title: NTC tumor DC2


title: 20220801_hpap_4_Pool_Well6_ADT, ADT derived library.

status: Public on Feb 05 2025

type: SRA

city: Philadelphia

first: Vincent

last: Wu

state: PA

address: 402 Johnson Pavilion

department: Microbiology

country: USA

institute: University of Pennsylvania

description: Library name: 20220801_hpap_4_Pool_Well6_ADT

library_source: other

data_processing:
Raw BCL files were converted to fastq files using either cellranger mkfastq (for RNA) or bcl2fastq (for ADT/HTO)
For RNA, fastq files were aligned to hg38, counted, and filtered for QC using cellranger count.
For ADT/HTO, fastq files were aligned to ADT or HTO catalog references. Alignments were barcode corrected and counted as part of the kallisto bustools pipeline (KITE; see https://github.com/betts-lab/scc-proc for snakemake pipeline).
Assembly: hg38
Supplementary files format and content: RNA: tar.gz archive of cellranger output (matrix.tsv.gz, features.tsv.gz, barcodes.tsv.gz). ADT/HTO: tar.gz archive of kallisto bustools output (output.genes.txt, output.mtx, output.barcodes.txt)
Library strategy: CITE-seq

molecule: protein

organism: Homo sapiens

source_name: mononuclear cells

extract_protocol:
Pooled samples were placed through the 3' scRNAseq v3.1 pipeline (10X Genomics) to generate single cell partitions sharing cDNA, antibody derived tag, and hashing antibody barcodes. Each well of a 10X chip was superloaded with ~1.75X manufacturer's recommended maximum cell count. cDNA extract protocol followed manufacturer's instructions. To extract antibody derived tag and hashing tag sequences, the supernatant from cDNA Cleanup - SPRIselect (Step 2.3d in Protocol CG000315 Rev C, or equivalent step) was saved for further processing following the standard CITEseq protocol (https://cite-seq.com/protocols/).
Dual indexed cDNA libraries were generated following manufacturer's instructions (10X Genomics Protocol CG000315 Rev C, or equivalent for high-throughput protocols). Dual indexed antibody derived tag and hashing tag libraries were generated following standard CITEseq protocol (https://cite-seq.com/protocols/) using primers recommended from Biolegend. Antibody derived tag and hashing tag sequences were enriched in the initial cDNA amplification step of the 3' scRNAseq v3.1 protocol via addition of additive primers (https://cite-seq.com/protocols/).

treatment_protocol: All samples were thawed from -150℃ cryopreservation. Individual tubes were gently shaken in a 37℃ water bath until the frozen cells were partially thawed. Cells were then quickly resuspended in at least 14 mL cold R10 + DNAse (RPMI-1640 supplemented with 10% fetal bovine serum, 1% L-glutamine, and 1% penicillin/streptomycin in the presence of 10 U/mL DNAse I) and spun down at 500 xg to pellet. The cell pellet was resuspended in R10 + DNase I and counted. Cells were then rested at 2E6 cells/mL in R10 + DNAse I for 2 hours. After resting, cells were washed in cold Cell Staining Buffer (Biolegend) 2 times, filtered through a 70 um filter, and counted. 5E5 cells from each sample were incubated with Human TruStain FcX (Biolegend) at 4℃ for 10 min at the manufacturer's recommended concentration of 10E6 cells/mL. Then, each individual sample was incubated with a unique TotalSeq-A compatible Hashing Antibody (Biolegend) at 0.5 ug antibody at 11.8E6 cells/mL. Then, samples were incubated with the TotalSeq-A Universal cocktail (Biolegend #399907) according to manufacturer's instructions. Samples were washed 3X with Cell Staining Buffer and counted. Cells from each sample were then pooled, concentrated to 2000 cells/uL, and filtered through a 40 um FlowMi filter (Bel-Art).

tag: cell type

value: mononuclear cells

tag: individuals and_tissues

tag: run number


title: NTC tumor DC1

city: Durham

first: Nicholas

last: DeVito

state: NC

address: 308 Research Drive

institute: Duke University

library_source: transcriptomic

data_processing:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification (NEBNext Ultra™ II RNA Library Prep Kit). The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on a Novaseq 6000 (Illumina), according to effective library concentration and data amount. Twenty million reads per sample were acquired at PE150 depth.
Assembly: grcmm39
Supplementary files format and content: xlsx FPKM

molecule: total RNA

organism: Mus musculus

source_name: tumor

growth_protocol: NTC and Gli2CA cells were grow in DMEM 10% FBS with 1x AA and 1 ug/mL of puromycin. These were implanted at 1e6 cells per 100 uL (1:1 with matrigel:pbs) into c57 bl/6 mice, and whole tumors were harvested at day d28

extract_protocol:
Tumors were taken at the time of experiment termination and digested in RPMI with collagenase (1 g/100mL HBSS, 10x stock solution, Sigma- Aldrich, C-5138) and DNase (20,000 U/100mL HBSS, 10x stock solution, Sigma-Aldrich, D-5025) at 37°C at 250 rpm in 15 mL conical tubes for 15 minutes. Tumors were processed through a 40 mM cell strainer (Corning, 431750) and CD11c selection was performed using FACS sorting (Sony DH800 Sorter). Selected cells were washed with PBS and lysed with RLT PLUS (QIAGEN, 1053393) with b-mercaptoethanol (VWR, VWRV0482-250ML). RNA was isolated using the RNAeasy Plus Micro kit (QIAGEN, 74034) per the manufacturer’s instructions.
NEBNext Ultra™ II RNA Library Prep Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: tissue

value: tumor

tag: cell line

value: dendritic cells

tag: genotype

value: NTC


title: Gli2CA Tumor DC1


title: 20220801_hpap_4_Pool_Well3_ADT, ADT derived library.

description: Library name: 20220801_hpap_4_Pool_Well3_ADT


title: Cas9-Gli2KO3

growth_protocol: NTC and Gli2CA cells were grow in DMEM 10% FBS with 1x AA and 1 ug/mL of puromycin; Cas9-NTC and Gli2KO cell media also contained blasticidin at 10 ug/mL

extract_protocol:
Rneasy Miniplus Kit from Qiagen
NEBNext Ultra™ II RNA Library Prep Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: melanoma


title: Cas9-Gli2KO2


title: Cas9-Gli2KO1


title: 20220531_hpap_2_Pool_Run2_Well9_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well9_ADT


title: 20220923_hpap_5_Pool_Well2_ADT, ADT derived library.

description: Library name: 20220923_hpap_5_Pool_Well2_ADT


title: 20220801_hpap_4_Pool_Well1_ADT, ADT derived library.

description: Library name: 20220801_hpap_4_Pool_Well1_ADT


title: Cas9-NTC3


title: NTC Replicate 1 scRNAseq

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the CellRanger software v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz

source_name: CD45+ cells from tumor

growth_protocol: see manuscript

extract_protocol:
Tumors were mechanically and enzymatically digested, CD45+ cells were selected by magnetic selection using the miltenyi biotec. Fllowing magentic selection, cells were washed and resuspended in 0.04% BSA in PBS prior to cell partitioning and library prep.
Libraries were constructed using 10x Genomics default protocols following the Next GEM Chromium 3' GEX v3.1

treatment_protocol: see manuscript

value: CD45+ cells from tumor

tag: treatment

value: IgG


title: 20220531_hpap_2_Pool_Run2_Well16_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well16_ADT


title: Cas9-NTC1


title: Gli2CA Tumor DC2


title: 20220531_hpap_2_Pool_Run2_Well14_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well14_ADT


title: 20220531_hpap_2_Pool_Run2_Well13_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well13_ADT


title: Gli2CA_03


title: 20220531_hpap_2_Pool_Run2_Well12_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well12_ADT


title: Gli2CA_02


title: 20220531_hpap_2_Pool_Run2_Well11_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well11_ADT


title: 20220801_hpap_4_Pool_Well4_ADT, ADT derived library.

description: Library name: 20220801_hpap_4_Pool_Well4_ADT


title: Gli2CA_01


title: NTC__03


title: 20220801_hpap_4_Pool_Well5_ADT, ADT derived library.

description: Library name: 20220801_hpap_4_Pool_Well5_ADT


title: 20220531_hpap_2_Pool_Run2_Well10_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well10_ADT


title: NTC__02


title: 20220531_hpap_2_Pool_Run1_Well8_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run1_Well8_ADT


title: NTC__01


title: Fetal liver, Input, rep2

city: Suzhou

first: Wen

last: Wei

state: Jiangsu Province

address: No. 199, Ren Ai Road

country: China

institute: Soochow University

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control and an initial threshold p-value of 0.001 as cutoff
Assembly: mm10
Supplementary files format and content: narrowPeak  file were generated using MACS2(2.2.7.1) (except for Input sample)

molecule: genomic DNA

source_name: E14.5 mouse fetal liver

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: E14.5 mouse fetal liver

tag: chip antibody


title: 20220531_hpap_2_Pool_Run1_Well6_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run1_Well6_ADT


title: Cas9-NTC2


title: 20220531_hpap_2_Pool_Run1_Well5_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run1_Well5_ADT


title: Gli2CA3

extract_protocol:
Rneasy Miniplus Kit from Qiagen, C-tube from miltenyi
NEBNext Ultra™ II RNA Library Prep Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: strain


title: 20220531_hpap_2_Pool_Run1_Well1_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run1_Well1_ADT


title: 20220531_hpap_2_Pool_Run1_Well2_ADT, ADT derived library.

description: Library name: 20220531_hpap_2_Pool_Run1_Well2_ADT


title: Gli2CA1


title: Gli2CA2


title: 20220119_hpap_1_Pool_A4_ADT, ADT derived library.

description: Library name: 20220119_hpap_1_Pool_A4_ADT


title: NTC2


title: NTC1


title: 20220119_hpap_1_Pool_A3_ADT, ADT derived library.

description: Library name: 20220119_hpap_1_Pool_A3_ADT


title: NTC3


title: Patient 8 Post-treatment_CD45_enriched

city: Barcelona

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

country: Spain

institute: CNAG

description: Library name: Patient 8_Post-treatment_CD45_enriched

data_processing:
Raw sequencing reads (paired-end fastq) were aligned to the GRCh38 genome and compressed into cram files.
Raw sequencing reads (fastq) were processed with 10X Genomics' software CellRanger version 6.0.1 to create processed files.
Assembly: GRCh38
Supplementary files format and content: tar.zip files raw count matrices per sample as produced by CellRanger

source_name: tumor biopsy

extract_protocol:
The extraction protocol involved enzymatic dissociation or thawing of biopsied or cryopreserved cells, followed by washing, filtration, and CD45+ cell enrichment to obtain viable single-cell suspensions for sequencing. More details are provided on the methods section of the paper.
Libraries were prepared following 10x Genomics’ 5-prime protocol.

value: tumor biopsy

value: tumor microenvironment

value: ImmTAC


title: 20220801_hpap_4_Pool_Well2_ADT, ADT derived library.

description: Library name: 20220801_hpap_4_Pool_Well2_ADT


title: Patient 8 Post-treatment

description: Library name: Patient 8_Post-treatment


title: 20220119_hpap_1_Pool_A2_ADT, ADT derived library.

