RNA, were also removed from consideration.
Assembly: mm10
Supplementary files format and content: Matrix files

source_name: Spleen and blood

extract_protocol:
Mouse cells were first pre-enriched by negative selection, using the EasySep™ Mouse naive CD4+ T Cell Isolation Kit. Cells were sorted as singlet, viability dye-, CD4+, CD8-, CD44lo, CD62L+, CD25-, CXCR3-.
Droplet-based 5′ end scRNA-seq was performed using the 10x Genomics platform and libraries were prepared and sequenced on a NextSeq2000 using 28×90bp reads for GEX libraries using the Chromium Single Cell NextGEM 5' v2 chemistry Reagent kit.

value: Spleen and blood

value: naive CD4+ T cells

value: untreated

value: HTO

tag: hto

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (CD45.1_spleen_1), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (CD45.2_spleen_1), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (CD45.1_spleen_2), TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (CD45.2_spleen_2), TotalSeq™-C0305 anti-mouse Hashtag 5 Antibody (Blood_1), TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody (Blood_2)


title: AAV-GFP, DRG SCI 3dpi, rep1

description: Library name: Sample 1


title: WT 40 M

value: M


title: Multiplexed, B6 spleen/blood, naive CD4+ T cells, host/recipient, mRNA

description:
Library name: tissue_transfer_mRNA
polyA RNA
tissue_transfer_matrix.mtx.gz
tissue_transfer_barcodes.tsv.gz
tissue_transfer_features.tsv.gz


title: 231-PT3-3

description: Library name: Sample 12

value: breast cancer cell

value: cluster T3 from primary tumor cells


title: HET 38 F

value: F


title: Multiplexed, B6 spleen, naive CD4+ T cells, untreated/CFA/LPS treated, HTO

description:
Library name: CFA_LPS_HTO
Hashtag-derived oligonucleotide (HTO)
CFA_LPS_barcodes.tsv.gz
CFA_LPS_features.tsv.gz
CFA_LPS_matrix.mtx.gz

source_name: Spleen

value: Spleen

value: mixed sample (CFA-treated, LPS-treated, untreated)

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (CFA_1), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (CFA_2), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (LPS_1), TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (LPS_2), TotalSeq™-C0305 anti-mouse Hashtag 5 Antibody (Untreated_1), TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody (Untreated_2)


title: Induced cardiomyocytes, shGrhl3, Day5, CUT&Tag 2

city: Wuhan

first: Xin

last: Wu

address: 115 Donghu Road, Wuchang District

institute: Wuhan university

description: Library name: Sample 8

data_processing:
For RNA-seq, the clean reads were filtered by Cutadapt (version 1.9.1), and mapped to the reference genome of mouse (mm10) using Hisat2(v2.0.1).
For CUT&Tag, raw reads were subjected to adapter removal (Cutadapt 1.9.1) and mapped to genome mm10 (bowtie2 2.2.6). The peak calling was performed by MACS2. Next, the CUT&Tag peaks were annotated with ChIPseeker.
Assembly: mm10
Supplementary files format and content: xls files inculde counts values for each RNA-seq sample
Supplementary files format and content: BigWig files for CUT&Tag samples
Library strategy: CUT&Tag

source_name: Induced cardiomyocytes(Neo)

extract_protocol: RNA were harvested in TRIzol for RNA-seq. For CUT&Tag, cells were harvested at day5 using Hyperactive Universal CUT&Tag Assay Kit (Vazyme, TD903) according to the manufacturer’s protocol.

value: Induced cardiomyocytes(Neo)

tag: cut&tag antibody


title: Induced cardiomyocytes, shGrhl3, Day5, CUT&Tag 1

description: Library name: Sample 7


title: Lung cell, aged, uninfected, GEX

description:
Library name: G2-1_GEX
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2

value: Lung

value: CD45 positive cells

value: male

value: 5 days post infection

value: mRNA


title: Multiplexed, B6 spleen, naive CD4+ T cells, untreated/CFA/LPS treated, mRNA

description:
Library name: CFA_LPS_mRNA
polyA RNA
CFA_LPS_barcodes.tsv.gz
CFA_LPS_features.tsv.gz
CFA_LPS_matrix.mtx.gz

value: naive CD4+ T cells


title: 231-LT1T2-2

description: Library name: Sample 14

value: cluster T1T2 from lung metastatic breast cancer cells


title: WT 38 F

value: liver

value: HOM flox/WT cre


title: HET 36 M

value: HOM flox/HET cre

value: M


title: WT 36 M


title: 231-PT3-2

description: Library name: Sample 11

value: breast cancer cell

value: cluster T3 from primary tumor cells


title: Induced cardiomyocytes, shGrhl3, Day5, RNA-seq 2

description: Library name: Sample 4

data_processing:
For RNA-seq, the clean reads were filtered by Cutadapt (version 1.9.1), and mapped to the reference genome of mouse (mm10) using Hisat2(v2.0.1).
For CUT&Tag, raw reads were subjected to adapter removal (Cutadapt 1.9.1) and mapped to genome mm10 (bowtie2 2.2.6). The peak calling was performed by MACS2. Next, the CUT&Tag peaks were annotated with ChIPseeker.
Assembly: mm10
Supplementary files format and content: xls files inculde counts values for each RNA-seq sample
Supplementary files format and content: BigWig files for CUT&Tag samples


title: Multiplexed, B6 spleen, naive CD4+ T cells, OT2/IFNAR, HTO

description:
Library name: OT2_IFNAR_HTO
Hashtag-derived oligonucleotide (HTO)
OT2_IFNAR_barcodes.tsv.gz
OT2_IFNAR_features.tsv.gz
OT2_IFNAR_matrix.mtx.gz

value: Spleen

value: untreated

value: HTO

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (OT2_3), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (OT2_4), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (IFNAR_1), TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (IFNAR_2)


title: Multiplexed, B6 spleen, naive CD4+ T cells, untreated/aMHC treated, mRNA

description:
Library name: MHC_mRNA
polyA RNA
MHC_barcodes.tsv.gz
MHC_features.tsv.gz
MHC_matrix.mtx.gz


title: Induced cardiomyocytes, shNT, Day5, CUT&Tag 2

description: Library name: Sample 6

value: Induced cardiomyocytes(Neo)

value: MGT+shNT


title: Multiplexed, B6 spleen, naive CD4+ T cells, untreated/aMHC treated, HTO

description:
Library name: MHC_HTO
Hashtag-derived oligonucleotide (HTO)
MHC_barcodes.tsv.gz
MHC_features.tsv.gz
MHC_matrix.mtx.gz

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (isotype_1), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (isotype_2), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (isotype_3), TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (aMHC_1), TotalSeq™-C0305 anti-mouse Hashtag 5 Antibody (aMHC_2), TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody (aMHC_3)


title: 231-PT3-1

description: Library name: Sample 10


title: Induced cardiomyocytes, shNT, Day5, CUT&Tag 1

description: Library name: Sample 5


title: HCC1806-LM3-3

description: Library name: Sample 6

value: lung metastatic breast cancer cells


title: 231-PT1T2-3

description: Library name: Sample 9

value: cluster T1T2 from primary tumor cells


title: HCC1806-LM3-2

description: Library name: Sample 5


title: WT 32 M


title: 231-PT1T2-1

description: Library name: Sample 7


title: WT 34 F

value: F


title: Multiplexed, B6 spleen, naive CD4+ T cells, RAG2GFP/OT2, mRNA

description:
Library name: RAG2GFP_OT2_mRNA
polyA RNA
RAG2GFP_OT2_barcodes.tsv.gz
RAG2GFP_OT2_features.tsv.gz
RAG2GFP_OT2_matrix.mtx.gz

value: naive CD4+ T cells

value: mRNA


title: HCC1806-PRI-3

description: Library name: Sample 3

value: primary tumor cells


title: RNA_HoxB8_pDC_CpGA_24h_02

city: New York City

first: Eduardo

last: Esteva

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq, Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools, bedgraph to bigwig performed using bedGraphToBigWig v4
Assembly: mm10
Supplementary files format and content: BigWig (coverage for mapped reads)

growth_protocol: The murine progenitor HoxB8-FL cell line (Redecke et al, PMC4131762) was maintained in the progenitor state by culturing in RPMI supplemented with 10% FCS, 10% B16-Flt3L supernatant, 1% L-glutamine, 1% penicillin-streptomycin, and 10 μM β-estradiol (Sigma-Aldrich). To induce progenitor differentiation into mature DCs, the cells were washed twice and replated in RPMI supplemented with 10% charcoal-stripped serum, 10% B16-Flt3L supernatant, 1% L-glutamine, and 1% penicillin-streptomycin in the absence of estrogen.

