title: LLO-tetr+ CD4+ Tconv WT mouse14

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: Library name: WTLLO-tetr+CD4+TconvSpleen277589

library_source: other

data_processing:
The CLC Genomics Workbench software (v23.0.3) provided by Qiagen was used to generate clonotype reads. Briefly, sequences with the same unique molecular index (UMI) were merged and those with UMI reads < 3 were excluded. Further quality control steps included merging and trimming of overlapping paired-end sequences. Results were annotated using the C57BL/6-specific functional TCRα genes extracted from the IMGT murine TCR database. Analyses were done using RStudio (Version 2023.06.1+524). A clonotype was defined as a unique combination of Trav gene, Traj gene and an in-frame CDR3 amino acid sequence. Clonotype abundance was defined as the number of clonotype-encoding unique cDNA molecules (distinguished by UMI) detected in a sample. TCR diversity was assessed using the approach of Chao et al. 78, wherein one unique cDNA molecule was defined as one ‘individual’ and one clonotype as one ‘species’. Rarefaction with Hill numbers was done using ‘iNEXT’ (Version 2.0.20). Shannon diversity is the exponential of Shannon entropy and is calculated in ‘iNEXT’ using q = 1. Shannon diversity (or effective number of TCR clonotypes) is the number of equally abundant clonotypes that would be needed to give the same Shannon diversity as the sample. As sampling completeness reached the maximum (coverage = 1) for each sample and sub-repertoire examined, the observed Shannon diversities were used to calculate ‘Relative diversity’. As adding 95% confidence intervals constructed from 5 bootstrap replications made a negligible difference to the appearance of the rarefaction curves and were smaller than the symbols on the ‘Relative diversity’ summaries, these details were omitted. To assess TCR overlap between pairs of samples we used ‘abdiv’ (Version 0.2.0) to calculate the Morisita Horn index. Quantification of nucleotide deletion or addition at Trav-Traj junctions was done using results from the IMGT Junction Analysis tool. The ‘# nucleotides deleted or added at the Trav-Traj junction’ was defined as the sum of the absolute values of the number of nucleotides deleted from the germline Trav and/or Traj gene(s) plus the number of P and/or N nucleotides added between the remaining germline Trav and/or Traj nucleotides. Due to duplication events at the TCRαβ locus in B6 mice, 23-30% of unique cDNA molecules per sample aligned with > 1 Trav paralog; these sequences were excluded from the analyses of chromosomal location of Trav gene usage and nucleotide deletion or addition at Trav-Traj junctions. Codes are available at the following link upon request:  https://github.com/srdaley/CathepsinL_TCRseq.
Assembly: Ensembl release version 106 for M. musculus
Supplementary files format and content: Table with clonotype counts
Library strategy: TCR-seq

molecule: other

source_name: Spleen+LNs

growth_protocol: Mice were maintained under SPF conditions in individually ventilated cages.

extract_protocol:
CD69-MHCI+ (M2) CD4SP thymocytes were FACS-sorted, pelleted and resuspended in RNA protect (Qiagen). All samples were stored at -80°C until RNA extraction. RNA isolation was performed by Qiagen, according to the RNeasy Mini/Micro kit (Qiagen).
QIAseq® Immune Repertoire RNA Library kit (Qiagen), modified to include only TCRα-specific primers for both the reverse transcription and the target enrichment steps.

value: Spleen+LNs

value: LLO-tetr+ CD4+ FoxP3-

value: Dereg Fixedbeta TCRalpha+/- (WT)


title: LLO-tetr+ CD4+ Tconv WT mouse13

status: Public on Jun 13 2025

type: SRA

country: Germany

description: Library name: WTLLO-tetr+CD4+TconvSpleen277588

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype


title: LLO-tetr+ CD4+ Tconv WT mouse12

description: Library name: WTLLO-tetr+CD4+TconvSpleen297663

source_name: Spleen

value: Spleen


title: Plate8_B12

city: Palo Alto

first: Rebeca

last: Arroyo Hornero

state: California

address: Campus Drive

country: USA

institute: Stanford

library_source: transcriptomic single cell

data_processing:
Data was processed with STAR
Assembly: hg19
Supplementary files format and content: feature_counts.csv (csv file)

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Plasmocytoid dendritic cells were magnetically enriched from peripheral blood of a healthy donor, cultured with IL-3 and CD40L for two days and single-cell FACS-sorted on a FACS Aria Fusion (BD Biosciences) into Takara Smart-Seq Single Cell kit lysis buffer and frozen at -80C.
The Illumina Nextera XT DNA Library Prep and Unique Dual Index Kits (Illumina) were used for library preparation according to manufacturer's instructions.

value: blood

value: plasmacytoid dendritic cell

tag: treatment

value: sorted as:day2_itDC_donor 2


title: LLO-tetr+ CD4+ Tconv WT mouse11

description: Library name: WTLLO-tetr+CD4+TconvSpleen297659


title: KP1233, DMSO-treated, Rep 2

city: Cambridge

first: Colin

middle: Emory

last: Fowler

state: MA

address: 500 Main Street

department: Biology

institute: Massachusetts Institute of Technology

description: Library name: 215002

library_source: transcriptomic

data_processing:
To generate counts for alternative splicing analysis, raw reads were mapped to the human GRCh38 genome using STAR (--runMode alignReads --runThreadN 16 --sjdbOverhang 149 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 70 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMstrandField intronMotif --outFilterType BySJout --twopassMode Basic) and Bowtie (-n 1 -l 30 -e 70 -t -p 4 -m 1 -X 500 -S).
Mapped reads were filtered using Bedtools to remove reads overlapping expressed repeats from the UCSC genome browser RNA repeats and Gencode hg38 and coding exons annotated in the Gencode hg38 annotations. Alternative and constitutive classifications were performed using custom Python scripts and are agnostic to existing annotations other than known gene boundaries. All three cell lines were run in parallel to ensure consistency between annotations. Alternative splicing events were quantified using DEXSeq.
Assembly: Gencode GRCh38 v33 and Gencode GRCm38 vM24
Supplementary files format and content: genes.results files are outputted raw count files from RSEM for each gene.
Supplementary files format and content: isoform.results files are outputted raw count files from RSEM for each isoform (Consensus/Coding or DI).
Supplementary files format and content: DEXSeq files are outputted exon count files from DEXSeq.
Supplementary files format and content: Supplementary files are gff files needed for DEXSeq alternative splicing analysis.

molecule: polyA RNA

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s media (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and cultured in 37℃ at 5% CO2. Η23 cells were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and cultured in 37℃ at 5% CO2. Cells were routinely tested for mycoplasma and were found to be negative.

extract_protocol:
For whole cell lysates, following 3-day treatment with either DMSO (vehicle), PRMT5i, or dTag-13, cells were harvested by scraping. RNA was purified using the RNeasy Mini Kit (Qiagen, 74106) according to manufacturer’s instructions, including the optional DNaseI addition to remove contaminating gDNA (Qiagen, 79254). For fractionated cells, after 3 days in drug, cells were harvested via trypsinization, pelleted, and separated into nuclear and cytoplasmic fractions. Briefly, cell pellets were resuspended in cytoplasmic lysis buffer [0.15% (v/v) NP40, 10 mM Tris (pH7), 150 mM NaCl] supplemented with 10 U SUPERase.IN (Thermo Fisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Cells were then incubated on ice for 5 minutes. Cell lysate was layered on top of sucrose buffer [0 mM Tris (pH7), 150 mM NaCl, 25% (w/v) sucrose] supplemented with 10 U SUPERase.IN (Thermo Fisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Cells were then centrifuged at 16,000 x g for 10 minutes at 4 °C. The supernatant contains the cytoplasmic fraction and was harvested for RNA extraction. The remaining pellet contains the nuclear fraction and was washed twice with 800 μL cold PBS, centrifuging at 16,000 x g for 1 minute at 4°C after each wash. The pellet was resuspended in cold RIPA buffer [50 mM Tris (pH 8), 150 mM NaCl, 1% (v/v) NP-40, 0.5% sodium deoxycholate, and 0.1% (w/v) SDS] supplemented with 10 U SUPERase.IN (ThermoFisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Lysate was incubated for 30 minutes on ice, with vortexing every 10 minutes, and then pelleted at 16,000 x g for 10 minutes at 4°C. The supernatant contains the nuclear fraction and was harvested for RNA extraction. The RNA from the nuclear and cytoplasmic fractions were extracted using TRIzol Reagent (Thermo Fisher, 15596026) according to manufacturer’s instructions. Briefly, to each aqueous fraction, 0.5 mL of isopropanol and 1 mL of TRIzol Reagent was added, followed by an incubation on ice for 10 minutes. Samples were then centrifuged for 10 minutes at 12,000 x g at 4 °C, pellets were washed in 1 mL 75% ethanol, and centrifuged again for 5 minutes at 7,500xg at 4 °C. Pellets were air dried for 10 minutes and resuspended in RNase-free water.
RNA-Seq libraries were prepared using the NEB Ultra II Directional RNA Kit with Poly(A) Selection per the manufacturer's protocol.

treatment_protocol: Cells were grown in the presence of PRMT5 inhibitor, dTag-13, or vehicle control.

tag: cell line

value: WT

value: DMSO

tag: time

value: Day 3


title: Plate8_B10


title: KP1233, DMSO-treated, Rep 1

description: Library name: 215001


title: Plate8_C02


title: Plate8_C01


title: Plate8_B11


title: Plate8_B09


title: Naive CD4+ Tconv WT mouse10

description: Library name: WTNaiveCD4+TconvSpleen296468

value: Naive CD4+ CD25-

value: Fixedbeta TCRalpha+/- (WT)


title: Naive CD4+ Tconv WT mouse9

description: Library name: WTNaiveCD4+TconvSpleen297661


title: Plate8_B08


title: Naive CD4+ Tconv WT mouse8

description: Library name: WTNaiveCD4+TconvSpleen297664


title: Plate8_B07


title: Plate8_C07

value: sorted as:day2_icDC2_donor 2


title: Plate8_B06


title: M2 CD5hi WT mouse10

description: Library name: WTM2Thymus296468_CD5hi

source_name: thymus

value: thymus

value: CD4SP CD25- M2 CD5hi thymocytes


title: Plate8_B05


title: M2 CD5lo WT mouse10

description: Library name: WTM2Thymus296468_CD5lo

value: CD4SP CD25- M2 CD5lo thymocytes


title: M2 CD5lo WT mouse9

description: Library name: WTM2Thymus297661_CD5lo


title: Plate8_B01

value: sorted as:day2_pDC_donor 2


title: Naive CD4+ Tconv WT mouse7

description: Library name: WTNaiveCD4+TconvSpleen297662


title: M2 CD5hi WT mouse8

description: Library name: WTM2Thymus297664_CD5hi


title: Plate8_A12


title: Plate8_B03


title: Plate8_B02


title: M2 CD5lo WT mouse8

description: Library name: WTM2Thymus297664_CD5lo


title: M2 CD5lo WT mouse7

description: Library name: WTM2Thymus297662_CD5lo


title: Plate8_A10


title: Plate8_A11


title: Plate8_A09


title: Upf1 RIP, upf3 delta, replicate 3

city: Paris

first: Gwenael

last: Badis

address: 46 rue d'Ulm

department: Genomique fonctionnelle (Section 2)

country: France

institute: IBENS

description:
Library name: Upf1_RIP_upf3delta_R3
Direct RNA sequencing

data_processing:
fast basecalling using guppy and options rna_r9.4.1_70bps_fast.cfg
Mapping to the SC288 reference genome Saccer3.fa using minimap2 with option -k14 -ax splice -uf -G 2000 -secondary=no
Assembly: Saccer3.fa
Supplementary files format and content: Bigwig files contain the profile of each experiment (strand 1 and strand 2 per replicatre) and were generated using deepTools bamCoverage option --binSize 1
Supplementary files format and content: Fastq files contains the raw data sequences after basecalling of fast5 files

organism: Saccharomyces cerevisiae BY4741

source_name: yeast

growth_protocol: 30°C in YPD, exponential phase (OD 600=0,7)

extract_protocol:
Phenol Chloroform extraction of total RNA (hot phenol and two supbsequent phenolChloroform extractions), or Immunoprecipitated (one phenol chloroform extraction) followed by a precipitation with NH4OAc/Ethanol.
Direct RNA sequencing (ONT SQK RNA002)

treatment_protocol: Immunoprecipitiation of the protein A tag using rabbit IgG coupled to magnetic beads (RIP-seq only)

value: yeast

tag: strain

value: MATa, ura3delta0, his3delta1, leu2delta0, met15delta0, UPF1(YMR080W)-TAP:HIS3, upf3(ygr072w)::KANMX6