description: Library name: 20220119_hpap_1_Pool_A2_ADT


title: ChIP-Seq_RPB1_CTDP1_degron_2h_DRB_40m_rep1

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

data_processing:
Raw ChIP-Seq reads with spike-in were firstly trimmed by Cutadapt software (v3.4) and then mapped to mm10 and hg19 genome by Bowtie2 software (v2.3.5.1) in end-to-end mode.
Only uniquely and concordantly mapped reads were kept for further analysis.
The bigwig files were generated using bamCoverage from Deeptools software (v3.5.1) normalized by the reads mapped to hg19 genome.
Assembly: mm10, hg19
Supplementary files format and content: bigwig

source_name: CTDP1-degron mES

growth_protocol: The cell were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma, D5796) with 15 % fetal bovine serum (FBS) (GeminiBio, 900-108), also supplemented with 1 mM L-glutamine (Gibco, 25030081), 1× nucleosides (Millipore, ES-008-D), 1× nonessential amino acids (Gibco, 11140050), 1× penicillin/ streptomycin (Gibco, 15140122), 1 mM Sodium Pyruvate (Gibco, 11360070), 0.1 mM β-mercaptoethanol (Sigma, M3148), 3 μM CHIR99021 (Selleck, S1036) and 1 μM PD0325901 (Selleck, S1263), 1000 U/ml mouse leukemia inhibiting factor (mLIF) (Milipore, ESG1107). All the cells were cultured in 0.2 % gelatin-coated plates at 37°C and 5% CO2 under humid environment.

extract_protocol:
The 1%(wt/vol) formaldehyde crosslinked, MNase digested and Qsonica sonicated chromatin fraction were incubated with indicated antibody overnight and Protein G magnetic beads (Thermo Fisher, 10004D) for another 3 h. After sufficient washing, elution and incubation at 65 °C overnight, DNA was purified through the DNA Extraction Reagent (phenol: chloroform: isoamyl alcohol (25: 24: 1) (pH8.0), Solarbio, P1012).
DNA library was constructed by NEB DNA Library Prep Kit for Illumina (NEB, E7645S), according to the manufacturer's instructions.

treatment_protocol: For RPB7 degradation, cells were treated with 2 μg/ml Dox for 12 h, then with 500 μM auxin for 3 h.  For transcription elongation inhibition, cells were pretreated with 0.5 μM CDK9 degrader THAL-SNS-032 (dCDK9, Selleck, S8979) for 2 h. Each sample was combiend with 10 % HEK293T cells for spike-in normalization.

value: CTDP1-degron mES

value: RPB7 degron 2h, DRB release 40m


title: ChIP-Seq_RPB1_CTDP1_degron_2h_DRB_40m_rep2


title: Patient 8 Sample 10

description: Library name: Patient 8_Sample 10


title: ChIP-Seq_RPB1_CTDP1_degron_2h_DRB_20m_rep2

value: RPB7 degron 2h, DRB release 20m


title: ChIP-Seq_RPB1_CTDP1_degron_2h_DRB_20m_rep1


title: Patient 8 Sample 9

description: Library name: Patient 8_Sample 9


title: ChIP-Seq_RPB1_CTDP1_degron_2h_DRB_0m_rep2

value: RPB7 degron 2h, DRB release 0m


title: Patient 7 Sample 8

description: Library name: Patient 7_Sample 8


title: ChIP-Seq_RPB1_CTDP1_degron_2h_DRB_0m_rep1


title: ChIP-Seq_RPB1_CTDP1_degron_0h_DRB_40m_rep2

value: RPB7 degron 0h, DRB release 40m


title: Patient 5 Sample 5

description: Library name: Patient 5_Sample 5


title: ChIP-Seq_RPB1_CTDP1_degron_0h_DRB_40m_rep1


title: Patient 6 Sample 6

description: Library name: Patient 6_Sample 6


title: ChIP-Seq_RPB1_CTDP1_degron_0h_DRB_20m_rep1

value: RPB7 degron 0h, DRB release 20m


title: ChIP-Seq_RPB1_CTDP1_degron_0h_DRB_20m_rep2


title: ChIP-Seq_RPB1_CTDP1_degron_0h_DRB_0m_rep2

value: RPB7 degron 0h, DRB release 0m


title: Patient 2 Sample 2

description: Library name: Patient 2_Sample 2


title: Patient 4 Sample 4

description: Library name: Patient 4_Sample 4


title: Patient 1 Sample 1

description: Library name: Patient 1_Sample 1


title: Patient 7 Sample 7

description: Library name: Patient 7_Sample 7


title: ChIP-Seq_RPB1_CTDP1_degron_0h_DRB_0m_rep1


title: RNA-Seq_Cul3KO_CTDP1_degron_12h_rep2

data_processing:
Raw RNA-Seq reads with spike-in were firstly trimmed by Cutadapt software (v3.4) and then mapped to mm10 and dm6 genome by STAR software (v2.7.10a).
Reads that were not primarily mapped, RCR duplicates and rRNA reads were discarded for further analysis.
Reads that mapped to each gene were counted by featureCounts software (v2.0.1).
Assembly: mm10, dm6
Supplementary files format and content: excel file include raw read counts for each Sample

molecule: polyA RNA

source_name: CTDP1-degron, Cul3KO mES

extract_protocol:
Total RNA was extracted by trizol according to the manufacturer’s instruction.
Samples were delivered to Novogene for poly(A) RNA library construction.

treatment_protocol: Cells were treated with 2 μg/ml Dox for 12 h, then with 500 μM auxin for another 12 h. For site-specific mutations of RPB7, 500 μM auxin treatment were prolonged for another 12 h. Each sample was combiend with 10 % Drosophila S2 cells for spike-in normalization.

value: CTDP1-degron, Cul3KO mES

value: CTDP1 degron for 12h


title: VIT030 Patient ATAC

city: Sevilla

first: Eloisa

last: Andujar

state: Sevilla

address: Avda Americo vespucio s/n

department: GENOMICS UNIT

institute: CABIMER-CSIC

description:
Library name: VIT030 scATAC-seq
10x genomics
Processed data for ATAC-seq data included in files on corresponding GEX sample.

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger ARC software v7.0  (https://www.10xgenomics.com/support/software/cell-ranger-arc/latest)
CellRanger count and aggr functions to aggregate reads across sequencing lanes into a single set of  barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (CellRanger ARC output files:  barcodes.tsv.gz, features.tsv.gz,matrix.mtx.gz)

source_name: Blood

extract_protocol:
Human peripheral blood mononuclear cells were isolated by Ficoll-Paque density gradient centrifugation and cryopreserved 2x10e6 cells per sample. Cell viability was 95% or greater for all samples. PBMCs were quickly thawed at 37°C in a water bath and washed with culture medium RPMI 1640 supplemented with 10% FBS. DNase treatment was done before the nuclei isolation. The nuclei isolation was conducted with an RNase inhibitor. Nuclei suspension was filtered with a 40μm cell strainer and counted in a Countess 3 FL Automated Cell Counter (Invitrogen); all samples had <5% live cells. High-quality nuclei were checked by 60x brightfield microscopy. The targeted number of nuclei was 5000 nuclei per sample. Finally, Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) was used to generate single-cell multiome data.
CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User Guide_RevF (Using a microfluidic chip, the nuclei of different patients are partitioned into nanoliterscale Gel Beads-in-emulsion (GEMs) with thousands of Barcodes to separately and uniquely index the transposed DNA and cDNA of each individual nucleus. ATAC and gene expression (GEX) libraries are generated from the same pool of pre-amplified transposed DNA/cDNA and sequenced)

value: Blood

value: PBMCs


title: RNA-Seq_Cul3KO_CTDP1_degron_0h_rep2

value: CTDP1 degron for 0h


title: VIT029 Patient ATAC

description:
Library name: VIT029 scATAC-seq
10x genomics
Processed data for ATAC-seq data included in files on corresponding GEX sample.


title: VIT027 Patient ATAC

description:
Library name: VIT027 scATAC-seq
10x genomics
Processed data for ATAC-seq data included in files on corresponding GEX sample.


title: RNA-Seq_Cul3KO_CTDP1_degron_0h_rep1


title: VIT028 Patient ATAC

description:
Library name: VIT028 scATAC-seq
10x genomics
Processed data for ATAC-seq data included in files on corresponding GEX sample.


title: VIT018 Patient ATAC

description:
Library name: VIT018 scATAC-seq
10x genomics
Processed data for ATAC-seq data included in files on corresponding GEX sample.


title: VIT017 Patient ATAC

description:
Library name: VIT017 scATAC-seq
10x genomics
Processed data for ATAC-seq data included in files on corresponding GEX sample.


title: VIT022 Patient ATAC

description:
Library name: VIT022 scATAC-seq
10x genomics
Processed data for ATAC-seq data included in files on corresponding GEX sample.


title: RNA-Seq_CTDP1_degron_0h_rep1


title: Patient 3 Sample 3

description: Library name: Patient 3_Sample 3


title: RNA-Seq_CTDP1_degron_12h_rep2


title: VIT011 Patient ATAC

description:
Library name: VIT011 scATAC-seq
10x genomics
Processed data for ATAC-seq data included in files on corresponding GEX sample.


title: RNA-Seq_CTDP1_degron_0h_rep2


title: VIT012 Patient ATAC

description:
Library name: VIT012 scATAC-seq
10x genomics
Processed data for ATAC-seq data included in files on corresponding GEX sample.


title: VIT010 Patient ATAC

description:
Library name: VIT010 scATAC-seq
10x genomics
Processed data for ATAC-seq data included in files on corresponding GEX sample.


title: VIT001 Patient ATAC

description:
Library name: VIT001 scATAC-seq
10x genomics
Processed data for ATAC-seq data included in files on corresponding GEX sample.


title: RNA-Seq_Cul3KO_CTDP1_degron_12h_rep1


title: POWV 3hr B

city: Syracuse

first: Saravanan

last: Thangamani

state: New York

address: 505 Irving Ave

institute: SUNY Upstate Medical University

description: Library name: 149

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Assembly: The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: CSV files include raw counts for each sample

source_name: Integument

extract_protocol:
RNA was extracted by homogenizing 4mm skin biopsies from the bite sites of tick feedings after fixation in Qiazol for 24 hours. After chlorophorm treatment and seperation of the aqueous layer, samples were extracted using an Rneasy kit (Qiagen) according to manufacturers' instructions.
Libraries were made using the NEBNext Ultra II RNA Library Prep Kit for Illumina based on the manufacturers instructions.

treatment_protocol: Ixodes scapularis ticks were allowed to feed on the backs of mice for 1, 3, or 6 hours. Ticks were either uninfected or infected with Powassan virus.