extract_protocol:
RNA was extracted from sort-purified cells using the QIAGEN RNeasy Mini Kit, QIAshredder homogenization columns, and the accompanying RNase-Free DNase Set according to the manufacturer protocol.
cDNA libraries were prepared using the low input Clontech SMART-Seq HT with Nxt HT kit according to the manufacturer protocol.

treatment_protocol: HoxB8-FL-derived pDCs were sorted using a FACSAria II (BD Biosciences) at the Cytometry & Cell Sorting Laboratory at NYUSoM. Flow cytometry was performed on sorted samples to confirm purity > 95% for populations of interest. pDCs = Live singlets CD11c+ MHC-II- B220+ Siglec-H+. Purified pDCs were stimulated with 1 μM CpG-A/ODN2216 (InvivoGen) for 6 hours and 24 hours or left unstimulated as a control for the same duration of time. Successful pDC activation was confirmed by flow cytometric analysis of CD69 upregulation and/or intracellular staining for IFN-α.

value: pDC

value: CpG-A (24h)


title: HET 34 F

value: liver

value: HOM flox/HET cre


title: Multiplexed, B6 spleen, naive CD4+ T cells, KBxN/RAG2GFP, mRNA

description:
Library name: KBxN_Rag2GFP_mRNA
polyA RNA
KBxN_Rag2GFP_barcodes.tsv.gz
KBxN_Rag2GFP_features.tsv.gz
KBxN_Rag2GFP_matrix.mtx.gz

value: Spleen


title: Induced cardiomyocytes, shNT, Day5, RNA-seq 2

description: Library name: Sample 2


title: WT 30 F

value: HOM flox/WT cre


title: HET 28 M

value: M


title: HCC1806-PRI-2

description: Library name: Sample 2

value: breast cancer cell


title: Induced cardiomyocytes, shGrhl3, Day5, RNA-seq 1

description: Library name: Sample 3

value: Induced cardiomyocytes(Neo)


title: Induced cardiomyocytes, shNT, Day5, RNA-seq 1

description: Library name: Sample 1

value: MGT+shNT


title: Multiplexed, B6 spleen, naive CD4+ T cells, OT2/IFNAR, mRNA

description:
Library name: OT2_IFNAR_mRNA
polyA RNA
OT2_IFNAR_barcodes.tsv.gz
OT2_IFNAR_features.tsv.gz
OT2_IFNAR_matrix.mtx.gz

value: untreated


title: RNA_HoxB8_pDC_US_24h_02

value: Unstimulated (24h)


title: HET 30 F


title: Multiplexed, B6 spleen, naive CD4+ T cells, RAG2GFP/OT2, HTO

description:
Library name: RAG2GFP_OT2_HTO
Hashtag-derived oligonucleotide (HTO)
RAG2GFP_OT2_barcodes.tsv.gz
RAG2GFP_OT2_features.tsv.gz
RAG2GFP_OT2_matrix.mtx.gz

value: HTO

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (Rag2GFP_1), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (OT2xRagKO_1), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (OT2_1), TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (OT2_2)


title: RNA_HoxB8_pDC_CpGA_24h_03


title: HET 32 M


title: HET 26 F

value: F


title: Multiplexed, B6 spleen, naive CD4+ T cells, SPF/Germ-free, mRNA

description:
Library name: Germ_free_mRNA
polyA RNA
Germ-free_barcodes.tsv.gz
Germ-free_features.tsv.gz
Germ-free_matrix.mtx.gz

value: naive CD4+ T cells

value: mRNA


title: HET 24 M


title: 231-PT1T2-2

description: Library name: Sample 8

value: cluster T1T2 from primary tumor cells


title: HCT116 ΔUIM scramble bio rep 1

city: Bethesda

first: Achim

last: Werner

state: MD

address: 30 Convent Dr. MSC 4340

department: NIDCR

institute: NIH

description:
Library name: UIM_siOTUD5_1
Sequenced by commercial vendor Genewiz/Azenta

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to a customized GRCh38v32 genome supplemented with ERCCs and commom mouse transgenes using STAR v2.7.3a in  single-pass mode with –outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.7.3a built-in counting option --quantMode GeneCounts against a customized Gencode GRCh38v32  genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: hg38
Supplementary files format and content: RawCountFile.txt, Raw counts expression matrix.
Supplementary files format and content: RawCountFile_filtered.txt, Filtered counts expression matrix. Genes with less than 5 counts in at least one sample were removed.
Supplementary files format and content: CPM_TMM_counts.txt, TMM-normalized Counts Per Million expression matrix.

growth_protocol: HCT116 cells were grown in McCoy 5A medium and periodically passaged at ~70% confluence.

extract_protocol:
RNA was extracted from samples with the Rneasy Mini Kit, from QIAgen, using the protocol provided by the manufacturer.
Propietary Nextera-XT based method. Sequenced by commercial vendor.

treatment_protocol: Transfection was done with the Lipofectamine RNAiMAX reagent, according to the manufacturer's protocol. Cells were reverse transfected with either a scrambled siRNA (Negative control) or with a mixture of 4 siRNA against OTUD5, both at a 50 nM concentration. Cells were transfected for 48 hours prior to extraction.

value: Colon Cancer Cell Line

value: Rpn10 truncation


title: RNA_HoxB8_pDC_CpGA_6h_02

value: pDC

value: CpG-A (6h)


title: Multiplexed, B6 spleen, naive CD4+ T cells, KBxN/RAG2GFP, HTO

description:
Library name: KBxN_Rag2GFP_HTO
Hashtag-derived oligonucleotide (HTO)
KBxN_Rag2GFP_barcodes.tsv.gz
KBxN_Rag2GFP_features.tsv.gz
KBxN_Rag2GFP_matrix.mtx.gz

value: Spleen

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (KBxN_1), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (KBxN_2), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (RAG2GFP_1)


title: RNA_HoxB8_pDC_CpGA_6h_01


title: RNA_HoxB8_pDC_CpGA_24h_01

value: CpG-A (24h)


title: HCT116 ΔUIMscramble bio rep 4

description:
Library name: UIM_siScramble_4
Sequenced by commercial vendor Genewiz/Azenta

value: siScramble


title: HCC1806-PRI-1

description: Library name: Sample 1

value: breast cancer cell

value: primary tumor cells


title: RNA_HoxB8_pDC_US_24h_03

value: Unstimulated (24h)


title: WT 26 F

value: liver

value: HOM flox/WT cre


title: HCC1806-LM3-1

description: Library name: Sample 4

value: lung metastatic breast cancer cells


title: Multiplexed, B6 spleen, naive CD4+ T cells, aged/smarta, mRNA

description:
Library name: aged_smarta_mRNA
polyA RNA
aged_smarta_barcodes.tsv.gz
aged_smarta_features.tsv.gz
aged_smarta_matrix.mtx.gz

value: naive CD4+ T cells

value: untreated


title: HCT116 ΔUIMscramble bio rep 3

description:
Library name: UIM_siScramble_3
Sequenced by commercial vendor Genewiz/Azenta


title: Multiplexed, B6 spleen, naive CD4+ T cells, aged/smarta, HTO

description:
Library name: aged_smarta_HTO
Hashtag-derived oligonucleotide (HTO)
aged_smarta_barcodes.tsv.gz
aged_smarta_features.tsv.gz
aged_smarta_matrix.mtx.gz

value: HTO

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (aged_1), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (aged_2), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (smarta_1), TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (smarta_2)