title: Plate8_A08


title: M2 CD5hi WT mouse7

description: Library name: WTM2Thymus297662_CD5hi


title: Upf1 RIP, upf3 delta, replicate 2

description:
Library name: Upf1_RIP_upf3delta_R2
Direct RNA sequencing


title: Plate8_A07


title: Upf1 RIP, upf3 delta, replicate 1

description:
Library name: Upf1_RIP_upf3delta_R1
Direct RNA sequencing


title: Plate8_A05


title: Plate8_A06


title: Input, upf3 delta, replicate 3

description:
Library name: Upf1_upf3delta_R3_Input
Direct RNA sequencing


title: Plate8_A04


title: Input, upf3 delta, replicate 2

description:
Library name: Upf1_upf3delta_R2_Input
Direct RNA sequencing


title: Input, upf3 delta, replicate 1

description:
Library name: Upf1_upf3delta_R1_Input
Direct RNA sequencing


title: Plate8_A03


title: Upf1 RIP, upf2 delta, replicate 3

description:
Library name: Upf1_RIP_upf2delta_R3
Direct RNA sequencing

value: MATa, ura3delta0, his3delta1, leu2delta0, met15delta0, UPF1(YMR080W)-TAP:HIS3, yhr077c::KANMX6


title: M2 CD5hi WT mouse9

description: Library name: WTM2Thymus297661_CD5hi


title: Upf1 RIP, upf2 delta, replicate 2

description:
Library name: Upf1_RIP_upf2delta_R2
Direct RNA sequencing


title: Upf1 RIP, upf2 delta, replicate 1

description:
Library name: Upf1_RIP_upf2delta_R1
Direct RNA sequencing


title: Plate8_A01


title: Plate7_D11


title: Plate7_D10


title: Plate7_D12


title: Input, upf2 delta, replicate 2

description:
Library name: Upf1_upf2delta_R2_Input
Direct RNA sequencing


title: Plate7_D08


title: upf1 delta, replicate 3

description:
Library name: upf1_delta_R3
Direct RNA sequencing

value: MATa, ura3delta0, his3delta1, leu2delta0, met15delta0, upf1(ymr080w)::KANMX6


title: Plate7_D07

value: blood


title: Plate7_D09

value: plasmacytoid dendritic cell


title: Input, upf2 delta, replicate 1

description:
Library name: Upf1_upf2delta_R1_Input
Direct RNA sequencing


title: Plate7_D06


title: eIF4G2 RIP, replicate 3

description:
Library name: eIF4G2_RIP_R3
Direct RNA sequencing

value: MATa, ura3delta0, his3delta1, leu2delta0, met15delta0, eIF4G2(YGL049C)-TAP:HIS3


title: upf1 delta, replicate 1

description:
Library name: upf1_delta_R1
Direct RNA sequencing


title: Plate7_D05


title: Plate7_D04


title: eIF4G2 RIP, replicate 1

description:
Library name: eIF4G2_RIP_R1
Direct RNA sequencing


title: eIF4G2 RIP, replicate 2

description:
Library name: eIF4G2_RIP_R2
Direct RNA sequencing


title: Plate7_D02


title: Plate8_A02


title: Plate7_D03


title: Upf1 RIP, replicate 2

description:
Library name: Upf1_RIP_R2
Direct RNA sequencing

value: MATa, ura3delta0, his3delta1, leu2delta0, met15delta0, UPF1(YMR080W)-TAP:HIS3


title: Upf1 RIP, replicate 3

description:
Library name: Upf1_RIP_R3
Direct RNA sequencing


title: Upf1 RIP, replicate 1

description:
Library name: Upf1_RIP_R1
Direct RNA sequencing


title: Input, upf2 delta, replicate 3

description:
Library name: Upf1_upf2delta_R3_Input
Direct RNA sequencing


title: Plate7_D01


title: Plate7_C12

value: sorted as:day2_itDC_donor 2


title: WT input, replicate 3

description:
Library name: WT_Input_R3
Direct RNA sequencing


title: Plate7_C11


title: WT input, replicate 2

description:
Library name: WT_Input_R2
Direct RNA sequencing


title: WT input, replicate 1

description:
Library name: WT_Input_R1
Direct RNA sequencing


title: Plate7_C09


title: upf1 delta, replicate 2

description:
Library name: upf1_delta_R2
Direct RNA sequencing


title: CRAMP1-KO + GFP1-CRAMP1, 20 μM etoposide 1 hour, CC-seq, Rep4

city: Brighton

first: William

last: Gittens

state: I am not in the U.S. or Canada

address: Science Park Road

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

library_source: genomic

data_processing:
Paired-end reads that passed filter were aligned to hg19 using bowtie2 (options: -X 1000 –no-discordant –very-sensitive –mp 5,1 –np 0), using MAPQ0 settings, then SAM files processed to FullMap files via terminalMapper (Perl, v5.22.1; https://github.com/Neale-Lab) that computes the coordinates of the protein-linked 5′-terminal nucleotide.
Assembly: hg19
Supplementary files format and content: FullMap files containing sparsely-formatted, 1bp histograms detailing the total number of Watson (+) and Crick (-) hits for all mapped base-pairs. 4-column format (Chr, Pos, Watson, Crick).
Library strategy: Top2 CC-seq

molecule: genomic DNA

growth_protocol: U2OS cells were seeded into 15 cm dishes and incubated for 24 hours before treatment with 0.1 μg/ml doxocyclin to induce GFP-CRAMP1 expression. After additional 24h, upon 70% confluence, the cells were treated for 1 h with 20 µM Etoposide then fixed with -20˚C 70 % C EtOH for 15 minutes. Afterwards, cells were spun down 1500 rpm at 4 C for 5 min, EtOH is aspirated and replaced with fresh -20 C EtOH, and the pellets are stored until extraction.

extract_protocol:
Ethanol fixed cell pellets were lysed with 2.4 ml 1× STE buffer (2% SDS, 0.5 M Tris pH 8.1, 10 mM EDTA, 0.05% bromophenol blue), for 10 min at 65 °C, before cooling to room temperature. Extractions were performed with 1.25 ml Phenol-Chloroform-isoamyl alcohol (25:24:1; Sigma) to remove bulk free protein, then DNA in the aqueous/interphase was precipitated by addition of 3.3ml ethanol, followed by centrifugation at 10,000g for 2 min. DNA pellets were washed once with 70% ethanol, before resuspension in 1 mL 1x TE buffer pH 7.5 overnight at 4 °C. Samples were fully resuspended, prior to sonication to an average fragment size of 300–400 bp with Covaris (duty cycle: 10%, intensity/peak power incidence: 75 W, cycles/burst: 200, time: 21 min). A sample of 12 uL was removed and incubated at 37˚C for 45 min with 3 uL of RNAse A (1 mg/ml). DNA shearing was checked by 1% agarose gel electrophoresis, and DNA was quantified in technical triplicate with the Qubit (ThermoFisher) and High Sensitivity reagents. Next, S.cerevisisae DNA spike was added to 950 uL of sample (Yeast:Human DNA weight ratio of 1:100), then the total volume was made up to 1 mL with 1x TE (pH 7.5). Triton-X100, N-Lauroylsarcosine sodium salt and NaCl were then added to complete the binding buffer (final concentrations: 0.3 M NaCl, 0.2% Triton-X100, 0.1% N-Lauroylsarcosine sodium salt). Each sample was divided over two QIAquick silica fibre membrane spin columns (QIAGEN). Under these conditions, protein, but not free nucleic acids, bind to the silica membrane, leading to selective retention of any protein-DNA CCs. Columns were washed six times with 600 µL of TEN (10 mM Tris pH 7.5, 1 mM EDTA, 0.3 M NaCl) per 1 min wash to remove any residual non-CC DNA fragments, prior to elution twice with 125 µL TES (10 mM Tris pH 7.5, 1 mM EDTA, 0.5% SDS). Eluted products were pooled to 500 µL in TES and incubated with 1 mg/mL Proteinase K (Sigma) for 60 min at 50 °C, prior to overnight ethanol precipitation at −20 °C with 1.41 mL ethanol, 0.2 mg/mL glycogen and 200 mM NaOAc. The DNA-glycogen precipitate was pelleted by centrifugation at 20,000 × g for 1 h at 4 °C, washed once with 1.5 mL 70% ethanol, and air-dried for 10 min at room temperature.
DNA was solubilised in 25 µL 10 mM Tris-HCl pH 7.5, and subjected to end repair and adapter ligation with NEBNext Ultra II DNA Library Preparation kit (NEB), according to manufacturer’s instructions, except all steps were conducted at half-scale and a custom P7 adapter was used. After ligation of the P7 adapter to the (non-CC) sonicated end, TE was added to a final volume of 90 uL. DNA was isolated with AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions (beads:input of 78:90 uL) and eluted in 85 µL water. Next, 10 uL of 10X Cutsmart buffer and 5 uL Shrimp Alkaline Phosphatase (rSAP; NEB) were added before incubation for 30 min at 37˚C. DNA was isolated again with AMPure XP beads (Beckman Coulter) (beads:input of 83:100 uL) and eluted in 50 µL 10 mM Tris-HCl. Samples were diluted twofold with 50 µL TDP2 reaction buffer (100 mM TrisOAc, 100 mM NaOAc, 2 mM MgOAc, 2 mM DTT, 200 µg/ml BSA) and incubated with 3 µL of 10 µM recombinant zebrafish TDP2 catalytic domain (Addgene plasmid #200512) for 1 h at 37 °C, to non-nucleolytically repair the Top2cc DNA end. DNA was isolated again with AMPure XP beads (beads:input of 83:103) and eluted in 26 µL 10 mM Tris-HCl. Next, a second round of adapter ligation was conducted using a custom adapter dp-P5 without prior end repair, to prevent dephosphorylation of DNA 3′-phosphate termini which may be generated by TDP2 activity on 3′-CCs. After ligation of the dp-P5 adapter to the Top2-cleaved end, sample volume was adjusted to 90 uL with Tris-HCl, DNA was isolated with AMPure XP beads (beads:input of 78:90) and eluted in 15 µL 10 mM Tris-HCl. This was used as template for the NEBNext Ultra II PCR step using universal primer (P5 end) and indexed primers for multiplexing (P7 end), according to manufacturer’s instructions (12–15 cycles). PCR reactions were diluted with 50 µL 10 mM Tris-HCl, DNA was isolated with AMPure XP beads (beads:input of 83:100) and eluted in 30 µL 1 mM Tris-HCl pH 8.1, 100 uM EDTA. Sample DNA molarities were quantified using the Bioanalyzer or Tapestation (Agilent).

treatment_protocol: U2OS cells were treated for 1 h with 20 µM Etoposide before fixation.

value: CRAMP-KO + GFP-CRAMP1

value: 20 μM etoposide (1 hour)


title: Plate7_C07


title: CRAMP1-KO, 20 μM etoposide 1 hour, CC-seq, Rep4


title: WT, 20 μM etoposide 1 hour, CC-seq, Rep4

value: WT


title: Plate7_C05


title: Plate7_C06


title: WT, 20 μM etoposide 1 hour, CC-seq, Rep3


title: Plate7_C02


title: Plate7_C03


title: Plate7_C01


title: CRAMP1-KO + GFP1-CRAMP1, 20 μM etoposide 1 hour, CC-seq, Rep2


title: CRAMP1-KO + GFP1-CRAMP1, 20 μM etoposide 1 hour, CC-seq, Rep1


title: CRAMP1-KO, 20 μM etoposide 1 hour, CC-seq, Rep2


title: WT, 20 μM etoposide 1 hour, CC-seq, Rep2


title: Plate7_B12


title: CRAMP1-KO, 20 μM etoposide 1 hour, CC-seq, Rep1


title: WT, 20 μM etoposide 1 hour, CC-seq, Rep1


title: Plate7_C10


title: Plate7_C04


title: Plate7_B11


title: Plate7_B08


title: Pod-TRECK DT 100ng day 21 kidney 3

city: Towada

first: Masaki

last: Watanabe

department: School of Veterinary Medicine

country: Japan

institute: Kitasato University

description: Library name: DT21D_3

data_processing:
Demultiplexing was performed using the DNBSEQ built-in software based on sample-specific barcodes. Quality control of raw reads was conducted using fastp v0.20.0. Adapter trimming was also performed with fastp, using the following adapter sequences:  Forward: AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA Reverse: AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG
Assembly: GRCm39 (GENCODE release M29)
Supplementary files format and content: Processed data (all.raw.count.xlsx) is an Excel file that contains raw read counts generated by featureCounts. Each row corresponds to a gene, and columns represent 12 RNA-seq samples. The file also includes gene annotations such as GeneID, GeneName, chromosome location, and strand information. Counts were derived using the GENCODE M29 annotation with the GRCm39 genome build.

source_name: kidney

growth_protocol: Mice were maintained under specific pathogen-free conditions with a 12 h light/dark cycle and provided ad libitum access to food and water.

extract_protocol:
Total RNA was extracted from whole kidney tissue using the NucleoSpin RNA kit (Macherey-Nagel), following the manufacturer's protocol, including on-column DNase I treatment to eliminate genomic DNA contamination.
RNA-seq libraries were constructed using the MGI RNA Library Prep kit, following the manufacturer’s protocol for mRNA enrichment via poly(A) selection. Barcodes were ligated for multiplexing. Libraries were assessed for quality and quantity before sequencing.

treatment_protocol: Diphtheria toxin (DT) was administered intraperitoneally at a dose of 100 ng to Pod-TRECK mice. Kidneys were harvested at 5, 14, and 21 days post-injection. Control mice received no treatment.