value: Integument

value: Balb/CJ

value: POWV infected Tick Bite


title: POWV 3hr A

description: Library name: 134


title: POWV 1hr C

description: Library name: 121


title: VIT030 Patient GEX

description:
Library name: VIT030 scRNA-seq
10x genomics


title: RNA-Seq_CTDP1_degron_12h_rep1


title: POWV 1hr B

description: Library name: 112


title: POWV 1hr A

description: Library name: 105


title: CDX2P-CreERT2Apcfl/fl Hmga1-/- mouse #284

city: Baltimore

first: LI

last: LUO

state: MD

address: 720 Rutland Ave, Ross Build

department: Hematology

institute: Johns Hopskins University

data_processing:
High thoughput sequencing was performed by Azenta HiSeq 2x150bp.
Trimmomatic 0.38 was used to trim the reads with default settings.
Sequencing reads were mapped back to mouse reference genome mm10 using Bowtie2.
Potential PCR duplicates were removed with samtools 1.9  to keep alignments that (1) have a minimum mapping quality of 30, (2) are aligned concordantly, and (3) are the primary called alignments. PCR or optical duplicates are marked using Picard 2.18.26 and removed.Prior to peak calling, reads mapping to mitochondria (mt) are called and filtered, and reads mapping to unplaced contigs are removed.. Peak calling was performed using Genrich (https://github.com/jsh58/Genrich) (0.6.1),  followed by DiffBind (http://bioconductor.org/packages/release/ bioc/html/DiffBind.html) (3.4.11) to identify differentially accessible regions of chromatin
MACS2 2.1.2 was used for peak calling to identify open chromatin regions. If a blacklist If a ‘blacklist’ of artefactual regions (areas with extremely high- or low-mappability) is available for the provided reference genome, called peaks are filtered for blacklisted regions to mitigate errors due to mappability. Valid peaks froms each group or condition are merged and peaks called in at least 66% of samples are kept for downstream analyses.
For each pair-wise comparison, peaks from condition A and condition B are merged and peaks found in either condition are kept for downstream analyses. Reads falling beneath peaks were counted in all samples, and these counts were used for differential peak analyses using the R package Diffbind.
Assembly: mm10
Supplementary files format and content: KO263.filtered.bam.tdf
Supplementary files format and content: KO266.filtered.bam.tdf
Supplementary files format and content: KO284.filtered.bam.tdf
Supplementary files format and content: WT260.filtered.bam.tdf
Supplementary files format and content: WT269.filtered.bam.tdf
Supplementary files format and content: WT279.filtered.bam.tdf

source_name: colon crypt cells

extract_protocol:
Enriched mouse colon crypt cells were washed once in 1x PBS, resuspended in ice-cold ATACseq lysis buffer (100 μl; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 and protease inhibitor) and centrifuged for 500 rpm, 10 minutes at 4 °C.  After centrifugation, pellets were washed briefly in 1x PBS before incubating in the transposase reaction mix (12.5 μl 2 × TD buffer, 2 μl transposase; Illumina) and nuclease-free water (10.5 μl) for 30 minutes at 37° C. Genomic DNAs were eluted using MinElute kit; QIAGEN.
After DNA purification (MinElute kit; QIAGEN), eluted DNA (1 μl) was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. Purified fragmented DNA was amplified by PCR.

value: colon crypt cells

value: CDX2P-CreERT2Apcfl/fl Hmga1-/-

value: tamoxifen induction at 12 weeks


title: VIT029 Patient GEX

description:
Library name: VIT029 scRNA-seq
10x genomics


title: POWV 6hr C

description: Library name: 110


title: CDX2P-CreERT2Apcfl/fl Hmga1-/- mouse #266


title: CDX2P-CreERT2Apcfl/fl Hmga1+/+ mouse #269

value: CDX2P-CreERT2Apcfl/fl Hmga1+/+


title: POWV 6hr A

description: Library name: 109


title: POWV 6hr B

description: Library name: 113


title: CDX2P-CreERT2Apcfl/fl Hmga1-/- mouse #263


title: VIT027 Patient GEX

description:
Library name: VIT027 scRNA-seq
10x genomics


title: Uninfected 6hr A

description: Library name: 217

value: Uninfected Tick Bite


title: VIT022 Patient GEX

description:
Library name: VIT022 scRNA-seq
10x genomics


title: CDX2P-CreERT2Apcfl/fl Hmga1+/+ mouse #279


title: VIT028 Patient GEX

description:
Library name: VIT028 scRNA-seq
10x genomics


title: POWV 3hr C

description: Library name: 127


title: Uninfected 6hr C

description: Library name: 218


title: AZD4

city: Nanjing

first: YUE

last: ZHAO

address: 305 East Zhongshan Road

institute: National Clinical Research Center of Kidney Diseases, Jinling Hospital

data_processing:
1、Data quality control The image data of the sequenced fragments measured by high-throughput sequencers are converted into sequence data (reads) by CASAVA base recognition, and the files are in fastq format, which mainly contain the sequence information of the sequenced fragments as well as their corresponding sequencing quality information. In order to ensure the quality and reliability of data analysis, we need to filter the raw data. To ensure the quality and reliability of the data analysis, we need to filter the raw data, including removing reads with adapters, removing reads containing N (N means that the information of bases cannot be determined), and removing low-quality reads (Qphred <= 20 bases accounted for more than 50% of the total length of the reads). At the same time, Q30 and GC content calculations were performed on clean data. All subsequent analyses were high-quality analyses based on clean data
2、Sequence alignment to a reference genome Download the reference genome and gene model annotation files directly from the genome website. The index of the reference genome was constructed using HISAT2 v2.0.5, and paired-end clean reads were compared to the reference genome using HISAT2 v2.0.5. We chose HISAT2 as the comparison tool because HISAT2 can generate a spliced linked database based on the gene model annotation files, and therefore has better comparison results than other non-spliced comparison tools.
3、Quantification of gene expression levels The FPKM of each gene is calculated based on the length of the gene and the number of reads mapped to that gene is calculated.FPKM refers to the expected number of fragments per kilobase per million base pairs of sequenced transcript sequence fragments. The effects of sequencing depth and gene length on read counts are also taken into account and are currently the most commonly used method for estimating gene expression levels.
4、Differential expression analysis For samples with biological duplicates, differential expression analyses between the two comparison combinations were performed using the DESeq2 software.DESeq2 provides statistical procedures for identifying differential expression in numerical gene expression data using models based on negative binomial distributions. The method of Benjamini and Hochberg was used to adjust the resulting p-values to control for false discovery rates. Genes with adjusted P-values <= 0.05 were found to be assigned as differentially expressed by DESeq2. For those without biological replicates were analysed using DESeq software.
5、Differential gene enrichment analysis GO enrichment analysis and KEGG pathway enrichment statistics of differentially expressed genes were achieved by clusterProfiler software, and GO terms and KEGG pathways with P < 0.05 were set as significant enrichment results
Assembly: Mus_musculus.GRCm38.91
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: renal tissue

extract_protocol:
Total RNA was isolated using an RNA extraction kit (Takara) and quantified using a NanoDrop 2000.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries
1) Total RNA samples were tested and then enriched for eukaryotic mRNA by Oligo(dT) magnetic beads; (2) Add Fragmentation Buffer for mRNA fragmentation; (3) One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; (4) Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; (5) PCR enrichment was performed to obtain cDNA libraries.

value: renal tissue


title: MT934_CHD3_WT_D18_CHIP_CHD3_rep1

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description:
Library name: MT934_CHD3_WT_D18_CHIP_CHD3_rep1
ChIP-Seq

data_processing:
[*RNA data processing step]  Adaptors were removed using TrimGalore!, reads were mapped and quantified using Kallisto and differential gene expression was analysed using DESeq2.
[ChIP data processing step]  ChIP-seq data were aligned to hg19 using BWA-mem. HOMER was used to call peaks using default parameters and FDR <5%
[ATAC data processing step]  ATAC-seq data were aligned to hg19 using BWA-mem. MACS2 was used to call peaks using default parameters and FDR <5%
Assembly: hg19 (homo sapiens)
Supplementary files format and content: kallisto quantified abundance files for RNA-seq data
Supplementary files format and content: bigwig files for ChIP-seq & ATAC-seq

source_name: BIONi010-A clone 3.3 (CHD3-WT 2)

growth_protocol: Human iPSCs were plated on Geltrex LDEV-Free hESC-qualified Reduced Growth Factoer Basement Membrane Matrix and maintained in feeder-free, serum-free mTeSR plus medium in small clusters

extract_protocol:
[*RNA extract protocol]  RNA was extracted using the Monarch Total RNA Miniprep Kit (New England Biolabs, T2010).
[*RNA-seq library construction protocol]  RNA libraries were constructed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760). 1 μg of total RNA input was used for each library. Libraries were sequenced on Illumina NextSeq 2000, producing 60bp paired-end reads.
[*ChIP-seq library construction protocol]  Barcoded libraries were made with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) using NEBNext Multiplex Oligos Dual Index Primers for Illumina (NEB, E7600S), and sequenced on Illumina NextSeq2000, producing 60 bp paired-end reads
[*ATAC-seq library construction protocol]  ATAC-seq was performed using 50,000 cells per sample. Libraries were prepared using the ATAC-seq Kit (Active Motif, 53150) and sequenced on either Illumina NextSeq2000, producing 60 bp paired-end reads or Illumina NovaSeq X Plus producing 150 bp paired-end reads.

treatment_protocol: iPSCs were cultured with CNCC specification media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 5 μg/ml bovine insulin, 20 ng/ml EGF, and 20 ng/ml hFGF for 6 days. At day ~7 when early migratory CNCCs first appeared, the cells were transitioned to CNCC early maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 1 mg/ml bovine serum albumin, serum replacement grade, 20 ng/ml EGF, and 20 ng/ml hFGF for 7 days. After 14 full days of CNCC specification, the cells were maintained in an “early CNCC” state for up to 18 days for subsequent experiments, or immediately transitioned to CNCC late maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 1 mg/ml bovine serum albumin, 20 ng/ml EGF, 20 ng/ml hFGF, 3uM ChIRON 99021, and 50pg/mL BMP2.

value: CHD3 Bethyl A301-220A

value: BIONi010-A clone 3.3 (CHD3-WT 2)

value: day 18 cranial neural crest cell - late maintenance media

value: cranial neural crest cell specification


title: AZD3


title: Uninfected 3hr C

description: Library name: 204


title: CDX2P-CreERT2Apcfl/fl Hmga1+/+ mouse #260


title: AZD2


title: Uninfected 3hr B

description: Library name: 207


title: MT933_CHD3_WT_D18_CHIP_INPUT

description:
Library name: MT933_CHD3_WT_D18_CHIP_INPUT
ChIP-Seq input


title: VIT018 Patient GEX

description:
Library name: VIT018 scRNA-seq
10x genomics


title: VIT017 Patient GEX

description:
Library name: VIT017 scRNA-seq
10x genomics


title: VIT012 Patient GEX

description:
Library name: VIT012 scRNA-seq
10x genomics


title: RNA_IF-3mt_KO_2

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

description: Library name: L8

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Assembly: Read quantitation using custom scripts
Supplementary files format and content: The human nuclear genomes (hg38) and custom-made mitochondrial transcript sequences
Supplementary files format and content: Fpcount text files contain three columns:  1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts.

