title: Wfdc21KO total lung cells, SeV d49

city: Saint Louis

first: Michael

last: Holtzman

address: 425 S Euclid Avenue

institute: Washington University in Saint Louis

description: 10x genomics

data_processing:
RNAseq was using a NovaSeq 6000 with S4 flow cell. Gene and transcript levels were quantified using the RSEM (version 1.3.2) pipeline, and the estimated counts were stored as the appropriate raw data to feed into the edgeR (version 3.24.3), limma (version 3.38.3), and voom (version 3.38.3) pipeline. The list of Ensemble gene ids was annotated by the biomaRt (version 2.38.0), which queried BioMart databases to retrieve additional information including entrezgene identifiers for gene symbol and chromosome. A DGEList appropriate for our data was declared, and filterByExpr function in edgeR was used to maintain 35% of the genes in the gene list by filtering out lowly expressed genes automatically and in a principled way. The data were then normalized to account for variability in sequencing depth, library size, and other external factors that are not of biological interest. After TMM normalization, unsupervised heirarchical clustering with the hclust function in base R (version 3.5.3) and principal component analysis with the prcomp function were conducted to identified treatment and control clusters. The correlations between replicate samples were also examined, with the lowest value of 0.94. We invoked voom software to compute precision weights and fitted linear models to the data using the lmFit function. Then, we refitted the model using the contrasts.fit function and computed moderated t- and F- statistics using the eBayes and treat functions, respectively. We chose the outputs from treat function for a more stringent definition of statistical significance to test against a fold change threshold. Two heatmaps were generated with heatmap.2 function in gplots (version 3.1.0), based on subsets of the top 100 most significant genes sorted separately by the F-statistic and fold change. We also generated scatter plots with ggplot2 (version 3.3.2) with the top genes ranked by fold change labelled of our interest.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Total lung

extract_protocol:
Total lung RNA
Lung tissue RNA was purified as described previously 11 from three mice per sample condition (12 or 21 d after SeV infection or PBS control challenge) and subjected to RNAseq using a NovaSeq 6000 with S4 flow cell (Illumina, San Diego, CA) in the Genome Technology Access Center in the McDonnell Genome Institute (Washington University, St. Louis). RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Total lung

value: SeV

tag: time point


title: ASP_TFE_P53_1

status: Public on Apr 11 2025

type: SRA

city: Heidelberg

first: Ana

last: Banito

address: Im Neuenheimer Feld 581

country: Germany

institute: KiTZ, DKFZ

library_source: transcriptomic

data_processing:
Sequencing was carried out on Illumina’s NovaSeq 6000 S1 or S4 flow cell with paired-end 50 bp reads, yielding an average of approximately 20 million reads per sample
Sequencing reads were aligned to the mouse reference genome (GRCm38mm10) by DKFZ’s Omics IT and Data Management Core Facility (ODCF) using the One Touch Pipeline (OTP)264 / RNAseq workflow pipeline, version 1.3.0 (STAR Version 2.5.3a, Merging/duplication marking program: Sambamba Version 0.6.5. SAMtools program: Version 1.6.), resulting in raw counts, RPKM, and TPM values.
Assembly: GRCm38mm10
Supplementary files format and content: TPM counts for all samples.txt

molecule: total RNA

organism: Mus musculus

source_name: Tumor

extract_protocol:
DNA and RNA were extracted from the same tumor tissue piece, approximately 20-30 mg in weight, using Qiagen’s DNA/RNA AllPrep kit (80204) following the manufacturer’s protocol.
Only samples with RNA integrity scores (RIN) exceeding 7 proceeded to library preparation using the TruSeq Stranded total mRNA protocol, starting with 50 μl of undegraded RNA at concentrations ranging from 50 to 80 ng/μl per sample.

tag: tissue

value: Tumor

tag: cell line

value: EPO P30

tag: genotype

value: ASPSCR1-TFE3, sgp53


title: Nf1_p53_5_SAM_3D

type: genomic

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing:
IDAT files were obtained and processed using the R package sesame, version 1.16.1 (SEnsible Step-wise Analysis of DNA MEthylation BeadChips)(Zhou et al., 2018) to generate normalized beta values. Probe intensities underwent background correction using the p-value with the out-of-band array hybridization approach, followed by a normal-exponential out-of-band approach. Dye bias correction was performed by aligning green and red to the midpoint using the dyeBiasCorrTypeINorm method in sesame. Probes targeting the X and Y chromosomes were excluded. Clustering analysis was performed with R packages Rtsne and umap based on the 2,000 or 10,000 most variably methylated probes, with perplexity values set to 5 for tSNE and 15 for umap clustering.
Average Beta values

molecule: genomic DNA

source_name: MPNST (Nf1_P53)

label_protocol: Illumina protocol

extract_protocol: A minimum of 500ng of genomic DNA extracted from frozen tissue was submitted per sample. DNA quality was ensured by digital gel electrophoresis (Agilent, G2939BA).

tag: gender

value: F

tag: location

value: Thigh

tag: type of gemm

value: EPO-GEMM

value: SAM 3D P6


title: 4h_IFNalpha_R1

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps-Universität Marburg

description: Lexogen Quantseq

data_processing:
CLC Genomics Workbench v 10.0.1
Sequence reads were trimmed using the CLC workbench with quality score limit set to 0.05 and 25 nt minimal read length
Trimmed sequences were mapped to the GRCh38 human reference genome using the CLC workbench with the following parameters: Mismatch cost: 2. Insertion cost: 3. Deletion cost: 3. Length fraction: 0.8. Similarity fraction: 0.8. Max. hits for a read: 10. Strand specific: both.
Normalized expression values (e.g. RPKM) were calculated based on the read counts obtained from the CLC genomics workbench analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file, including gene identifiers and coordinates, read counts and RPKM values for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

growth_protocol: AEC II cells were cultured on ThinCert™ transwells in SAGM medium (Lonza), supplemented with 2% FCS. Primary macrophages were cultured in X-Vivo-15 medium (Lonza), supplemented with 5 % FCS.  THP1 cells were cultivated in RPMI Glutamax medium, supplemented with 5 % FCS. All cells were cultured at 37 °C with humidified 5% CO2 atmosphere.

extract_protocol:
RNA was extracted with Trizol reagent and DNaseI-treated, using established protocols. PolyA RNA was selected using magnetic beads.
Libraries were generated using the TruSeq Stranded mRNA Kit (Illumina) or the QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen), as indicated.

treatment_protocol:
Blood-derived monocytes (CD14 MACS purification) were differentiated into macrophages using 15 ng / ml recombinant GM-CSF or M-CSF for 7 days. THP1 cells were differentiated with PMA (20 nM) for two days.
Upon differentiation / attachment, cells were treated with different immune-stimuli at the following concentrations: Flagellin: 1 µg / ml. LPS: 100 ng / ml. Pam3csk4: 200 ng / ml. IFNalpha: 100 ng / ml.
For inhibitor experiments, cells were pre-treated with for 2 hours as follows, prior to further stimulations: - (DMSO only as solvent control). BAY 11-7082: 5 or 10 µM. Ruxolitinib: 1 or 5 µM, BX795: 1 or 5 µM

value: blood

tag: cell type

value: blood-derivedmacrophage

tag: source

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: WT

tag: treatment

value: IFNalpha

tag: time

value: 4 h


title: Nf1_p53_5_SAM_2D

value: SAM 2D P6


title: AAV genomes – CMV promoter

city: Salt Lake City

first: Justin

middle: G

last: English

state: UT

address: 15 N Medical Drive East RM 4100

department: Biochemistry

country: USA

institute: University of Utah

description: Library name: Sample 34

library_source: other

data_processing:
Basecalling of raw nanopore trace files was performed after sequencing with Guppy or during sequencing with MinKNOW software. In both cases, the ‘super accuracy’ basecalling algorithm was utilized. Default software read quality thresholds were maintained throughout.
Basecalled reads in fastq format were processed into bins by our ConSeqUMI according to unique 5’ and 3’ sequence tags. Each bin was exported as a single fastq file containing all basecalled reads belonging to the bin.
ConSeqUMI was then used to derive a consensus sequence for each individual bin based on constituent sequences therein.
Assembly: GRCh38/hg38 (Ded. 2013)
Supplementary files format and content: FASTA files contain consensus sequences generated by ConSeqUMI

molecule: other

organism: mixed DNA library

source_name: Input

growth_protocol: 293 cells were maintained in DMEM supplemented with 10% FBS and 200 ug/mL Geneticin.

extract_protocol:
Target amplicons were purified after polymerase chain reactions using gel extraction or column purification.
Sequencing libraries were prepared using Native Ligation kits and protocols developed by Oxford Nanopore Technologies according to their instructions.

value: Input


title: Nf1_p53_5_SAM_fragments

value: SAM primary fragments


title: DPTP -  200 uM

description: Library name: Sample 33

value: 200 uM dPTP


title: Wfdc21KO total lung cells, SeV d21

description: 10x genomics

library_source: transcriptomic single cell

value: Total lung

value: SeV


title: Wfdc21KO total lung cells, SeV d12

description: 10x genomics


title: 4h_LPS_R1

description: Lexogen Quantseq

value: LPS


title: DPTP -  80 uM

description: Library name: Sample 32

value: 80 uM dPTP


title: Nf1_p53_5

value: F

value: Thigh


title: Nf1_p53_5_SAM_cells

value: EPO-GEMM

value: SAM primary cells


title: 2h_IFNalpha_R1

description: Lexogen Quantseq

value: blood

value: blood-derivedmacrophage

value: 2 h


title: Wfdc21KO total lung cells, PBS

description: 10x genomics

value: PBS


title: 10h_LPS_R1

description: Lexogen Quantseq

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: WT


title: 8h_LPS_R1

description: Lexogen Quantseq

value: 8 h


title: DPTP -  16 uM

description: Library name: Sample 31

value: Input

value: 16 uM dPTP


title: AAV genomes – EF1a promoter

description: Library name: Sample 35


title: DPTP -  3.2 uM

description: Library name: Sample 30

value: 3.2 uM dPTP


title: WT total lung cells, SeV d21

description: 10x genomics

value: Total lung

value: SeV


title: 2h_Pam3csk4_R1

description: Lexogen Quantseq


title: Kras_p53_5_2D

source_name: eRMS (KrasG12V-P53)

value: M

value: 2D cell line


title: 2h_LPS_R1

description: Lexogen Quantseq

value: LPS


title: WT total lung cells, SeV d12

description: 10x genomics


title: 1h_LPS_R1

description: Lexogen Quantseq

value: 1 h


title: 4h_Pam3csk4_R1

description: Lexogen Quantseq

value: 4 h


title: Kras_p53_5_SAM_3D

value: Thigh

value: EPO-GEMM

value: SAM 3D P6


title: Kras_p53_5_SAM_2D

value: SAM 2D P6


title: WT total lung cells, PBS

description: 10x genomics

value: PBS


title: DPTP -  0 uM

description: Library name: Sample 27

value: 0 uM dPTP


title: DPTP -  0.128 uM

description: Library name: Sample 28

value: 0.128 uM dPTP


title: 0.5h_Ctrl_R1

description: Lexogen Quantseq

value: blood

value: blood-derivedmacrophage

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days

value: WT

value: control


title: 0.5h_LPS_R1

description: Lexogen Quantseq


title: Kras_p53_5_SAM_fragments

value: M

value: SAM primary fragments


title: SuperFi – PCR round 3

description: Library name: Sample 25

value: Input


title: SuperFi – PCR round 2

description: Library name: Sample 24


title: Kras_p53_5_3D

value: 3D cell line


title: LINC01268_ChIRP

description: Vertis gDNA-seq

library_source: genomic

data_processing:
CLC Genomics Workbench v 10.0.1
Sequence reads were trimmed using the CLC workbench with quality score limit set to 0.05 and 25 nt minimal read length
Trimmed sequences were mapped to the GRCh38 human reference genome using the CLC workbench with the following parameters: Mismatch cost: 2. Insertion cost: 3. Deletion cost: 3. Length fraction: 0.8. Similarity fraction: 0.8. Max. hits for a read: 10. Strand specific: both.
Peak calling was done using the CLC Genomics workbench, with the control ChIRP dataset as a background control, minimum peak length = 300 bases and p-value cutoff at 0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file, including chromosomal coordinates, peak shape score and p-value and nearby gene information.