value: kidney

value: Pod-TRECK

value: DT 100ng 21D

tag: batch


title: Plate7_B10


title: Plate7_C08


title: Pod-TRECK DT 100ng day 21 kidney 1

description: Library name: DT21D_1


title: Plate7_B09


title: Pod-TRECK DT 100ng day 21 kidney 2

description: Library name: DT21D_2


title: CRAMP1-KO + GFP1-CRAMP1, 20 μM etoposide 1 hour, CC-seq, Rep3


title: Plate7_B07


title: Plate7_B06


title: CRAMP1-KO, 20 μM etoposide 1 hour, CC-seq, Rep3


title: Plate7_B05


title: Pod-TRECK DT 100ng day 14 kidney 3

description: Library name: DT14D_3

value: DT 100ng 14D


title: Plate7_B04

value: sorted as:day2_pDC_donor 2


title: Pod-TRECK DT 100ng day 14 kidney 2

description: Library name: DT14D_2


title: Pod-TRECK DT 100ng day 14 kidney 1

description: Library name: DT14D_1


title: Plate7_B03


title: Pod-TRECK DT 100ng day 5 kidney 3

description: Library name: DT5D_3

value: DT 100ng 5D


title: Pod-TRECK DT 100ng day 5 kidney 2

description: Library name: DT5D_2


title: Pod-TRECK DT 100ng day 5 kidney 1

description: Library name: DT5D_1


title: Plate7_B01


title: Plate7_A12


title: Pod-TRECK control mouse kidney 2

description: Library name: Ctrl_2

value: Control


title: Plate7_A11


title: Pod-TRECK control mouse kidney 1

description: Library name: Ctrl_1


title: Plate7_A10


title: Pod-TRECK control mouse kidney 3

description: Library name: Ctrl_3


title: Plate7_A09


title: Plate7_A08


title: Plate7_A06


title: Plate7_A07


title: Plate7_A05


title: Plate7_A02


title: 2w_Perio-1

city: Ann Arbor

first: Yeji

last: Kim

state: Michigan

address: 1150 W Medical Center Dr

institute: University of Michigan

description: Library name: 13104-YK-26

data_processing:
University of Michigan Bioinformatics Core RNA-seq pipeline "Watermelon" version 2.4.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v4.8.
FastQC v0.11.8 was used to ensure the quality of data
Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a
Quantitative count estimates to genes performed with RSEM v1.3.3
Assembly: GRCm38
Supplementary files format and content: counts_rawCounts.txt
Supplementary files format and content: tab-delimited text with include expected counts values for each Sample

source_name: small intestine

extract_protocol:
Small intestinal tissue samples were harvested and RNA was extracted using E.Z.N.A. Total RNA Kit I (Omega Bio-tek).
Illumina RNA (PolyA-enrichment) library prep kit was used according to manufacturer's directions.

value: small intestine

tag: age

value: 2 weeks

value: periodontitis


title: 2w_Perio-5

description: Library name: 13104-YK-30


title: 2w_Perio-4

description: Library name: 13104-YK-29


title: 2w_Perio-3

description: Library name: 13104-YK-28


title: 2w_Perio-2

description: Library name: 13104-YK-27


title: Plate7_A04

value: blood

value: plasmacytoid dendritic cell


title: 2w_Ctrl-5

description: Library name: 13104-YK-25

value: control


title: 2w_Ctrl-4

description: Library name: 13104-YK-24


title: Plate7_A01


title: Plate7_A03


title: 2w_Ctrl-3

description: Library name: 13104-YK-23


title: Plate7_B02


title: 2w_Ctrl-1

description: Library name: 13104-YK-21


title: Plate6_D11

value: sorted as:day2_icDC2_donor 2


title: 7w_Perio-5

description: Library name: 13104-YK-20

value: 7 weeks


title: 2w_Ctrl-2

description: Library name: 13104-YK-22


title: 7w_Perio-3

description: Library name: 13104-YK-18


title: 7w_Perio-1

description: Library name: 13104-YK-16


title: 7w_Perio-4

description: Library name: 13104-YK-19


title: Plate6_D05


title: Plate6_D07


title: Plate6_D08


title: Plate6_D09


title: Plate6_D06


title: 7w_Perio-2

description: Library name: 13104-YK-17


title: 7w_Ctrl-5

description: Library name: 13104-YK-15


title: 7w_Ctrl-4

description: Library name: 13104-YK-14


title: Plate6_D04


title: 7w_Ctrl-3

description: Library name: 13104-YK-13


title: 7w_Ctrl-1

description: Library name: 13104-YK-11


title: Plate6_C11

value: sorted as:day2_itDC_donor 2


title: 7w_Ctrl-2

description: Library name: 13104-YK-12


title: 3311_Control_Replicate2

city: Salt Lake City

first: Gabriela

last: Fort

state: UT

address: 2000 Circle of Hope Drive

institute: Huntsman Cancer Institute, University of Utah

description:
Library name: 3311_Control_Replicate2
RNAseq

data_processing:
Optical duplicates were removed from Fastq files using Clumpify v38.34.
Adaptor sequences were trimmed using Cutadapt v3.5 with a minimum overlap of 6 bp and minimum trimmed read length of 20.
Reads were aligned to the reference using STAR v2.7.6a in two pass basic mode.
Mapped reads were assigned to annotated genes using featureCounts v1.6.3 in paired-end mode.
Raw counts were filtered to remove features with zero counts and features with five or fewer reads in every sample.
Assembly: mm10; for murine 1027B and 3311 MEKi experiments, and 3154 Hnf4a deletion experiments
Assembly: mm39; for murine 3154 MRTX1133 +/- Hnf4a experiment
Assembly: hg38; for all human samples
Supplementary files format and content: tab-delimited text files with raw counts for each experiment

growth_protocol: Organoid cultures were grown in 50% L-WRN conditioned media (Miyoshi and Stappenbeck, 2013). H358 cells were cultured in RPMI/10% FBS. H1651 cells were cultured in Advanced DMEM F-12/10% FBS/10mM HEPES. 3311 cells were cultured in DMEM/10% FBS.

extract_protocol:
RNA was isolated via Trizol-chloroform extraction followed by column-based purification. The aqueous phase was brought to a final concentration of 35% ethanol, and RNA was purified using the PureLink RNA Mini kit according to the manufacturer’s instructions (ThermoFisher Scientific).
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA isolation. Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

treatment_protocol: For Hnf4a deletion RNA-seq, 3154 organoids were treated with 2mM 4OHT (or ethanol) for 2 days to delete Hnf4a, and RNA was harvested 2 weeks later. For H1651 RNA-seq, H1651 cells harboring lentiviral HNF4α overexpression construct were treated with 1μg/mL doxycycline for 7 days. For MEKi RNA-seq, 3311 cells were treated with 50nM Trametinib for 48h, 1027B organoids were treated with 10nM Trametinib or 20nM MRTX1133 for 48h, H358 cells and H1651 cells were treated with 20nM Trametinib for 48h. For 3154 MEKi/Hnf4a deletion RNA-seq, 3154 organoids were treated with 3nM MRTX1133 and/or 4OHT to delete Hnf4a for 48 hours.

value: Lung cell line


title: Plate6_D02


title: 3311_MEKi_Replicate2

description:
Library name: 3311_MEKi_Replicate2
RNAseq

value: Trametinib


title: Plate6_D01


title: Plate6_D03


title: Plate6_D10


title: Plate6_D12


title: Plate6_C09


title: 3311_Control_Replicate1

description:
Library name: 3311_Control_Replicate1
RNAseq


title: Plate6_C10


title: K27m3_ScLZ_WT_r2

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description: Library name: Sample22

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to mm10 using STAR
Duplicated reads were removed using SAMtools
Read count extraction and normalization were performed using QuasR/limma
Assembly: mm10
Supplementary files format and content: BigWig files created using the function qExportWig from the QuasR package for 100bp  tiles in the mm10 genome.

source_name: Testis

extract_protocol:
To profile histone modifications in spermatogonia cells we followed the previously published ULI-NChIP protocol (Brind'Amour, Liu et al. 2015) with minor modifications. Briefly 5000-7500 spermatogonia cells were FACS-sorted directly in 20 μl nuclear isolation buffer (Sigma-Aldrich NUC101) in Eppendorf® LoBind microcentrifuge tubes. The nuclei were centrifuged at 500g for 5 minutes at 4°C in a swing bucket centrifuge and the volume of the sample was reduced to 10 μl. The sample was snap frozen in liquid nitrogen and stored at –80°C freezer until further processing. The sample was thawed on ice and 1 μl of TS buffer (5% Triton X-100, 5% Sodium deoxycholate) was added for 10 minutes to ensure permeabilization of nuclei. 40 μl of MNAse digestion buffer (3.33 gelUnits/μl Micrococcal Nuclease (NEB M0247S), 1.25X Micrococcal Nuclease buffer, 6.25% PEG 6000, 0.85mM DTT) was added to the sample for 10 minutes at 25 °C to fragment the chromatin. Reaction was stopped by addition of 5 μl 100 uM EDTA and the sample was placed on ice. The sample was diluted by addition of 145 μl ChIP buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1X EDTA-free protease inhibitor cocktail). To ensure release of chromatin fragments, the sample was sonicated using the Diagenode Bioruptor Plus® for 3 cycles of 5 seconds ON and 30 seconds OFF at low output. Then chromatin was pre-cleared with 10 μl of 1:1 protein A:protein G Dynabeads (Thermo Fisher Scientific, 10001D and 10003D). The precleared chromatin sample was incubated with 0.5 μg of anti-H3K4me3 or 1 μg anti-H3K36me2 or 1 μg anti-H3K27me3 conjugated with 10 μl of 1:1 protein A: protein G Dynabeads overnight at 4 °C on a rotator. Chromatin-Antibody-Dynabeads complexes were washed once with 500 μl of ChIP buffer, 3 times with 1ml of Low Salt wash buffer (20 mM Tris-HCl (pH 8.0), 0.05% SDS, 1% Triton X-100, 2 mM EDTA and 150 mM NaCl) and 3 times with 1 ml High Salt buffer (20 mM Tris-HCl (pH 8.0), 0.05% SDS, 1% Triton X-100, 2 mM EDTA and 250 mM NaCl). Chromatin was eluted in 40 μl of Elution buffer (100 mM NaHCO3 and 1% SDS) for 90 minutes at 65 °C. DNA from eluted material was purified by 2X volumes of Ampure XP DNA purification beads (Beckman Coulter, A63881) and resuspended in 25 μl nuclease free H2O.
For library construction the ChIP purified DNA was used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645L) with modifications of the manufacturer instruction as we assembled half volume reactions and we doubled reaction incubation times. For adaptor ligation we used 1:15 adaptor dilution. We amplified the ligated fragments for 12 cycles using single indexed primers.

treatment_protocol: Activation of the CreERT2 was achieved by tamoxifen administration (Sigma-Aldrich #T5648; 1mg, dissolved in corn oil, per 20g mouse body weight, dosed by IP injection) on 5 consecutive days. Testis were collected 10 days after the first injection. Differentiated spermatogonia cells (SgD) were isolated from single-cell testicular suspension by FACS (BD FACSAria II; Hoechst 33342 mid/ CD117 positive /CD324 negative/ CD49f negative)

value: Testis

tag: antibody

value: anti-H3K27me3 (Cell Signaling 9733)

value: Leptotene/Zygotene Spermatocytes

value: Kdm2a +/+ ; cre-ERt2 -

value: No treatment


title: K27m3_SgU_WT_r2

description: Library name: Sample18

value: Undifferentiated Spermatogonia


title: 3311_ChIPreChIP_HNF4a:NKX2-1_Replicate2

description: Library name: 25932X16

data_processing:
Fastq alignments were pre-processed with the merge_umi_fastq application from the UMIScripts package (https://github.com/HuntsmanCancerInstitute/UMIScripts) to associate the UMI sequence, provided as a third Fastq file, into the read comment.
Reads were aligned using Bowtie2 v2.2.9 to the standard chromosomes of the mouse genome (version mm10) or the human genome (version hg38).
Duplicate alignments based on the UMI code were removed using the bam_umi_dedup application (UMIScripts) allowing for 1 mismatch.
Peaks were called using MACS2 v2.2.7 with a significance of q-value < 0.01.
Coverage tracks were generated with MACS2 as Reads Per Million.
Assembly: mm10; for murine samples
Assembly: hg38; for human samples
Supplementary files format and content: bigwig, BED files (except for Input samples)

growth_protocol: Organoid cultures grown in 50% L-WRN conditioned media (Miyoshi and Stappenbeck, 2013). H358 cells were cultured in RPMI/10% FBS. H1651 cells were cultured in Advanced DMEM F-12/10% FBS/10mM HEPES. 3311 cells were cultured in DMEM/10% FBS.