extract_protocol:
Cells in a 10-cm dish were lysed with 600 µl of lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol) and treated with 25 U/ml TURBO DNase (Thermo Fisher Scientific). Then, the lysate was clarified by centrifugation at 20,000 × g for 10 min at 4°C.
Ribo-seq: RNase treatment, ribosome pelleting, Ribo-FilterOut, size selection, 1st preadenylated linker ligation, rRNA depletion, in vitro transcription, 2nd preadenylated linker ligation, reverse transcription, and PCR amplification. RNA-seq: the libraries were prepared by a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).

value: IF-3mt KO


title: AZD1


title: Uninfected 3hr A

description: Library name: 201


title: vehicle3


title: Uninfected 6hr B

description: Library name: 211


title: VIT011 Patient GEX

description:
Library name: VIT011 scRNA-seq
10x genomics

value: Blood


title: RNA_HEK293_1

description: Library name: L5

value: Naive


title: RNA_HEK293_2

description: Library name: L6


title: Uninfected 1hr B

description: Library name: 206


title: vehicle1


title: VIT001 Patient GEX

description:
Library name: VIT001 scRNA-seq
10x genomics

value: PBMCs


title: Ribo_IF-3mt_KO_2

description: Library name: L4

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Assembly: Read quantitation using custom scripts
Supplementary files format and content: The human nuclear genomes (hg38) and custom-made mitochondrial transcript sequences
Supplementary files format and content: Fpcount text files contain three columns:  1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts.
Library strategy: Ribo-Seq


title: Uninfected 1hr A

description: Library name: 203

value: Integument


title: Naïve Control 3

description: Library name: 703

value: Balb/CJ


title: Ribo_IF-3mt_KO_1

description: Library name: L3


title: VIT010 Patient GEX

description:
Library name: VIT010 scRNA-seq
10x genomics


title: RNA-seq_inner medulla, NFAT5-KO, rep6

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

country: Germany

institute: University Hospital Halle (Saale)

data_processing:
Clean reads were obtained from raw reads of FASTQ format by removing reads containing adapter and poly-N sequences and reads with low quality.
Paired-end clean reads were mapped to the reference genome (ensembl_mus_musculus_grcm38_p6_gca_000001635_8) using HISAT2 software. HTSeq was used to count the read numbers mapped of each gene, including known and novel genes. The FPKMs (Fragments Per Kilobase per Million mapped fragments) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each group
Supplementary files format and content: tab-delimited text files include FPKM values for each single sample

source_name: renal inner medulla

growth_protocol: KspCre+/-Nfat5fl/fl mice, Nfat5fl/fl mice, WT mice and Aqp2-Cre+/- mice from strain C57BL/6N were used.

extract_protocol:
Fresh kidneys were removed from the mice. A small piece of renal cortex tissue (approx. 2 mm) and the renal inner medulla from each single kidney were extracted. Total RNA was isolated with the Gene Elute Mammalian Total RNA prep kit (Sigma Aldrich) according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs, USA) 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. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, USA). Then 3 μl USER Enzyme (New England Biolabs, 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. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina, USA) according to the manufacturer’s instructions.

value: renal inner medulla


title: RNA-seq_inner medulla, NFAT5-KO, rep5


title: Ribo_HEK293_2

description: Library name: L2


title: SM4-4-5 iPSC-derived motor neurons, MN Day45

city: Bunkyo-ku

first: Selena

last: Setsu

state: Tokyo

department: Institute for Quantitative Bioscience

institute: University of Tokyo

description: SMART-seq

data_processing:
Quality Control of the sequences was performed by fastp (version 0.23.2).
Read counts were calculated by salmon (version 1.7.0), and the read count data outputs by salmon were processed by tximport (version 1.22.0).
The processed data were subjected to Transcripts Per Million (TPM) normalization among groups.
Assembly: GRCh38.p13
Supplementary files format and content: Quantitative read count data prossecced by salmon in .sf format.

extract_protocol:
RNA was harvested using Rneasy Micro Kit (Qiagen). 0.2 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nextera XT DNA Library Prep Kit following manufacturer's protocols.

value: iPSC-derived motor neurons

value: TARDBP N345K hetero

value: non

tag: time

value: MN Day45


title: 414C2 iPSC-derived motor neurons, MN Day45

description: SMART-seq

value: WT


title: Naïve Control 2

description: Library name: 702


title: RNA-seq_inner medulla, NFAT5-KO, rep4


title: WaGa_RIP_IMP3_rep3

city: Solna

first: Yajie

last: Yang

address: BioClinicum J6:20, Karolinska University Hospital Solna, Visionsgatan 4

country: Sweden

institute: Karolinska Institute

data_processing:
RNA sequencing reads were aligned to the human reference genome (GRCh38) and MCPyv genome (Nc 010277.2) using STAR aligner (v2.7.9a), which generated the raw count matrix.
The bam files aligned to transcriptome were submitted to RSEM method for quantifying transcript abundances frrm RNA-seq data
The quantification process utilized the human gene annotation from GENCODE v37.
Assembly: Human genome (GRCh38) and MCPyv genome (Nc 010277.2)
Supplementary files format and content: tab_delimited text files includes raw counts, TPM and FPKM for each sample

source_name: WaGa

growth_protocol: WaGa cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37

extract_protocol:
RNA immunoprecipitation (RIP) was performed using 5 µg IGF2BP3  or IgG antibody and 100 µL of Protein G Sepharose 4 Fast Flow beads, following overnight incubation at 4°C. To digest the proteins, 1 mg/mL proteinase K was added and incubated for 30 minutes at 55°C, followed by RNA extraction using Trizol Reagent.
Library preparation and sequencing was performed by Novogene Company Limited (Cambridge, UK) on an Illumina HiSeq platform with 150 bp paired end reads.

treatment_protocol: No treatment

value: WaGa

value: Merkel cell carcinoma cell line


title: RNA_IF-3mt_KO_1

description: Library name: L7


title: Ribo_HEK293_1

description: Library name: L1


title: Naïve Control 1

description: Library name: 701


title: RNA-seq_inner medulla, NFAT5-KO, rep3


title: WaGa_RIP_IgG_rep3


title: vehicle2

value: renal tissue


title: Sora3

first: Chunxiao

last: Li

address: Huayuan Road

institute: Peking University Third Hospital

data_processing:
The sequencing data were filtered with SOAPnuke (v1.5.2) (Li et al., 2008)by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) was more than 20%; (3) Removing reads whose unknown base ('N' base) ratio was more than 5%, and afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)(Kim et al., 2015). Bowtie2 (v2.2.5)(Langmead and Salzberg, 2012) was applied to align the clean reads to the reference coding gene set，and then expression level of gene was calculated by RSEM (v1.2.12)(Li and Dewey, 2011).
The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Assembly: mm9
Supplementary files format and content: counts.txt

source_name: Myeloid-derived suppressor cells

extract_protocol:
Total RNA was extracted from the muscle tissues using Trizol (Invitrogen, Carlsbad, California, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, and then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, and then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from the previous step were amplified by PCR, and products were purified by Ampure XP Beads, and then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from the previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Myeloid-derived suppressor cells

value: wildtye

value: Sora


title: Uninfected 1hr C

description: Library name: 209

value: Uninfected Tick Bite


title: Sora2


title: WaGa_RIP_IMP3_rep2


title: WaGa_RIP_IgG_rep2


title: RNA-seq_inner medulla, NFAT5-KO, rep1


title: WaGa_RIP_IMP3_rep1


title: Control3

value: Vehicle


title: RNA-seq_inner medulla, WT, rep11


title: HEK293, RPB1, shRPRD1B, rep2

city: Austin

first: Svetlana

last: Panina

state: TX

address: 101 East 21st St.

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
After initial assessment of read quality, RPB1-Pol II ChIP-Seq data was mapped onto human reference genome, hg38, with Bowtie2 v. 2.5.0 aligner for paired-end reads using default parameters.
Bigwig files (CPM format) were generated using the bamCoverage function (--normalizeUsing CPM --smoothLength 150 --binSize 50 --scalefactor 1) from deeptools.
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
For RPB1 samples,  HEK293T cells expressing shControl or shRPRD1B cells were crosslinked by 1% formaldehyde for 10 min. Crosslinking was quenched with 0.125 M glycine for 5 min. Cells were successively lysed in lysis buffer LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× PI), LB2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× PI) and LB3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1× PI). Chromatin was sonicated to an average size of ~200–500 bp using UCD-200 Biorupter (30s on and 30 s off for 30 min). A total of 5 μg of RPB1 antibody (cat: ab76123) was pre-mixed in a 50μl volume of Dynabeads protein A (Invitrogen) and was added to each sonicated chromatin sample and incubated overnight at 4°C. The chromatin-bound beads were washed two times with low salt buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 150mM NaCl), once with high salt wash buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 500mM NaCl), once with LiCl wash buffer (250mM LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, 1mM EDTA, 10mM Tris-Cl pH 8.0) and twice in TE buffer. The chromatin was reverse crosslinked overnight at 65°C with shaking at 750rpm. After DNA extraction using phenol-chloroform, the DNA was resuspended in 10mM Tris-HCl pH 8.0. The purified DNA was subjected to qPCR to confirm target region enrichment before moving on to deep sequencing library preparation.
For sequencing, the extracted DNA was used to construct the ChIP-seq library using the NEBNext Ultra II DNA Library Prep Kit followed by sequencing with an Illumina NovaSeq X Plus system.

treatment_protocol: HEK293T cells were infected at a multiplicity of infection 1 using MISSION shRNA lentiviral particles (Sigma, clone: TRCN0000130891) against RPRD1B. Hexadimethrine bromide was added to the cells at a final concentration of 8 μg/ml. Transduced cells were selected with puromycin at a concentration of 1 μg/ml for 7 days. In parallel, the control cells were transfected with MISSION non-mammalian shRNA negative control plasmid (Sigma, Cat: SHC002) using Fugene (Promega, Wadison, WI, USA) with a DNA to Fugene ratio of 1:3 for the same duration of time.

value: Human embryonic kidney


title: HEK293, RPB1, shRPRD1B, rep1


title: Control2


title: WaGa_RIP_IgG_rep1


title: Control1


title: HLA02-T7, CD45+ skin biopsy cells from pt with gamma/delta mycosis fungoides, scRNA-seq VDJ-T library

city: Palo Alto

first: Michael

last: Khodadoust

state: CA

address: 1701 Page Mill Rd

department: Medicine (Oncology)

institute: Stanford University School of Medicine

data_processing:
Demultiplexing of bulk sequencing FASTQs was performed using internal pipelines.
Barcode processing, gene counting, and aggregation were accomplished using Cell Ranger 6.1.2 and 7.0.1 (10x Genomics).
Assembly: hg38
Supplementary files format and content: Tab-delimited gzipped value files (*barcodes.tsv.gz, *features.tsv.gz), comma-delimited value files (*filtered_contig_annotations.csv, *cell_barcodes.json), and gzipped matrix files (*matrix.mtx.gz)

source_name: Skin

extract_protocol:
Fresh peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using Ficoll-Paque density-gradient centrifugation and cryopreserved in a solution of 50% fetal bovine serum, 40% RPMI 1640 media, and 10% dimethyl sulfoxide. At a later time, PBMCs were thawed. Skin biopsies were dissociated into single cell suspensions using either the Tumor Dissociation Reagent (BD Biosciences) or gentleMACS Tumor Dissociation Kit (Miltenyi Biotec). For both PBMC and skin samples, dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec). Cells from skin samples additionally underwent CD45+ enrichment using CD45 (TIL) MicroBeads (Miltenyi Biotec). Remaining viable cells were resuspended in 0.04% BSA in DPBS (no Ca2+/Mg2+).
Library construction was performed according to the manufacturer's instructions (Single Cell Next GEM 5' v2 protocol, 10x Genomics). Briefly, PBMCs were resuspended in the master mix and loaded 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 contained an Illumina R1 primer sequence, 10x barcode, and unique molecular identifier (UMI). The pooled barcoded DNA was then cleaned up using Silane Dynabeads, amplified by PCR, and then the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Illumina R2 primer sequences, paired-end constructs with P5 and P7 sequences, and a sample index were added.