growth_protocol: THP1 cells were differentiated with PMA (20 nM) for two days.

extract_protocol:
Genomic DNA was isolated using a ChIRP-seq anti-sense affinity purification protocol, with an oligo pool binding LINC01268 RNA or a control oligo pool.
Libraries were generated using a ChIP-seq library generation protocol (Vertis Biotech AG).

treatment_protocol: Upon differentiation, cells were treated with LPS (100 ng / ml) for 8 h.

value: monocytic

value: ATTC TIB-202; PMA-differentiated

value: LPS

value: 8 h


title: Kras_p53_5_SAM_cells

value: Thigh

value: EPO-GEMM

value: SAM primary cells


title: WT total lung cells, SeV d49

description: 10x genomics

value: Total lung

value: SeV


title: A6

city: San Francisco

first: Karishma

middle: Joanne Bhatia

last: Pratt

state: CA

address: 513 Parnassus Ave, Med. Sci. Bldg, Room S1364

institute: UCSF

data_processing:
sequencing reads were trimmed and checked for QC using STAR
reads were mapped and aligned using kallisto
downstream differential gene expression analysis was performed using DESeq2
Assembly: mm10 with introns included
Supplementary files format and content: excel file

source_name: MEC brain

extract_protocol:
RNA was extracted using TriZol/chloroform.
RNA seq libraries were prepared using SmartSeq library manufacturer instructions.

value: MEC brain

value: neuronal nuclei

value: aged


title: A7


title: A12


title: Ctrl_ChIRP

description: Vertis gDNA-seq

value: blood

value: WT


title: Kras_p53_5

value: M


title: DPTP -  0.64 uM

description: Library name: Sample 29

value: Input

value: 0.64 uM dPTP


title: E10.5 otic vesice, rep4

city: Ann Arbor

first: Robert

middle: K

last: Duncan

state: MI

address: 1150 W Medical Center Dr, 5315D Med Sci I

department: Otolaryngology - Head & Neck Surgery

institute: University of Michigan

description:
Library name: Sample_85617
Column name in raw_counts_HTSeq_all_samples: E10-4

data_processing:
Sequence reads were trimmed for adaptors and low-quality using Trim Galore! (v0.4.3.1) and Cutadapt (v1.14), removing reads shorter than 20bp and Phred scores below 20 (about 0.6% of reads).
Reads aligned to GrCM38/mm10 with HISAT2 (v2.0.5.2). Each sample was originally split across two lanes, so BAM files merged in Galaxy Merge BAM Files (v1.2.0).
Raw counts were determined with HTSeq Count (v0.6.1)
Raw counts were normalized for differential expression aanlysis with DESeq2 (v2.11.39)
Gene ontology enrichment was assessed on HTSeq counts with iPathway Guide .
Assembly: mm10
Supplementary files format and content: Comma-delimited text file contains raw counts for all samples
Supplementary files format and content: Tab-delimited text files with normalized counts from DESeq2 for each sample

source_name: Native Otic Vesicle

growth_protocol: R1/E mouse embryonic stem cells were maintained in 1:1 Advanced DMEM/F12 and Neurobasal media with 0.5X B-27 without vitamin A, 1X N-2, and 1X GlutaMAX with 1000 U/mL LIF, 1 µM PD0325901, and 3 µM CHIR99021, passaged at 60-80% confluence with TrypLE.

extract_protocol:
Isolated otic vesicles from mouse embryos (2-6 pooled per sample) and organoid cultures (30-50 pooled per sample) were placed in RLT Buffer (Qiagen) and stored at -80°C until total RNA was extracted using RNeasy Mini Kits (Qiagen). RNA quality was evaluated on Agilent 2200 TapeStation before library construction.
RNA libraries for RNASeq were prepared using TruSeq LT RNA Sample Prep Kit 2 (Illumina).

treatment_protocol: To derive otic vesicles in organoid cultures, R1/E mouse embryonic stem cells were aggregated into a spheroid in GMEM, 1.5% KnockOut serum replacement, 15 mM HEPES, 1X non-essential amino acids, 1mM sodium pyruvate, and 0.1 mM β-mercaptoethanol. On day-in-vitro 1 (D1), growth-factor reduced Matrigel was added (2% final). On D3, BMP4 (10 ng/ml) and the TGFβ inhibitor SB431542 (1 µM) were added to BSFL samples; the TGFβ inhibitor was omitted in BFL samples. On D4.5 the BMP inhibitor LDN193189 (1 µM) and FGF2 (100 ng/ml) were added. On D8, aggregates were trasferred to maturation media (Advanced DMEM/F12, 1X N-2, 15 mM HEPES, 1X GlutaMAX) with 1% growth-factor reduced Matrigel and 3 µM CHIR99021. Half volume was exchanged with fresh maturation media on D10 and D11 before harvesting aggregates for isolating otic vesicles on D12.

value: Native Otic Vesicle


title: SuperFi – PCR round 1

description: Library name: Sample 23


title: NTRK_p53_1_3D

source_name: P53-dominated IFS (ETV6-NTRK3_P53)

value: 3D cell line


title: A5


title: E10.5 otic vesice, rep3

description:
Library name: Sample_85616
Column name in raw_counts_HTSeq_all_samples: E10-3


title: SuperFi – parent plasmid

description: Library name: Sample 22


title: NTRK_p53_1_2D

value: 2D cell line


title: A4


title: E10.5 otic vesice, rep2

description:
Library name: Sample_85615
Column name in raw_counts_HTSeq_all_samples: E10-2


title: NTRK_p53_1_SAM_3D

value: SAM 3D P6


title: A13


title: PrimeSTAR – PCR round 4

description: Library name: Sample 21


title: NTRK_p53_1_SAM_2D

value: Thigh

value: SAM 2D P6


title: PrimeSTAR – PCR round 3

description: Library name: Sample 20


title: A3


title: SuperFi – PCR round 4

description: Library name: Sample 26


title: E10.5 otic vesice, rep1

description:
Library name: Sample_85614
Column name in raw_counts_HTSeq_all_samples: E10-1


title: PrimeSTAR – PCR round 2

description: Library name: Sample 19


title: Y19

value: young


title: NTRK_p53_1_SAM_fragments

value: EPO-GEMM

value: SAM primary fragments


title: D12 inner ear organoid culture, otic vesicle, TGFβ inhibition on D3, BSFL rep 3

description:
Library name: Sample_85613
Column name in raw_counts_HTSeq_all_samples: BSFL3

source_name: Derived Otic Vesicle

value: Derived Otic Vesicle

value: Differentiated ESC


title: Y18

value: MEC brain

value: neuronal nuclei


title: PrimeSTAR – PCR round 1

description: Library name: Sample 18


title: D12 inner ear organoid culture, otic vesicle, TGFβ inhibition on D3, BSFL rep 2

description:
Library name: Sample_85612
Column name in raw_counts_HTSeq_all_samples: BSFL2


title: NTRK_p53_1_SAM_cells

value: SAM primary cells


title: NTRK_p53_1

value: M


title: Y16


title: D12 inner ear organoid culture, otic vesicle, TGFβ inhibition on D3, BSFL rep 1

description:
Library name: Sample_85611
Column name in raw_counts_HTSeq_all_samples: BSFL1


title: Pax-Foxo_P53_1_3D

source_name: aRMS (Pax3-Foxo1)

value: F


title: Longitudinal – week 6

description: Library name: Sample 16

value: Input


title: D12 inner ear organoid culture, otic vesicle, no TGFβ inhibition, BFL rep 4

description:
Library name: Sample_85610
Column name in raw_counts_HTSeq_all_samples: BFL4

value: Vehicle, DMSO (0.1%)


title: PrimeSTAR – parent plasmid

description: Library name: Sample 17


title: Pax-Foxo_P53_1_2D


title: Y11


title: D12 inner ear organoid culture, otic vesicle, no TGFβ inhibition, BFL rep 3

description:
Library name: Sample_85609
Column name in raw_counts_HTSeq_all_samples: BFL3


title: Y3


title: Longitudinal – week 5

description: Library name: Sample 15


title: Y2


title: Kras_p53_6


title: Longitudinal – week 3

description: Library name: Sample 13


title: D12 inner ear organoid culture, otic vesicle, no TGFβ inhibition, BFL rep 2

description:
Library name: Sample_85608
Column name in raw_counts_HTSeq_all_samples: BFL2


title: lgG_2cell_rep2

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

data_processing:
Trimmed sequencing reads were aligned to the reference genome using HISAT2 with no-spliced-alignment and no-temp-splicesite parameters. PCR duplicates were removed using Picard mark duplicates. Peaks were called using MACS2 and annotated using HOMER(Zhang et al., 2008). Differential expression analysis was performed using the DiffBind package(Stark and Brown, 2011). A heatmap was generated using deeptools(Ramírez et al., 2014). Motif enrichment analysis and GREAT analysis were performed using HOMER and GREAT, respectively.
Assembly: mm9
Supplementary files format and content: bigwig file

source_name: embryo

extract_protocol:
A hyperactive in-situ ChIP assay was performed in accordance with manufacturer’s instructions (Vazyme, TD901-01). Briefly, ConA-beads were washed once with binding buffer and incubated with zona pellucida-removed 2-cell embryos. Bead-bound cells were resuspended in antibody buffer containing a primary rabbit monoclonal anti-POLR1 antibody (24799, Cell Signaling Technology) or negative control IgG (sc-2025, Santa Cruz) for 2 h with slow rotation. The primary antibody was removed using a magnet stand. Then, bead-bound cells were incubated in Dig-wash buffer containing a secondary rabbit anti-mouse IgG H&L antibody (ab6709, abcam). Cells were incubated with Hyperactive pA-Tn5 Transposase adapter mix and then resuspended in tagmentation buffer. DNA was purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation, and treated with RNase A. Then, library amplification and PCR product purification were performed.
A hyperactive in-situ ChIP assay was performed in accordance with manufacturer’s instructions (Vazyme, TD901-01). Briefly, ConA-beads were washed once with binding buffer and incubated with zona pellucida-removed 2-cell embryos. Bead-bound cells were resuspended in antibody buffer containing a primary rabbit monoclonal anti-POLR1 antibody (24799, Cell Signaling Technology) or negative control IgG (sc-2025, Santa Cruz) for 2 h with slow rotation. The primary antibody was removed using a magnet stand. Then, bead-bound cells were incubated in Dig-wash buffer containing a secondary rabbit anti-mouse IgG H&L antibody (ab6709, abcam). Cells were incubated with Hyperactive pA-Tn5 Transposase adapter mix and then resuspended in tagmentation buffer. DNA was purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation, and treated with RNase A. Then, library amplification and PCR product purification were performed.

