title: combo_gskj4_23

description: Library name: S23


title: ROI 58, Patient 9, Lymph node, MPR

status: Public on Jun 29 2026

type: SRA

city: Beijing

first: Rongzhen

last: Li

state: 北京Beijing

address: Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China

country: China

institute: Peking Union Medical College

description: Library name: ROI 58

library_source: transcriptomic

data_processing:
The raw FASTQ files were run through GeoMx NGS pipelines to acquire digital count conversions and initial data files for further analysis.
The initial data were further processed using quality control (QC) and normalization. RNA data were normalized using Total Count normalization with a scaling factor set at 10,210.
Assembly: mm10
Supplementary files format and content: csv file include normalized count data

molecule: total RNA

organism: Homo sapiens

source_name: Non-small cell lung cancer, Lymph node

extract_protocol:
Formalin-fixed and paraffin-embedded (FFPE) tissues were used to construct tissue microarrays (TMAs). Cores (2.0 mm in diameter) were punched from each FFPE block and arrayed across two recipient TMA blocks. Five-μm-thick TMA sections were deparaffinized and rehydrated, and regions of interest (ROIs) were selected based on immunofluorescence morphology markers.
RNA extraction was performed using the NanoString GeoMx Digital Spatial Profiler according to the manufacturer’s protocol. Briefly, TMA sections were processed and regions of interest (ROIs) were selected based on immunofluorescence morphology markers. Each ROI was sequentially decoupled from the oligonucleotides using ultraviolet (UV) light. UV-cleavable oligos coupled with individual genes were cleaved and collected from all ROIs using a digital mirror device-guided UV illumination. The resultant oligos were amplified by polymerase chain reaction (PCR) amplified (Bio-Rad Laboratories, Hercules, CA, USA) using GeoMx Seq Code primers for downstream library construction.

treatment_protocol: Interventions included pembrolizumab at a fixed dose of 200 mg combined with carboplatin (area under the curve 5) or cisplatin 75mg/m2, pemetrexed at 500 mg/m2 for nonsquamous cell carcinoma, and paclitaxel at 175 mg/m2 or nab-paclitaxel at 260 mg/m2 for squamous cell carcinoma. Surgery was performed after at least two cycles of neoadjuvant therapy. All patients received adjuvant pembrolizumab for up to one year after surgery. To ensure that all patients received four cycles of perioperative chemotherapy, adjuvant chemotherapy was given to patients who had not received adequate neoadjuvant therapy. The surgical approaches were chosen by the surgeon.

tag: tissue

value: Non-small cell lung cancer, Lymph node

tag: batch


title: ROI 57, Patient 9, Lymph node, MPR

description: Library name: ROI 57


title: combo_gskj4_22

city: Cambridge

first: Simon

last: Koplev

address: Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way

department: Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: Library name: S22

data_processing:
Resulting .fastq raw files were quality checked using FASTQC v. 0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MULTIQC v. 1.14. (https://github.com/MultiQC/MultiQC), before quantification using KALLISTO (https://github.com/pachterlab/kallisto) v. 0.48.0 with default settings. Processing of raw files was run in a Python virtual (v. 3.10.8) environment using CGATcore v. 12.2.0 pipeline framework (https://doi.org/10.12688/f1000research.18674.2).
Assembly: hg38
Supplementary files format and content: matrix of kallisto unnormalised counts for all samples (.csv)

source_name: intestine

growth_protocol: The Ccd-18Co colon fibroblast cell line was obtained from ATCC (#CRL-1459) up to passage 20. Ccd-18Co were maintained and expanded and maintained in full growth medium (MEM-alpha Sigma #12571063), Penicillin-Streptomycin (Thermo # 15140148) and 20% FBS (Thermo #A5209501). For experiments, fibroblast cultures were seeded at 25,000 cells in 200ul full growth medium in 48-well format tissue culture plates, unless stated otherwise.

extract_protocol:
RNA was isolated using the Qiagen RNeasey Mini kit (Qiagen #74104) or Zymo Quick-RNA 96 kits (ZymoResearch #R-1052) with the optional on-column DNA digestion step. Isolates from cell cultures were prepared by direct lysis in RNA lysis buffer, followed by RNA isolation with the Zymo RNA extraction kits including on-column DNase treatment. Isolated RNA was stored at –80C until further processing or shipped to service providers.
Libraries were prepared according to manufacturer's instructions, using NEBNext Ultra II RNA Library Prep Kit for Illumnia. Resulting libraries were sequenced on an Illumina NextSeq500.