title: RNA_HoxB8_pDC_CpGA_6h_03


title: Multiplexed, B6 blood and BALBc spleen, naive CD4+ T cells, HTO

description:
Library name: BALBspl_B6blood_HTO
Hashtag-derived oligonucleotide (HTO)
BALBspl_B6blood_barcodes.tsv.gz
BALBspl_B6blood_features.tsv.gz
BALBspl_B6blood_matrix.mtx.gz

value: Spleen and blood

value: BALBc and C57BL/6

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (BALBc_1), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (BALBc_2), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (B6_Blood_1), TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (B6_Blood_2)


title: Multiplexed, B6 spleen, naive CD4+ T cells, SPF/Germ-free, HTO

description:
Library name: Germ_free_HTO
Hashtag-derived oligonucleotide (HTO)
Germ-free_barcodes.tsv.gz
Germ-free_features.tsv.gz
Germ-free_matrix.mtx.gz

value: Spleen

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (SPF_1), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (SPF_2), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (Germ-free_1), TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (Germ-free_2)


title: WT 28 M

value: HET flox/WT cre

value: M


title: Multiplexed, B6 spleen, naive CD4+ T cells, pre/post IFNb treatment, HTO

description:
Library name: IFNb_HTO
Hashtag-derived oligonucleotide (HTO)
IFNb_barcodes.tsv.gz
IFNb_features.tsv.gz
IFNb_matrix.mtx.gz

value: mixed sample (untreated, IFNb treated, rested 5 days after IFNb)

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (untreated_1), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (untreated_2), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (IFNb_rested_1), TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (IFNb_rested_2), TotalSeq™-C0305 anti-mouse Hashtag 5 Antibody (IFNb_no_rest_1), TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody (IFNb_no_rest_2)


title: RNA_HoxB8_pDC_US_24h_01

value: pDC

value: Unstimulated (24h)


title: HCT116 ΔUIM scramble bio rep 4

description:
Library name: UIM_siOTUD5_4
Sequenced by commercial vendor Genewiz/Azenta

value: Colon Cancer Cell Line

value: Rpn10 truncation


title: HCT116 ΔUIM scramble bio rep 2

description:
Library name: UIM_siOTUD5_2
Sequenced by commercial vendor Genewiz/Azenta


title: WT 22 F

value: liver

value: HOM flox/WT cre

value: F


title: HCT116 ΔUIM scramble bio rep 3

description:
Library name: UIM_siOTUD5_3
Sequenced by commercial vendor Genewiz/Azenta


title: WT 24 M


title: HCT116 ΔUIMscramble bio rep 1

description:
Library name: UIM_siScramble_1
Sequenced by commercial vendor Genewiz/Azenta

value: siScramble


title: Multiplexed, B6 spleen, naive CD4+ T cells, pre/post IFNb treatment, GEX

description:
Library name: IFNb_mRNA
polyA RNA
IFNb_barcodes.tsv.gz
IFNb_features.tsv.gz
IFNb_matrix.mtx.gz

value: naive CD4+ T cells

value: mRNA


title: HET 18 F

value: HOM flox/HET cre


title: RNA_HoxB8_pDC_US_6h_03

value: Unstimulated (6h)


title: Sgo2-KO 2

city: Tianjin

first: Jie

last: Li

address: Wei Jin Road Nankai District No. 94

department: Department of Cell Biology and Genetics

institute: Nankai University

data_processing:
Raw reads were processed using trim-galore and clean reads were mapped to mm10 from UCSC genome by Hisat2 with default parameters .
Uniquely mapped reads annotated in Gencode vM17 were calculated by Featurecounts , with default parameters.
Raw counts were normalized by library size via transcripts per kilobase of exon model per million mapped reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols manufacturer's protocols.

value: mouse embryonic stem cells

value: Sgo2 knockout


title: HET 22 F


title: RNA_HoxB8_pDC_US_6h_02


title: HET 20 M

value: M


title: WT 2

value: E3 WT


title: WT 18 F


title: HCT116 WTsiOTUD5 bio rep 2

description:
Library name: WT_siOTUD5_2
Sequenced by commercial vendor Genewiz/Azenta

value: Control


title: Multiplexed, spleen, B6, naive CD4+ T cells, HTO

description:
Library name: naive_mouse_HTO
Hashtag-derived oligonucleotide (HTO)

data_processing:
The CellRanger Single-Cell Software Suite (10x Genomics) versions v2.1.1 to v7.1.0 were used to perform barcode processing and transcript counting after alignment to the mm10 reference genome with default parameters. Sample barcode hashtags were matched to cells using the HTODemux function of the Seurat package. Droplets containing reads from multiple hashtags were deemed doublets or triplets and filtered out. Hashtags associated with low numbers of reads, likely suggestive of free-floating RNA, were also removed from consideration.
Assembly: mm10
Supplementary files format and content: Matrix files
Library strategy: CITE-seq

value: Spleen

value: untreated

value: ADT

tag: adt

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody, TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody, TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody, TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody, TotalSeq™-C0305 anti-mouse Hashtag 5 Antibody, TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody, Ms.CD4, Ms.CD8a, Ms.CD366, Ms.CD279, Ms.Ly.6C, HuMs.CD11b, Ms.Ly.6G, HuMs.CD49f, HuMs.CD44, Ms.CD54, Ms.CD90.2, Ms.CD73, Ms.CD49d, Ms.CD200, Isotype_MOPC.21, Isotype_MOPC.173, Isotype_MPC.11, Ms.CD19, Isotype_RTK4530, Ms.CD45, Ms.CD25, HuMs.CD45R_B220, Ms.CD115, Ms.CD11c, Ms.CD21_CD35, Ms.CD23, Ms.CD43, Ms.CD5, Ms.CD62L, Ms.CD93, Ms.F4_80, Ms.FceRIa, Ms.I.A_I.E, Ms.NK.1.1, Ms.Siglec_H, Ms.TCR.Bchain, Ms.TCR.RD_GL3, Ms.TER.119, Ms.Ly.6A_E, Ms.CD45.2, HuMsRt.CD278, Ms.CD3, Ms.CD274, HuMsRt.CD27, Ms.CD20, Ms.CD357, Ms.CD137, Ms.CD134, Ms.CD69, Ms.CD127, Ms.CD86, Ms.CD103, Ms.CD150, Ms.CD24, HuMs.integrin.b7, Ms.CD106, Ms.CD183, Ms.CD8b, Ms.TCR.Vb8.1_8.2, Isotype_RTK2071, Isotype_G0114F7, Isotype_RTK2758, Isotype_RTK4174, Isotype_HTK888, HuMs.KLRG1, Ms.TCR.Vb5.1_5.2, Ms.CD223, Ms.CD163, Ms.CD49b, Ms.CD172a, Ms.CD48, Ms.CD170, Ms.CD169, Ms.CD71, Ms.CD41, Ms.CD304, Ms.CD38, Ms.CD55, Ms.CD63, Ms.CD301b, Ms.Tim.4, MsRt.CD29, Ms.IgD, Ms.CD11a, Ms.CD200R, Ms.CCR3, Ms.CD138, Ms.CD317, Ms.CD9, Ms.CD371, Ms.CD22, Ms.Ly49H, Ms.Ly49D, Ms.Ly.49A, Ms.CD185, Ms.CD49a, Ms.CD1d, Ms.CD226_10E5, Ms.CD272, Ms.CD2, Ms.CD120b, Ms.CD40, Ms.CD31, Ms.CD107a, Ms.CD182, MsRt.CD61, Ms.VISTA, Ms.CD186, Ms.Ly108, Ms.TCR.Va2, Ms.TCR.Va8.3_KT50, Ms.TCR.GD_UC7, Ms.CD98, Ms.CD160, Ms.CD51, Ms.CD94, Ms.CD205, Ms.CD155, Ms.CD88, Ms.FR4, Ms.CD45RB, MsRt.CD81


title: Multiplexed, B6 blood and BALBc spleen, naive CD4+ T cells, GEX

description:
Library name: BALBspl_B6blood_mRNA
polyA RNA
BALBspl_B6blood_barcodes.tsv.gz
BALBspl_B6blood_features.tsv.gz
BALBspl_B6blood_matrix.mtx.gz