tag: passages

tag: strain

tag: antibody

value: anti-IgG antibody


title: D12 inner ear organoid culture, otic vesicle, no TGFβ inhibition, BFL rep 1

description:
Library name: Sample_85607
Column name in raw_counts_HTSeq_all_samples: BFL1


title: SS18-SSX1_Pten_neo_6

source_name: Synovial Sarcoma


title: SS18-SSX1_Pten_neo_5


title: E7_2 [HTO]

city: Würzburg

first: Milas

last: Ugur

state: Bayern

address: Versbacherstr. 9

department: Institute of Systems Immunology

institute: Universität Würzburg

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.1.
Assembly: mm10-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lymph node

extract_protocol:
Single cell suspensions were generated in 2 % v/v FCS in PBS by mashing fresly isolated lymph nodes, incubated with fluorochrome labelled antibodies for 30 minutes on ice and sorted with a BD FACSAria sorter. After the sorting, cells from the infected and uninfected samples labelled with different hashtag (HTO) antibodies (Uninfected steady state with TotalSeq-A301, infected with TotalSeq-A306, BioLegend).
Library construction was performed according to manufacturer's instructions (Single Cell 3' v3, 10x Genomics). Briefly, single cells were encapsulated into droplets with the ChromiumTM Controller (10x Genomics) and processed following manufacturer’s specifications. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Next GEM Single Cell 3’ Reagent Kit (10x Genomics) following the detailed protocol provided by the manufacturer.

value: lymph node

value: T cell

value: infected and uninfected mixed


title: Longitudinal – week 2

description: Library name: Sample 12


title: Y17


title: E7_2 [GEX]

description: 10X Genomics


title: SS18-SSX1_Pten_neo_4

value: Thigh


title: Foxo1 iKO Spleen P14 CD8+ T cells ADT

city: San Diego

first: John

last: Chang

address: UCSD

institute: UC San Diego

description:
spleen_KO.barcodes.tsv.gz
spleen_KO.features.tsv.gz
spleen_KO.matrix.mtx.gz

data_processing:
Cell Ranger (v6.1.2) was used to process sequencing information and single cell barcodes.
Gene and cell filtering, clustering, differential and average expression using Seurat (v4.1.1)
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: spleen

extract_protocol:
Control and Foxo1 iKO CD8 T cells were harvested by mechanical and enzymatic digestion from spleen, small intestines, and colon at 5 weeks post-infection, FACS purified, and prepared for single-cell libraries
CITE-seq was performed using the TotalSeq-A Antibodies and Cell Hashing with 10x Single Cell 3’ Reagent Kit (Dual Index) (Biolegend).

value: spleen

value: T cells

tag: library type

value: ADT

value: Foxo1 iKO, CD8+

tag: antibodies/tags


title: SS18-SSX1_Pten_neo_3

value: EPO-GEMM


title: Longitudinal – week 1

description: Library name: Sample 11


title: lgG_2cell_rep1

growth_protocol: A hyperactive in-situ ChIP assay was performed in accordance with manufacturer’s instructions (Vazyme, TD901-01). Briefly, ConA-beads were washed once with binding buffer and incubated with zona pellucida-removed 2-cell embryos. Bead-bound cells were resuspended in antibody buffer containing a primary rabbit monoclonal anti-POLR1 antibody (24799, Cell Signaling Technology) or negative control IgG (sc-2025, Santa Cruz) for 2 h with slow rotation. The primary antibody was removed using a magnet stand. Then, bead-bound cells were incubated in Dig-wash buffer containing a secondary rabbit anti-mouse IgG H&L antibody (ab6709, abcam). Cells were incubated with Hyperactive pA-Tn5 Transposase adapter mix and then resuspended in tagmentation buffer. DNA was purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation, and treated with RNase A. Then, library amplification and PCR product purification were performed.


title: Longitudinal – parent plasmid, replicate 2

description: Library name: Sample 10


title: POLR1A_8cell_rep2

treatment_protocol: A hyperactive in-situ ChIP assay was performed in accordance with manufacturer’s instructions (Vazyme, TD901-01). Briefly, ConA-beads were washed once with binding buffer and incubated with zona pellucida-removed 2-cell embryos. Bead-bound cells were resuspended in antibody buffer containing a primary rabbit monoclonal anti-POLR1 antibody (24799, Cell Signaling Technology) or negative control IgG (sc-2025, Santa Cruz) for 2 h with slow rotation. The primary antibody was removed using a magnet stand. Then, bead-bound cells were incubated in Dig-wash buffer containing a secondary rabbit anti-mouse IgG H&L antibody (ab6709, abcam). Cells were incubated with Hyperactive pA-Tn5 Transposase adapter mix and then resuspended in tagmentation buffer. DNA was purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation, and treated with RNase A. Then, library amplification and PCR product purification were performed.

value: anti-PLOR1A antibody from CST, Catalog number:24799


title: Longitudinal – parent plasmid, replicate 1

description: Library name: Sample 9


title: Foxo1 iKO Spleen P14 CD8+ T cells RNA

value: RNA


title: SS18-SSX1_Pten_neo_2


title: Control Spleen P14 CD8+ T cells RNA

description:
spleen_WT.barcodes.tsv.gz
spleen_WT.features.tsv.gz
spleen_WT.matrix.mtx.gz


title: Control Spleen P14 CD8+ T cells ADT


title: POLR1A_8cell_rep1


title: POLR1A_2cell_late_rep2


title: Plasmid pool, 10^5 input molecules, replicate 3

description: Library name: Sample 8


title: Longitudinal – week 4

description: Library name: Sample 14


title: SS18-SSX1_Pten_neo_1


title: Plasmid pool, 10^6 input molecules, replicate 3

description: Library name: Sample 7


title: Foxo1 iKO siLPL P14 CD8+ T cells ADT

description:
siLPL_KO.barcodes.tsv.gz
siLPL_KO.features.tsv.gz
siLPL_KO.matrix.mtx.gz

source_name: small intestinal lamina propria

value: small intestinal lamina propria


title: Plasmid pool, 10^5 input molecules, replicate 2

description: Library name: Sample 6


title: POLR1A_2cell_early_rep3


title: NTRK_p53_neo_5


title: Foxo1 iKO siLPL P14 CD8+ T cells RNA


title: NTRK_p53_neo_6

value: M


title: NTRK_p53_neo_4

source_name: Fusion-dominated IFS (ETV6-NTRK3_P53)

value: F


title: POLR1A_2cell_early_rep2


title: Control siLPL P14 CD8+ T cells ADT

description:
siLPL_WT.barcodes.tsv.gz
siLPL_WT.features.tsv.gz
siLPL_WT.matrix.mtx.gz


title: POLR1A_2cell_early_rep1


title: POLR1A_2cell_cx5461_rep2


title: Plasmid pool, 10^6 input molecules, replicate 2

description: Library name: Sample 5

value: Input


title: Plasmid pool, 10^6 input molecules, replicate 1

description: Library name: Sample 3


title: NTRK_p53_neo_3


title: NTRK_p53_neo_2


title: Foxo1 iKO siIEL P14 CD8+ T cells ADT

description:
siIEL_KO.barcodes.tsv.gz
siIEL_KO.features.tsv.gz
siIEL_KO.matrix.mtx.gz

source_name: small intestinal intraepithelial

value: small intestinal intraepithelial


title: Plasmid pool, 10^5 input molecules, replicate 1

description: Library name: Sample 4


title: Foxo1 iKO siIEL P14 CD8+ T cells RNA


title: POLR1A_1cell_rep2


title: NTRK_p53_neo_1


title: NTRK_p53_6


title: POLR1A_2cell_cx5461_rep1


title: Barcoded amplicon, 10^5 input molecules

description: Library name: Sample 2


title: Barcoded amplicon, 10^6 input molecules

description: Library name: Sample 1


title: POLR1A_2cell_late_rep1


title: POLR1A_1cell_rep1


title: Control siIEL P14 CD8+ T cells RNA

description:
siIEL_WT.barcodes.tsv.gz
siIEL_WT.features.tsv.gz
siIEL_WT.matrix.mtx.gz


title: NTRK_p53_5


title: Control siLPL P14 CD8+ T cells RNA


title: NTRK_p53_4


title: reCRAC N-FH Pin4, stress, Rep3

city: Edinburgh

first: Michaela

last: Ristova

address: Old College, South Bridge

country: United Kingdom

institute: University of Edinburgh

description: Library name: Sample 12

data_processing:
reCRAC: pyBarcodeFilter - demultiplexing, Flexbar- adapter trimming and quality filtering (--removal-tags -at RIGHT -ao 4 -u 3 -m 7 -n 16 -t) , pyFastqDuplicateRemover.py - PCR duplicates removal, Novoalign (V2.07.00) - alignment to the reference genome (SGD v64) with  genome annotation from Ensembl (EF4.74) applying the Random -r method, pyReadCounters.py - read counting using Ensembl GTF version EF4.74
RNAseq: The paired-end Illumina RNA-seq data were first pre-processed using Flexbar to trim low quality bases and adapters from raw reads. The specific parameters set for Flexbar included quality filtering of tail bases with a quality threshold of 30 (Sanger scale), adapter removal with a minimum overlap of four bases, and discarding of reads shorter than 18 bases after trimming (-q TAIL -qf sanger -qt 30 -aa TruSeq -ao 4 -m 18 -n 16). The cleaned reads were then aligned to the S. cerevisiae transcriptome using Salmon to quantify transcript abundances. For this, the genome GTF file and FASTA files for genes, cDNAs, and ncRNAs were downloaded from Ensembl (version GCF_000146045.2_R64-1-1). These files were used with Salmon’s generateDecoyTranscriptome.sh script to create a hybrid FASTA containing decoy genome sequences concatenated with the transcriptome. Indices for this decoy-aware transcriptome were built using the Salmon indexer. The salmon quant command was then employed to quantify the processed reads against this index. The resulting data were imported into R and processed with the edgeR package.
Assembly: reCRAC: reference genome (SGD v64) with  genome annotation from Ensembl (EF4.74). RNAseq: Ensembl (version GCF_000146045.2_R64-1-1)
Supplementary files format and content: reCRAC: gtf output file from pyReadCounters containing raw counts for each genomic feature; one processed file per sample
Supplementary files format and content: RNAseq: quant.sf output file from Salmon containing raw counts for each genomic feature; one processed file per sample
Library strategy: reCRAC