extract_protocol:
For cell line ChIP-seq, ~1 x 107 cells were collected per ChIP experiment. For organoid ChIP-seq, ~4 x 106 cells were collected per ChIP experiment. For ChIP-re-ChIP, ~3 x 107 cells were collected per ChIP experiment. For organoid ChIP experiments, organoids were first collected in Cell Recovery Solution and incubated on ice for 30 mins. Organoids were then washed three times in cold PBS. On the second wash, PBS was supplemented with DNase solution (containing a final concentration of 200U/ml DNase [Worthington], 2.5 mM MgCl2, 500 mM CaCl2). 2D adherent cell lines were washed 2X in cold PBS, then cells were scraped and collected and washed once more. Cell/organoid pellets were then resuspended in 5 ml of 2 mM DSG buffer (1X PBS, 1 mM MgCl2) containing 40μL of 0.25 M disuccinimidyl glutarate (DSG) (Thermo Fisher Scientific) and rotated at room temperature for 35 min. Methanol-free formaldehyde was then added to a final concentration of 1% and cells were crosslinked for 10 min. The cross-linking reaction was quenched with the addition of glycine to a final concentration of 125mM. Cells were washed with cold PBS, then the cell pellet was snap frozen in liquid nitrogen and stored at -80°C. Cell pellets were thawed on ice for 5 minutes then lysed in 1 mL of Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40) with Pierce Protease Inhibitor (PPI, ThermoFisher Scientific, A32959). Samples were centrifuged at 4°C (1000G) then resuspended in 1mL of RIPA lysis buffer (1X PBS, 1% NP40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate) with PPI. Chromatin was sonicated with a QSonica Q800R (pulse: 30 s on/30 s off; sonication time: 20 minutes; amplitude: 70%). After sonication, samples were centrifuged at 17,000 x g for 15 minutes and an input was collected from each sample of sheared chromatin. Chromatin from each sample was then immunoprecipitated overnight with 5ug of the following antibodies (per sample) premixed with Protein G Dynabeads (for mouse antibodies; ThermoFisher Scientific, 10004D) or Protein A Dynabeads (for rabbit antibodies; ThermoFisher Scientific, 10002D): HNF4α (Perseus Proteomics PPH1415), NKX2-1 (Abcam ab133737), FoxA1 (Abcam, ab170933), FoxA2 (CST 8186). The next day, bound chromatin was washed 5 times with LiCl Wash Buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate). At this point, ChIP-re-ChIP samples were subjected to an extra processing step: samples were resuspended in 10mM DTT and incubated with agitation at 37°C for 40 minutes. DTT was diluted by adding 1mL RIPA buffer with PPI, and diluted chromatin was immunoprecipitated for a second time overnight with the reciprocal antibody (either NKX2-1 or HNF4α). For all samples, crosslinks were reversed by incubating samples in IP Elution Buffer (1% SDS, 0.1% NaHCO3) overnight at 65°C. ChIP DNA was purified using Zymo ChIP DNA Clean and Concentrator Kit (Zymo, D5205).
Library preparation was performed using the ChIP-seq with NEBNext DNA Ultra II library prep kit using Unique Molecular Indexes (UMIs). Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

treatment_protocol: For Hnf4a deletion ChIP-seq, 3154 organoids were treated with 2mM 4OHT (or ethanol) for 6 days to delete Hnf4a. For H1651 ChIP-seq, H1651 cells harboring lentiviral HNF4α overexpression construct were treated with 1μg/mL doxycycline for 7 days. For MEKi ChIP-seq, 3311 cells were treated with 50nM Trametinib for 48h, and 1027B organoids and H358 cells were treated with 20nM Trametinib for 48h.

value: Control

tag: chip antibody

value: HNF4a (Perseus Proteomics PPH1415), NKX2-1 (Abcam ab133737)


title: Plate6_C04


title: 3311_ChIPreChIP_NKX2-1:HNF4a_Replicate2

description: Library name: 25932X14

value: NKX2-1 (Abcam ab133737), HNF4a (Perseus Proteomics PPH1415)


title: Plate6_C06

value: blood


title: Plate6_C03

value: plasmacytoid dendritic cell


title: Plate6_C12


title: 3311_ChIPreChIP_HNF4a:NKX2-1_Replicate1

description: Library name: 25932X8


title: 3311_ChIPreChIP_Input_Replicate1

description: Library name: 25932X1

value: No antibody


title: Plate6_C05


title: Plate6_C01


title: 3311_ChIPreChIP_Input_Replicate2

description: Library name: 25932X9


title: 3311_MEKi_Replicate1

description:
Library name: 3311_MEKi_Replicate1
RNAseq


title: Plate6_B12

value: sorted as:day2_pDC_donor 2


title: Plate6_B10


title: Plate6_C02


title: 3311_ChIPreChIP_NKX2-1:HNF4a_Replicate1

description: Library name: 25932X6


title: Plate6_B07


title: Plate6_B06


title: Plate6_B09


title: Plate6_B04


title: Plate6_B05


title: Plate6_B08


title: Plate6_B03


title: Plate6_C08


title: MPC-5 podocytes exposed to HG/BCAA plus TEPP46 for 24 hrs

city: Xi’an, China

first: zhao

last: huishou

state: Please select...

address: 127 West Changle Rd, Xi’an, China, 710032

country: China

institute: Xijing Hospital

description:
Library name: HG_B_T3
Column name in raw counts All samples.txt: HG_B_T3

data_processing:
Illumina Casava2.19 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the librar
Assembly: http://ftp.ensembl.org/pub/release-97/fasta/mus_musculus_c57bl6nj/
Supplementary files format and content: csv files  includes FPKM values for each Sample

growth_protocol: Podocytes were cultured in RPMI medium with 10% FBS at 33 °C and then thermo-shifted to 37 °C for 10 d before they were used for experiments.

extract_protocol:
RNA  was harvested using Rneasy plus kit (Qiagen), 1 μg of total RNA was used for the construction of sequencing  libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: MPC-5 podocytes were exposed to 25 mM glucose, 25 mM glucose plus 3 mM BCAAs (HG/BCAAor HG/BCAA plus 20 nM TEPP46 for 24 hours

value: podocytes

value: WT

value: HG/BCAA plus TEPP46


title: Plate6_B02


title: Plate6_C07

value: sorted as:day2_itDC_donor 2


title: MPC-5 podocytes under HG/BCAA withTEPP46 for 24 hrs

description:
Library name: HG_B_T2
Column name in raw counts All samples.txt: HG_B_T2


title: Plate6_B01


title: MPC-5 podocytes under HG/BCAA plus TEPP46 for 24 hours

description:
Library name: HG_B_T1
Column name in raw counts All samples.txt: HG_B_T1


title: Plate6_A11


title: Plate6_B11


title: MPC-5 podocytes under HG/BCAA for 24 hrs

description:
Library name: HG_B3
Column name in raw counts All samples.txt: HG_B3

value: HG/BCAA


title: Plate6_A12


title: MPC-5 podocytes under 25 mM HG/BCAA for 24 hrs

description:
Library name: HG_B2
Column name in raw counts All samples.txt: HG_B2


title: Plate6_A10


title: Plate6_A09


title: MPC-5 podocytes under 25 mM HG for 24 hrs

description:
Library name: HG_2
Column name in raw counts All samples.txt: HG3

value: HG


title: Plate6_A08


title: Plate6_A07


title: KPH_pre_depletion

description:
10X Genomics
20463X3

data_processing:
Single-cell RNA-seq data from both KP (n=2) and KPH (n=2) tumors were demultiplexed using the 10x cellranger mkfastq version 7.2.0 to create fastq files with the I1 sample index, R1 cell barcode+UMI, and R2 sequence.
Reads were aligned to the mouse genome (mm10 with custom CRE-ERT2 reference) and UMIs were generated using cellranger count 7.2.0 with include-introns set to true.
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: lung tumor

extract_protocol:
Individual macroscopic tumors were removed from the lungs and broken down into single cell suspensions. Pre-depletion cells were viably cryopreserved in 5% DMSO/FBS. The remaining cells were depleted of CD45-positive and CD31-positive cells using MACS with Miltenyi microbeads (CD45:130-052-301; CD31:130-097-418) and LD columns (130-042-901) following manufacturer recommendations. Post-depletion cells were viably cryopreserved in 5% DMSO/FBS. The day of library preparation, cells were thawed, washed in cold PBS, and resuspended in PBS + 0.5% BSA. Cells were stained with DAPI and sorted for single, live cells using a BD FACSAria cell sorter.
Protocols used to generate scRNA-seq data with 10x Genomics Chromium platform can be found at https://support.10xgenomics.com/single-cell-gene-expression. In brief, the Chromium Single Cell Gene Expression Solution with 3’ chemistry, version 3 (PN-1000075) was used to barcode individual cells with 16bp 10X barcodes and to tag cell specific transcript molecules with 10bp Unique Molecular Identifier (UMI) according to the manufacturer’s instructions. The following protocol was performed at the High-Throughput Genomics Shared Resource at Huntsman Cancer Institute, University of Utah. Single cells were suspended in PBS with 0.04% BSA, and the cell suspension was passed through a 40 micron cell strainer. Viability and cell count were assessed on Countess II (Thermo Scientific). Suspensions were equilibrated to targeted cell recovery of 10,000 cells. 10x Gel Beads and reverse transcription reagents were added and cell suspensions were loaded to Chromium Single Cell A (PN-120236) to form Gel Beads-in emulsions (GEMs) - the nano-droplets. Within individual GEMs, cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing, end repair, adaptor ligation and sample indexing were performed in bulk according to the manufacturer’s instructions. The resulting barcoding libraries were qualified on Agilent D1000 ScreenTape on Agilent Technology 2200 TapeStation system and quantified by quantification PCR using KAPA Biosystems Library Quantification Kit for Illumina Platforms (KK4842). Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2 × 150 PE mode.

treatment_protocol: KPH mice were injected with tamoxifen or corn oil 10 weeks after intubation with Adenoviral mSPC-FlpO, and two weeks later, single cells were collected from lung tumors.

value: lung tumor

value: Tamoxifen


title: KPH_post_depletion

description:
10X Genomics
20463X4


title: MPC-5 podocytes under 25 mM high glucose(HG) for 24 hrs

description:
Library name: HG_1
Column name in raw counts All samples.txt: HG2

value: high glucose (HG)


title: Plate6_A06


title: Plate6_A05


title: KP_post_depletion

description:
10X Genomics
20463X2

value: Ethanol


title: Plate6_A03


title: Plate6_A04


title: Plate6_A01


title: Plate6_A02


title: KP_pre_depletion

description:
10X Genomics
20463X1


title: 3154_4OHT_KRASi_Replicate2

description: RNAseq

value: Lung organoids


title: 3154_4OHT_KRASi_Replicate1

description: RNAseq


title: 3154_4OHT_Control_Replicate1

description: RNAseq


title: Plate5_E07

value: sorted as:fresh tDC_donor 2


title: Plate5_E08


title: MPC-5 podocytes under 25 mM glucose plus 3 mM BCAAs (HG/BCAA) for 24 hrs

description:
Library name: HG_B1
Column name in raw counts All samples.txt: HG_B1

value: 25 mM glucose plus 3 mM BCAAs (HG/BCAA)


title: Plate5_E06

value: blood


title: 3154_EtOH_KRASi_Replicate1

description: RNAseq


title: Plate5_E05

value: plasmacytoid dendritic cell


title: 3154_EtOH_Control_Replicate2

description: RNAseq

value: Ethanol/Control


title: 3154_EtOH_Control_Replicate1

description: RNAseq


title: 1027B_KRASi_Replicate2

description: RNAseq


title: Plate5_E02


title: 1027B_KRASi_Replicate1

description: RNAseq


title: Plate5_E03


title: Plate5_E01


title: Plate5_D12


title: 3154_4OHT_Control_Replicate2

description: RNAseq


title: Plate5_D11


title: 1027B_Control_Replicate2

description: RNAseq

value: Control


title: Plate5_D10


title: Plate5_D09


title: 1027B_Control_Replicate1

description: RNAseq


title: 3154_4OHT_Replicate2

description: RNAseq


title: 3154_EtOH_KRASi_Replicate2

description: RNAseq


title: 3154_EtOH_Replicate2

description: RNAseq


title: 3154_4OHT_Replicate1

description: RNAseq


title: Plate5_D07

value: sorted as:fresh pDC_donor 2


title: Plate5_D06


title: 1027B_MEKi_NKX2-1_Replicate2

description:
ChIPseq
25605X8

extract_protocol:
For cell line ChIP-seq, ~1 x 107 cells were collected per ChIP experiment. For organoid ChIP-seq, ~4 x 106 cells were collected per ChIP experiment. For ChIP-re-ChIP, ~3 x 107 cells were collected per ChIP experiment. For organoid ChIP experiments, organoids were first collected in Cell Recovery Solution and incubated on ice for 30 mins. Organoids were then washed three times in cold PBS. On the second wash, PBS was supplemented with DNase solution (containing a final concentration of 200U/ml DNase [Worthington], 2.5 mM MgCl2, 500 mM CaCl2). 2D adherent cell lines were washed 2X in cold PBS, then cells were scraped and collected and washed once more. Cell/organoid pellets were then resuspended in 5 ml of 2 mM DSG buffer (1X PBS, 1 mM MgCl2) containing 40μL of 0.25 M disuccinimidyl glutarate (DSG) (Thermo Fisher Scientific) and rotated at room temperature for 35 min. Methanol-free formaldehyde was then added to a final concentration of 1% and cells were crosslinked for 10 min. The cross-linking reaction was quenched with the addition of glycine to a final concentration of 125mM. Cells were washed with cold PBS, then the cell pellet was snap frozen in liquid nitrogen and stored at -80°C. Cell pellets were thawed on ice for 5 minutes then lysed in 1 mL of Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40) with Pierce Protease Inhibitor (PPI, ThermoFisher Scientific, A32959). Samples were centrifuged at 4°C (1000G) then resuspended in 1mL of RIPA lysis buffer (1X PBS, 1% NP40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate) with PPI. Chromatin was sonicated with a QSonica Q800R (pulse: 30 s on/30 s off; sonication time: 20 minutes; amplitude: 70%). After sonication, samples were centrifuged at 17,000 x g for 15 minutes and an input was collected from each sample of sheared chromatin. Chromatin from each sample was then immunoprecipitated overnight with 5ug of the following antibodies (per sample) premixed with Protein G Dynabeads (for mouse antibodies; ThermoFisher Scientific, 10004D) or Protein A Dynabeads (for rabbit antibodies; ThermoFisher Scientific, 10002D): HNF4α (Perseus Proteomics PPH1415), NKX2-1 (Abcam ab133737), FoxA1 (Abcam, ab170933), FoxA2 (CST 8186). The next day, bound chromatin was washed 5 times with LiCl Wash Buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate). At this point, ChIP-re-ChIP samples were subjected to an extra processing step: samples were resuspended in 10mM DTT and incubated with agitation at 37°C for 40 minutes. DTT was diluted by adding 1mL RIPA buffer with PPI, and diluted chromatin was immunoprecipitated for a second time overnight with the reciprocal antibody (either FoxA1 or HNF4α). For all samples, crosslinks were reversed by incubating samples in IP Elution Buffer (1% SDS, 0.1% NaHCO3) overnight at 65°C. ChIP DNA was purified using Zymo ChIP DNA Clean and Concentrator Kit (Zymo, D5205).
Library preparation was performed using the ChIP-seq with NEBNext DNA Ultra II library prep kit using Unique Molecular Indexes (UMIs). Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