value: Spleen and blood

value: BALBc and C57BL/6


title: HCT116 ΔUIMscramble bio rep 2

description:
Library name: UIM_siScramble_2
Sequenced by commercial vendor Genewiz/Azenta

value: Colon Cancer Cell Line

value: Rpn10 truncation


title: Multiplexed, spleen, B6, naive CD4+ T cells, GEX

description:
Library name: naive_mouse_mRNA
polyA RNA

value: naive CD4+ T cells


title: HCT116 WTsiOTUD5 bio rep 1

description:
Library name: WT_siOTUD5_1
Sequenced by commercial vendor Genewiz/Azenta


title: naive CD4+ T cells, Nur77-GFP-LOW, rep_3

description:
Library name: Nur77-GFPlo_rep_3
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_110
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_110

data_processing:
Bulk sequencing data was analyzed using the edgeR function in R, with at least an n=2 for each group.
Assembly: mm10
Supplementary files format and content: Raw data in readcounts.raw tsv files
Supplementary files format and content: Normalized data in rpkm tsv files

extract_protocol:
Mouse cells were first pre-enriched by negative selection, using the EasySep™ Mouse naive CD4+ T Cell Isolation Kit. Cells were sorted as singlet, viability dye-, CD4+, CD8-, CD44lo, CD62L+, CD25-, CXCR3- and either GFP low or high expressors. Cells from Mx1-GFP mice were sorted on the Mx1-GFP+, with a gate set using WT mice, which was the top 1% of cells. The Mx1-GFP- population was sorted using a gate set on the bottom 10-15% of naive CD4+ T cells. For Nur77 and KLF2, the top and bottom 10-15% of GFP was sorted.
Samples were sorted into buffer RTL. Then, RNA was isolated and prepared for sequencing using the Takara Pico v3 kit


title: RNA_HoxB8_pDC_US_6h_01

value: pDC


title: naive CD4+ T cells, Nur77-GFP-TOTAL, rep_3

description:
Library name: Nur77-GFPtot_rep_3
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_111
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_111


title: naive CD4+ T cells, Nur77-GFP-TOTAL, rep_2

description:
Library name: Nur77-GFPtot_rep_2
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_108
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_108


title: WT 20 M

value: liver

value: HOM flox/WT cre


title: naive CD4+ T cells, Nur77-GFP-HI, rep_3

description:
Library name: Nur77-GFPhi_rep_3
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_109
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_109


title: Multiplexed, LN and spleen, B6, naive CD4+ T cells, GEX

description:
Library name: B6spleen_B6ln_mRNA
polyA RNA
B6spleen_B6ln_barcodes.tsv.gz
B6spleen_B6ln_features.tsv.gz
B6spleen_B6ln_matrix.mtx.gz

source_name: Spleen and Lymph node

value: Spleen and Lymph node

value: mRNA


title: WT 12 M

value: M


title: naive CD4+ T cells, Nur77-GFP-LOW, rep_2

description:
Library name: Nur77-GFPlo_rep_2
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_107
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_107


title: HCT116 WTsiOTUD5 bio rep 4

description:
Library name: WT_siOTUD5_4
Sequenced by commercial vendor Genewiz/Azenta


title: HET 12 M

value: HOM flox/HET cre


title: HCT116 WTscramble bio rep 1

description:
Library name: WT_siScramble_1
Sequenced by commercial vendor Genewiz/Azenta

value: Control

value: siScramble


title: Multiplexed, LN and spleen, B6, naive CD4+ T cells, HTO

description:
Library name: B6spleen_B6ln_HTO
Hashtag-derived oligonucleotide (HTO)
B6spleen_B6ln_barcodes.tsv.gz
B6spleen_B6ln_features.tsv.gz
B6spleen_B6ln_matrix.mtx.gz

value: untreated

value: HTO

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (B6_Spleen_1), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (B6_Spleen_2), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (B6_LN_1), TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (B6_LN_2)


title: HCT116 WTsiOTUD5 bio rep 3

description:
Library name: WT_siOTUD5_3
Sequenced by commercial vendor Genewiz/Azenta


title: naive CD4+ T cells, Nur77-GFP-HI, rep_2

description:
Library name: Nur77-GFPhi_rep_2
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_106
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_106

value: Spleen


title: Sgo2-KO 1

value: mouse embryonic stem cells

value: Sgo2 knockout


title: WT 1

value: E3 WT


title: HET 16 M


title: HET 10 F

value: F


title: WT 16 M


title: naive CD4+ T cells, Nur77-GFP-TOTAL, rep_1

description:
Library name: Nur77-GFPtot_rep_1
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_105
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_105

value: naive CD4+ T cells


title: Osi-1, snRNA-Seq

city: Duarte

first: June-Wha

last: Rhee

address: 1500 E Duarte Rd

department: Division of Cardiology, Department of Medicine

institute: City of Hope

description: 10x Genomics

data_processing:
The barcoded processing and gene counting were made using the Cell Ranger software v7.0.1 with --include-introns=true
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: snRNA-Seq

molecule: nuclear RNA

source_name: left ventricular tissue

extract_protocol:
All equipment were washed by RNase Zap before use. Remove heart tissue from -80°C storage and place in pre-chilled petri dish filled with cold Dissociation Buffer (5mM CaCl2, 3mM MgAc, 2mM EDTA, 0.5mM EGTA, 10mM Tris-HCl, 1mM DTT, 0.4% Triton x-100 in RNase-free water) on ice, cut it into small pieces, then transfer to Dounce Homogenizer contains 1mL dissociation buffer, homogenize for 5-10 times, with loose and tight heads, respectively. After homogenization, incubate the lysate on ice for 5 minutes, then centrifuge at 40g for 2minutes at 4°C to remove remaining large fragments. Filter lysate through 70µM and 40µM Flowmi filters (Sigma), centrifuge at 1000g for 5 minutes at 4°C to collect the nuclei. Resuspend the pellet in 1.5mL Sucrose Buffer (1M sucrose, 3mM MgAc, 10mM Tris-HCl, 1mM DTT in RNase-free water), then centrifuge another 5 minutes at 1000g. Resuspend nuclei with 100µL Resuspension Buffer (2%BSA, 1mM DTT in 1xPBS), aliquot 10µL of it for imaging in Trypan Blue. After calculation of nuclei number, the resuspension is centrifuged at 1000g for 5 minutes at 4°C, discard the supernatant and store the nuclei in -80°C until further use.
Eight mouse snRNA-Seq libraries were prepared from four treatment groups (n=2 per group) – Sham, Osimertinib (Osi), Transverse aortic constriction (TAC), and TAC-Osi – using Next GEM 10x Genomics Chromium Single Cell 3' Reagent Kit v3.1 chemistry, and sequenced on Illumina NovaSeq 6000 at Translational Genomics Research Institute (TGen), an affiliate of City of Hope.

value: left ventricular tissue

tag: agent

value: Osi


title: TAC-Osi-2, snRNA-Seq

description: 10x Genomics

value: TAC-Osi


title: HCT116 WTscramble bio rep 4

description:
Library name: WT_siScramble_4
Sequenced by commercial vendor Genewiz/Azenta

value: Colon Cancer Cell Line


title: TAC-1, snRNA-Seq

description: 10x Genomics

value: TAC


title: HET 14 F

value: liver

value: HOM flox/HET cre


title: WT 10 F

value: HOM flox/WT cre


title: naive CD4+ T cells, Nur77-GFP-HI, rep_1

description:
Library name: Nur77-GFPhi_rep_1
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_103
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_103

value: untreated


title: WT 8 M

value: M


title: iPSCdNK_NT_1

city: La Jolla

first: Virginia

middle: Chu

last: Cheung

state: CA

address: 2880 Torrey Pines Scenic Dr.