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: For reCRAC, yeast cells were grown in 800 mL of pre-warmed glucose medium (2%glucose, 2% YNB, 2% single dropout -Trp) until they reached OD600 of 0.45. For RNAseq, the yeast cells were grown in 100 mL of the same growth medium as for reCRAC until they reached OD600 of 0.45.

extract_protocol:
reCRAC: Cells were lysed with denaturing lysis buffer containing 6 M Guanidine HCl, with subsequent purification performed on Ni-NTA beads. The adapter ligation, radiolabeling with 32P and partial Benzonase digestion to generate protein-protected RNA fragments were performed on the beads. A second purification on anti-FLAG beads was performed. The samples were then visualized via autoradiography, the RNA bound to the target protein was cut out and treated with Proteinase K. RNAseq: RNA was extracted from 10 OD600 units of cells using TRIzol reagent with the addition of 0.5% final β-mercaptoethanol. Cells were lysed by bead beating in screw-cap tubes three times in a Fast Prep-24 machine (MP Biomedicals) using 200 µL of Zirconia beads at a setting of 6 m/s for 40 sec. RNA was cleaned twice by chloroform extraction and precipitation was performed using 0.8 vol isopropanol. RNA concentration was quantified using Nanodrop (OD280). 6 µg of RNA was treated with DNase I for 30 min and further purified using RNA Clean and Concentrator kit. RNA integrity and quality were assessed using an Agilent 2100 Electrophoresis Bioanalyser Instrument
reCRAC: The pulled RNA was converted to cDNA. We used an Illumina MiniSeq system, with single end sequencing and 75 bp read length, using the High Output Reagent Cartridge and followed the manufacturer’s instructions.RNAseq: Libraries were prepared from 500 ng of total RNA per sample using the NEBNEXT Ultra II Directional RNA Library Prep kit and the Poly-A mRNA Magnetic Isolation Module following the manufacturer’s protocols. Sequencing was carried out on the NextSeq 2000 platform  using NextSeq 2000 P3 Reagents (200 Cycles)with paired-end, 2x 100 nt outputs.

treatment_protocol: reCRAC: upon reaching the exponential growth, cultures were UV crosslinked at 254 nm to stabilize RNA-protein interactions either in glucose medium or shifted to glucose-deprived medium (2% glycerol, 2% ethanol) for 16 min. Immediately following crosslinking, the cells were harvested by filtration and put into 50 mL of ice-cold water, and centrifuged at 4,600 rpm for 2  min at 4°C. RNAseq: For glucose samples, cells were rapidly filtered and immediately immersed in 50 mL of ice-cold water, centrifuged at 4,600 rpm for 2 min at 4°C. For glucose starvation stress, cells were filtered and incubated in SD-Trp medium without glucose but supplemented with 2% glycerol and 2% ethanol. At the 16 min timepoint, cells were filtered and immersed in 50 mL of ice-cold water, after which they were spun down as described for glucose samples.

value: BY4741 background

value: Saccharomyces cerevisiae

value: N-terminal FLAG-Ala4-His8 (FH) tagged Pin6

value: 2% glycerol plus ethanol (Gly/EtOH) medium for 16 min


title: reCRAC N-FH Pin4, stress, Rep2

description: Library name: Sample 11

value: N-terminal FLAG-Ala4-His8 (FH) tagged Pin5


title: CX45_rep1

data_processing:
For RNA pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using Hisat2 (version 4.8.2) (Pertea et al., 2016) with default parameters
Gene expression FPKM was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) using the RefSeq database from the UCSC genome browser. Sequencing depth was normalized.
Assembly: mm9
Supplementary files format and content: bigwig

growth_protocol: RNA-sequencing (RNA-seq) was conducted by the Smart-seq method(Hu et al., 2016; Picelli et al., 2014). Briefly, mouse embryo samples were lysed, followed by reverse transcription into cDNA, and then pre-amplified using KAPA HiFi HotStart polymerase. After purification, amplified cDNA was used for library construction. A single-strand circularization process was subsequently performed to generate a single-stranded circular DNA library harboring >200 copies of DNA nanoballs, which was sequenced on the BGISEQ500 platform.

extract_protocol:
The total RNA of cells was extracted, followed the manufacturer’s instruction of Trizol Reagent (Invitrogen). KAPA HiFi HotStart DNA Polymerase (Roche) was used to amplify the cDNA.
The RNA-seq library was prepared using Nextera XT DNA Library Preparation Kit (Illumina), followed by the manufacturer’s instruction.


title: reCRAC N-FH Pin4, stress, Rep1

description: Library name: Sample 10

value: N-terminal FLAG-Ala4-His8 (FH) tagged Pin4


title: NTRK_p53_3

value: Thigh


title: CX22_rep2


title: CD45-positive, Dura, MCAO_3w

city: Fukuoka

first: Mitsuhiro

last: Kanamori

state: Fukuoka

address: Higashi-ku Maidashi 3-1-1

department: Allergy and Immunology

country: Japan

institute: Kyushu University

description:
Sample_C
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the cellranger multi function of the Cell Ranger software to obtain the processed tsv and mtx files.
The processed files were analyzed using Seurat (version 4.0.0) in the RStudio platform (Version 1.4.1717).
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dura mater

extract_protocol:
Mice were perfused with PBS containing heparin 1 week and 3 weeks after MCAO or the sham treatment. Five mice were pooled per sample. The ipsilateral non-sinus area of the dura mater was digested with Liberase DH (0.2 mg/ml) and DNase I (0.2 mg/ml) to prepare single-cell suspension. After blocking with CD16/CD32 Monoclonal Antibody, the cells were stained with Fixable Viability Dye, antibodies for surface antigens, and Totalseq™-C0306 to -C0310 (Biolegend, 155871, 155873, 155875, 155877, and 155879) for 20 min on ice. The tags were assigned as follows: C0306, Sham 1w dura; C0307, MCAO 1w dura; C0308, Sham 3w dura; C0309, MCAO 3w dura; C0310, MCAO 3w brain. Live, singlet CD45+ and CD45– cells were purified by FACSMelody. The ipsilateral cerebral hemisphere without the superficial leptomeninges was dissected only from the mice subjected to MCAO 3 weeks earlier. The brains were homogenized in 6 ml of RPMI supplemented with 15 mM HEPES and 0.27 % glucose on ice with a Potter-Elehjem Tissue Grinder. The samples were forced through 70 um strainers, and leukocytes were obtained by centrifugation in 37% Percoll. Brain samples were stained as the dura samples, and live, singlet CD45+CD11b– cells were purified by FACSMelody.
Libraries were prepared according to the protocol of Chromuim Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) using a Chromium controller. Briefly, GEMs were first generated by Master Mix with barcoded Single Cell VDJ 5' Gel Beads, cells and distribution to Oil to Chromium Next GEM Chip K. Barcoded cDNA was then generated from the GEM. This cDNA was amplified by PCR reaction to generate V(D)J library, 5' Gene Expression library and Feature Barcode library.

value: Dura mater

value: CD45-positive cells

value: C57BL/6J WT

value: MCAO


title: NTRK_p53_2

value: EPO-GEMM


title: reCRAC WT, stress, Rep2

description: Library name: Sample 8

value: WT


title: Pax-Foxo_P53_2

value: M


title: reCRAC WT, stress, Rep3

description: Library name: Sample 9


title: Control siIEL P14 CD8+ T cells ADT

value: T cells

value: ADT


title: CD45-negative, Dura, Sham_1w, MCAO_1w, Sham_3w, MCAO_3w

description:
Sample_B
10x Genomics

value: CD45-negative cells

value: Sham or MCAO, identified by HashTags


title: reCRAC WT, stress, Rep1

description: Library name: Sample 7

value: BY4741 background

value: Saccharomyces cerevisiae


title: 8C_rep1


title: Nf1_p53_4

source_name: MPNST (Nf1_P53)

value: F


title: CD45-positive, Dura, Sham_1w, MCAO_1w, Sham_3w

description:
Sample_A
10x Genomics


title: 8C_rep2


title: reCRAC N-FH Pin4, glucose, Rep3

description: Library name: Sample 6

value: N-terminal FLAG-Ala4-His8 (FH) tagged Pin6

value: glucose


title: shHifN43

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

institute: Anhui Normal University

data_processing:
trim_galore
Hisat2
Stringtie
Assembly: GRCm38
Supplementary files format and content: csv files include read counts values for each Sample

source_name: Embryonic stem cells

extract_protocol:
Total RNA samples were extracted using the Total RNA Isolation Reagent (Biosharp).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cells

value: ESC


title: Smarcb1_p53_3

source_name: MRT (SMARCB1_P53)

value: Thigh


title: shHifN42


title: reCRAC N-FH Pin4, glucose, Rep2

description: Library name: Sample 5

value: N-terminal FLAG-Ala4-His8 (FH) tagged Pin5


title: 2C_rep2


title: shHifN41


title: Pax-Foxo_P53_1


title: reCRAC N-FH Pin4, glucose, Rep1

description: Library name: Sample 4

value: N-terminal FLAG-Ala4-His8 (FH) tagged Pin4


title: CX45_rep2


title: 2C_rep1


title: CD45-positive, Brain, MCAO_3w

description:
Sample_D
10x Genomics

source_name: Brain

value: Brain

value: CD45-positive CD11b-negative cells

value: C57BL/6J WT

value: MCAO


title: Smarcb1_p53_2

value: M

value: EPO-GEMM


title: Rifampicin 2.5ng replicate 3

city: Tampere

first: Rahul

last: Jagadeesan

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

data_processing:
RNA sequencing reads were trimmed to remove possible adapter sequences and nucleotides with poor quality with Trimmomatic v.0.39
Trimmed reads were then mapped to the reference genome (E. coli MG1655, NC_000913.3) using using the Bowtie2 aligner v.2.3.5.1
featureCounts from Rsubread R package (v.2.8.2) was used to calculate unique gene hit counts. Genes with less than 5 counts in more than 3 samples, and genes whose mean counts are less than 10, were removed.
Gene hit counts were used for subsequent differential expression analysis, using DESeq2 R package (v.1.34.0) to compare gene expression between samples and calculate log2 of fold changes (LFC) using Wald tests (function nbinomWaldTest).
P-values were adjusted for multiple hypotheses testing (Benjamini–Hochberg, BH procedure)
Assembly: Escherichia coli str. K-12 substr. MG1655 (NC_000913.3
Supplementary files format and content: .csv file containing raw counts
Supplementary files format and content: .csv file containing normalized raw counts
Supplementary files format and content: .csv file containing results from differential expression analysis

organism: Escherichia coli

growth_protocol: Growth rates were measured by spectrophotometry (BioTek Synergy HTX Multi-Mode Microplate Reader). From a glycerol stock (-80 °C), cells were streaked on LB agar plates (2%) and incubated at 37 °C, overnight. Next, a single colony was picked, inoculated in LB medium with antibiotics and incubated at 30°C overnight with shaking. Overnight cultures were diluted into fresh medium to an optical density of 600 nm (O.D.600) of 0.03 and incubated for growth by shaking at 250 rpm at 37°C. We used Luria-Bertani (LB) medium with 10 g peptone, 10 g NaCl, and 5 g yeast extract in 1000 ml distilled water and the antibiotics kanamycin and chloramphenicol from Sigma Aldrich, U.S.A. Cells were grown until reaching either the exponential or stationary growth phases.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen).
RNA-seq libraries were constructed according to the Illumina's protocol.