value: Trametinib


title: Plate5_D05


title: Plate5_D04


title: Plate5_E04


title: Plate5_D03


title: 1027B_MEKi_Input_Replicate2

description:
ChIPseq
25605X6

value: No antibody


title: 1027B_MEKi_Replicate2

description: RNAseq


title: 1027B_MEKi_Input_Replicate1

description:
ChIPseq
25605X2


title: 1027B_MEKi_Replicate1

description: RNAseq


title: 1027B_Control_NKX2-1_Replicate2

description:
ChIPseq
25605X7


title: Plate5_C12


title: Plate5_D08


title: 1027B_Control_NKX2-1_Replicate1

description:
ChIPseq
25605X3


title: Plate5_D01


title: 1027B_Control_Input_Replicate1

description:
ChIPseq
25605X1


title: Plate5_C09


title: Plate5_C08


title: 3311_MEKi_NKX2-1_Replicate2

description:
ChIPseq
20585X7

value: Lung cell line


title: Plate5_C07


title: 3154_EtOH_Replicate1

description: RNAseq


title: 3311_MEKi_NKX2-1_Replicate1

description:
ChIPseq
20556X7


title: Plate5_D02


title: 1027B_Control_Input_Replicate2

description:
ChIPseq
25605X5


title: Plate5_C05


title: 3311_MEKi_Input_Replicate2

description:
ChIPseq
20585X6


title: Plate5_C11


title: Plate5_C06


title: Plate5_C04


title: 3311_Control_FoxA1_Replicate2

description:
ChIPseq
20585X3

value: FoxA1 (Abcam, ab170933)


title: Plate5_C03


title: Plate5_C02


title: 3311_MEKi_Input_Replicate1

description:
ChIPseq
20556X6


title: 1027B_MEKi_NKX2-1_Replicate1

description:
ChIPseq
25605X4


title: 3311_Control_HNF4a_Replicate1

description:
ChIPseq
20556X4

value: HNF4a (Perseus Proteomics PPH1415)


title: Plate5_C01


title: 3311_Control_HNF4a_Replicate2

description:
ChIPseq
20585X4


title: Plate5_B12


title: 3311_Control_NKX2-1_Replicate2

description:
ChIPseq
20585X2


title: Plate5_C10


title: 3311_Control_NKX2-1_Replicate1

description:
ChIPseq
20556X2


title: Plate5_B11


title: 3154_4OHT_FoxA2_Replicate1

description:
ChIPseq
20606X8

value: FoxA2 (CST 8186)


title: 3311_Control_Input_Replicate2

description:
ChIPseq
20585X1


title: Plate5_B10


title: 3154_4OHT_FoxA2_Replicate2

description:
ChIPseq
20667X9


title: Plate5_B06


title: Plate5_B05


title: Plate5_B08


title: 3154_4OHT_NKX2-1_Replicate1

description:
ChIPseq
20606X6


title: 3154_4OHT_Input_Replicate2

description:
ChIPseq
20667X2


title: Plate5_B02


title: 3154_4OHT_FoxA1_Replicate2

description:
ChIPseq
20667X7


title: 3154_4OHT_Input_Replicate1

description:
ChIPseq
20606X5


title: 3154_4OHT_FoxA1_Replicate1

description:
ChIPseq
20606X7


title: 3311_Control_FoxA1_Replicate1

description:
ChIPseq
20556X3


title: Plate5_B04


title: Plate5_A12


title: Plate5_B03


title: Plate5_B01


title: Plate5_A11


title: Plate5_B07


title: 3154_EtOH_FoxA2_Replicate1

description:
ChIPseq
20606X4


title: Plate5_B09


title: 3154_4OHT_NKX2-1_Replicate2

description:
ChIPseq
20667X6


title: Plate5_A08


title: 3311_Control_Input_Replicate1

description:
ChIPseq
20556X1


title: 3154_EtOH_NKX2-1_Replicate2

description:
ChIPseq
20667X4


title: Plate5_A10


title: 3154_EtOH_NKX2-1_Replicate1

description:
ChIPseq
20606X2


title: Plate5_A09


title: 3154_EtOH_HNF4a_Replicate2

description:
ChIPseq
20667X3


title: 3154_EtOH_HNF4a_Replicate1

description:
ChIPseq
20606X10


title: 3154_EtOH_FoxA1_Replicate1

description:
ChIPseq
20606X3


title: Plate5_A07


title: Plate5_A03


title: Plate5_A06


title: G-CSF TINs, replicate 2, plate 13, scRNAseq

city: Bunkyo-ku

first: Osamu

last: Sugahara

state: Tokyo

address: Yushima 1-5-45

department: Advanced Research Initiative

institute: Institute of Science Tokyo

data_processing:
The FASTQ files obtained from CEL-seq2 analysis were processed with celseq2 software. The reads were thus “demultiplexed” and mapped to the mouse genome (Mm10, Genome Reference Consortium GRCm38) with the use of Bowtie2 software, and gene counting was then performed with HTSeq software. The resultant gene (UMI)-cell matrices for each experiment were concatenated with R software.
Assembly: mm10
Supplementary files format and content: Gene (UMI)-cell matrices

source_name: cholangiocarcinoma (CCA) tumor

extract_protocol:
For isolation of single tumor cells, tumors were mechanically dissociated with scissors and digested by incubation for 30 min at 37°C with collagenase at 1 mg/mL in HBSS. Cells were then isolated by vigorous pipetting of the tumor fragments and passage through a 70-μm cell strainer. For analysis of CCA tumors, erythrocytes were lysed with hemolysis buffer (0.14 M NH4Cl and 0.01 M Tris-HCl at pH 7.5), and the remaining cells were stained with antibodies against CD45.2 (clone 104, BioLegend), CD11b (clone M1/70, BioLegend), Ly6G (clone 1A8, BioLegend). Cell sorting was performed with a FACS Aria II instrument fitted with a 100-μm nozzle. After gating for forward scatter and side scatter and exclusion of doublets, the 7AAD–CD45+CD11b+Ly6G+ fraction was collected as neutrophils.
For single-cell RNA sequencing (scRNA-seq) library preparation, single TINs were processed and barcoded with the use of the CEL-seq2 technique as performed with minor modifications. In brief, each single cell was directly sorted into a well of a 96-well PCR plate containing primer mix including reverse transcription (RT) primers with unique molecular identifiers (UMI) and cell barcodes, deoxynucleoside triphosphates, RNase inhibitors, and 0.3% Nonidet P-40. The cells were lysed by incubation at 65°C for 5 minutes and then subjected to room temperature with SuperScript III Reverse Transcriptase. Samples from each plate were pooled into a single library, from which cDNAs were purified with the use of Agencourt AMPure XP Beads and subjected to second-strand synthesis. The resultant libraries were again bead-purified and then used as templates for in vitro transcription with a MEGAscript T7 Transcription Kit. The amplified RNAs were subjected to RT followed by PCR amplification (20 cycles) with Illumina TruSeq Small RNA primers to generate the final cDNA libraries, which were subjected to paired-end sequencing with an Illumina NovaSeq6000 instrument.

value: cholangiocarcinoma (CCA) tumor

value: tumor-infiltrating neutrophils (TINs)

value: WT

value: rhG-CSF


title: Plate5_A04


title: Plate5_A02


title: 3154_EtOH_Input_Replicate2

description:
ChIPseq
20667X1

value: Lung organoids

value: Ethanol


title: 3154_EtOH_Input_Replicate1

description:
ChIPseq
20606X1


title: S3-7_S8

city: Boston

first: Yonglin

last: Zhu

address: 300 Longwood Ave

department: Cardiac Surgery

institute: Boston Children's Hospital

data_processing:
For bulk RNA-seq, raw 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 Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file.
For scRNA-seq, the demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text files include count values for all samples (bulk RNA-seq)
Supplementary files format and content: tab-delimited text files include count matrix for each samples (scRNA-seq)

source_name: Cell line

extract_protocol:
For bulk RNA-seq, total RNA was extracted from fresh frozen cell pellet samples using Qiasymphony RNA kit following manufacturer’s instructions (Qiagen, Hilden, Germany). For scRNA-seq, single-cell RNA samples were prepared using the Chromium Next 10X genomics kits (10xgenomics, PN-1000128, PN-1000127) following the manufacture's protocols.
For bulk RNA-seq, RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA). For scRNA-seq, RNA sequencing libraries were prepared using the dual index kit (10xgenomics, PN-100021310x following the manufacturer's protocols.

value: Cell line

value: mixed cell population


title: dox1_S6


title: G-CSF TINs, replicate 2, plate 12, scRNAseq


title: dox3_S7


title: VO-iMC-rep3

value: mural cell


title: VO-iMC-rep2


title: Plate4_D04

value: blood

value: plasmacytoid dendritic cell

value: sorted as:day2_icDC2_donor 1


title: G-CSF TINs, replicate 2, plate 11, scRNAseq


title: Plate5_A01

value: sorted as:fresh pDC_donor 2


title: G-CSF TINs, replicate 2, plate 10, scRNAseq


title: VO-iMC-rep1


title: VO-iEC-rep3

value: endothelial cell


title: VO-iEC-rep2


title: Plate5_A05


title: Plate4_D03


title: G-CSF TINs, replicate 2, plate 09, scRNAseq


title: VO-iEC-rep1


title: Plate4_D02


title: 2D-iMC-rep3


title: 2D-iMC-rep2


title: 2D-iMC-rep1


title: G-CSF TINs, replicate 2, plate 08, scRNAseq


title: Plate4_D01


title: 2D-iEC-rep3


title: G-CSF TINs, replicate 2, plate 07, scRNAseq


title: Plate4_C12


title: 2D-iEC-rep2


title: 2D-iEC-rep1


title: 941

city: Amsterdam

first: Joe

last: Butler

address: Meibergdreef 9

department: Infectious diseases

country: Netherlands

institute: Amsterdam UMC

data_processing:
Libraries were sequenced using the Illumina HiSeq4000 (Illumina, San Diego, CA, USA) to generate 50bp single-end reads.
The sequence read quality was assessed using FastQC methods (version 0.11.5; Babraham Institute, Babraham, Cambridgeshire, UK).
Trimmomatic version 0.39 was used to trim the Illumina adapters and filter low quality reads and ambiguous nucleotide-containing sequences.
The remaining high-quality reads were aligned against the human Genome Reference Consortium Build 38 (GRCh38, Ensembl 84) using Hisat2 (2.2.0) with default parameters
Count data were generated using the HTSeq method.
Assembly: Human Genome Reference Consortium Build 38 (GRCh38, Ensembl 84)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: N/A

source_name: Whole blood

extract_protocol:
Total RNA was extracted using the PAXgene blood mRNA kit (Qiagen, Venlo, the Netherlands).
Sequencing libraries were prepared by means of the KAPA RNA HyperPrep with RiboErase (Roche) as per manufacturer’s instructions.