treatment_protocol: Ccd-18Co were seeded at 25,000 cells in 200ul of full growth medium in 48-well format tissue culture plates. After attachment, cells were subjected to three pulses (1 pulse: 72h of cytokines in serum-free medium followed by 96h of recovery in full growth medium) of cytokine cocktail (TNF, OSM and IL-17A at 10ng/ml each; IL-1B at 0.1 ng/ml) stimulations. After a resting period of 1 week, Ccd-18Co were subjected to either DMSO, 250nM Belinostat or 10uM GSKJ4, each diluted 1:5000 in serum-free medium for a total of 5 days. After the 5 days, cells were returned to full growth medium. Cell extracts for RNAseq were prepared 2 weeks after the final epigenetic modulator treatment.

value: intestine

tag: cell line

tag: cell type

value: fibroblast


title: ROI 56, Patient 9, Lymph node, MPR

description: Library name: ROI 56


title: E13.5-Cramp1-KO-AZT-DNA-nanopore

city: Shanghai

first: Yu

last: Liang

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

description: Library name: sample6

library_source: genomic

data_processing:
Sequencing data were aligned to Drosophila melanogaster reference genome dm6/mm10 and corresponding transposon sequences via Minimap2 (v 2.17-r941). After mapping, two files, "dm6/mm10 PAF file" and "TE PAF file", were generated. The alignments with mapping quality less than 30 or target sequence length less than 200bp were filtered. Python script was written to process two filtered PAF files to find insertions.
Assembly: dm6 and Drosophila TE consensus sequence for fruitfly; mm10 and repBase sequence for mouse.
Supplementary files format and content: bed files contain TE insertion sites

molecule: genomic DNA

organism: Mus musculus

source_name: E13.5d Liver

extract_protocol:
Genomic DNA from fly samples was extracted using Buffer A (100 mM Tris-HCl pH7.5, 100 mM EDTA, 100 mM NaCl, 0.5% SDS) and Buffer B (28.6% 5 M potassium acetate and 71.4% 6 M lithium chloride) reagents. Genomic DNA from fetal livers was extracted by using lysis buffer (100 mM Tris-HCl pH7.5, 50 mM NaCl, 5 mM EDTA, 0.2% SDS) with Protease K.
Genomic DNA extracted from Drosophila hindguts, ovaries and mouse fetal livers was sent toBenagen for quality control and Nanopore Sequencing.

value: E13.5d Liver

tag: genotype

value: Cramp1 mutant

tag: treatment

value: AZT


title: ROI 55, Patient 9, Primary tumor bed, MPR

description: Library name: ROI 55

source_name: Non-small cell lung cancer, Primary tumor bed


title: combo_gskj4_21

description: Library name: S21


title: ROI 54, Patient 9, Primary tumor bed, MPR

description: Library name: ROI 54

value: Non-small cell lung cancer, Primary tumor bed


title: E13.5-Cramp1-KO-DNA-nanopore

data_processing:
Sequencing data were aligned to Drosophila melanogaster reference genome dm6/mm10 and corresponding transposon sequences via Minimap2 (v 2.17-r941). After mapping, two files, "dm6/mm10 PAF file" and "TE PAF file", were generated. The alignments with mapping quality less than 30 or target sequence length less than 200bp were filtered. Python script was written to process two filtered PAF files to find insertions.
Assembly: dm6 and Drosophila TE consensus sequence for fruitfly; mm10 and repBase sequence for mouse.
Supplementary files format and content: bed files contain TE insertion sites
Library strategy: Nanopore DNA seq


title: ROI 53, Patient 9, Primary tumor bed, MPR

description: Library name: ROI 53


title: ROI 52, Patient 10, Primary tumor bed, MPR

description: Library name: ROI 52


title: A0_Patient_2_Region _4

type: RNA

city: St. Louis

first: Daniel

last: Kreisel

state: Missouri

address: 660 Euclid Ave

country: USA

institute: Washington University School of Medicine

hyb_protocol: The Xenium Human Lung Gene Expression hLung_v1.1 was used with 289 genes.  Hybridization was performed by 10X Genomics Protocol CG000582_XeniumInSitu_GeneExpression_UserGuide_RevH

scan_protocol: Imaging, processing, decoding, QC, and multimodal cell segmentation was performed onboard the Xenium Analyzer . The instrument software version was 2.0.1.0 and the analysis version was xenium-2.0.0.10

data_processing: Onboard Analysis: xenium-2.0.0.10

label: Xenium probe set

source_name: lung

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: FFPE blocks were sectioned at 5 microns thickness onto Xenium Slides. Tissue was deparrafinized and decrosslinkd by 10x Genomics Protocl CG000580_Demonstrated_Protocol_Xenium_FFPE_Deparaffinization_Decrosslinking_RevB