treatment_protocol: Cells from 3 independent biological replicates of E. coli MG1655 in exponential and stationary growth phase conditions were treated with RNA protect bacteria reagent (Qiagen, Germany), to prevent degradation of RNA.


title: ctrlN43

value: scramble shRNA


title: reCRAC WT, glucose, Rep3

description: Library name: Sample 3

value: BY4741 background

value: WT


title: Rifampicin 2.5ng replicate 1


title: p53_3

source_name: UPS (P53)


title: N23

value: normoxia


title: RNAseq pin4Δ, stress, Rep3

description: Library name: Sample 24

data_processing:
reCRAC: pyBarcodeFilter - demultiplexing, Flexbar- adapter trimming and quality filtering (--removal-tags -at RIGHT -ao 4 -u 3 -m 7 -n 16 -t) , pyFastqDuplicateRemover.py - PCR duplicates removal, Novoalign (V2.07.00) - alignment to the reference genome (SGD v64) with  genome annotation from Ensembl (EF4.74) applying the Random -r method, pyReadCounters.py - read counting using Ensembl GTF version EF4.74
RNAseq: The paired-end Illumina RNA-seq data were first pre-processed using Flexbar to trim low quality bases and adapters from raw reads. The specific parameters set for Flexbar included quality filtering of tail bases with a quality threshold of 30 (Sanger scale), adapter removal with a minimum overlap of four bases, and discarding of reads shorter than 18 bases after trimming (-q TAIL -qf sanger -qt 30 -aa TruSeq -ao 4 -m 18 -n 16). The cleaned reads were then aligned to the S. cerevisiae transcriptome using Salmon to quantify transcript abundances. For this, the genome GTF file and FASTA files for genes, cDNAs, and ncRNAs were downloaded from Ensembl (version GCF_000146045.2_R64-1-1). These files were used with Salmon’s generateDecoyTranscriptome.sh script to create a hybrid FASTA containing decoy genome sequences concatenated with the transcriptome. Indices for this decoy-aware transcriptome were built using the Salmon indexer. The salmon quant command was then employed to quantify the processed reads against this index. The resulting data were imported into R and processed with the edgeR package.
Assembly: reCRAC: reference genome (SGD v64) with  genome annotation from Ensembl (EF4.74). RNAseq: Ensembl (version GCF_000146045.2_R64-1-1)
Supplementary files format and content: reCRAC: gtf output file from pyReadCounters containing raw counts for each genomic feature; one processed file per sample
Supplementary files format and content: RNAseq: quant.sf output file from Salmon containing raw counts for each genomic feature; one processed file per sample

value: Saccharomyces cerevisiae

value: Deletion of PIN4 gene

value: 2% glycerol plus ethanol (Gly/EtOH) medium for 16 min


title: p53_2

value: F


title: KRAS_Bcor_4

source_name: eRMS (KrasG12V_BCOR)

value: Thigh


title: ctrlN42

value: Embryonic stem cells

value: ESC


title: N22


title: Rifampicin 0ng replicate 2


title: Rifampicin 2.5ng replicate 2


title: reCRAC WT, glucose, Rep2

description: Library name: Sample 2

value: glucose


title: Muscle_6

source_name: Muscle Control

value: Thigh muscle

value: Normal muscle control


title: Rifampicin 0ng replicate 1


title: Smarcb1_p53_1


title: CX22_rep1


title: RNAseq WT, stress, Rep3

description: Library name: Sample 21


title: reCRAC WT, glucose, Rep1

description: Library name: Sample 1


title: H23

value: hypoxia


title: H22


title: RNAseq pin4Δ, stress, Rep1

description: Library name: Sample 22


title: Muscle_4

value: M


title: Novobiocin 500ng replicate 3


title: Novobiocin 500ng replicate 2


title: Rifampicin 0ng replicate 3


title: Muscle_3


title: RNAseq WT, stress, Rep2

description: Library name: Sample 20


title: ctrlN41


title: H21


title: Novobiocin 500ng replicate 1


title: Muscle_2


title: RNAseq pin4Δ, stress, Rep2

description: Library name: Sample 23


title: Novobiocin 100ng replicate 3


title: N21


title: Muscle_5


title: HEI-OC1_LMX1A_c.915dup_rep3

first: Shanhe

last: Yu

address: 197# Rui Jin Road II

institute: Shanghai Institute of Hematology，Rui Jin Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCm38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCm38

growth_protocol: HEI-OC1 cells were maintained as monolayer cultures in DMEM supplemented with 10% fetal bovine serum, 20 U/mL penicillin and 20μg/mL streptomycin, with a 5% CO2 concentration at 37°C.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cochlear hair cell line

value: HEI-OC1 cells transduced with LMX1A c.915dup


title: Muscle_1


title: RNAseq pin4Δ, glucose, Rep3

description: Library name: Sample 18

value: BY4741 background


title: Novobiocin 100ng replicate 2


title: Nf1_p53_3

value: EPO-GEMM


title: Novobiocin 100ng replicate 1


title: HEI-OC1_LMX1A_c.915dup_rep1


title: RNAseq pin4Δ, glucose, Rep2

description: Library name: Sample 17


title: Novobiocin 0ng replicate 3


title: HEI-OC1_LMX1A_WT_rep3

value: HEI-OC1 cells transduced with LMX1A


title: Nf1_p53_1


title: HEI-OC1_LMX1A_WT_rep2


title: RNAseq pin4Δ, glucose, Rep1

description: Library name: Sample 16

value: Saccharomyces cerevisiae


title: Novobiocin 0ng replicate 1


title: Novobiocin 0ng replicate 2


title: RNAseq WT, glucose, Rep2

description: Library name: Sample 14

value: WT


title: HEI-OC1_LMX1A_WT_rep1


title: RNAseq WT, stress, Rep1

description: Library name: Sample 19

value: 2% glycerol plus ethanol (Gly/EtOH) medium for 16 min


title: RNAseq WT, glucose, Rep1

description: Library name: Sample 13


title: KRAS_p53_2

source_name: eRMS (KrasG12V-P53)


title: HEI-OC1_EV_rep3

value: HEI-OC1 cells transduced with empty vector


title: Zea mays gDNA homozygous N siblings backcrossed into W22

first: Annis

middle: Elizabeth

last: Richardson

address: Max Borne Crescent, Kings Buildings

department: Institute of Molecular Plant Sciences, School of Biological Sciences

description:
Library name: TrfN5
2 lanes of sequencing used (L1 and L3)

data_processing:
Raw reads were passed through FASTQ for quality checks and read trimming.
Trimmed reads were aligned to the Zea mays NAM5.0 B73 genome using Bowtie2, with default settings
.sam files were converted to .bam files and indexed using samtools
sequence variants between the Trf or N sequence (based on the .bam files), and the reference genome, were called using bcftools mpileup to generate .bcf files
.bcf files were converted to .vcf files using bcftools view
.vcf files containing all the sequence variants compared to the reference genome for N and for Trf pools were converted to .txt using PyVCF
Assembly: Zea mays NAM5.0 B73 genome (Zm-B73-REFERENCE-NAM-5.0)
Supplementary files format and content: .txt file for the N and for the Trf prool, which contains all the sequence variants when compared to the reference genome

organism: Zea mays

source_name: leaf discs

growth_protocol: The Truffula seed was provided by Gerry Neuffer, and originally called Ts-2620, found in an EMS mutagenised Mo17 population. The phenotype of Trf was analyzed in backcrosses into W22 and Mo17 advanced to generation 10. Field grown plants were grown at UC Berkeley Gill Tract, UC Davis and UMass Amherst during summer field seasons. All plants used for molecular analysis were backcrossed into W22 10 times. Seedlings grown for RNA and DNA extractions were grown under greenhouse conditions in 30x45x2.5cm trays with peat free soils plus osmocote.

extract_protocol:
Leaf discs were collected from 80 Trf and N siblings in the W22 backcross population (at least 10 introgressions). High-quality gDNA was extracted using a urea-based extraction method which is as follows. Tissue was ground in urea extraction buffer (4M urea, 4M NaCl, 1M Tris pH8, 0.5M EDTA, 34mM n-lauroyl sarcosine). Then an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1), was added and vortexed to mix. After centrifugation, the supernatant was decanted and mixed with an equal volume of chloroform. After centrifugation, the supernatant was decanted and mixed with 1/10th volume of 4.4 M NH4OAc pH 5.2 and 0.7 volume of isopropanol. Strands of DNA were then collected and washed with 70% ethanol in a separate tube. The dried pellet was resuspended in 100μl of TE. DNA integrity was checked using gel electrophoresis and quantified using qubit before sending for library preparation and 150bp PE sequencing by Novogene. Sequencing was for 10 x coverage of the maize genome.
A total amount of 1.0μg DNA per sample was used as input material for the DNA sample preparations. Sequencing libraries were generated using NEBNext® DNA Library Prep Kit following manufacturer's recommendations and indices were added to each sample. The genomic DNA is randomly fragmented to a size of 350bp by shearing, then DNA fragments were end polished, A-tailed, and ligated with the NEBNext adapter for Illumina sequencing, and further PCR enriched by P5 and indexed P7 oligos. The PCR products were purified (AMPure XP system) and resulted libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified using real-time PCR.

value: leaf discs

value: Homozygous N sibling from segregating Trf population in W22 background

value: pool of leaf discs from 80 individuals


title: Nup54_siRNA1_96h_rep1

city: Cambridge

first: Azad

last: Alizada

state: Cambridgeshire

address: University of Cambridge Li Ka Shing Centre, Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

description:
nup54 siRNA in OSC
DEseq2_gene_te_normalized_counts.txt
DEseq2_Nup54_vs_renilla_siRNA_96h.txt

data_processing:
The reads were trimmed of adapter sequences AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT using Cutadapt tool (v1.18; -m 1 specified to not have reads trimmed to zero).
The trimmed reads were aligned to the genome assemblies using the RNA-seq aligner STAR (v2.7.3a).
Gene counts were calculated with the featureCounts tool (Subread package v1.5.3; -s 2 for stranded libraries prepared by dUTP method). D. mel gene annotations were taken from Drosophila_melanogaster.BDGP6.28.100.gtf in the Ensembl genome database.
Differential gene expression analysis was performed using DESeq2 (v1.30.1) package.
Assembly: dm6
Supplementary files format and content: tab-delimited text files showing normalized gene counts for each sample
Supplementary files format and content: tab-delimited text files for differential RNA-seq analysis showing DESeq2-computed fold-change values between the contrasted samples

organism: Drosophila melanogaster

source_name: OSC

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Cat. No. 74106, QIAGEN) with RNase-Free DNase Set (Cat. No. 79254, QIAGEN) for DNase digestion during RNA purification as per manufacturer’s instruction. Reverse transcription was performed with 100 ng to 1 µg RNA using SuperScript™ IV Reverse Transcriptase (Cat. No. 18090010, Thermo Fisher Scientific).
poly(A) selection was done using Poly(A) mRNA Magnetic Isolation Module (NEB # E7490) with 500 ng of total RNA as input. Libraries were prepared using The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (#E7420L).