value: Skin

value: CD45+ cells from skin biopsy


title: HEK293, RPB1, Control, rep1


title: RNA-seq_inner medulla, WT, rep10

value: renal inner medulla


title: RNA-seq_inner medulla, WT, rep9


title: Sora1


title: Pten p53 5mo [scRNA-seq]

first: Gilles

last: Laverny

address: 1 rue Laurent fries

country: France

institute: IGBMC

description:
MNGC383
10x Genomics

data_processing:
Cell Ranger 7.0.0 count was used for alignment, barcode and UMI filtering and counting, with a reference created with Cell Ranger 7.0.0 mkref using GRCm39 assembly of Mus musculus genome, Ensembl release 107 annotations and CreERT2 sequence.
Assembly: GRCm39
Supplementary files format and content: Gzipped tsv files with feature and barcode sequences corresponding respectively to row and column indices from the matrix.

source_name: Prostate

extract_protocol:
Mouse prostates were dissociated into single cells as described (DOI:10.1126/sciadv.abo2295). Cells from 3 prostates were pooled, stained with DAPI and living cells (DAPI-negative) were FACS-sorted using a BD FACSAriaTM Fusion flow cytometer. Trypan blue exclusion assay was used to determine cell number and viability of prostatic FACS-sorted cells using a Neubauer Chamber.
Sixteen thousand cells were loaded on the Chromium Controller (10X Genomics, Leiden, The Netherlands). Single-cell 3′ mRNA-seq library was generated according to User guide Chromium Next GEM Single Cell 3 prime Reagent Kits v3.1 (Dual index) (10X Genomics, PN CG000315 - Rev.D).

value: Prostate


title: RNA-seq_inner medulla, WT, rep8


title: DDC6Wks-2-DKO-[D_243]

city: San Francisco

first: Jessica

middle: M

last: Herrera

address: 513 Parnassus Ave, HSE 590

department: Surgery

institute: UCSF

data_processing:
Library construction, quality control, sequence alignment, and high- throughput sequencing were performed by Novogene (Sacramento, CA) in accordance with their standard protocol.
Poly-N, low-quality reads, and adaptor reads were removed from the raw reads in FASTQ format; Q20, Q30, error rate distribution, and GC content of filtered data were determined.
STAR alignment software was used to map the quality- controlled reads to the mouse reference genome (mm10).
Raw reads were normalized by DESeq2 algorithm using R
Assembly: mm10
Supplementary files format and content: Excel table with raw gene counts for every gene in every sample.
Supplementary files format and content: Excel table with Deseq2 normalized counts for every gene in every sample.

source_name: Liver

growth_protocol: Liver epithelial-specific ROCK deficient mice were generated when Rock1fl/fl, Rock2fl/fl, and Rock1fl/fl;Rock2fl/fl mice were injected with adeno-associated virus serotype 8 (AAV8)-thyroid hormone-binding globulin (TBG)-Cre for targeted gene deletion in hepatocytes, or injected with AAV8-TBG-Null to generate littermate controls (WT).

extract_protocol:
Livers were removed, preserved in RNALater for at least 24 hours, and then RNA was harvested using the RNeasy Plus Mini Kit (QIAGEN, Germantown, MD) following the manufacturer’s instructions. RNA quantity and purity were quantified by NanoDrop1000 (Thermo Fisher Scientific, Waltham, MA). 1μg of total RNA was used for the construction of sequencing libraries.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) was used to create the sequencing libraries.

treatment_protocol: Gradual cholestatic injury was induced by providing mice with 0.1% w/w DDC diet (TestDiet, St. Louis, MO) ad libitum for 4-8 weeks.

value: Liver

tag: genotype abbreviation

value: DKO

value: DDC

tag: Sex

value: Male


title: HEK293T,shRPRD1B, rep1

first: Yan

middle: Jessie

last: Zhang

address: 100 E. 24th Street

institute: University of Texas-Austin

data_processing:
Sequence reads were trimmed using TrimGalore! to omit adaptor sequences
trimmed sequences were mapped to hg38 using HISAT2
read count extraction was conducted using featurecounts
Assembly: hg38
Supplementary files format and content: text file including raw counts for each sample

growth_protocol: HEK293T cells were maintained in DMEM supplemented in 10% FBS and antibiotics in a humidified chamber with 5% CO2 at 37°C

extract_protocol:
RNA was isolated from HEK293T cells (at least ~106 cells per sample) using DirectZol RNA Miniprep kit (Zymo Research).
Libraries were prepared at Novogene Co. according to manufacturer’s instructions for the NEBNext Ultra RNA Library kit for Illumina.

treatment_protocol: Cells were transduced with shRNA to knockdown RPRD1B via lentivirus transduction or shControl in HEK293T cells

value: human embryonic kidney cells


title: HEK293T, shCtrl, rep2

value: shCtrl


title: HLA19-T5, CD45+ skin biopsy cells from pt with Sézary syndrome, scRNA-seq VDJ-T library


title: DDC6Wks-2-DKO-[D_203]


title: RNA-seq_inner medulla, WT, rep7


title: HLA02-T7, CD45+ skin biopsy cells from pt with gamma/delta mycosis fungoides, scRNA-seq GEX library


title: RNA-seq_inner medulla, NFAT5-KO, rep2


title: HEK293, RPB1, Control, rep2


title: HLA19-T5, CD45+ skin biopsy cells from pt with Sézary syndrome, scRNA-seq GEX library


title: HEK293, Input


title: RNA-seq_inner medulla, WT, rep12


title: DDC6Wks-2-DKO-[D_202]


title: A549 cells,Knockdown2,DDX24

city: Dalian

first: Wang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

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

source_name: Lung

growth_protocol: A549 cells were maintained at standard culture conditions (37°C, 5% CO2) in F12K medium with 10% FBS.

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

value: Lung

value: lung cancer cells


title: HEK293T, shRPRD1B, rep2


title: A549 cells,Knockdown1,DDX24


title: HLA20-T2, CD45+ skin biopsy cells from pt with mycosis fungoides, scRNA-seq VDJ-T library


title: HEK293T, shCtrl, rep1


title: HLA20-T2, CD45+ skin biopsy cells from pt with mycosis fungoides, scRNA-seq GEX library


title: DDC6Wks-2-DKO-[D_201]


title: RNA-seq_inner medulla, WT, rep4

value: WT


title: RNA-seq_inner medulla, WT, rep6


title: DDC6Wks-4-DKO-[D_207]


title: HLA21-T1, peripheral blood mononuclear cells from pt with Sézary syndrome, scRNA-seq VDJ-T library

value: Blood

value: Peripheral blood mononuclear cells


title: DDC6Wks-4-DKO-[D_205]


title: S3, sample5, BCR

city: New Haven

first: Liza

last: Konnikova

state: CT

address: 375 Congress Ave

institute: Yale University

data_processing:
Raw sequence reads were aligned to the human reference dataset GRCh38 to generate gene expression using Cell Ranger v6.1.2 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
Cryopreserved samples are thawed slightly, and cells with a viability of >70% were used 10X single cell RNA sequencing.
Single-cell cDNA with matched TCR and BCR VDJ libraries were prepared using the 10x Chromium Next GEM 5′ reagent kit (v2) according to the manufacturer’s instructions. Sequencing was performed on the NovaSeq 6000 sequencer (Illumina) to obtain paired end reads.
scRNA-seq, scTCR-seq, scBCR-seq

tag: Stage

value: 1 month

value: blood

value: primary cells

value: immune cells

tag: library type

value: BCR


title: RNA-seq_inner medulla, WT, rep2

value: renal inner medulla


title: HLA21-T1, peripheral blood mononuclear cells from pt with Sézary syndrome, scRNA-seq GEX library


title: DDC6Wks-4-DKO-[D_98]

value: Liver


title: S3, sample5, TCR

value: TCR


title: MT810_CHD3_KO_D18_CNCC_ATAC_rep2

description:
Library name: MT810_CHD3_KO_D18_CNCC_ATAC_rep2
ATAC-seq

source_name: BIONi010-A clone 2.12 (CHD3-KO 1)

value: BIONi010-A clone 2.12 (CHD3-KO 1)

value: day 18 cranial neural crest cell - late maintenance media

value: cranial neural crest cell specification


title: RNA-seq_inner medulla, WT, rep1


title: MT809_CHD3_KO_D18_CNCC_ATAC_rep1

description:
Library name: MT809_CHD3_KO_D18_CNCC_ATAC_rep1
ATAC-seq


title: S3, sample5, GEX

value: GEX


title: DDC6Wks-4-DKO-[D_26]

value: DKO

value: DDC

value: Male


title: RNA-seq_cortex, NFAT5-KO, rep6

source_name: renal cortex

value: renal cortex


title: MT808_CHD3_WT_D18_CNCC_ATAC_rep2

description:
Library name: MT808_CHD3_WT_D18_CNCC_ATAC_rep2
ATAC-seq

source_name: BIONi010-A clone 3.2 (CHD3-WT 1)

value: BIONi010-A clone 3.2 (CHD3-WT 1)


title: S5, sample4, BCR

value: 2 months


title: DDC6Wks-2-WT-[D_218]

value: WT


title: S5, sample4, TCR

value: blood

value: primary cells


title: MT807_CHD3_WT_D18_CNCC_ATAC_rep1

description:
Library name: MT807_CHD3_WT_D18_CNCC_ATAC_rep1
ATAC-seq


title: DDC6Wks-2-WT-[D_216]


title: RNA-seq_cortex, NFAT5-KO, rep5


title: RNA-seq_inner medulla, WT, rep5


title: MT804_CHD3_KO_D14_CNCC_ATAC_rep2

description:
Library name: MT804_CHD3_KO_D14_CNCC_ATAC_rep2
ATAC-seq

value: day 14 cranial neural crest cell


title: A549 cells,Knockdown,Control

value: Lung

value: lung cancer cells


title: S2, sample2, BCR

value: 1 month

value: immune cells

value: BCR


title: RNA-seq_cortex, NFAT5-KO, rep4


title: RNA-seq_cortex, NFAT5-KO, rep2


title: RNA-seq_cortex, NFAT5-KO, rep3


title: S2, sample2, TCR

value: TCR


title: MT802_CHD3_WT_D14_CNCC_ATAC_rep2

description:
Library name: MT802_CHD3_WT_D14_CNCC_ATAC_rep2
ATAC-seq

value: cranial neural crest cell specification


title: DDC6Wks-2-WT-[D_219]