value: Whole blood

tag: gender

value: male

tag: bsi group

value: EC


title: Plate4_C11


title: 7673222

value: OTH


title: G-CSF TINs, replicate 2, plate 05, scRNAseq

value: cholangiocarcinoma (CCA) tumor

value: tumor-infiltrating neutrophils (TINs)


title: 7605503

value: female

value: STR


title: 7549906

value: SA


title: G-CSF TINs, replicate 2, plate 04, scRNAseq

value: WT

value: rhG-CSF


title: 7548204

value: MIX


title: 7540639

value: VI


title: 7452000


title: G-CSF TINs, replicate 2, plate 03, scRNAseq


title: Plate4_C09

value: blood

value: plasmacytoid dendritic cell


title: Plate4_C08

value: sorted as:day2_icDC2_donor 1


title: G-CSF TINs, replicate 2, plate 02, scRNAseq


title: 7433964


title: 3154_EtOH_FoxA2_Replicate2

description:
ChIPseq
20667X8

value: Lung organoids

value: Ethanol

value: FoxA2 (CST 8186)


title: Plate4_C07


title: 7263743

value: Whole blood

value: EC


title: G-CSF TINs, replicate 2, plate 01, scRNAseq

value: cholangiocarcinoma (CCA) tumor


title: 7310676


title: 7449219

value: male

value: CoNS


title: 7235477

value: OTH


title: G-CSF TINs, replicate 2, plate 06, scRNAseq

value: tumor-infiltrating neutrophils (TINs)


title: 7219393


title: Plate4_C05


title: G-CSF TINs, replicate 1, plate 13, scRNAseq

value: WT


title: Plate4_C10


title: G-CSF TINs, replicate 1, plate 12, scRNAseq

value: rhG-CSF


title: Plate4_C04

value: sorted as:day2_itDC_donor 1


title: 7023105

value: MIX


title: 7100733

value: female


title: G-CSF TINs, replicate 1, plate 11, scRNAseq


title: 7186495


title: Plate4_C03

value: blood

value: plasmacytoid dendritic cell


title: 6845

value: NI


title: G-CSF TINs, replicate 1, plate 10, scRNAseq


title: Plate4_C02


title: 6822618


title: G-CSF TINs, replicate 1, plate 09, scRNAseq


title: Plate4_C01


title: Plate4_C06

value: sorted as:day2_icDC2_donor 1


title: G-CSF TINs, replicate 1, plate 08, scRNAseq


title: 6744

value: STR


title: 6749

value: Whole blood

value: SA


title: 6773


title: Plate4_B12


title: 6710954


title: 6689

value: VI


title: Plate4_B11


title: G-CSF TINs, replicate 1, plate 07, scRNAseq

value: cholangiocarcinoma (CCA) tumor


title: 6643

value: male


title: Plate4_B10


title: 6631


title: Plate4_B09


title: G-CSF TINs, replicate 1, plate 05, scRNAseq


title: 6893056


title: 6580878


title: G-CSF TINs, replicate 1, plate 04, scRNAseq


title: 6598586


title: 6445

value: OTH


title: Plate4_B08


title: G-CSF TINs, replicate 1, plate 03, scRNAseq

value: tumor-infiltrating neutrophils (TINs)


title: 6425


title: 6431240


title: 6733


title: Plate4_B07


title: G-CSF TINs, replicate 1, plate 02, scRNAseq

value: WT


title: 6365424


title: Plate4_B06


title: 6359


title: 6332966


title: 6317


title: 6676761


title: G-CSF TINs, replicate 1, plate 06, scRNAseq

value: rhG-CSF


title: G-CSF TINs, replicate 1, plate 01, scRNAseq


title: 6131636

value: EC


title: Plate4_B05

value: sorted as:day2_itDC_donor 1


title: Plate4_B04

value: sorted as:day2_pDC_donor 1


title: Control TINs, replicate 2, plate 12, scRNAseq

value: PBS


title: 6116

value: MIX


title: 6040


title: Plate4_B03

value: blood

value: plasmacytoid dendritic cell


title: Control TINs, replicate 2, plate 11, scRNAseq


title: 6010469

value: NI


title: 5960698

value: Whole blood

value: female


title: Control TINs, replicate 2, plate 10, scRNAseq


title: Plate4_B02


title: 5960204

value: STR


title: Control TINs, replicate 2, plate 09, scRNAseq

value: cholangiocarcinoma (CCA) tumor


title: 5928786

value: VI


title: 5905189

value: male


title: Plate4_B01


title: 5902601


title: Plate4_A12


title: 5875


title: Control TINs, replicate 2, plate 07, scRNAseq

value: tumor-infiltrating neutrophils (TINs)


title: Control TINs, replicate 2, plate 08, scRNAseq

value: WT


title: 5770186


title: 5764

value: CoNS


title: Control TINs, replicate 2, plate 06, scRNAseq


title: Plate4_A10


title: 5753125


title: 6037


title: Plate4_A11


title: Control TINs, replicate 2, plate 05, scRNAseq


title: 5693718

value: ENT


title: Control TINs, replicate 2, plate 04, scRNAseq


title: Plate4_A08


title: Plate4_A09


title: Control TINs, replicate 2, plate 03, scRNAseq


title: 5608450

value: EC


title: 5745


title: 5595


title: 5642

value: SA


title: 5529379

value: OTH


title: Control TINs, replicate 2, plate 02, scRNAseq

value: PBS


title: Plate4_A06

value: blood

value: sorted as:day2_pDC_donor 1


title: 5516297


title: 5871556


title: Control TINs, replicate 2, plate 01, scRNAseq


title: 5486

value: NI


title: 5401364

value: Whole blood


title: 5305


title: Plate4_A04

value: plasmacytoid dendritic cell


title: 5299084

value: female


title: Plate4_A03


title: Control TINs, replicate 1, plate 13, scRNAseq

value: cholangiocarcinoma (CCA) tumor


title: Control TINs, replicate 1, plate 12, scRNAseq


title: Plate4_A07


title: 5298783

value: VI


title: Plate4_A02


title: 5157005

value: male


title: 5084

value: STR


title: 5074279


title: Plate4_A01


title: 5041


title: Control TINs, replicate 1, plate 11, scRNAseq

value: tumor-infiltrating neutrophils (TINs)

value: WT


title: 3154_EtOH_FoxA1_Replicate2

description:
ChIPseq
20667X5

value: Lung organoids

value: Ethanol

value: FoxA1 (Abcam, ab170933)


title: Plate4_A05


title: Plate3_D12

value: sorted as:day2_icDC2_donor 1


title: 4931

value: MIX


title: 4922

value: OTH


title: Plate3_D11

value: blood


title: 4908

value: ENT


title: Control TINs, replicate 1, plate 09, scRNAseq

value: PBS


title: Control TINs, replicate 1, plate 08, scRNAseq


title: 4882

value: Whole blood


title: 5177

value: NI


title: 4828

value: female


title: Control TINs, replicate 1, plate 07, scRNAseq

value: cholangiocarcinoma (CCA) tumor


title: Plate3_D10

value: plasmacytoid dendritic cell


title: 4782

value: male

value: EC


title: 4787


title: Plate3_D09


title: Control TINs, replicate 1, plate 10, scRNAseq

value: tumor-infiltrating neutrophils (TINs)

value: WT


title: Control TINs, replicate 1, plate 06, scRNAseq


title: Plate3_D08


title: 4674


title: Plate3_D07


title: 5062363

value: STR


title: Control TINs, replicate 1, plate 05, scRNAseq


title: 4622


title: 4755


title: Control TINs, replicate 1, plate 04, scRNAseq


title: Plate3_D06


title: 4534

value: VI


title: Plate3_D05

value: sorted as:day2_icDC2_donor 1


title: 4570


title: 454


title: Control TINs, replicate 1, plate 03, scRNAseq


title: 448


title: Plate3_D04


title: 4463


title: 4434


title: 4777


title: Plate3_D03


title: 4171


title: 4075109

value: CoNS


title: Plate3_D02


title: 4596


title: Plate3_D01


title: M2_CtslΔTEC mouse5,6,7

data_processing:
The CLC Genomics Workbench software (v23.0.3) provided by Qiagen was used to generate clonotype reads. Briefly, sequences with the same unique molecular index (UMI) were merged and those with UMI reads < 3 were excluded. Further quality control steps included merging and trimming of overlapping paired-end sequences. Results were annotated using the C57BL/6-specific functional TCRα genes extracted from the IMGT murine TCR database. Analyses were done using RStudio (Version 2023.06.1+524). A clonotype was defined as a unique combination of Trav gene, Traj gene and an in-frame CDR3 amino acid sequence. Clonotype abundance was defined as the number of clonotype-encoding unique cDNA molecules (distinguished by UMI) detected in a sample. TCR diversity was assessed using the approach of Chao et al. 78, wherein one unique cDNA molecule was defined as one ‘individual’ and one clonotype as one ‘species’. Rarefaction with Hill numbers was done using ‘iNEXT’ (Version 2.0.20). Shannon diversity is the exponential of Shannon entropy and is calculated in ‘iNEXT’ using q = 1. Shannon diversity (or effective number of TCR clonotypes) is the number of equally abundant clonotypes that would be needed to give the same Shannon diversity as the sample. As sampling completeness reached the maximum (coverage = 1) for each sample and sub-repertoire examined, the observed Shannon diversities were used to calculate ‘Relative diversity’. As adding 95% confidence intervals constructed from 5 bootstrap replications made a negligible difference to the appearance of the rarefaction curves and were smaller than the symbols on the ‘Relative diversity’ summaries, these details were omitted. To assess TCR overlap between pairs of samples we used ‘abdiv’ (Version 0.2.0) to calculate the Morisita Horn index. Quantification of nucleotide deletion or addition at Trav-Traj junctions was done using results from the IMGT Junction Analysis tool. The ‘# nucleotides deleted or added at the Trav-Traj junction’ was defined as the sum of the absolute values of the number of nucleotides deleted from the germline Trav and/or Traj gene(s) plus the number of P and/or N nucleotides added between the remaining germline Trav and/or Traj nucleotides. Due to duplication events at the TCRαβ locus in B6 mice, 23-30% of unique cDNA molecules per sample aligned with > 1 Trav paralog; these sequences were excluded from the analyses of chromosomal location of Trav gene usage and nucleotide deletion or addition at Trav-Traj junctions. Codes are available at the following link upon request:  https://github.com/srdaley/CathepsinL_TCRseq.
Assembly: Ensembl release version 106 for M. musculus
Supplementary files format and content: Table with clonotype counts.
Library strategy: TCR-seq

value: thymus

value: CD4SP M2 thymocytes

value: Fixedb TCRa+/- CtsldTEC


title: 4044191


title: M2_CtslΔTEC mouse3,4


title: 3859


title: Plate3_C12

value: blood

value: sorted as:day2_itDC_donor 1


title: 3884866

value: Whole blood

value: MIX


title: Control TINs, replicate 1, plate 02, scRNAseq

value: cholangiocarcinoma (CCA) tumor

value: PBS


title: Plate3_C11

value: plasmacytoid dendritic cell


title: M2_WT mouse5,6

value: Fixedb TCRa+/- (WT)


title: 3803135

value: female


title: M2_WT mouse3,4


title: 3789940

value: SA


title: Plate3_C10


title: Control TINs, replicate 1, plate 01, scRNAseq

value: tumor-infiltrating neutrophils (TINs)

value: WT


title: 3936540

value: male

value: EC


title: 3749057

value: CoNS


title: M2_WT mouse1,2

value: thymus

value: CD4SP M2 thymocytes


title: 3734678

value: OTH


title: Plate3_C09

value: blood

value: sorted as:day2_itDC_donor 1


title: WT 40Hz 1hr Rep7 VC

city: Atlanta

first: Levi

middle: B.

last: Wood

state: GA

address: 315 Ferst Dr NW Rm 3303

institute: Georgia Institute of Technology

description: 94 VC

data_processing:
Alignment was performed by Molecular Research Lab (https://mrdnalab.com) and data was validated for fastq integrity and quality. Each library was split between four lanes and .fastq.gz files were merged using DNAstar ArrayStar. Next, Qseq reads were mapped using the mouse reference genome GRCm39 (GCF_000001635.27). For the read assignment, the threshold was set at 20bp and 80% of the bases matching within each read. Duplicated reads were eliminated and genes with less than 20 total raw counts were removed from analysis. Gene counts were normalized using DESeq2 in R.
Assembly: mouse reference genome GRCm39 (GCF_000001635.27)
Supplementary files format and content: Raw count values in csv format.

source_name: Brain Tissue

extract_protocol:
RNAwasisolated from mouse brain tissue  tissues using Qiagen RNeasy kit(217804; Qiagen; Hilden, Germany)according to the manufacturer’s protocols.
Libraries were sequenced for paired-end mRNA using the NovaSeq 6000 sequencing system to obtain a sequencing depth of 30 to 40 million reads per sample. Before sequencing, quality control was performed using a bioanalyzer for RNA integrity number greater than seven. The NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit were used to prepare sequencing libraries.

value: Brain Tissue

tag: tissue region

value: VC

tag: Sex

value: Male

value: WT 40Hz 1hr


title: 3939657

value: Whole blood

value: MIX


title: Plate3_C08

value: plasmacytoid dendritic cell


title: CRAMP1-KO + GFP-CRAMP1-∆GB-N cells, RNA, exp2, rep3

city: Copenhagen

first: Niels

last: Mailand

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

data_processing:
Basecalls were performed using bcl2fastq (version 2.20.0)
Reads underwent filtering for adapters and low quality using TrimGalore (version 0.6.7).
Reads were aligned to the human (hg38) genome using STAR (version 2.6.1d).
Duplicate reads were removed with MarkDuplicates (version 2.7.4). Only reads with a mapping quality above 30 were retained for subsequent downstream analyses.
Reads were quantified using Salmon (version 1.6.9) and normalized using TPM.
Assembly: hg38
Supplementary files format and content: Raw counts
Supplementary files format and content: Transcript per million (TPM) counts