treatment_protocol: Sense and anti-sense siRNA sequences (21 nt) for target genes were designed using the DSIR tool (http://biodev.cea.fr/DSIR/DSIR.html). The designed sequences were ordered from IDT. The RNA oligonucleotides were resuspended to 400 μM final concentration in RNase-free water. Equal volumes of the resuspended sense and antisense siRNA were mixed then added to an equal amount of 2x annealing buffer (60 mM potassium acetate; 200 mM HEPES, pH 7.5). The mix was boiled for 5 min. at 75 °C, then ramped down to 25 °C (-0.1 °C/second) to anneal the siRNA sequences into the siRNA duplex (100 μM final concentration =200 pmoles). 2 μL of the final 100 μM siRNA duplex was mixed with 100 μL of Nucleofection solution V (VVCA-1003, Lonza) and transfected into 10 million cells using NucleofectorTM 2b Device (T-029 program) (Lonza). Cells were plated into 12-well plates and the media was changed after 24 hr. RNA was harvested at 48 and 96 hrs.

value: OSC

value: ovarian somatic cell


title: KRAS_p53_1

data_processing:
IDAT files were obtained and processed using the R package sesame, version 1.16.1 (SEnsible Step-wise Analysis of DNA MEthylation BeadChips)(Zhou et al., 2018) to generate normalized beta values. Probe intensities underwent background correction using the p-value with the out-of-band array hybridization approach, followed by a normal-exponential out-of-band approach. Dye bias correction was performed by aligning green and red to the midpoint using the dyeBiasCorrTypeINorm method in sesame. Probes targeting the X and Y chromosomes were excluded. Clustering analysis was performed with R packages Rtsne and umap based on the 2,000 or 10,000 most variably methylated probes, with perplexity values set to 5 for tSNE and 15 for umap clustering.
Average Beta values

extract_protocol: A minimum of 500ng of genomic DNA extracted from frozen tissue was submitted per sample. DNA quality was ensured by digital gel electrophoresis (Agilent, G2939BA).

value: Thigh


title: HEI-OC1_LMX1A_c.915dup_rep2


title: p53_1


title: HEI-OC1_EV_rep2


title: Nf1_p53_2


title: Zea mays gDNA heterozygous Trf siblings backcrossed into W22

description:
Library name: TrfM6
2 lanes of sequencing used (L1 and L3)

value: Heterozygous Truffula, backcrossed in to W22


title: Nup54_siRNA1_48h_rep2

description:
nup54 siRNA in OSC
DEseq2_gene_te_normalized_counts.txt
DEseq2_Nup54_vs_renilla_siRNA_48h.txt


title: HEI-OC1_EV_rep1


title: Lola-I[KO-2] D. mel. 16-24h embryonic neurons, Hi-C rep1

city: Lausanne

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description:
Library name: Lola_KO2-1
Hi-C library

data_processing:
FASTQ files were mapped to the dm6 reference genome using distiller v0.3.3 (https://github.com/open2c/distiller-nf).
For each biological replicate, unique pairs of reads with MAPQ ≥ 30 on both sides were aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction using cooler v0.8.11 (https://github.com/open2c/cooler).
For each sample, unique pairs of reads with MAPQ ≥ 30 on both sides from all replicates were aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction using cooler v0.8.11 (https://github.com/open2c/cooler).
Assembly: dm6
Supplementary files format and content: Multi-resolution cooler file format (mcool): unique pairs of reads with MAPQ ≥ 30 on both sides, aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction (cooler v0.8.11, https://github.com/open2c/cooler).

source_name: neurons

growth_protocol: standard Drosophila culture at 25°C

extract_protocol:
0.3-1 million neurons were FACS-purified from formaldehyde-crosslinked embryos, then subjected to Hi-C, cutting with Csp6I and MseI restrictrion enzymes.
NEBNext Ultra II DNA Library Prep kit for Illumina

treatment_protocol: Animals were not subjected to any particular treatment.

value: neurons

tag: developmental stage

value: 16-24-hour embryos


title: Lola-I[KO-6] D. mel. 16-24h embryonic neurons, Hi-C rep2

description:
Library name: Lola_KO6-1
Hi-C library


title: Kras_1

value: F


title: RNAseq WT, glucose, Rep3

description: Library name: Sample 15

value: BY4741 background

value: glucose


title: Nup54_siRNA1_48h_rep1


title: WT D. mel. 16-24h embryonic neurons, Hi-C rep2

description:
Library name: WT-2
Hi-C library

value: wildtype


title: KRAS_p53_3

value: EPO-GEMM


title: KRAS_Bcor_3

value: M


title: KRAS_Bcor_1


title: RenillaLuc_siRNA1_96h_rep2

description:
renilla siRNA in OSC
DEseq2_gene_te_normalized_counts.txt


title: KRAS_Bcor_2


title: WT D. mel. 16-24h embryonic neurons, Hi-C rep1

description:
Library name: WT-1
Hi-C library


title: Cp190[0] D. mel. 16-24h embryonic neurons, Hi-C rep1

description:
Library name: Cp190_0_rep1
Hi-C library


title: RenillaLuc_siRNA1_48h_rep3


title: RenillaLuc_siRNA1_48h_rep2


title: Cp190[0] D. mel. 16-24h embryonic neurons, Hi-C rep2

description:
Library name: Cp190_0_rep2
Hi-C library


title: CTCF[0] D. mel. 16-24h embryonic neurons, Hi-C rep2

description:
Library name: CTCF_0_rep2
Hi-C library


title: Psoriasis4

type: RNA

city: Jinan

first: Q

last: Sun

state: Shandong

address: Medical College of Shandong University 44 Wenhua West Road, Lixia District,

department: Dermatology

institute: Shandong University; Qilu hospital

description: miRNAs expression in Serum extracellular vesicles

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Serum extracellular vesicles

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen).

treatment_protocol: Whole blood (5-10 mL) from patients and healthy control were centrifuged at 3000 rpm for 10 minutes to separate serum. The serum was collected, centrifuged at 300g for 10 min, and then at 16,500g for 30 min, and later filtered through a 0.22 mm pore size filter to remove cell debris. The final supernatant was ultracentrifuged at 100,000g for 70 min and recentrifuged at the same speed. The purified EVs were resuspended in PBS.

value: Serum extracellular vesicles

value: male

tag: disease state

value: Psoriasis


title: Psoriasis3

tag: tissue

value: female


title: SS18-SSX1_1

first: Ana

last: Banito

address: Im Neuenheimer Feld 581

source_name: Synovial Sarcoma


title: SS18-SSX2_Pten_2


title: Kras_p53_Neo_5_groin

value: Soft-tissue groin


title: CTCF[0] D. mel. 16-24h embryonic neurons, Hi-C rep1

description:
Library name: CTCF_0_rep1
Hi-C library


title: Psoriasis1


title: RenillaLuc_siRNA1_96h_rep1

tag: cell line

value: OSC


title: tj_siRNA3_96h_rep1

description:
tj siRNA in OSC
DEseq2_gene_te_normalized_counts.txt
DEseq2_tj_vs_renilla_siRNA_96h.txt

value: ovarian somatic cell


title: RenillaLuc_siRNA1_48h_rep1


title: Psoriasis2


title: WT[0] D. mel. 16-24h embryonic neurons, Hi-C rep2

description:
Library name: WT_0_rep1_2
Hi-C library

tag: genotype


title: ctr4

tag: gender

value: healthy


title: ctr3


title: tj_siRNA2_96h_rep1


title: ctr2


title: RenillaLuc_siRNA1_48h_rep4


title: WT[0] D. mel. 16-24h embryonic neurons, Hi-C rep1

description:
Library name: WT_0_rep1
Hi-C library


title: Kras_p53_Neo_4_groin

tag: location


title: KRAS_D_p53_3N

source_name: eRMS (KrasG12D-P53)

value: Thigh

tag: type of gemm


title: tj_siRNA1_96h_rep1

tag: cell type


title: ctr1


title: Ovaries - TjGal80ts Gal4 ; RNAi white (BL#33644)

data_processing:
Adapters were trimmed.
size selection was performed to retain only 18-29 nucleotide reads.
small RNA pipeline sRNAPipe (Pogorelcnik et al., 2018)
Assembly: release 6.03
Supplementary files format and content: .txt read counts at piRNA clusters

source_name: ovaries

growth_protocol: Flies were kept at standard conditon at 25°C

extract_protocol:
Total RNA extraction with TRIzolTM (Invitrogen) Polyacrylamide gel size selection of 18-30 nucleotides
Library preparation using illumina TruSeq small RNA kit, Specific treatment anti 2S

treatment_protocol: Ovary dissections

value: ovaries

value: ;TjGal80ts Gal4 ; RNAi white (BL#33644)


title: SS18-SSX2_Pten_3


title: tj_siRNA3_48h_rep2

description:
tj siRNA in OSC
DEseq2_gene_te_normalized_counts.txt
DEseq2_tj_vs_renilla_siRNA_48h.txt


title: KRAS_D_p53_2N

value: F


title: HA ChIP, WT, rep3

description:
Library name: WT_3_antiHA
ChIP-seq library

data_processing:
Reads were aligned against Drosophila melanogaster genome assembly release 6 (dm6).
Samtools v1.10 was used to identify duplicate reads
Coverage (in reads per million) was evaluated after truncating each paired end read to the 50nt region centered on the its midpoint, ignoring duplicate reads.
Assembly: dm6
Supplementary files format and content: bigWig files were generated using R package rtracklayer v1.42.2. Score represent coverage in reads per million.

source_name: central nervous system

extract_protocol:
30 third-instar larval CNSs per biological replicate (two biological replicates per sample) were dissected in ice-cold PBS. Chromatin was prepared as described in (Gambetta, Oktaba and Müller, 2009) with the following modifications: inverted larval cuticles were cross-linked for 15 minutes at room temperature in 1.8% (v/v) paraformaldehyde, and dissected brains were sonicated in 120 µl of previously described RIPA140 buffer in AFA microtubes in a Covaris S220 sonicator (Covaris) for 5 minutes with a peak incident power of 140W, a duty cycle of 5% and 200 cycles per burst. Sonicated chromatin was centrifuged to pellet insoluble material and snap-frozen.  ChIP was performed with rabbit polyclonal anti-HA antibody (Abcam Ab9110). ChIP was performed as previously described in (Gambetta, Oktaba and Müller, 2009) except that Protein A and G Dynabeads were used. ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep kit for Illumina. An equimolar pool of multiplexed ChIP-seq libraries was sequenced 150 bp paired-end.
Standard ChIP-seq libraries were prepared with the NEBNext Ultra II DNA Library Prep kit for Illumina.