value: Liver


title: DDC6Wks-4-WT-[D_209]

value: DDC


title: S2, sample2, GEX

value: GEX


title: RNA-seq_cortex, WT, rep12

value: renal cortex


title: RNA-seq_inner medulla, WT, rep3

value: renal inner medulla


title: RNA-seq_cortex, NFAT5-KO, rep1


title: MT801_CHD3_WT_D14_CNCC_ATAC_rep1

description:
Library name: MT801_CHD3_WT_D14_CNCC_ATAC_rep1
ATAC-seq

value: BIONi010-A clone 3.2 (CHD3-WT 1)


title: S5, sample3, BCR

value: 2 months


title: RNA-seq_cortex, WT, rep11


title: DDC6Wks-2-WT-[D_215]

value: WT

value: Male


title: DDC6Wks-4-WT-[D_30]


title: MT906_CHD3_KO_D14_CHIP_DLX5_35

description:
Library name: MT906_CHD3_KO_D14_CHIP_DLX5_35
ChIP-Seq

source_name: BIONi010-A clone 3.5 (CHD3-KO 2)

value: DLX5 Abcam ab109737

value: BIONi010-A clone 3.5 (CHD3-KO 2)

value: day 14 cranial neural crest cell


title: DDC6Wks-4-WT-[D_900]


title: MT803_CHD3_KO_D14_CNCC_ATAC_rep1

description:
Library name: MT803_CHD3_KO_D14_CNCC_ATAC_rep1
ATAC-seq

value: BIONi010-A clone 2.12 (CHD3-KO 1)


title: MT903_CHD3_WT_D14_CHIP_DLX5_32

description:
Library name: MT903_CHD3_WT_D14_CHIP_DLX5_32
ChIP-Seq


title: DDC6Wks-4-WT-[D_208]


title: S5, sample4, GEX

value: blood

value: primary cells

value: immune cells


title: S2, sample1, BCR

value: 1 month

value: BCR


title: MT900_CHD3_WT_D14_CHIP_CHD3_33

description:
Library name: MT900_CHD3_WT_D14_CHIP_CHD3_33
ChIP-Seq

value: CHD3 Bethyl A301-220A

value: BIONi010-A clone 3.3 (CHD3-WT 2)

value: cranial neural crest cell specification


title: DDC6Wks-R2KO-[S_470]

value: Liver

value: DDC


title: RNA-seq_cortex, WT, rep8

value: renal cortex


title: S5, sample3, TCR

value: 2 months

value: TCR


title: RNA-seq_cortex, WT, rep7


title: MT905_CHD3_KO_D14_CHIP_DLX5_212

description:
Library name: MT905_CHD3_KO_D14_CHIP_DLX5_212
ChIP-Seq

value: DLX5 Abcam ab109737


title: RNA-seq_cortex, WT, rep6


title: MT819_CHD3_KO_D14_CNCC_RNA_rep3

description:
Library name: MT819_CHD3_KO_D14_CNCC_RNA_rep3
RNA-Seq


title: DDC6Wks-R2KO-[S_472]

value: Male


title: MT898_CHD3_WT_D14_CHIP_INPUT

description:
Library name: MT898_CHD3_WT_D14_CHIP_INPUT
ChIP-Seq input

value: day 14 cranial neural crest cell


title: RNA-seq_cortex, WT, rep10


title: DDC6Wks-R2KO-[S_471]


title: S5, sample3, GEX

value: GEX


title: S2, sample1, TCR

value: blood


title: RNA-seq_cortex, WT, rep5


title: MT818_CHD3_KO_D14_CNCC_RNA_rep2

description:
Library name: MT818_CHD3_KO_D14_CNCC_RNA_rep2
RNA-Seq

value: BIONi010-A clone 2.12 (CHD3-KO 1)


title: RNA-seq_cortex, WT, rep9


title: MT817_CHD3_KO_D14_CNCC_RNA_rep1

description:
Library name: MT817_CHD3_KO_D14_CNCC_RNA_rep1
RNA-Seq


title: S1, sample5, GEX

value: 1 week

value: primary cells

value: immune cells


title: DDC6Wks-R1KO-[S_474]


title: MT899_CHD3_WT_D14_CHIP_CHD3_32

description:
Library name: MT899_CHD3_WT_D14_CHIP_CHD3_32
ChIP-Seq

value: CHD3 Bethyl A301-220A

value: BIONi010-A clone 3.2 (CHD3-WT 1)


title: DDC6Wks-R2KO-[S_419]


title: S1, sample5, BCR

value: BCR


title: RNA-seq_cortex, WT, rep2

value: WT


title: S2, sample1, GEX

value: 1 month


title: S5, sample2, TCR


title: MT811_CHD3_WT_D14_CNCC_RNA_rep1

description:
Library name: MT811_CHD3_WT_D14_CNCC_RNA_rep1
RNA-Seq

value: cranial neural crest cell specification


title: S1, sample5, TCR


title: DDC6Wks-R1KO-[S_490]

value: Liver

value: DDC


title: MT738_CHD3_HET_D20_CNCC_RNA_rep3

description:
Library name: MT738_CHD3_HET_D20_CNCC_RNA_rep3
RNA-Seq

source_name: BIONi010-A clone 1.9 (CHD3-HET-KO 1)

value: BIONi010-A clone 1.9 (CHD3-HET-KO 1)

value: day 18 cranial neural crest cell - early maintenance media


title: DDC6Wks-R1KO-[S_475]

value: Male


title: MT726_CHD3_HET_D20_CNCC_RNA_rep2

description:
Library name: MT726_CHD3_HET_D20_CNCC_RNA_rep2
RNA-Seq


title: S3, sample4, BCR


title: RNA-seq_cortex, WT, rep4

value: renal cortex


title: DDC6Wks-R2WT-[S_422]


title: RNA-seq_cortex, WT, rep3


title: S5, sample2, BCR

value: 2 months

value: blood


title: M4

city: Shanghai

first: Cenxi

last: Liu

address: Songhu Road 2005

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for  low-quality sequence, then mapped to mm10 whole genome using Hisat2
Stringtie was used to quantify
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Adipose

extract_protocol:
Total RNA was extracted from tissues by using TRIzol reagent (Invitrogen). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adipose

value: depleted Ntsr2


title: S3, sample4, GEX

value: primary cells

value: immune cells

value: GEX


title: DDC6Wks-R1KO-[S_492]


title: MT812_CHD3_WT_D14_CNCC_RNA_rep2

description:
Library name: MT812_CHD3_WT_D14_CNCC_RNA_rep2
RNA-Seq

value: BIONi010-A clone 3.2 (CHD3-WT 1)

value: day 14 cranial neural crest cell


title: DDC6Wks-R2WT-[S_493]


title: RNA-seq_cortex, WT, rep1

value: WT


title: posterior eye, aged, OVX, animal 23

city: Atlanta

first: Andrew

middle: J

last: Feola

address: 1365B Clifton Road NE

institute: Emory University

data_processing:
Transcript abundance estimates were calculated internally to the STAR aligner using the htseq-count algorithm. Gene counts were normalized using DESeq2 in R.
Assembly: Alignment was performed using STAR version 2.7.3a and transcripts were annotated using Rnor_6.0 Ensembl release 95.
Supplementary files format and content: Raw count values in csv

organism: Rattus norvegicus

source_name: Posterior Eye

extract_protocol:
All samples were stored at 25°C and processed within 48 hours of dissection. Tissues were homogenized in 700 µL of QIAzol and extracted using the miRNeasy Mini kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using a TapeStation 4200 (Agilent) and 10 ng of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a Fragment Analyzer (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding 30 million reads per sample on average.
RNA quality was assessed using a TapeStation 4200 (Agilent) and 10 ng of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a Fragment Analyzer (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding 30 million reads per sample on average.

value: Posterior Eye

value: Female

value: Aged, OVX


title: S5, sample2, GEX


title: MT724_CHD3_WT_D20_CNCC_RNA_rep2

description:
Library name: MT724_CHD3_WT_D20_CNCC_RNA_rep2
RNA-Seq

value: cranial neural crest cell specification


title: M5


title: C4

value: control


title: DDC6Wks-R1WT-[S_486]

value: Liver

value: DDC

value: Male


title: DDC6Wks-R1WT-[S_485]


title: MT694_CHD3_WT_D20_CNCC_RNA_rep1

description:
Library name: MT694_CHD3_WT_D20_CNCC_RNA_rep1
RNA-Seq

value: day 18 cranial neural crest cell - early maintenance media


title: S3, sample4, TCR

value: 1 month

value: blood

value: TCR


title: MT696_CHD3_HET_D20_CNCC_RNA_rep1

description:
Library name: MT696_CHD3_HET_D20_CNCC_RNA_rep1
RNA-Seq

value: BIONi010-A clone 1.9 (CHD3-HET-KO 1)


title: S1, sample3, BCR

value: 1 week

value: primary cells

value: immune cells

value: BCR


title: MT736_CHD3_WT_D20_CNCC_RNA_rep3

description:
Library name: MT736_CHD3_WT_D20_CNCC_RNA_rep3
RNA-Seq

value: BIONi010-A clone 3.2 (CHD3-WT 1)


title: C5

value: Adipose


title: SP_tumor_rep4_ATAC

city: Saint Louis

first: Changxu

last: Fan

state: Missouri

address: 4515 McKinley Avenue, Room 5213

department: Genetics

institute: Washington University in St. Louis

data_processing:
Data were processed using the "count" function of cellranger-arc (v2.0)
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene-by-cell expression matrices and peak-by-cell chromatin accessibility matrices
Supplementary files format and content: fragments.tsv.gz: ATAC fragments
Supplementary files format and content: .arrow: arrow files created by ArchR
Library strategy: single cell multiome ATAC + GEX

source_name: Spleen

extract_protocol:
BM samples: Lin- cells were sorted. Spleen samples: Lin-Kit+ and Lin-Kit+Sca+ cells were sorted and combined at a ratio of 1:1.
Nuclei were isolated following the 10x protocol CG000365 • Rev B. Isolated nuclei were further processed using the 10x “Single Cell Multiome ATAC + Gene Expression” platform (CG000338 Rev B).

treatment_protocol: Tumor: mice were subcutaneously injected with PyMT-B6 cancer cell line. Ctrl: PBS was injected instead of cancer cells. Samples were collected 29 days (BM_ctrl_rep1, BM_tumor_rep1) or 21 days (all other samples) after injection.