department: Pathology

institute: Univeristy of California, San Diego

description:
Library name: Sample1
10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the CellRanger software v 7.2.0
Assembly: GRCh38, version 32
Supplementary files format and content: barcodes.tsv:  tab-separated values for cell barcodes
Supplementary files format and content: features.tsv:  tab-separated values list of gene IDs
Supplementary files format and content: matrix.mtx:  gene expression count data in Matrix Market Exchange Format

growth_protocol: iPSC were differentiated to dNK and were cultured in an expansion condition for two weeks in the presence or absence of TGFB

extract_protocol:
Single cell suspensions were washed, filtered for cell debris, counted, and stained with a viability marker to ensure correct loading concentration and a high percentage of live cells. Cell suspensions were then loaded onto the 10x Genomics Controller for GEM generation.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: iPSC derived dNK were treated with 500units/mL IL-2, 10ng/mL IL-15 alone, or 500units/mL IL-2, 10ng/mL IL-15, and 10gn/mL TGF-beta 1 for 2 weeks

value: iPSC derived dNK

value: No treatment


title: iPSCdNK_NT_2

description:
Library name: Sample2
10x genomics


title: TAC-2, snRNA-Seq

description: 10x Genomics


title: HCT116 WTscramble bio rep 3

description:
Library name: WT_siScramble_3
Sequenced by commercial vendor Genewiz/Azenta

value: Control

value: siScramble


title: WT 14 F


title: Osi-2, snRNA-Seq

description: 10x Genomics


title: WT 6 F


title: HCT116 WTscramble bio rep 2

description:
Library name: WT_siScramble_2
Sequenced by commercial vendor Genewiz/Azenta


title: iPSCdNK_TGFB_2

description:
Library name: Sample4
10x genomics

value: TGF-beta treatment


title: Sham-2, snRNA-Seq

description: 10x Genomics

value: Sham


title: lonp-1(cmh24) bio rep 2

city: Worcester

first: Junhui

state: MA

address: 364 Plantation St

institute: University of Massachusetts Medical School

description: Library name: lonp-1-2

data_processing:
The analysis were performed on the OneStopRNASeq platform.
Specifically, paired-end RNASeq reads were aligned to WBcel235 with STAR
Gene expression were quantified with featureCounts
Genome annotation file used was WBcel235.90
Differential analysis processed with DESeq2
Assembly: WBcel235
Supplementary files format and content: Gene expression matrix: This is a tabular file that represents the gene expression levels for each sample in the dataset. It typically includes rows representing genes or transcripts and columns representing individual samples. The values in the matrix can be raw read counts, normalized expression values (e.g., TPM or FPKM), or log-transformed expression values.
Supplementary files format and content: Differential expression analysis results: These files contain the results of differential gene expression analysis, identifying genes that show significant expression differences between different conditions or groups. The files may include statistics such as fold change, p-values, adjusted p-values, and gene annotations.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Worms were grown on HT115 E. coli bacteria and harvested at the L4 stage.

extract_protocol:
Trizol Reagent whole worm RNA extraction.
P_Stranded Library&Seq(PE100)

value: whole organism


title: TAC-Osi-1, snRNA-Seq

description: 10x Genomics

value: left ventricular tissue


title: HET 6 F

value: F


title: iPSCdNK_TGFB_1

description:
Library name: Sample3
10x genomics


title: HET 4 M


title: HET 8 M


title: naive CD4+ T cells, Nur77-GFP-LOW, rep_1

description:
Library name: Nur77-GFPlo_rep_1
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_104
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_104

value: Spleen

value: naive CD4+ T cells


title: lonp-1(cmh24) bio rep 3

description: Library name: lonp-1-3


title: naive CD4+ T cells, Nur77-GFP-WT, rep_3

description:
Library name: Nur77-GFP-WT_rep_3
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_102
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_102


title: Sham-1, snRNA-Seq

description: 10x Genomics


title: Human intestinal organoid cultured in matrigel or type I collagen (hashtag library)

description:
Library name: Human_Hashtag library
hashtag index A951: matrigel organoid Day7 hashtag index A952:collagen organoid Day2 hashtag index A953:collagen organoid Day4

data_processing:
Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) were processed as follows: Adapter trimming, quality filtering, and phase-shift base removal of sequencing data was performed by using Cutadapt 4.1. Filtered cell barcode and cDNA reads were annotated and mapped to reference genome (build GRCh38 release-107) by using STARsolo (2.7.10a) and known BD Rhapsody cell barcodes by the following parameters:–clipAdapterType CellRanger4 –outSAMmultNmax 1 –outFilterScoreMinOverLread 0 –outFilterMatchNminOverLread 0 –outFilterMultimapScoreRange 0 –seedSearchStartLmax 30 –soloType CB_UMI_Complex –soloUMIdedup NoDedup –soloMultiMappers Rescue –soloFeatures Gene GeneFull –soloCBmatchWLtype EditDist_2 –soloUMIlen 8 –soloAdapterSequence NNNNNNNNNGTGANNNNNNNNNGACA –soloCBposition 2_0_2_8 2_13_2_21 3_1_3_9 –soloUMIposition 3_10_3_17. We do not perform UMI compression because BD Rhapsody UMI length (8-base and directly attatched polyT) is not sufficient to avoid UMI collision (minimum 10-base is required, Perukhov et al. Genome Biol 2018). Resulted non-umi count data was converted to genes x cells matrix file and inflection threshold of the barcode rank plot was detected by using DropletUtils package in R version 4.3.0 (2023-04-21). Valid cell barcodes and backgrounds from inflection threshold * 0.9 to inflection threshold * 1.1 were separated by Dropkick package (Heiser et al Genome Biol 2022). For STAR index build, small RNA annotations were filtered out from gencode.v41 gtf file.
For assignment of each tag to each cell barcode, read counts of each tag in each valid cell barcode, which defined by the cDNA matrix, were extracted from tag/cell barcode expression matrix. Unassigned cell barcodes were labeled as “not-detected” cells. Then, sum of the total read counts of each tags were normalized to 10M reads, and log2 fold-change between first most counted tags and second most counted tags within each cell barcode. Doublet cells (double-positive cells of any pair of Tags (identified by flowDensity package) and log2 fold-change between first and second most counted tags < 0.38025 were identified as doublets. Finally, remained cell barcodes were assigned to the first most counted tags.
For DBEC correction (mRNA leak-derived backgroud subtraction of gene expression), genes of which log2(x+1)-transformed maximum expression over 8 were selected, and biexponential transformation was performed by using FlowTrans package in R version 4.3.0 (2023-04-21). Next, normal mixture components (model E) was detected by using mclust package in R version 4.3.0 (2023-04-21), average expression of each component were calculated, and genes of which the maximum average expression over 5.5 were selected for background subtration. Then, if the components of which difference of the maximum average expression against maximal average expression under 5 were detected, the expression value of the components set as 0 for background subtracion.
Assembly: GRCh38 release-107
Supplementary files format and content: tab-separated values file

growth_protocol: Surgical specimens of human proximal small intestine were obtained from the Institute of Science Tokyo Hospital with approval from the Medical Research Ethics Committee of Institute of Science Tokyo (approval number: M2023-195). Crypts were isolated from the epithelial layer of the proximal small intestine. The epithelial tissue was dissected and cut into small fragments, which were washed twice in 30 mL of PBS and once in 2% Mucofilin (Eisai). The tissue was then incubated in 15 mM EDTA at 4 °C for 20 minutes. After an additional wash with 30 mL of PBS, the fragments were digested in 10 mL of collagenase solution (0.5 mg/mL in PBS; Sigma-Aldrich, #C7657) at 37 °C for 20 minutes. Following digestion, the supernatant was passed through a 70 μm mesh filter and transferred to a fresh 50 mL conical tube. The volume was adjusted to 10 mL with 0.1% (v/v) BSA/PBS, transferred to a 15 mL conical tube, and centrifuged at 500 × g for 3 minutes. The resulting pellet was resuspended in Matrigel and plated into 24-well plates. Organoids were cultured in 20% cWRNE medium consisting of Advanced DMEM/F12 supplemented with 1% (v/v) penicillin/streptomycin, 1% (v/v) GlutaMAX, 20% (v/v) L-WRN conditioned medium, recombinant murine EGF (50 ng/mL), nicotinamide (10 mM), 1X N2 supplement, 1X B27 supplement, N-acetyl-L-cysteine (1 mM; Sigma-Aldrich, #A9165), gastrin I (10 nM; Sigma-Aldrich, #G9145), and A83-01 (500 nM; Tocris, #2939). Matrigel-grown organoids were subsequently passaged into collagen matrices and maintained in the same 20% cWRNE medium.