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) GlutaMax containing 10% fetal bovine serum (FBS; Gibco) and 100 U/ml penicillin-streptomycin (Gibco) and incubated at 37ºC with 5% CO2

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen X) and quality checked on a TapeStation. 500 ng total RNA was used for the next steps.
Ribosomal RNA was depleted using the NEBNext rRNA depletion kit v2 (New England Biolabs, E7405). Libraries were constructed using the NEBNext Ultra II Directional RNA library prep kit (New England Biolabs, E7760) with the NEBNext Multiplex Oligos for Illumina (New England Biolabs, E6440). Libraries were amplified with 8 PCR cycles, size selected using AMPure XP beads (Beckman Coulter, A63881) and quality was assesed using the HS D1000 kit on a TapeStation (Agilent).


title: 3690470


title: M2_CtslΔTEC mouse1,2

extract_protocol:
CD69-MHCI+ (M2) CD4SP thymocytes were FACS-sorted, pelleted and resuspended in RNA protect (Qiagen). All samples were stored at -80°C until RNA extraction. RNA isolation was performed by Qiagen, according to the RNeasy Mini/Micro kit (Qiagen).
QIAseq® Immune Repertoire RNA Library kit (Qiagen), modified to include only TCRα-specific primers for both the reverse transcription and the target enrichment steps.

value: Fixedb TCRa+/- CtsldTEC


title: CRAMP1-KO + GFP-CRAMP1-∆GB-N  cells, RNA, exp2, rep2


title: Plate3_C07

data_processing:
Data was processed with STAR
Assembly: hg19
Supplementary files format and content: feature_counts.csv (csv file)

extract_protocol:
Plasmocytoid dendritic cells were magnetically enriched from peripheral blood of a healthy donor, cultured with IL-3 and CD40L for two days and single-cell FACS-sorted on a FACS Aria Fusion (BD Biosciences) into Takara Smart-Seq Single Cell kit lysis buffer and frozen at -80C.
The Illumina Nextera XT DNA Library Prep and Unique Dual Index Kits (Illumina) were used for library preparation according to manufacturer's instructions.


title: 3652

value: female

value: ENT


title: WT 40Hz 1hr Rep6 VC

description: 178 VC

value: WT


title: Plate3_C06


title: CRAMP1-KO + GFP-CRAMP1-∆GB-N cells, RNA, exp2, rep1


title: 3813826

value: male

value: CoNS


title: 3637616

value: STR


title: 3827994


title: CRAMP1-KO + GFP-CRAMP1-∆SANT cells, RNA, exp2, rep3


title: Plate3_C05


title: 3624123


title: WT 40Hz 1hr Rep6 Hip

description: 178 Hip

value: Hip


title: WT 40Hz 1hr Rep5 VC

description: 153 VC


title: 3620743


title: Plate3_C04

value: blood


title: CRAMP1-KO + GFP-CRAMP1-∆SANT  cells, RNA, exp2, rep2


title: WT 40Hz 1hr Rep5 Hip

description: 153 Hip


title: CRAMP1-KO + GFP-CRAMP1-∆SANT cells, RNA, exp2, rep1


title: Plate3_C03

value: sorted as:day2_itDC_donor 1


title: 3614667

value: EC


title: WT 40Hz 1hr Rep7 Hip

description: 94 Hip

value: Brain Tissue


title: CRAMP1-KO + GFP-CRAMP1  cells, RNA, exp2, rep2


title: Plate3_C02


title: WT 40Hz 1hr Rep4 Hip

description: 143 Hip

value: Male


title: 3601684


title: CRAMP1-KO + GFP-CRAMP1 cells, RNA, exp2, rep1


title: Plate3_C01


title: 3577

value: OTH


title: WT 40Hz 1hr Rep3 VC

description: 142 VC

value: VC

value: WT 40Hz 1hr


title: CRAMP1-KO cells, RNA, exp2, rep3


title: Plate3_B12

value: plasmacytoid dendritic cell

value: sorted as:day2_pDC_donor 1


title: WT 40Hz 1hr Rep3 Hip

description: 142 Hip


title: Plate3_B11


title: CRAMP1-KO cells, RNA, exp2, rep2


title: 3552905

value: Whole blood

value: MIX


title: Plate3_B10


title: CRAMP1-KO cells, RNA, exp2, rep1


title: WT 40Hz 1hr Rep2 Hip

description: 121 Hip

value: WT


title: Plate3_B09


title: WT cells, RNA, exp2, rep3


title: 3455833

value: male


title: WT 40Hz 1hr Rep4 VC

description: 143 VC


title: WT 40Hz 1hr Rep1 VC

description: 119 VC


title: 3443597


title: Plate3_B08


title: WT cells, RNA, exp2, rep2


title: WT 40Hz 1hr Rep1 Hip

description: 119 Hip


title: WT cells, RNA, exp2, rep1


title: Plate3_B07


title: 3428745

value: VI


title: WT 20Hz 1hr Rep8 VC

description: 180 VC

value: WT 20Hz 1hr


title: Plate3_B06


title: 3557924

value: female

value: STR


title: WT 20Hz 1hr Rep8 Hip

description: 180 Hip

value: Hip


title: CRAMP1-KO cells, RNA, exp1, rep3


title: CRAMP1-KO cells, RNA, exp1, rep2


title: Plate3_B05

value: blood


title: 3404773


title: WT 20Hz 1hr Rep7 VC

description: 177 VC

value: Brain Tissue


title: WT 40Hz 1hr Rep2 VC

description: 121 VC

value: Male


title: CRAMP1-KO cells, RNA, exp1, rep1


title: 3404682


title: Plate3_B04


title: WT 20Hz 1hr Rep7 Hip

description: 177 Hip


title: Plate3_B03


title: WT 20Hz 1hr Rep6 VC

description: 176 VC


title: Plate3_B02


title: WT cells, RNA, exp1, rep2


title: WT cells, RNA, exp1, rep3


title: 3317

value: EC


title: 3406


title: WT 20Hz 1hr Rep6 Hip

description: 176 Hip


title: WT cells, RNA, exp1, rep1


title: Plate3_B01


title: 3286

value: OTH


title: CRAMP1-KO + GFP-CRAMP1-∆SANT cells, CUT&RUN, rep3

data_processing:
Basecalls were performed using bcl2fastq (version 2.20.0)
Reads underwent filtering for adapters and low quality using  TrimGalore! (version 0.6.6).
Reads were aligned to the human (hg38) and S. cerevisiae (R64-1-1) genomes using bowtie2 (version 2.4.4).
Duplicate reads were removed with MarkDuplicates (version 3.0.0), and ENCODE hg38 blacklist regions were masked. Only reads with a Phred quality above 30 were retained for subsequent downstream analyses.
Reads were normalized to spike-in using deeptools bamCoverage (v.3.5.5) tool and bedgraph files were created using bedtools (version 2.31.0).
Coverage files were created using UCSC tool bedGraphToBigWig function and replicates were merged after evaluating correlation using bigwigCompare UCSC function.  Replicates were merged for visualization.
To identify CRAMP1 binding location, narrow peaks were called using macs3 (v.3.0.0) in callpeak mode with specific parameters. Replicates were merged for visualization and further analysis.
Assembly: hg38 and R64-1-1
Supplementary files format and content: bigwigs: bam files were normalized to the number of million of reads (RPM), saved as bedgraph and converted to bigwig using UCSC BedGraphToBigWig
Supplementary files format and content: peaks: narrow peak files in bed format generated using the MACS3 algorithm to identify open and close chromatin regions
Library strategy: CUT&RUN

extract_protocol:
Cells were permeabilised with NaCl and Triton-X before incubating with indicated antibodies and subsequently with MNase-pAG. Spike-in DNA was added before releasing and purifying the fragments.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7760) with the Multiplex Oligos for Illumina (New England Biolabs, E6440). DNA was amplified with 12 PCR cycles. PCR products were purified and size selected using AMPure XP beads (Beckman Coulter, A63881) ). The quality was checked on a TapeStation 4200 using D1000 HS kit.

tag: cut&run antibody

value: GFP (Takara, 632592)


title: WT 20Hz 1hr Rep5 VC

description: 155 VC

value: VC


title: Plate3_A12

value: plasmacytoid dendritic cell

value: sorted as:day2_pDC_donor 1


title: 3277

value: Whole blood

value: NI


title: WT 20Hz 1hr Rep5 Hip

description: 155 Hip

value: WT


title: Plate3_A11


title: CRAMP1-KO + GFP-CRAMP1-∆SANT cells, CUT&RUN, rep2


title: 2846788

value: male

value: SA


title: WT 20Hz 1hr Rep4 VC

description: 149 VC

value: WT 20Hz 1hr


title: CRAMP1-KO + GFP-CRAMP1-∆SANT cells, CUT&RUN, rep1


title: Plate3_A10


title: 278


title: 3359


title: CRAMP1-KO + GFP-CRAMP1-∆GB-N cells, CUT&RUN, rep3


title: WT 20Hz 1hr Rep4 Hip

description: 149 Hip


title: 3336297


title: 2302349

value: female

value: MIX


title: WT 20Hz 1hr Rep3 Hip

description: 145 Hip

value: Hip


title: Plate3_A09

value: blood


title: Plate3_A08


title: 2168288


title: CRAMP1-KO + GFP-CRAMP1-∆GB-N cells, CUT&RUN, rep2


title: CRAMP1-KO + GFP-CRAMP1-∆GB-N cells, CUT&RUN, rep1


title: 2166


title: WT 20Hz 1hr Rep2 Hip

description: 144 Hip

value: Brain Tissue

value: Male


title: CRAMP1-KO + GFP-CRAMP1 cells, CUT&RUN, rep3


title: Plate3_A06


title: 1434


title: WT 20Hz 1hr Rep1 Hip

description: 141 Hip


title: CRAMP1-KO + GFP-CRAMP1 cells, CUT&RUN, rep1


title: WT 20Hz 1hr Rep2 VC

description: 144 VC


title: Plate3_A07


title: 1104


title: 5xFAD LightHz 1hr Rep6 VC

description: 292 VC

value: 5xFAD LightHz 1hr


title: WT 20Hz 1hr Rep1 VC

description: 141 VC


title: Plate3_A03


title: 1063

value: CoNS


title: CRAMP1-KO cells, ATAC, rep3

data_processing:
Basecalls were performed using bcl2fastq (version 2.20.0)
Reads underwent filtering for adapters and low quality using cutadapt (version 3.4)
Reads were aligned to the human (hg19) genome using bwa-mem (version 0.7.17-r1188).
Duplicate reads were removed with MarkDuplicates (version 3.0.0), and ENCODE hg19 blacklist regions were masked. Only reads with a Phred quality above 30 were retained for subsequent downstream analyses.
To identify accessible chromatin regions, peaks were called using macs3 with specific parameters. Replicates were merged for visualization and further analysis
Assembly: hg19
Supplementary files format and content: bigwigs: bam files were normalized to the number of million of reads (RPM) saved as bedgraph and converted to bigwig using UCSC BedGraphToBigWig
Supplementary files format and content: peaks: peak files in bed format generated using the MACS3 algorithm to identify open and close chromatin regions

extract_protocol:
50 000 cells per condition were collected by centrifugation and lysed using NP-40, Tween-20 and digitonin to isolate nuclei. Nuclei pellets were incubated with transposase for 30 min before stopping the tagmentation reaction.
Libraries were constructed using NEBNext High-Fidelity 2X PCR Master Mix (New Englands Biolabs, M0541S) and ATAC-seq primers (from 2013 PMID: 24097267), and amplified with 7 PCR cycles. DNA was purified and size selected using AMPure XP beads (Beckman Coulter, A63881) ). The quality was checked on a TapeStation 4200 using HS D5000 kits.


title: 5xFAD LightHz 1hr Rep6 Hip

description: 292 Hip


title: 1856


title: CRAMP1-KO + GFP-CRAMP1 cells, CUT&RUN, rep2

value: GFP (Takara, 632592)


title: CRAMP1-KO cells, ATAC, rep2


title: Plate3_A02

value: plasmacytoid dendritic cell


title: 5xFAD LightHz 1hr Rep5 VC

description: 263 VC

value: VC


title: CRAMP1-KO cells, ATAC, rep1


title: 42_D1_Ad26.MVA

city: Oxford

first: Daniel

last: O'Connor

state: Oxfordshire

address: Churchill Hospital

department: Paediatrics

institute: University of Oxford

data_processing:
The sequencing data were aligned against the whole human (Homo sapiens) genome build GRCh38 (https://ccb.jhu.edu/software/hisat2/index.shtml), using STAR (version 2.6.1d). Gene features were counted using HTSeq (version 0.11.1), using human gene annotation general transfer format version GRCh38.92 (www.ensembl.org).  Genes with low counts across most libraries were removed by only retaining genes with abundance greater than 3 counts per million in 4 or more samples. Ribosomal RNA (rRNA), sex chromosome genes, mitochondrial RNA and haemoglobin genes were excluded from downstream analysis.
Assembly: human (Homo sapiens) genome build GRCh38 (
Supplementary files format and content: The expression E value is the gene expression value derived from the voom‐limma workflow

extract_protocol:
Venous peripheral blood (up to 3ml) was collected directly in TempusTM RNA tube immediately pre-vaccination, then 10 days post-first vaccine and 7 days post-second vaccine. RNA was extractedusing theTempus™spin RNAisolationkit(Invitrogen, USA).Eluted RNA was quantifiedusingQubit™ RNA BR Assay Kit(Invitrogen, USA) and quality control was conducted usingthe Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent, USA). RNA was ribodepleted and globin depleted usingRibo-ZeroTM Gold rRNA removal Kit (Illumina, USA).
RNA was converted to cDNA, second-strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated and prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and quality controlled before 75bp paired-end sequencing (HiSeq4000). Sequencing was conducted at the Wellcome Trust Centre for Human Genetics (Oxford, UK).