value: Spleen

value: Hematopoietic progenitors

value: WT C57BL/6J

value: subcutaneous MMTV-PyMT tumor


title: M3

value: depleted Ntsr2


title: S1, sample4, BCR


title: posterior eye, aged, OVX, animal 22

value: Posterior Eye

value: Female

value: Aged, OVX


title: S1, sample4, TCR

value: blood


title: S1, sample3, TCR

value: TCR


title: C3

value: control


title: posterior eye, aged, sham, animal 18

value: Aged, Sham


title: S1, sample3, GEX

value: 1 week

value: primary cells

value: GEX


title: MT822_CHD3_KO_D18_CNCC_RNA_rep3

description:
Library name: MT822_CHD3_KO_D18_CNCC_RNA_rep3
RNA-Seq

data_processing:
[*RNA data processing step]  Adaptors were removed using TrimGalore!, reads were mapped and quantified using Kallisto and differential gene expression was analysed using DESeq2.
[ChIP data processing step]  ChIP-seq data were aligned to hg19 using BWA-mem. HOMER was used to call peaks using default parameters and FDR <5%
[ATAC data processing step]  ATAC-seq data were aligned to hg19 using BWA-mem. MACS2 was used to call peaks using default parameters and FDR <5%
Assembly: hg19 (homo sapiens)
Supplementary files format and content: kallisto quantified abundance files for RNA-seq data
Supplementary files format and content: bigwig files for ChIP-seq & ATAC-seq

value: BIONi010-A clone 2.12 (CHD3-KO 1)

value: day 18 cranial neural crest cell - late maintenance media

value: cranial neural crest cell specification


title: posterior eye, aged, OVX, animal 21


title: posterior eye, aged, OVX, animal 24


title: SP_tumor_rep3_GEX

value: Spleen

value: Hematopoietic progenitors


title: posterior eye, aged, OVX, animal 19


title: MT821_CHD3_KO_D18_CNCC_RNA_rep2

description:
Library name: MT821_CHD3_KO_D18_CNCC_RNA_rep2
RNA-Seq


title: MT820_CHD3_KO_D18_CNCC_RNA_rep1

description:
Library name: MT820_CHD3_KO_D18_CNCC_RNA_rep1
RNA-Seq


title: SP_tumor_rep3_ATAC

value: WT C57BL/6J

value: subcutaneous MMTV-PyMT tumor


title: posterior eye, aged, OVX, animal 20

value: Posterior Eye


title: MT815_CHD3_WT_D18_CNCC_RNA_rep2

description:
Library name: MT815_CHD3_WT_D18_CNCC_RNA_rep2
RNA-Seq

value: BIONi010-A clone 3.2 (CHD3-WT 1)


title: MT814_CHD3_WT_D18_CNCC_RNA_rep1

description:
Library name: MT814_CHD3_WT_D18_CNCC_RNA_rep1
RNA-Seq


title: posterior eye, aged, sham, animal 17

value: Female


title: S1, sample2, BCR

value: blood

value: immune cells

value: BCR


title: posterior eye, aged, sham, animal 15

value: Aged, Sham


title: SP_tumor_rep2_GEX


title: S1, sample4, GEX

value: 1 week


title: SP_tumor_rep2_ATAC


title: S1, sample2, GEX

value: primary cells


title: posterior eye, aged, sham, animal 16


title: SP_tumor_rep4_GEX


title: MT725_CHD3_HET_D0_CNCC_RNA_rep2

description:
Library name: MT725_CHD3_HET_D0_CNCC_RNA_rep2
RNA-Seq

value: BIONi010-A clone 1.9 (CHD3-HET-KO 1)

value: induced pluripotent stem cell


title: SP_tumor_rep1_ATAC


title: S1, sample2, TCR

value: TCR


title: MT695_CHD3_HET_D0_CNCC_RNA_rep1

description:
Library name: MT695_CHD3_HET_D0_CNCC_RNA_rep1
RNA-Seq


title: posterior eye, aged, sham, animal 14


title: PTCB, sample5, BCR

value: preterm cord blood


title: posterior eye, aged, sham, animal 13


title: SP_tumor_rep1_GEX

value: Spleen


title: MT739_CHD3_KO_D0_CNCC_RNA_rep3

description:
Library name: MT739_CHD3_KO_D0_CNCC_RNA_rep3
RNA-Seq

value: BIONi010-A clone 2.12 (CHD3-KO 1)


title: BM_tumor_rep2_ATAC

source_name: Bone Marrow

value: Bone Marrow

value: Hematopoietic progenitors

value: WT C57BL/6J


title: posterior eye, young, OVX, animal 12

value: Posterior Eye

value: Young, OVX


title: PTCB, sample5, GEX

value: blood

value: GEX


title: MT727_CHD3_KO_D0_CNCC_RNA_rep2

description:
Library name: MT727_CHD3_KO_D0_CNCC_RNA_rep2
RNA-Seq


title: BM_tumor_rep2_GEX

value: subcutaneous MMTV-PyMT tumor


title: PTCB, sample4, BCR

value: immune cells

value: BCR


title: MT697_CHD3_KO_D0_CNCC_RNA_rep1

description:
Library name: MT697_CHD3_KO_D0_CNCC_RNA_rep1
RNA-Seq


title: MT737_CHD3_HET_D0_CNCC_RNA_rep3

description:
Library name: MT737_CHD3_HET_D0_CNCC_RNA_rep3
RNA-Seq


title: posterior eye, young, OVX, animal 11

value: Female


title: BM_tumor_rep1_ATAC


title: posterior eye, young, OVX, animal 10


title: PTCB, sample4, TCR

value: primary cells


title: BM_tumor_rep1_GEX


title: posterior eye, young, OVX, animal 9


title: MT735_CHD3_WT_D0_CNCC_RNA_rep3

description:
Library name: MT735_CHD3_WT_D0_CNCC_RNA_rep3
RNA-Seq

value: BIONi010-A clone 3.2 (CHD3-WT 1)

value: induced pluripotent stem cell


title: PTCB, sample4, GEX

value: preterm cord blood


title: MT723_CHD3_WT_D0_CNCC_RNA_rep2

description:
Library name: MT723_CHD3_WT_D0_CNCC_RNA_rep2
RNA-Seq


title: posterior eye, young, OVX, animal 8


title: BM_ctrl_rep2_ATAC

value: control


title: PTCB, sample3, BCR


title: MT693_CHD3_WT_D0_CNCC_RNA_rep1

description:
Library name: MT693_CHD3_WT_D0_CNCC_RNA_rep1
RNA-Seq


title: BM_ctrl_rep2_GEX


title: PTCB, sample5, TCR

value: TCR


title: PTCB, sample3, TCR


title: posterior eye, young, sham, animal 6

value: Young, Sham


title: posterior eye, young, OVX, animal 7


title: PTCB, sample3, GEX


title: BM_ctrl_rep1_ATAC

value: Bone Marrow

value: Hematopoietic progenitors


title: BM_ctrl_rep1_GEX

value: WT C57BL/6J


title: scRNA-seq,AV_plus_P,CMO

middle: S.

last: Diamond

state: MO

address: 425 S. Euclid Ave

department: Immunology and Pathology

institute: Washington University School of Medicine

description:
Library name: AV_plus_P_CMO
CMO library:hashtag antibodies

data_processing:
Data was demultiplexed and proccessed using Cell Ranger multi pipeline version 8.0.1
Subsequent analysis was performed using the Seurat package (version 5.1.0)
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output filtered_bc(gex) files: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz
Supplementary files format and content: CellRanger output files(cmo): matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz, feature_reference.csv

source_name: ipsilateral feet

extract_protocol:
At 5 days post infection, single cell suspensions were obtained from joint-associated tissue specimens by digestion in RPMI with 10% FBS, 15 mM HEPES, type I collagenase (Thermo; 2.5 mg/mL) and DNase (Sigma-Aldrich; 10 µg/mL) for 1 h at 37oC, followed by filtration through a 70 µm nylon filter. Cells were blocked with TruStain FcX™ PLUS (anti-mouse CD16/32, Biolegend) and then stained with TotalSeq anti-mouse hashtag antibodies (Biolegend B0302, B0304, B0306, B0308; one distinct hastag per mouse sample in each group following manufacturer’s instructions) and fluorescently conjugated antibodies against cell surface antigens. After washing, individual samples were pooled according to experimental group and resuspended in sorting buffer (PBS with 1% FBS, 1mM EDTA, and 25 mM HEPES). Fluorescence activated cell sorting was performed using a BD FACSAria II flow cytometer (BD Biosciences). Sorted cell populations were pooled according to experimental group and resuspended in PBS with 0.04% BSA prior to processing for single cell RNA sequencing. RNA was extracted according to the 10x v3 3' Expression library kit.
Libraries were prepared according to the 10x v3 3' Expression library kit, following manufacturer's instructions.

treatment_protocol: 3-4-week-old conventionally housed mice were provided with water or antibiotics (0.5 g/L vancomycin and/or 1 g/L ampicillin) in drinking water ad libitum for 3 days. For antibiotic-treated mice receiving oral propionate supplementation, sodium propionate (37 mM, Sigma-Aldrich) was added to drinking water at the time of antibiotic initiation and continued after cessation of antibiotics. For CD4 T cell depletion, antibiotic-treated mice were administered 25 ug of anti-CD4 mAb (clone GK1.5; BioXCell) via intraperitoneal injection every 3 days for 1 week prior to and continued after infection. At 3 days after cessation of antibiotics, mice were infected with Mayaro virus via subcutaneous footpad injection.

value: ipsilateral feet

value: antibiotics and propionate

tag: t cell_depletion

value: no

value: CMO

tag: cmo

value: Biolegend B0302(Hashtag_2_TotalSeqB), B0304(Hashtag_4_TotalSeqB), B0306(Hashtag_6_TotalSeqB), B0308(Hashtag_8_TotalSeqB)


title: posterior eye, young, sham, animal 5

value: Posterior Eye


title: scRNA-seq,W,CMO

description:
Library name: W_CMO
CMO library:hashtag antibodies

value: water


title: PTCB, sample2, BCR

value: blood

value: primary cells

value: immune cells

value: BCR


title: D14_CITE-seq HTO

city: Dallas

first: Siyuan

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

description:
HTO reads
D14_features.tsv.gz
D14_matrix.mtx.gz
D14_barcodes.tsv.gz

data_processing:
Demultiplexing: cellranger mkfastq
10x genomics Cellranger V7.2 was used for alignment, filtering, barcoding counting, cDNA UMI counting and antibody counting
Cellranger V7.2 was used for ADT/HTO feature count
HTO1-6 were used for sample level demultiplexing and group assignment. In each separate library (separated by time points into four groups), control (vehicle) sample replicates were stained with HTOs 1-3 and ABX sample replicates were stained with HTOs 4-6. HTO1: control brain, replicate 1; HTO2: control brain, replicate 2; HTO3: control brain, replicate 3; HTO4: ABX brain, replicate 1; HTO5: ABX brain, replicate 2; HTO6: ABX brain, replicate 3.
After generating the digital gene expression data matrices, the Seurat v5 R package was used to perform data normalization, integration, dimension reduction, clustering and differential expression analysis.
Assembly: mm10-3.0.0 (10x genomics)
Supplementary files format and content: tab-delimited text files that include UMI values for gene UMI, HTO and ADT counts
Supplementary files format and content: processed data contains cell ranger output files in "filtered_feature_bc_matrix" folder.
Library strategy: CITE-seq

source_name: brain

extract_protocol:
Mice were perfused with cold PBS and brains extracted. Brains digested with multi tissue dissocation kit (Miltenyi). Brain infiltrating immune cells were enriched by 70%/37%/30% percoll gradient centrifugation.
For RNA expression (cDNA), we followed 10x genomics single cell 3’ v3 assay standard protocol. For ADT and HTO, we followed CITE-seq and Cell hashing protocol as provided here:https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf
10x genomics single cell 3’ v3 assay with Total-seq A CITE-seq protocol