extract_protocol:
Single-cell suspensions were obtained from Matrigel-embedded organoids on day 7, while collagen-embedded organoids were collected on days 2 and 4 after the start of culture. For Matrigel-embedded organoids, Cell Recovery Solution (Corning, #354253) was used to dissolve the matrix. For collagen-embedded organoids, digestion was performed using collagenase solution (0.5 mg/mL in PBS; Sigma-Aldrich, #C7657). After matrix removal, organoids were incubated in TrypLE Express (Thermo Fisher) for 15–30 minutes. Mechanical dissociation was carried out by pipetting or using a 5 mL syringe to generate single-cell suspensions. The resulting cells were filtered through a 40 μm cell strainer (Falcon, #352340) to eliminate debris and cell aggregates. Isolated cells were stained with biotinylated anti-human CD298 and CD147 antibodies, followed by incubation with TotalSeq PE-conjugated streptavidin (BioLegend).
Library construction was conducted by ImmunoGeneTeqs, Inc. Briefy, obtained single-cell suspensions were subjected to a BD Rhapsody system according to the manufacturer’s protocol. The reverse-transcribed, exonuclease-I treated BD Rhapsody beads were subjected to TAS-Seq protocol (Shichino et al. Commun Biol. 2022) for cDNA and hashtag library amplification. Whole-transcriptome library was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs). Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer (Illumina).

value: small intestine

value: intestinal epithelial cells

value: Intestinal epithelium isolated fromhuman proximal small intestine were cultured in matrige or collagen with conditioned medium.


title: naive CD4+ T cells, Nur77-GFP-WT, rep_1

description:
Library name: Nur77-GFP-WT_rep_1
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_100
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_100


title: naive CD4+ T cells, Mx1-GFP, GFP-HI, rep 3

description:
Library name: Mx1-GFP-HI_rep_3
Column name in Mx1-GFP_featurecounts.readcounts.raw.tsv file: 164630-03
Column name in Mx1-GFP_featurecounts.readcounts_rpkm.tsv: 164630-03


title: naive CD4+ T cells, Nur77-GFP-WT, rep_2

description:
Library name: Nur77-GFP-WT_rep_2
Column name in Nur77-GFP_featurecounts.readcounts.raw.tsv file: AS_101
Column name in Nur77-GFP_featurecounts.readcounts_rpkm.tsv file: AS_101


title: mrps-38(P210L) bio rep 2

description: Library name: P-2


title: lonp-1(cmh24)_mrps-38(P210L) bio rep 3

description: Library name: PL-3


title: lonp-1(cmh24) bio rep 1

description: Library name: lonp-1-1


title: mrps-38(P210L) bio rep 3

description: Library name: P-3


title: WT 0 M

value: liver

value: HOM flox/WT cre


title: naive CD4+ T cells, Mx1-GFP, GFP-low, rep 2

description:
Library name: Mx1-GFP-LO_rep_2
Column name in Mx1-GFP_featurecounts.readcounts.raw.tsv file: 164630-02
Column name in Mx1-GFP_featurecounts.readcounts_rpkm.tsv: 164630-02

value: untreated


title: naive CD4+ T cells, Mx1-GFP, GFP-low, rep 4

description:
Library name: Mx1-GFP-LO_rep_4
Column name in Mx1-GFP_featurecounts.readcounts.raw.tsv file: 164630-06
Column name in Mx1-GFP_featurecounts.readcounts_rpkm.tsv: 164630-06


title: WT 2 F


title: EPZ_1uM_2_Days_3_22Rv1

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Library name: MR678

data_processing:
Raw fastq files were aligned using STAR v2.7.1. Raw counts were calculated by STAR, FPKM values were calculated by in-house perl script
Assembly: hg38
Supplementary files format and content: txt files of raw counts and FPKM values

source_name: Prostate

growth_protocol: VCaP and 22Rv1 prostate cancer cell line was maintained in Dulbecco’s modified Eagle’s medium (DMEM) and Roswell Park Memorial Institute Medium (RPMI), respectively, supplemented with 10% fetal bovine serum (FBS), penicillin sodium (100 U/mL), and streptomycin sulfate (100 µg/mL).

extract_protocol:
Total RNA was isolated from cells using NucleoSpin RNA isolation kit (Takara) following the manufacturer’s instructions.
RNA-seq libraries were prepared from 0.5 μg of high-quality DNA-free RNA using NEBNext Ultra RNA Library Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: VCaP and 22Rv1 cells were treated with either DMSO, VHL-inactive control compound 6286 (1µM), EZH2 PROTAC degrader PROTAC-6272 (1µM), or EZH2 enzymatic inhibitor EPZ-6438 (1µM) for 48 hours and then collected for RNA analysis.

value: Prostate

value: Prostate cancer cell

value: WT

value: EZH2 enzymatic inhibitor EPZ-6438


title: PROTAC-6272_1uM_2_Days_2_22Rv1

description: Library name: MR674

value: EZH2 PROTAC degrader PROTAC-6272


title: lonp-1(cmh24)_mrps-38(P210L) bio rep 2

description: Library name: PL-2


title: naive CD4+ T cells, Mx1-GFP, GFP-HI, rep 2

description:
Library name: Mx1-GFP-HI_rep_2
Column name in Mx1-GFP_featurecounts.readcounts.raw.tsv file: 164630-01
Column name in Mx1-GFP_featurecounts.readcounts_rpkm.tsv: 164630-01


title: wildtype bio rep 3

description: Library name: N2-3


title: naive CD4+ T cells, Mx1-GFP, GFP-HI, rep 4

description:
Library name: Mx1-GFP-HI_rep_4
Column name in Mx1-GFP_featurecounts.readcounts.raw.tsv file: 164630-05
Column name in Mx1-GFP_featurecounts.readcounts_rpkm.tsv: 164630-05


title: EPZ_1uM_2_Days_2_22Rv1

description: Library name: MR677


title: HET 2 F

value: HOM flox/HET cre


title: EPZ_1uM_2_Days_1_22Rv1

description: Library name: MR676


title: Human intestinal organoid cultured in matrigel or type I collagen (cDNA library)

description:
Library name: Human_cDNA library
hashtag index A951: matrigel organoid Day7 hashtag index A952:collagen organoid Day2 hashtag index A953:collagen organoid Day4


title: WT 4 M

value: M


title: 8hLD1

city: BOSTON

first: Birol

last: Ay

state: Massachusetts

address: 50 BLOSSOM STREET

institute: MASSACHUSETTS GENERAL HOSPITAL

description: Library name: 8h-LPA/1,25D-1

data_processing:
https://bioconductor.org/packages/release/workflows/vignettes/RNAseq123/inst/doc/limmaWorkflow.html
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: xlsx files include all results

source_name: Bone

extract_protocol:
RNA was harvested by Rneasy mini plus kit (Qiagen).
DNBSEQ Fast RNA Library Prep Set was used to prepare libraries.

value: Bone

value: Ocy454 cells

value: Osteocytic Cells


title: naive CD4+ T cells, KLF2-GFP ho, GFP-LO, rep 4

description:
Library name: Klf2GFPlo_HO_rep_4
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X172906.4
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X172906.4

value: Spleen

value: naive CD4+ T cells


title: HET 0 F

value: F


title: 8hL3

description: Library name: 8h-LPA-3


title: PROTAC-6272_1uM_2_Days_1_22Rv1

description: Library name: MR673


title: naive CD4+ T cells, Mx1-GFP, GFP-low, rep 3

description:
Library name: Mx1-GFP-LO_rep_3
Column name in Mx1-GFP_featurecounts.readcounts.raw.tsv file: 164630-04
Column name in Mx1-GFP_featurecounts.readcounts_rpkm.tsv: 164630-04