value: Whole blood

value: blood cells

tag: visit


title: 42_D36_Ad26.MVA

tag: tissue


title: 5xFAD LightHz 1hr Rep5 Hip

description: 263 Hip


title: WT cells, ATAC, rep3

value: WT


title: Plate3_A05

tag: cell type

value: sorted as:day2_pDC_donor 1


title: Plate2_D12

value: sorted as:day2_icDC2_donor 1


title: 42_D11_Ad26.MVA


title: Plate3_A04


title: 5xFAD LightHz 1hr Rep4 VC

description: 228 VC

tag: genotype


title: Plate2_D11

tag: treatment


title: 41_D36_Ad26.MVA


title: 5xFAD LightHz 1hr Rep4 Hip

description: 228 Hip


title: Plate2_D10


title: WT cells, ATAC, rep1

tag: cell line


title: 41_D1_Ad26.MVA


title: 5xFAD LightHz 1hr Rep3 VC

description: 146 VC


title: Plate2_D08


title: Plate2_D09


title: 5xFAD LightHz 1hr Rep2 VC

description: 128 VC


title: Plate2_D07


title: 5xFAD LightHz 1hr Rep3 Hip

description: 146 Hip


title: 41_D11_Ad26.MVA


title: Plate3_A01


title: 40_D1_Ad26

value: Female


title: 5xFAD LightHz 1hr Rep2 Hip

description: 128 Hip


title: 40_D11_Ad26


title: Plate2_D06


title: Plate2_D05


title: 40_D36_Ad26


title: 39_D11_Ad26.MVA


title: 5xFAD 40Hz 4hr Rep7 VC

description: 253 VC

value: 5xFAD 40Hz 4hr


title: 5xFAD LightHz 1hr Rep1 Hip

description: 123 Hip


title: 39_D1_Ad26.MVA


title: Plate2_D03


title: WT cells, ATAC, rep2


title: Plate2_D04


title: 39_D36_Ad26.MVA


title: 5xFAD 40Hz 4hr Rep7 Hip

description: 253 Hip


title: Plate2_D02


title: 38_D1_Ad26.MVA


title: Plate2_D01


title: 38_D11_Ad26.MVA


title: Plate2_C12

value: sorted as:day2_itDC_donor 1


title: 5xFAD 40Hz 4hr Rep6 Hip

description: 239 Hip

value: Hip


title: 38_D36_Ad26.MVA


title: Plate2_C10

value: blood


title: Plate2_C11


title: 5xFAD 40Hz 4hr Rep5 Hip

description: 229 Hip

value: Brain Tissue


title: 5xFAD 40Hz 4hr Rep5 VC

description: 229 VC

value: Male


title: 5xFAD 40Hz 4hr Rep4 VC

description: 140 VC


title: 37_D1_Ad26.MVA


title: 5xFAD LightHz 1hr Rep1 VC

description: 123 VC

value: 5xFAD LightHz 1hr


title: 37_D36_Ad26.MVA


title: 37_D11_Ad26.MVA


title: Plate2_C08


title: Plate2_C09


title: 36_D1_Ad26.MVA


title: Plate2_C07


title: Monocytes, 1,25D+LPS, non-primed, RNA replicate 2

city: Olsztyn

first: Mariusz

last: Jankowski

address: Trylińskiego

country: Poland

institute: Institute of Animal Reproduction and Food Research

description: Library name: DL-np_RNA_R2

data_processing:
RNA-seq: Single-end reads were aligned using STAR aligner. Read quantification performed with FeatureCounts (version 2.0.6) with settings for reverse-strand.
Assembly: GRCh38.p13
Supplementary files format and content: Gene_count_matrix.csv - raw gene counts matrix with counts of protein coding genes with an expression level > 0.5 CPM, without mitochondrially encoded genes and genes missing HGNC symbols

source_name: peripheral blood

extract_protocol:
RNA-seq: cells were preserved in TRIzol (1 ml per 5 × 10⁶ cells; Zymo Research) at -80 °C overnight before RNA extraction. Total RNA was isolated using the High Pure RNA Isolation Kit (Roche) with minor modifications. Chloroform (1:5 ratio) was added to thawed TRIzol samples to induce phase separation. Phase-lock gel heavy tubes (5Prime) were used to efficiently separate proteins into the organic phase, DNA at the interface, and RNA in the aqueous phase. RNA quality and quantity were assessed using a Bioanalyzer (Agilent 2100; RNA Nano 6000 Assay), ensuring a RIN (RNA integrity number) > 8. Ribosomal RNA (rRNA) was depleted using the NEBNext rRNA Depletion Kit, and complementary DNA (cDNA) libraries were prepared from the rRNA-depleted RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, following the manufacturer’s protocol. Library quality was confirmed using the Agilent DNA 1000 Chip, and indexed libraries were pooled prior to sequencing.
RNA-seq libraries were sequenced on an Illumina NextSeq500 system (Illumina) at 75 bp read length using standard protocols at the Gene Core facility of the EMBL (Heidelberg, Germany).

treatment_protocol: Cells treated with either 10 nM 1,25(OH)2D3 or 100 ng/ml LPS (both from Sigma-Aldrich), or with the respective vehicle controls (0.1% ethanol [EtOH] or 0.1% dimethyl sulfoxide [DMSO]).

value: peripheral blood

value: monocytes


title: 5xFAD 40Hz 4hr Rep6 VC

description: 239 VC


title: Plate2_C06

value: plasmacytoid dendritic cell


title: 5xFAD 40Hz 4hr Rep4 Hip

description: 140 Hip


title: 5xFAD 40Hz 4hr Rep3 VC

description: 139 VC

value: VC


title: Monocytes, 1,25D+LPS, LPS-primed, RNA replicate 2

description: Library name: DL-Lp_RNA_R2


title: 36_D11_Ad26.MVA

value: Whole blood


title: 5xFAD 40Hz 4hr Rep2 VC

description: 137 VC


title: Plate2_C05


title: 5xFAD 40Hz 4hr Rep3 Hip

description: 139 Hip


title: 36_D92_Ad26.MVA

value: blood cells


title: 35_D64_Ad26.MVA


title: Plate2_C04


title: 5xFAD 40Hz 4hr Rep1 VC

description: 114 VC


title: 35_D11_Ad26.MVA


title: 5xFAD 40Hz 4hr Rep2 Hip

description: 137 Hip


title: Monocytes, 1,25D+LPS, 1,25D-primed, RNA replicate 3

description: Library name: DL-Dp_RNA_R3


title: Monocytes, 1,25D+LPS, LPS-primed, RNA replicate 1

description: Library name: DL-Lp_RNA_R1


title: 35_D1_Ad26.MVA


title: 5xFAD 40Hz 4hr Rep1 Hip

description: 114 Hip


title: Plate2_C02


title: Plate2_C03


title: 34_D1_Ad26.MVA


title: 5xFAD 40Hz 1hr Rep13 VC

description: 526 VC

value: 5xFAD 40Hz 1hr


title: Monocytes, 1,25D+LPS, 1,25D-primed, RNA replicate 1

description: Library name: DL-Dp_RNA_R1


title: Monocytes, 1,25D+LPS, non-primed, RNA replicate 1

description: Library name: DL-np_RNA_R1


title: Plate2_C01


title: 5xFAD 40Hz 1hr Rep13 Hip

description: 526 Hip


title: Monocytes, LPS, non-primed, RNA replicate 2

description: Library name: L-np_RNA_R2

value: LPS


title: 34_D36_Ad26.MVA


title: Plate2_B12

value: sorted as:day2_pDC_donor 1


title: Plate2_B11


title: Monocytes, LPS, non-primed, RNA replicate 1

description: Library name: L-np_RNA_R1


title: 5xFAD 40Hz 1hr Rep12 VC

description: 518 VC


title: 34_D11_Ad26.MVA


title: 5xFAD 40Hz 1hr Rep12 Hip

description: 518 Hip


title: Monocytes, LPS, LPS-primed, RNA replicate 3

description: Library name: L-Lp_RNA_R3


title: Plate2_B10


title: 33_D92_Placebo.Placebo

value: Female


title: 5xFAD 40Hz 1hr Rep11 VC

description: 5 VC


title: Plate2_B09


title: Monocytes, 1,25D+LPS, 1,25D-primed, RNA replicate 2

description: Library name: DL-Dp_RNA_R2


title: 33_D1_Placebo.Placebo


title: Plate2_B08


title: 5xFAD 40Hz 1hr Rep11 Hip

description: 5 Hip


title: Monocytes, LPS, 1,25D-primed, RNA replicate 3

description: Library name: L-Dp_RNA_R3


title: 32_D92_Ad26.MVA


title: Monocytes, LPS, 1,25D-primed, RNA replicate 2

description: Library name: L-Dp_RNA_R2


title: 32_D11_Ad26.MVA


title: 5xFAD 40Hz 1hr Rep10 Hip

description: 4 Hip


title: 5xFAD 40Hz 1hr Rep10 VC

description: 4 VC


title: Monocytes, LPS, 1,25D-primed, RNA replicate 1

description: Library name: L-Dp_RNA_R1


title: Plate2_B06


title: Monocytes, 1,25D, non-primed, RNA replicate 3

description: Library name: D-np_RNA_R3


title: 32_D1_Ad26.MVA


title: 33_D11_Placebo.Placebo


title: 5xFAD 40Hz 1hr Rep9 VC

description: 3 VC


title: 31_D1_Ad26.MVA


title: Plate2_B05


title: 5xFAD 40Hz 1hr Rep8 VC

description: 298 VC


title: 5xFAD 40Hz 1hr Rep9 Hip

description: 3 Hip


title: Monocytes, 1,25D, non-primed, RNA replicate 2

description: Library name: D-np_RNA_R2


title: Monocytes, 1,25D, non-primed, RNA replicate 1

description: Library name: D-np_RNA_R1


title: Monocytes, LPS, LPS-primed, RNA replicate 2

description: Library name: L-Lp_RNA_R2


title: 31_D11_Ad26.MVA


title: Plate2_B03


title: 31_D92_Ad26.MVA


title: 5xFAD 40Hz 1hr Rep8 Hip

description: 298 Hip


title: Plate2_B07


title: Monocytes, 1,25D, LPS-primed, RNA replicate 2

description: Library name: D-Lp_RNA_R2


title: 30_D36_Ad26.MVA


title: Monocytes, 1,25D, LPS-primed, RNA replicate 3

description: Library name: D-Lp_RNA_R3


title: Plate2_B01


title: Plate2_B02


title: 5xFAD 40Hz 1hr Rep7 Hip

description: 295 Hip


title: 30_D11_Ad26.MVA


title: Monocytes, 1,25D, LPS-primed, RNA replicate 1

description: Library name: D-Lp_RNA_R1


title: Plate2_A12


title: 5xFAD 40Hz 1hr Rep6 Hip

description: 282 Hip


title: Monocytes, 1,25D, 1,25D-primed, RNA replicate 3

description: Library name: D-Dp_RNA_R3


title: 30_D1_Ad26.MVA


title: Plate2_B04


title: Plate2_A11


title: Monocytes, 1,25D, 1,25D-primed, RNA replicate 1

description: Library name: D-Dp_RNA_R1


title: 5xFAD 40Hz 1hr Rep5  VC

description: 264 VC


title: Plate2_A10


title: 29_D64_Ad26.MVA


title: Plate2_A09


title: Monocytes, solvent, 24 hours, RNA replicate 3

description: Library name: Solvent_24_RNA_R3

value: control


title: Plate2_A08


title: 5xFAD 40Hz 1hr Rep7 VC

description: 295 VC


title: 28_D11_Ad26.MVA


title: 5xFAD 40Hz 1hr Rep5 Hip

description: 264 Hip


title: 29_D1_Ad26.MVA


title: 5xFAD 40Hz 1hr Rep4 VC

description: 258 VC


title: Monocytes, solvent, 24 hours, RNA replicate 2

description: Library name: Solvent_24_RNA_R2


title: Plate2_A07


title: 5xFAD 40Hz 1hr Rep4 Hip

description: 258 Hip


title: Monocytes, solvent, 48 hours, RNA replicate 3

description: Library name: Solvent_48_RNA_R3


title: 29_D11_Ad26.MVA


title: 28_D64_Ad26.MVA


title: 27_D64_Ad26.MVA


title: 5xFAD 40Hz 1hr Rep3 Hip

description: 241 Hip


title: Monocytes, 1,25D, 1,25D-primed, RNA replicate 2

description: Library name: D-Dp_RNA_R2


title: Monocytes, solvent, 48 hours, RNA replicate 1

description: Library name: Solvent_48_RNA_R1


title: Plate2_A06


title: 5xFAD 40Hz 1hr Rep6 VC

description: 282 VC