treatment_protocol: See experimental design for details

value: brain

tag: mouse strain

tag: tumor stage

value: late D14

value: Ctrl/ABX


title: posterior eye, young, sham, animal 4

value: Female

value: Young, Sham


title: D14_CITE-seq ADT

description:
ADT reads
D14_features.tsv.gz
D14_matrix.mtx.gz
D14_barcodes.tsv.gz

tag: cell type


title: PTCB, sample2, GEX

value: preterm cord blood

value: GEX


title: posterior eye, young, sham, animal 3


title: scRNA-seq,AV-T,CMO

description:
Library name: AV-T_CMO
CMO library:hashtag antibodies

value: ipsilateral feet

value: antibiotics

value: yes


title: posterior eye, young, sham, animal 2


title: D14_CITE-seq mRNA/cDNA

description:
GEX 3'. R1 contains cell barcode and UMI. R2 contains gene expression reads
D14_features.tsv.gz
D14_matrix.mtx.gz
D14_barcodes.tsv.gz


title: S5, sample1, BCR

value: 2 months


title: D08_CITE-seq HTO

description:
HTO reads
D08_matrix.mtx.gz
D08_features.tsv.gz
D08_barcodes.tsv.gz

value: mid D08


title: posterior eye, young, sham, animal 1

value: Posterior Eye


title: scRNA-seq,AV_plus_P,GEX

description:
Library name: AV_plus_P_mRNA
GEX(3' 10x v3) library:4 mice pulled

value: antibiotics and propionate

value: no

value: mRNA


title: S5, sample1, TCR

value: blood

value: primary cells

value: immune cells

value: TCR


title: scRNA-seq,W,GEX

description:
Library name: W_mRNA
GEX(3' 10x v3) library:4 mice pulled

value: water


title: scRNA-seq,AV,GEX

description:
Library name: AV_mRNA
GEX(3' 10x v3) library:4 mice pulled


title: retina, aged, OVX, animal 24

source_name: Retina

value: Retina

value: Female

value: Aged, OVX


title: S5, sample1, GEX

value: GEX


title: D08_CITE-seq mRNA/cDNA

description:
GEX 3'. R1 contains cell barcode and UMI. R2 contains gene expression reads
D08_matrix.mtx.gz
D08_features.tsv.gz
D08_barcodes.tsv.gz

value: brain

value: Ctrl/ABX


title: S3, sample3, BCR

value: 1 month

value: BCR


title: retina, aged, OVX, animal 23


title: scRNA-seq,AV,CMO

description:
Library name: AV_CMO
CMO library:hashtag antibodies

value: ipsilateral feet

value: antibiotics

value: CMO

value: Biolegend B0302(Hashtag_2_TotalSeqB), B0304(Hashtag_4_TotalSeqB), B0306(Hashtag_6_TotalSeqB), B0308(Hashtag_8_TotalSeqB)


title: D08_CITE-seq ADT

description:
ADT reads
D08_matrix.mtx.gz
D08_features.tsv.gz
D08_barcodes.tsv.gz

value: mid D08


title: retina, aged, OVX, animal 22


title: PTCB, sample2, TCR

value: preterm cord blood

value: blood

value: primary cells


title: D04_CITE-seq ADT

description:
ADT reads
D04_matrix.mtx.gz
D04_features.tsv.gz
D04_barcodes.tsv.gz

value: immune cells

value: early D04


title: iKRAS_Day4_Control,scRNAseq, gene_exp

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

description: 10x Genomics

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) with default settings. Gene expression reads were aligned to the mouse reference genome version gex-mm10-2020-A. Graph-based clustering results produced by Cell Ranger were used for differential expression calculations.
Secondary analysis was carried out using Loupe Browser (10X Genomics)
Assembly: GRCm38
Supplementary files format and content: Gene expression: Single cell 3' cell/gene matrices in .mtx format generated by Cell Ranger for individual samples.  Cell Ranger graph-based clustering results and UMAP coordinates are included for each individual sample

source_name: Pancreatic ductal adenocarcinoma, dissociated orthotopic tumor

extract_protocol:
Single cell suspensions were prepared by treating tumor tissues with 1x collagenase/hyaluronidase (StemCell Technology), 0.5 mg/ml Liberase-DL (Roche), and 0.1 mg/ml DNase I (Sigma) for 45 minutes at 37C with continuous mixing.
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 the 10x Genomics Chromium Controller and libraries prepared according to the manufacturer’s instructions. Libraries were paired end sequenced using the Illumina NextSeq2000 sequencing system with 28x10x10x90bp reads to a mean depth of ~45,000 reads per cell.

treatment_protocol: Orthotopic injections into the pancreas of FVB mice were performed with 104 iKRAS parental control (A9993) or iKRAS STAT3 KO cells in Matrigel diluted 1:10 with Opti-MEM using standard procedures (Kim et al 2009). For tumor formation, the drinking water was provided ad libitum and supplemented with 2% sucrose, doxycycline hyclate (0.5 mg/ml), neomycin (0.5 mg/mL) and ampicillin (1 mg/mL). The animals were observed for tumor development by palpation and orthotopic tumors were pooled from 2-3 individual mice at day 0 (~150-350mg) or following doxycycline removal for 4 days (day 4) (100-200mg).

value: iKRAS pancreatic ductal adenocarcinoma

value: FVB syngeneic male mouse

tag: age

value: 8-10 weeks


title: retina, aged, OVX, animal 21

tag: tissue

value: Retina

value: Female

value: Aged, OVX


title: S3, sample3, TCR

value: 1 month

tag: cell line

value: TCR


title: iKRAS_Day4_STAT3KO,scRNAseq, gene_exp

description: 10x Genomics

value: STAT3 knockout in iKRAS pancreatic ductal adenocarcinoma

value: Pancreatic ductal adenocarcinoma, dissociated orthotopic tumor


title: S3, sample3, GEX

value: GEX


title: iKRAS_Day0_STAT3KO,scRNAseq, gene_exp

description: 10x Genomics


title: retina, aged, OVX, animal 20

tag: genotype


title: D04_CITE-seq mRNA/cDNA

description:
GEX 3'. R1 contains cell barcode and UMI. R2 contains gene expression reads
D04_matrix.mtx.gz
D04_features.tsv.gz
D04_barcodes.tsv.gz

value: brain

tag: treatment

value: Ctrl/ABX


title: S3, sample2, BCR

value: blood

value: BCR


title: D00_CITE-seq HTO

description:
HTO reads
D00_matrix.mtx.gz
D00_features.tsv.gz
D00_barcodes.tsv.gz

value: immune cells

value: naive D00


title: retina, aged, OVX, animal 19


title: S3, sample2, TCR

value: primary cells


title: iKRAS_Day0_Control,scRNAseq, gene_exp

description: 10x Genomics

value: iKRAS pancreatic ductal adenocarcinoma

value: FVB syngeneic male mouse


title: Pten/p53 5 mo [scATAC-Seq]

description:
LWHR3
10x Genomics

data_processing:
Cell Ranger ATAC 2.0.0 and the mouse reference cellranger-arc-mm10-2020-A-2.0.0 were used for demultiplexing, alignment, barcode filtering and counting
Assembly: mm10
Supplementary files format and content: tsv files with peaks and barcode sequences corresponding respectively to row and column indices from the matrix.

source_name: Prostate

extract_protocol:
Mouse dorso-lateral prostate was dissociated into single cells as described (DOI:10.1126/sciadv.abo2295).). Nuclei were isolated from 800 000 cells by applying Nuclei isolation buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0,1% Tween-20, 0,1% IGEPAL CA-630, 0,01% Digitonin, 1% BSA) for 5 min and washed according to the 10X Demonstrated Protocol (CG000169).
16 000 nuclei were loaded on a 10X Chromium Controller (10X Genomics, Leiden, The Netherlands) to recover 10 000 nuclei. Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10X Genomics ref. CG000209 Rev C) were used to generate single-cell libraries.

value: Prostate


title: scRNA-seq,AV-T,GEX

description:
Library name: AV-T_mRNA
GEX(3' 10x v3) library:4 mice pulled

value: ipsilateral feet

value: antibiotics

value: yes

value: mRNA


title: D00_CITE-seq ADT

description:
ADT reads
D00_matrix.mtx.gz
D00_features.tsv.gz
D00_barcodes.tsv.gz


title: S3, sample2, GEX

value: 1 month


title: D04_CITE-seq HTO

description:
HTO reads
D04_matrix.mtx.gz
D04_features.tsv.gz
D04_barcodes.tsv.gz

value: early D04


title: retina, aged, sham, animal 17

value: Retina

value: Female

value: Aged, Sham


title: D00_CITE-seq mRNA/cDNA

description:
GEX 3'. R1 contains cell barcode and UMI. R2 contains gene expression reads
D00_matrix.mtx.gz
D00_features.tsv.gz
D00_barcodes.tsv.gz

value: brain

value: Ctrl/ABX


title: retina, aged, sham, animal 18


title: Calu-3/2B4, Mock, 48 hpi, Rep 3

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

description: Mock, 48 hpi, Rep 3

data_processing:
STAR v. 2.7.10a was used to map filtered/trimmed reads to GRCh38 and generated gene reads counts.
sequencing reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v.1.15
Assembly: GRCh38
Supplementary files format and content: tab delimited text file containg raw gene level read counts

growth_protocol: Calu-3/2B4 cells were maintained in 1X MEM supplemented with 20% fetal bovine serum (FBS), 0.01% L-Glutamine, and 0.01% Penicillin-Streptomycin in an incubator with 5% CO2 at 37 degrees Celsius.

extract_protocol:
RNA was harvested following the Invitrogen TRIzol™ Reagent Protocol at 12-, 24-, and 48-hours post-infection.
RNA libraries were prepared using NEBNext polyA mRNA Magnetic Isolation Module and NEB Ultra II RNA library preparation kit for illumina following manufacturer's protocol

treatment_protocol: Calu-3/2B4 cells were infected with the Urbani strain of SARS-CoV-1 or the USA-WA1/2020 strain of SARS-CoV-2 at a MOI of 1.0. Uninfected cells served as controls.

value: bronchial epithelial cells

tag: infection status

value: Mock

value: 48 hpi


title: Calu-3/2B4, Mock, 48 hpi, Rep 2

description: Mock, 48 hpi, Rep 2


title: Replicate 3, AsGM1- Group 1 ILCs

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010).
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive
quality control report (Ewels et al., 2016).
Assembly: GRCm38 (ENSEMBL 102)
Supplementary files format and content: Tabular count table

source_name: Liver

extract_protocol:
Total RNA was isolated from AsGM1+ and AsGM1- ILC subsets using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s procedure. RNA samples were treated with the DNA-free kit (Ambion) to remove any traces of genomic DNA.
According to the manufacturer’s protocol (Illumina NovaSeq).

value: Liver

value: B6.Cg-Rag2tm1.1Cgn/J (RAG2 KO)


title: retina, aged, sham, animal 16