title: DMSO_1uM_2_Days_3_22Rv1

description: Library name: MR669

value: DMSO


title: 6286_1uM_2_Days_3_22Rv1

description: Library name: MR672

value: VHL-inactive control compound 6286


title: 8hL2

description: Library name: 8h-LPA-2


title: lonp-1(cmh24)_mrps-38(P210L) bio rep 1

description: Library name: PL-1

value: whole organism


title: PROTAC-6272_1uM_2_Days_3_22Rv1

description: Library name: MR675


title: mrps-38(P210L) bio rep 1

description: Library name: P-1


title: 8hL1

description: Library name: 8h-LPA-1


title: 8hLD3

description: Library name: 8h-LPA/1,25D-3


title: naive CD4+ T cells, Mx1-GFP, GFP-low, rep 1

description:
Library name: Mx1-GFP-LO_rep_1
Column name in Mx1-GFP_featurecounts.readcounts.raw.tsv file: 134993_0002
Column name in Mx1-GFP_featurecounts.readcounts_rpkm.tsv: 134993_0002

value: untreated


title: wildtype bio rep 2

description: Library name: N2-2


title: naive CD4+ T cells, KLF2-GFP ho, GFP-HI, rep 3

description:
Library name: Klf2GFPhi_HO_rep_3
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X172906.1
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X172906.1


title: P8 testis, Daxx knockdown, biol rep2

first: shen

last: jin

state: Hubei

address: No. 299, Bayi Road, Wuchang District, Wuhan City

description:
Library name: SAMPLES4
Daxx_2

data_processing:
For analysis of differentially expressed genes , raw sequence reads were trimmed using Trim Galore (0.6.10, parameters:–paired–length 25--stringency 4--clip_R1 12 --clip_R2 12 ). Then, clean sequence reads were mapped to the UCSC mm39 genome  with default parameters using HISAT2(2.2.1) , mapped reads per gene were counted with FeatureCount (1.5.3), providing a GTF file, and differential expression analysis was performed by DESeq2(1.46.0). For analysis of differentially expressed TEs, similar to the analysis mentioned above, and the GTF file was acquired from Gale-Hammell lab.
Assembly: UCSC mm39
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

source_name: testis

extract_protocol:
The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA). RNA concentration and purity was measured using NanoDrop 2000                                                                                (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: testis

value: DAXX knockdown


title: naive CD4+ T cells, Mx1-GFP, GFP-HI, rep 1

description:
Library name: Mx1-GFP-HI_rep_1
Column name in Mx1-GFP_featurecounts.readcounts.raw.tsv file: 134993_0001
Column name in Mx1-GFP_featurecounts.readcounts_rpkm.tsv: 134993_0001


title: 8hLD2

description: Library name: 8h-LPA/1,25D-2


title: naive CD4+ T cells, KLF2-GFP het, GFP-LO, rep 2

description:
Library name: Klf2GFPlo_HET_rep_2
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X155951.8
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X155951.8


title: VIL_3

first: Shiro

address: 1-5-45, Yushima, Bunkyo-ku

description: Library name: Sample 18

data_processing:
Raw sequencing data were converted to FASTQ files using bcl2fastq2 v2.20. Reads were aligned to the mouse reference genome (GRCm39; GENCODE release M38) using the DRAGEN Bio-IT Platform v4.3.6, and gene-level read counts and TPM values were quantified.
Assembly: mm39
Supplementary files format and content: Tab-separated values files

source_name: Small intestine

growth_protocol: Mouse small intestinal crypt–derived organoids were established and maintained as previously described (Yui et al., Cell Stem Cell, 2018). Briefly, small intestines from C57BL/6 wild-type mice were harvested, flushed with cold PBS (Nacalai Tesque, 14249-24), and opened longitudinally. The tissues were cut into 2–5 mm fragments and incubated in PBS containing 2 mM EDTA (Invitrogen, #AM9260G) at 4 °C for 30 minutes in a 50 mL conical tube (VIOLAMO, 1-3500-22) to dissociate the epithelial layer. Epithelial fractions were collected by vigorous shaking, passed through a 70 µm cell strainer (Falcon, #352350), and centrifuged at 500 × g for 3 minutes in a 15 mL conical tube (Falcon, #188271-013). Isolated crypts were resuspended in either Matrigel (Corning, 356231) or collagen type I (Cellmatrix Type I-A; Nitta Gelatin, 631-00651) and plated as 30 µL domes in pre-warmed 24-well plates (Corning, 3524). After polymerization at 37 °C for 30 minutes, Matrigel domes were overlaid with 500 µL ENR medium (MG). For collagen-embedded organoids, domes were overlaid with 500 µL ENRW medium (COL) for 5-FU treatment or 25% cWRNE medium (COL-cWRNE) for comparison with V-organoids. For V-organoid cultures, villi within 3 cm distal to the pylorus were gently scraped using a glass coverslip (MATSUNAMI, #MAS-01), washed in PBS, and centrifuged at 100 × g for 3 minutes to separate intact villi from single cells. Villi were washed by transferring a 70 µm cell strainer (Falcon, #353046) sequentially through wells of a 6-well plate filled with PBS and gently pipetting. After washing, villi remaining in the strainer were collected into a 15 mL tube, centrifuged at 500 × g for 3 minutes, resuspended in 20 µL collagen matrix, and plated in 24-well plates. Cultures were maintained in 25% cWRNE medium (VIL).  Medium Compositions ENR medium: Advanced DMEM/F12 supplemented with 1% penicillin/streptomycin, 1% GlutaMAX, 1× B27, 1× N2, EGF (50 ng/mL), Noggin (100 ng/mL), and R-spondin 1 (400 ng/mL). ENRW medium: ENR medium supplemented with Wnt3a (100 ng/mL), nicotinamide (10 mM), and 1% BSA. cWRNE medium: Advanced DMEM/F12 supplemented with 1% penicillin/streptomycin, 1% GlutaMAX, 1× B27, 1× N2, EGF (50 ng/mL), NAC (1 mM), and 25% L-WRN conditioned medium concentrated with a 10-kDa filter.

extract_protocol:
On day 6, organoids were released from the ECM and total RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
Whole-transcriptome libraries were generated using the SMART-Seq mRNA kit (Takara Bio) based on the SMART (Switching Mechanism at the 5′ End of RNA Template) method. cDNA libraries were purified using AMPure XP beads (Beckman Coulter). Tagmentation and adapter ligation were performed using the Nextera XT DNA Library Prep Kit (Illumina) together with Illumina DNA-RNA UD Indexes. Pooled libraries were sequenced on an Illumina NovaSeq X Plus system.

treatment_protocol: For 5-FU treatment, 40 µM 5-fluorouracil (Selleck Chemicals, #S-1209) was added to the culture medium of MG- or COL-embedded crypt-derived organoids on days 4–6 of culture.

value: Small intestine

value: intestinal epithelial cells

value: C57BL/6J WT


title: naive CD4+ T cells, KLF2-GFP het, GFP-HI, rep 2

description:
Library name: Klf2GFPhi_HET_rep_2
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X155951.7
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X155951.7


title: PROTAC-6272_1uM_2_Days_3_VCaP

description: Library name: MR655

value: Prostate

value: VCaP

value: Prostate cancer cell

value: WT

value: EZH2 PROTAC degrader PROTAC-6272


title: P8 testis, Wild type, biol rep2

description:
Library name: SAMPLES2
Control_2


title: 6286_1uM_2_Days_1_22Rv1

description: Library name: MR670


title: P8 testis, Wild type, biol rep1

description:
Library name: SAMPLES1
Control_1


title: naive CD4+ T cells, KLF2-GFP het, GFP-HI, rep 1

description:
Library name: Klf2GFPhi_HET_rep_1
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X155951.5
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X155951.5

value: Spleen


title: wildtype bio rep 1

description: Library name: N2-1


title: naive CD4+ T cells, KLF2-GFP ho, GFP-HI, rep 4

description:
Library name: Klf2GFPhi_HO_rep_4
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X172906.3
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X172906.3

value: naive CD4+ T cells


title: COL_cWRNE_3

description: Library name: Sample 15


title: PROTAC-6272_1uM_2_Days_2_VCaP

description: Library name: MR654


title: DMSO_1uM_2_Days_2_22Rv1

description: Library name: MR668


title: 6286_1uM_2_Days_2_22Rv1

description: Library name: MR671


title: COL_cWRNE_2

description: Library name: Sample 14


title: naive CD4+ T cells, KLF2-GFP ho, GFP-HI, rep 2

description:
Library name: Klf2GFPhi_HO_rep_2
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X155951.3
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X155951.3