value: central nervous system

value: third instar larva

tag: chip antibody

value: rabbit polyclonal anti-HA (Abcam Ab9110)


title: HA ChIP, WT, rep2

description:
Library name: WT_2_antiHA
ChIP-seq library

value: wildtype


title: Ovaries - flam {-515; +6334} Tomato


title: tj_siRNA2_48h_rep2

tag: treatment


title: Ovaries - flam {-515; +1200} Tomato


title: KRAS_D_p53_1N

value: M

value: EPO-GEMM


title: HA ChIP, WT, rep1

description:
Library name: WT_1_antiHA
ChIP-seq library


title: Kras_p53_Neo_2


title: Ovaries - flam {-515; +718} Tomato


title: HA ChIP, HA-Lola-I, rep3

description:
Library name: HALola_3_antiHA
ChIP-seq library

value: lola-I[KO]+HA-lola-I rescue


title: Ovaries - flam deltaProm/flam DeltaProm

value: flam deltaProm/flam deltaProm


title: Kras_p53_Neo_1


title: tj_siRNA2_48h_rep1

tag: time


title: Ovaries - flam deltaProm/WT

value: flam deltaProm/WT


title: tj_siRNA1_48h_rep1


title: tj_siRNA3_48h_rep1


title: HA ChIP, HA-Lola-I, rep1

description:
Library name: HALola_1_antiHA
ChIP-seq library


title: Ovaries - TjGal80ts Gal4 ; RNAi TJ (BL34595)

value: ;TjGal80ts Gal4 ; RNAi TJ (BL34595)


title: HA ChIP, HA-Lola-I, rep2

description:
Library name: HALola_2_antiHA
ChIP-seq library


title: cell-free DNA from CAR T cells of patient CF-027

status: Public on Apr 10 2025

type: other

city: Berlin

first: Charlotte

last: Junkuhn

address: Föhrer Str. 15

institute: Charité Universitätsmedizin Berlin

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standart recommended Illumina scanner settings

data_processing:
Normalization was performed using the minfi preprocessNoob function, beta values were obtained using the getBeta function in an R environment (v4.3.1)
Processed file beta_p_matrix.csv (Beta value) is linked as a supplementary file on the Series record.

label: Cy3 and Cy5

source_name: CAR T cells

label_protocol: Standart Illumina Protocol

extract_protocol: DNA was extracted from T cell samples using the Research Quick DNA Microprep Kit (Zymo)

tag: age

tag: Sex

value: CAR T cells

value: pre-therapy


title: cell-free DNA from CAR T cells of patient CF-024


title: cell-free DNA from CAR T cells of patient CF-026

value: post-therapy


title: cell-free DNA from CAR T cells of patient CF-025


title: cell-free DNA from CAR T cells of patient CF-022


title: cell-free DNA from CAR T cells of patient CF-023


title: cell-free DNA from T cells of patient CF-018

source_name: T cells

value: T cells


title: cell-free DNA from CAR T cells of patient CF-020


title: cell-free DNA from T cells of patient CF-042


title: cell-free DNA from T cells of patient CF-036


title: cell-free DNA from T cells of patient CF-031


title: Kras_p53_Neo_3

institute: KiTZ, DKFZ

value: Thigh


title: cell-free DNA from T cells of patient CF-033


title: cell-free DNA from T cells of patient CF-011


title: cell-free DNA from T cells of patient CF-016


title: cell-free DNA from T cells of patient CF-022


title: cell-free DNA from T cells of patient CF-004


title: cell-free DNA from T cells of patient CF-019


title: cell-free DNA from T cells of patient CF-023


title: cell-free DNA from T cells of patient CF-009


title: cell-free DNA from T cells of patient CF-028


title: cell-free DNA from T cells of patient CF-029


title: cell-free DNA from T cells of patient CF-027


title: cell-free DNA from T cells of patient CF-025


title: cell-free DNA from T cells of patient CF-008


title: cell-free DNA from T cells of patient CF-017


title: cell-free DNA from T cells of patient CF-005


title: cell-free DNA from T cells of patient CF-021


title: H01_24Gy (5)

city: London

first: Silvia

last: Marino

address: 4 Newark Street

department: Blizard Institute

institute: Queen Mary University of London

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
data were analysed using a cross-package Bioconductor workflow in R, employing the methylation specific packages wateRmelon, bigmelon, IlluminaHumanMethylationEPICanno.ilm10b5.hg38 and DMRcate
raw data were imported in R using wateRmelon
quality control was performed by removing probes associated with sex and mitochondrial chromosomes (chrX, Y, MT) and single nucleotide polymorphisms (SNPs)
Normalization was performed using wateRmelon’s adjusted Dasen method.
Probe-wise differential methylation analysis was performed using cpg.annotate function (analysis.type = “differential”) within the DMRcate package. Probes with Benjamini and Hochberg adjusted p-value < 0.05 were considered statistically significant
Differential methylation analysis of regions was performed using the dmrcate function of R package DMRcate based on the annotated probes obtained in the previous step (a region should contain at least 6 probes in a manner that two consecutive probes should not exceed a separation of 400 BPs, with a p-value cutoff at 0.01 ).
The *bvals.csv files represent normalized Average Beta values obtained using the adjusted-Dasen method.

label: Cy3, Cy5

source_name: Homo sapiens

growth_protocol: COs were developed from patient-derived expanded potential stem cell lines and were maintained in Stemcell™ mTeSR Plus medium.  For the development of COs, the STEMdiff™ Cerebral Organoid Kit was utilised and 1X Pen/Strep was added during the maintenance phase.

extract_protocol: DNA from the FFPE tissue was extracted using Norgen FFPE RNA/DNA Purification plus kit. COs were dissociated with Sigma-Aldrich accutase and Norgen RNA/DNA/Protein Purification Plus Kit was utilised for the DNA extraction.

treatment_protocol: Irradiation was performed using X-Ray Biological Irradiator from Queen Mary Biological Science Unit and radiation dose of 24Gy was administered at 8.5Gy/min. CO-related data were collected 4 weeks after the irradiation.

value: Cerebral organoid (CO)

value: Irradiated


title: G01_24Gy (4)

label_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting


title: cell-free DNA from CAR T cells of patient CF-021

value: F


title: F01_24Gy (3)


title: cell-free DNA from T cells of patient TC-48


title: cell-free DNA from CAR T cells of patient CF-019


title: E01_24Gy (1)


title: A01_0Gy (1)

value: Control


title: B01_0Gy (2)


title: C01_0Gy (3)


title: D01_0Gy (4)


title: cell-free DNA from T cells of patient CF-020


title: Cnt9

value: Formalin-fixed Paraffin-embedded (FFPE) brain


title: Cnt10


title: RT12


title: RT11


title: Cnt12


title: RT13


title: Cnt11


title: RT9


title: Cnt4


title: Cnt3


title: Cnt7


title: RT3


title: Cnt5


title: RT6


title: Cnt8


title: RT4


title: RT7


title: RT8


title: Cnt2


title: RT14


title: Cnt1


title: RT1


title: RT2


title: neurons,mut,rep2

first: Shigeki

last: Iwase

state: Michigan

address: 1241 E. Catherine St.

department: Human Genetics

description: Library name: neurons_mut_rep2

data_processing:
Sequence were trimmed using Trimgalore
Reads were aligned to the UCSC hg38 genome using Bowtie2.
bigWig files were generated using bamCoverage (deepTools), with files normalized to BPM for each replicate with bin size of 1.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Cortical Neurons

extract_protocol:
Total RNA was extracted using the Trizol-Chloroform method, treated with DNase (Promega #M6101, US), and cleaned up using RNeasy Plus Mini kit (Qiagen Valencia, CA). We synthesized cDNA using ProtoScript II Reverse Transcriptase (New England BioLab, US) and performed RT-qPCR using Applied Biosystems™ Power SYBR™ Green PCR Master Mix (Thermo Fisher Scientific, US) on an Applied Biosystems 7500 Instrument.
Libraries for MiSeq were prepared by Massachusetts General Hospital, Center for Computational and Integrative Biology

treatment_protocol: or HEK293T cell experiments, we transfected PGK-promoter constructs using Lipofectamine 2000 and harvested cells one day post-transfection. For neuronal experiments, we packaged hSYN1-promoter constructs into lentivirus and introduced them into DIV3 mouse cortical neurons at MOI of 1, and harvested the neurons at DIV6.

value: Cortical Neurons


title: neurons,wt,rep2

description: Library name: neurons_wt_rep2

value: WT


title: RT10


title: neurons,mut,rep1

description: Library name: neurons_mut_rep1


title: neurons,wt,rep1

description: Library name: neurons_wt_rep1


title: 293T,wt,rep2

description: Library name: 293T_wt_rep2

source_name: 293T cells

value: 293T cells


title: 293T,mut,rep1

description: Library name: 293T_mut_rep1


title: 293T,wt,rep1

description: Library name: 293T_wt_rep1


title: Cnt6


title: Ex12-15, wt

description: Library name: Ex12_wt

source_name: Patient sample

treatment_protocol: For HEK293T cell experiments, we transfected PGK-promoter constructs using Lipofectamine 2000 and harvested cells one day post-transfection. For neuronal experiments, we packaged hSYN1-promoter constructs into lentivirus and introduced them into DIV3 mouse cortical neurons at MOI of 1, and harvested the neurons at DIV6. Blood samples derived from patients were used to establish lymphoblastoid cell lines

value: Lymphoblastoid cells


title: 293T,mut,rep2

description: Library name: 293T_mut_rep2


title: 35S:MiEFF12_2

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

country: France

institute: CNRS

description: Illumina NextSeq 500

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq preprocessing included the trimming of library adapters and quality controls with Trimmomatic. Paired-end reads with a Phred Quality Score Qscore > 20 and a read length > 30 bases were retained, and ribosomal RNA sequences were removed with SortMeRNA. Processed reads were aligned using Tophat2 with the following arguments: --max-multihits 1 -i 20 --min-segment-intron 20 --min-coverage-intron 20 --library-type fr-firststrand --microexon-search -I 1000 --max-segment-intron 1000 --max-coverage-intron 1000 --b2-very-sensitive.
Reads overlapping exons were counted per gene with the FeatureCounts function of the Rsubreads package, using the GTF annotation files from the Araport11 repository (https://www.araport.org/downloads/Araport11_Release_201606/annotation/Araport11_GFF3_genes_transposons.201606.gff.gz). Read counts were normalized with DESeq2
Assembly: Tair10
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: roots

extract_protocol:
Root were harveseted and flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: roots


title: 35S:MiEFF12_1

description: Illumina NextSeq 500


title: PBMC, library GD007_2, CITE

city: La Jolla

first: Kendall

last: Kearns

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description:
Library name: GD007_2_CITE
GD007_2
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv

data_processing:
Sequencing reads were aligned to the GRCh38 human reference genome and gene counting was performed using the multi pipeline in CellRanger (v5.0).
Downstream analyses were performed using Seurat (v5.0.0).
Seurat's MULTIseqDEMUX was used for hashtag demultiplexing and singlet assignment.
Assembly: GRCh38
Supplementary files format and content: tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
After overnight resting PBMCs were stimulated with extracts (10 µg/ml) or HDMPP (10 µg/ml), or medium alone as negative control, and incubated for 24h at 37ºC. After the incubation, cells were surface stained with fluorochrome-conjugated antibodies, for 40 minutes at 4°C using: anti-CD3 (AF700) (UCHT1), anti-CD4 (APCef780) (RPA-T4), anti-CD8 (PerCP-Cy5.5) (RPA-T8), anti-CD14 (V500) (M5E2), anti-CD19 (V500) (HIB19), anti-TCRγδ (PE-DA594) (IP26), anti-TCRδ1 (FITC) (TS8.2), anti-TCRδ2 (BV421) (B6), anti-CD137 (APC) (4B4-1), and anti-CD69 (BV605) (FN50) antibodies. TotalSeq-C oligonucleotide-conjugated antibodies (BioLegend) were also added at this step at 0.01mg/mL final concentration (one distinct antibody per sample). After two washes in PBS, cells were resuspended into 500 μl of MACS buffer (PBS containing 2mM EDTA (pH 8.0) and 0.5% BSA) and stored at 4ºC until flow cytometry acquisition. AIM+ (CD69+CD137+) Vδ1 and Vδ2 cells were captured by fluorescence-activated cell sorting (FACS), using a BD FACSAria Fusion cell sorter (Becton Dickinson).
Samples were processed using 10x Genomics 5’ end mRNA capture reagents (5v2.0 single cell gene expression profiling chemistry) as per manufacturer’s recommendations; after droplet generation, and in-droplet based reverse transcription, cDNA was amplified by PCR for 13 cycles and gene expression library preparation followed. After quantification, equal molar concentration of each library was pooled and sequenced using the NovaSeq6000 Illumina sequencing platform to obtain 28- and 100-bp paired-end reads using the following read length: read 1, 100 cycles; read 2, 100 cycles; i7 index, 10 cycles and i5 index 10 cycles. Each gene expression library was sequenced aiming at a minimum mean sequencing depth of 30,000 reads per cell. Separate libraries were prepared to identify the DNA-Barcode that will allow de-multiplexing and linking each cell to a donor. Briefly, amplified DNA generated from antibody-DNA oligos was separated from transcriptomic cDNA based on size-selection following amplification. Antibody-DNA amplified fragments were less than 300 bp. Library preparation was followed in accordance with the manufacturer’s recommendations. Each library was sequenced aiming for 5,000 reads per cell.

value: PBMC


title: PBMC, library GD007_1, CITE

description:
Library name: GD007_1_CITE
GD007_1
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: PBMC, library GD009_1, CITE

description:
Library name: GD009_1_CITE
GD009_1
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: PBMC, library GD006_2, CITE

description:
Library name: GD006_2_CITE
GD006_2
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: RT5


title: PBMC, library GD006_1, CITE

description:
Library name: GD006_1_CITE
GD006_1
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: Ex12-15, variant

institute: University of Michigan

description: Library name: Ex12_mut


title: PBMC, library GD005_2, CITE

description:
Library name: GD005_2_CITE
GD005_2
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: PBMC, library GD004_2, CITE

description:
Library name: GD004_2_CITE
GD004_2
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: PBMC, library GD004_1, CITE

description:
Library name: GD004_1_CITE
GD004_1
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: PBMC, library GD005_1, CITE

description:
Library name: GD005_1_CITE
GD005_1
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: PBMC, library GD002, CITE

description:
Library name: GD002_CITE
GD002
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: PBMC, library GD001_2, CITE

description:
Library name: GD001_2_CITE
GD001_2
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: PBMC, library GD001_1, CITE

description:
Library name: GD001_1_CITE
GD001_1
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: PBMC, library GD009_2, GEX

description:
Library name: GD009_2_GEX
GD009_2
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD009_1, GEX

description:
Library name: GD009_1_GEX
GD009_1
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD007_2, GEX

description:
Library name: GD007_2_GEX
GD007_2
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD007_1, GEX

description:
Library name: GD007_1_GEX
GD007_1
GEX_SCT_counts.tsv
metadata.csv


title: 35S:MiEFF12_3

description: Illumina NextSeq 500


title: PBMC, library GD006_1, GEX

description:
Library name: GD006_1_GEX
GD006_1
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD005_2, GEX

description:
Library name: GD005_2_GEX
GD005_2
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD006_2, GEX

description:
Library name: GD006_2_GEX
GD006_2
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD005_1, GEX

description:
Library name: GD005_1_GEX
GD005_1
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD004_2, GEX

description:
Library name: GD004_2_GEX
GD004_2
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD009_2, CITE

description:
Library name: GD009_2_CITE
GD009_2
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: PBMC, library GD004_1, GEX

description:
Library name: GD004_1_GEX
GD004_1
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD001_2, GEX

description:
Library name: GD001_2_GEX
GD001_2
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD002, GEX

description:
Library name: GD002_GEX
GD002
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD001_1, GEX

description:
Library name: GD001_1_GEX
GD001_1
GEX_SCT_counts.tsv
metadata.csv


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep9

city: Glasgow

first: Kieran

last: Woolcock

address: Sir Graeme Davies Building, 120 University Place

department: School of Infection & Immunity

institute: University of Glasgow

description: Library name: RA_R60

data_processing:
The fastQ files were quality control checked using FastQC (Andrews, GitHub, v0.11.7) and then aligned to the reference genome and transcriptome GRCh38 (release 102) using STAR (v2.6)
Assembly: GRCh38 (release 102)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Peripheral Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from fresh human blood samples by density gradient centrifugation using Ficoll® Paque Plus (Sigma-Aldrich). To isolate CD14+ monocytes, the EasySep human CD14 positive selection kit II (StemCell Technologies) was used following manufacturer’s instructions.

extract_protocol:
Cells were lysed in RLT buffer (Qiagen) containing 1% beta-mercaptoethanol. RNA was extracted using the PureLinkTM RNA Mini Kit (Invitrogen), as per manufacturer’s instructions. Quality control was performed on the RNA samples using the high sensitivity RNA Analysis Kit (Agilent) on the 2100 Bioanalyzer Instrument (Agilent).
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) following the manufacturer’s instructions. Quality control was performed on the RNA libraries using a high sensitivity DNA Chip (Agilent) on the 2100 Bioanalyzer Instrument (Agilent).

value: Peripheral Blood

tag: subject status

value: Rheumatoid Arthritis

value: Monocyte


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep5

description: Library name: RA_R55


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep7

description: Library name: RA_R57


title: T126899

city: Chengdu

first: Chunjie

last: Li

state: Sichuan

address: No.14, Section 3rd, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

description: Library name: Sample 1

data_processing:
Raw data were processed using Cell Ranger with default parameters to generate gene-barcode matrices, followed by downstream analysis in Scanpy.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing gene expression matrices with genes in rows and cells in columns.

source_name: Tumor

extract_protocol:
Fresh surgical specimens were immediately transferred to the laboratory in ice-cold RPMI 1640 medium.  Tissues were manually minced and enzymatically dissociated using a cocktail of collagenase type I, DNase I, and hyaluronidase at 37°C with gentle agitation to generate single-cell suspensions.  Following enzymatic digestion, cell suspensions were filtered through a 40 μm strainer, centrifuged, and resuspended in PBS with 0.04% BSA.  Cell viability was assessed using trypan blue staining, and samples with viability >85% were processed for library preparation using the 10x Genomics Chromium Single Cell 3' protocol according to the manufacturer’s instructions.
Single-cell suspensions were processed using the 10x Genomics Chromium Single Cell 3ʹ v3 (or v3.1, if applicable) protocol. Cells were loaded onto the Chromium Controller to generate gel bead-in-emulsions (GEMs), enabling barcoding of individual cells. Reverse transcription, cDNA amplification, and library construction were performed according to the manufacturer’s instructions. Final libraries were quantified using a Bioanalyzer (Agilent) and Qubit (Thermo Fisher), and sequenced on an Illumina NovaSeq 6000 platform with paired-end reads.

value: Tumor

value: Parotid gland


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep8

description: Library name: RA_R59


title: T0309

description: Library name: Sample 2


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep6

description: Library name: RA_R56


title: T1213

description: Library name: Sample 5

value: Buccal gland


title: A1213

description: Library name: Sample 3

source_name: Normal

value: Normal

value: Labial gland


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep3

description: Library name: RA_R53


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep2

description: Library name: RA_R52


title: T99352

description: Library name: Sample 4

value: Palatal gland


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep1

description: Library name: RA_R51


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep14

description: Library name: HC_R64_4

value: Healthy Control


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep15

description: Library name: HC_R65_5


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep4

description: Library name: RA_R54


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep13

description: Library name: HC_R63_3


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep10

description: Library name: HC_R30


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep11

description: Library name: HC_R61_1


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep12

description: Library name: HC_R62_2


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep9

description: Library name: HC_R29


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep6

description: Library name: HC_R26


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep7

description: Library name: HC_R27


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep5

description: Library name: HC_R25


title: A126899

description: Library name: Sample 6


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep3

description: Library name: HC_R23


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep4

description: Library name: HC_R24


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep2

description: Library name: HC_R22


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep1

description: Library name: HC_R21


title: HC3

first: Kristina

middle: Elizabeth Neergaard

last: Clark

state: England

address: Royal Free Hospital, Pond Street

institute: UCL

description:
Library name: TY38
10X genomics

data_processing:
FASTQ files were demultiplexed for each 10× library using the Cell Ranger (V.3.1.0) mkfastq function. Reads were mapped to the GRCh38 human genome
Assembly: GRCh38 human genome
Supplementary files format and content: Tab separated values files and matrix files

source_name: Skin

extract_protocol:
The sample was dissociated using the Human Whole Skin Dissociation Kit (Miltenyi Biotech Inc) with Enzyme P, with overnight incubation as per manufacturers guidelines. The dissociated cells were stored in CryoStor CS10 (StemCell Technologies) at −80°C, then transferred to liquid nitrogen after 24 hours.
Thawing occurred just prior to 7-AAD staining (BioLegend 420404) and viable cell sorting by the SH800 Cell sorter (Sony Biotechnology). Viable cells in single-cell suspension were resuspended in 1% BSA in phosphate-buffered saline (PBS) at a concentration of 1000 cells/µL. A maximum of 20 000 cells were counted using the fluorescence cell counter LUNA-FX7 (Logos Biosystems) and loaded onto a single 10× lane and processed with the 10× Genomics Single Cell 3’ kit (V.3.1) following manufacturer user guide (CG000330). Only 3 samples did not reach this target, and about 17 000 cells were loaded. Sequencing was carried out by the Oxford Genomics Centre, using Illumina NovaSeq 6000 (V.1.5 chemistry, 28 bp/98 bp) and libraries were sequenced to a minimum of 50 000 reads/cell. Cells were analysed in 2 batches.

value: Skin

tag: disease

value: HC

tag: batch


title: Pt12

description:
Library name: TY45
10X genomics

value: SSc


title: HC2

description:
Library name: TY34
10X genomics


title: Pt10

description:
Library name: TY35
10X genomics


title: Pt8

description:
Library name: TY39
10X genomics


title: Pt7

description:
Library name: TY43
10X genomics


title: Pt9

description:
Library name: TY44
10X genomics


title: Pt3

description:
Library name: CLA8821A3
10X genomics


title: Pt11

description:
Library name: TY40
10X genomics


title: Pt4

description:
Library name: TY36
10X genomics


title: Pt5

description:
Library name: TY41
10X genomics


title: Pt2

description:
Library name: CLA8821A2
10X genomics


title: HC1

description:
Library name: CLA8821A4
10X genomics