title: 6286_1uM_2_Days_3_VCaP

description: Library name: MR652


title: naive CD4+ T cells, KLF2-GFP ho, GFP-LO, rep 3

description:
Library name: Klf2GFPlo_HO_rep_3
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X172906.2
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X172906.2


title: naive CD4+ T cells, KLF2-GFP ho, GFP-LO, rep 1

description:
Library name: Klf2GFPlo_HO_rep_1
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X155951.2
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X155951.2


title: EPZ_1uM_2_Days_3_VCaP

description: Library name: MR658

value: EZH2 enzymatic inhibitor EPZ-6438


title: 2hLD2

description: Library name: 2h-LPA/1,25D-2

value: Bone

value: Ocy454 cells

value: Osteocytic Cells


title: DMSO_1uM_2_Days_1_22Rv1

description: Library name: MR667

value: DMSO


title: naive CD4+ T cells, KLF2-GFP ho, GFP-HI, rep 1

description:
Library name: Klf2GFPhi_HO_rep_1
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X155951.1
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X155951.1

value: untreated


title: P8 testis, Daxx knockdown, biol rep1

description:
Library name: SAMPLES3
Daxx_1

value: testis

value: DAXX knockdown


title: COL_5FU_2

description: Library name: Sample 11

value: Small intestine

value: intestinal epithelial cells


title: VIL_2

description: Library name: Sample 17

value: C57BL/6J WT


title: EPZ_1uM_2_Days_1_VCaP

description: Library name: MR656

value: Prostate

value: VCaP


title: 8hD3

description: Library name: 8h-1,25D-3


title: 8hVeh3

description: Library name: 8h-Veh-3


title: EPZ_1uM_2_Days_2_VCaP

description: Library name: MR657

value: Prostate cancer cell

value: WT


title: 8hD2

description: Library name: 8h-1,25D-2


title: naive CD4+ T cells, KLF2-GFP het, GFP-LO, rep 1

description:
Library name: Klf2GFPlo_HET_rep_1
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X155951.6
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X155951.6

value: Spleen


title: 2hL3

description: Library name: 2h-LPA-3


title: VIL_1

description: Library name: Sample 16


title: naive CD4+ T cells, KLF2-GFP ho, GFP-LO, rep 2

description:
Library name: Klf2GFPlo_HO_rep_2
Column name in Klf2GFP_featurecounts.readcounts.raw.tsv file: X155951.4
Column name in Klf2GFP_featurecounts.readcounts_rpkm.tsv: X155951.4

value: naive CD4+ T cells


title: 8hVeh2

description: Library name: 8h-Veh-2


title: PROTAC-6272_1uM_2_Days_1_VCaP

description: Library name: MR653

value: EZH2 PROTAC degrader PROTAC-6272


title: 8hVeh1

description: Library name: 8h-Veh-1

value: Bone


title: COL_Control_3

description: Library name: Sample 9

value: non-treat


title: DMSO_1uM_2_Days_1_VCaP

description: Library name: MR647


title: COL_cWRNE_1

description: Library name: Sample 13


title: DMSO_1uM_2_Days_3_VCaP

description: Library name: MR649


title: 2hLD3

description: Library name: 2h-LPA/1,25D-3

value: Ocy454 cells

value: Osteocytic Cells


title: COL_Control_2

description: Library name: Sample 8


title: COL_5FU_3

description: Library name: Sample 12


title: 6286_1uM_2_Days_2_VCaP

description: Library name: MR651

value: VHL-inactive control compound 6286


title: 2hL1

description: Library name: 2h-LPA-1


title: 6286_1uM_2_Days_1_VCaP

description: Library name: MR650


title: 2hD2

description: Library name: 2h-1,25D-2


title: SN13_S79_KC,scRNAseq,gene_exp

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

description:
Library name: SN13_S79_KC
10x Genomics
CP_Norm_annot.csv

data_processing:
Sequencing reads were demultiplexed with matrices using 10X Genomics' Cell Ranger mkfastq software v6.0.0.
Gene expression count matrices were generated with STARsolo version 2.7.11a using mouse reference genome 2.7.4a (gex-mm10-2020-A, 10X Genomics) with default parameters. Barcodes were filtered for cell-containing droplets with STAR. Ambient RNA was subtracted using Cellbender 0.2.0.
Scanpy version 1.9.1 was used for normalization, dimensionality reduction, clustering and projection. Cell types were assigned to clusters based on differential expression of a curated list of marker genes.
Assembly: GRCm38
Supplementary files format and content: Gene expression: Single cell 3' cell/gene matrices in .mtx format generated by STAR for individual samples. Aggregated, Cellbender-corrected count matrices representing fibroblast populations provided as .csv.gz files

source_name: Pancreas

extract_protocol:
For tumor digestion: Pancreatic tumors from KPC (Kras+/LSL-G12D; Trp53+/LSL-R172H; Pdx1-Cre),  from KC (Kras+/LSL-G12D; Pdx1-Cre) mice were minced and enzymatically digested in DMEM supplemented with Collagenase D,Liberase DL, DNase I  at 37°C for 40 minutes. KPC tumor suspensions were then stained for CD45,CD31, EPCAM, and FACS sorted. Fibroblasts were enriched by sorting viable (DAPI-) cells from the population negative for all three markers (triple-negative, "TN"). Alternatively, all viable cells were enriched from the DAPI- fraction ("DN").  KC pancreata were harvested for single-cell RNAseq without sorting.  For KC samples, (from KC (Kras+/LSL-G12D; Pdx1-Cre mice), pancreata were minced in mincing media and enzymatically digested in DMEM supplemented with Collagenase D,Liberase DL, DNase I, Soybean trypsin inhibitor and HEPES  at 37°C for 20 minutes with refreshed enzyme media at 20 minutes for a total of 40 minutes. Samples were then stained and sorted for 70% Live,CD45-, and 30% Live, CD45+ and submitted for single cell sequencing.
Single-cell RNA sequencing was performed using 10X Genomics NextGEM v3.1 3' Gene Expression kits by the Cold Spring Harbor Laboratory Single-Cell Biology Shared Resource. Cells were loaded into a 10x Genomics Chromium instrument and libraries prepared according to the manufacturer’s instructions. Unique dual-indexe libraries were paired end sequenced using the Illumina NextSeq2000 sequencing system with 28x10x10x90bp reads to a mean depth of ~40,000 reads per cell.

value: Dissociated single cells

value: Pancreas

value: KrasG12D/+;Pdx1-Cre (KC)

tag: age

value: 6-14 weeks


title: 2hD1

description: Library name: 2h-1,25D-1


title: 2hLD1

description: Library name: 2h-LPA/1,25D-1


title: MG_5FU_2

city: Tokyo

last: Yui

institute: Institute of Science Tokyo

description: Library name: Sample 5

value: Small intestine

value: intestinal epithelial cells

value: C57BL/6J WT


title: SN12_S27_KC,scRNAseq,gene_exp

description:
Library name: SN12_S27_KC
10x Genomics
CP_Norm_annot.csv


title: 2hVeh3

description: Library name: 2h-Veh-3


title: 2hVeh2

description: Library name: 2h-Veh-2


title: COL_5FU_1

description: Library name: Sample 10


title: OGO_Wnt7b-mut_5548M,scRNAseq,gene_exp

description:
Library name: OGO_Wnt7b-mut_5548M
10x Genomics
OGO_Wnt7b_annot.csv

source_name: Pancreas Orthotopic Tumor

value: Pancreas Orthotopic Tumor


title: SN13_S78_KC,scRNAseq,gene_exp

description:
Library name: SN13_S78_KC
10x Genomics
CP_Norm_annot.csv


title: 4976_KPC-TN,scRNAseq,gene_exp

description:
Library name: 4976_KPC-TN
10x Genomics
KPC_KC_annot.csv

source_name: Pancreas Tumor

value: Pancreas Tumor

value: KrasG12D/+;Trp53R172H/+;Pdx1-Cre (KPC)


title: 4903_KPC-TN,scRNAseq,gene_exp

description:
Library name: 4903_KPC-TN
10x Genomics
KPC_KC_annot.csv