value: lung

tag: tissue preservation method

value: FFPE

tag: rejection grade


title: ROI 51, Patient 8, Lymph node, MPR

description: Library name: ROI 51


title: combo_belinostat 19

description: Library name: S19


title: ROI 50, Patient 8, Lymph node, MPR

description: Library name: ROI 50


title: ROI 49, Patient 8, Lymph node, MPR

description: Library name: ROI 49


title: combo_belinostat 18

description: Library name: S18


title: ROI 48, Patient 8, Primary tumor bed, MPR

description: Library name: ROI 48


title: A0_Patient_2_Region _3


title: ROI 47, Patient 8, Primary tumor bed, MPR

description: Library name: ROI 47


title: combo_belinostat 17

description: Library name: S17


title: ROI 46, Patient 8, Primary tumor bed, MPR

description: Library name: ROI 46


title: A0_Patient_2_Region _2


title: ROI 45, Patient 7, Lymph node, MPR

description: Library name: ROI 45


title: combo_dmso 16

description: Library name: S16


title: ROI 44, Patient 7, Lymph node, MPR

description: Library name: ROI 44


title: ROI 43, Patient 7, Lymph node, MPR

description: Library name: ROI 43


title: A0_Patient_2_Region _1


title: combo_dmso 15

description: Library name: S15


title: ROI 42, Patient 7, Primary tumor bed, MPR

description: Library name: ROI 42


title: ROI 41, Patient 7, Primary tumor bed, MPR

description: Library name: ROI 41


title: combo_dmso 14

description: Library name: S14


title: ROI 40, Patient 7, Primary tumor bed, MPR

description: Library name: ROI 40


title: ROI 39, Patient 6, Lymph node, MPR

description: Library name: ROI 39


title: combo_dmso 13

description: Library name: S13


title: A3_Patient_1_Region _2


title: ROI 37, Patient 6, Lymph node, MPR

description: Library name: ROI 37


title: unstim_dmso 4

description: Library name: S4


title: ROI 35, Patient 6, Primary tumor bed, MPR

description: Library name: ROI 35


title: unstim_dmso 3

description: Library name: S3


title: ROI 34, Patient 6, Primary tumor bed, MPR

description: Library name: ROI 34


title: Granuloma at 90 days_2

city: Stony Brook

first: Maurizio

last: Del Poeta

state: NY

address: 150 Life Science Building

department: Molecular Genetics and Microbiology

institute: Stony Brook University

hyb_protocol: For cell segmentation, sections were stained with a cocktail of antibodies directed against nuclear, membrane, and cytoplasmic markers (E-cadherin, ATP1A1, CD45, vimentin, α-SMA), after a blocking step to limit nonspecific binding. Staining was carried out overnight, followed by washes and the incubation with a signal enhancement reagent for 20 min at RT. Autofluorescence quenching was performed to reduce background derived from the lung matrix and FFPE processing by incubating the slides at RT in the dark for 10 minutes with a quenching solution provided with the Xenium kit. Nuclei were counterstained with DAPI, and slides were assembled into Xenium Cassettes v2 for imaging.

scan_protocol: The cassette assemblies prepared as described above were loaded onto the Xenium Prime Analyzer. The instrument performs automated hybridization, imaging, and stripping cycles according to the standard workflow for the Mouse 5K + custom panel (the latter loaded on the instrument as a .JSON file). During each cycle, fluorescent readout probes are hybridized to the amplified barcodes, imaged across all channels, and removed prior to the next cycle. Imaging is conducted with the default optical configuration of the instrument, which provides ~200 nm/pixel resolution. Z-stacks are collected through the full tissue thickness using a 0.75 µm step size. Raw image data are processed by the onboard Xenium software. Molecule detection, barcode identification, and initial quality control are performed automatically, and molecule-resolved output files are generated for downstream analysis.

data_processing: Xenium Explorer 4 (version 4.0.0)

source_name: Lung

extract_protocol: tissue preparation protocol: Spatial profiling was conducted on formalin-fixed paraffin-embedded (FFPE) samples from mouse control lung, and from lungs containing granulomatous lesions. Sections were cut at 5 µm, mounted on Xenium slides, and selected regions from each FFPE section were placed in the 10.45 x 22.45 mm sample area on Xenium slides, dried for 3 hrs at 42°C, and then kept at room temperature in a desiccator for 18h to 1 week. Once ready for processing, the sections were first deparaffinized and decrosslinked according to the Xenium FFPE demonstrated protocol (CG000580). After these initial steps, the tissue was incubated with the Xenium Prime priming oligos (standard Mouse 5K set and custom 47-gene oligos, which anneal to the RNA targets for 1.5 hrs at 50°C, followed by a wash of the excess primers for 30 min at 50°C. An RNase digestion step to release the RNA strand from the bound primers was carried out for 20 min at 37°C, followed by a 1-hour polishing step (also at 37°C), which prepared the cleaved RNA template for efficient probe hybridization. The Xenium Prime probe mix was then added to the sections and allowed to hybridize to the prepared RNA template for 16-24 hrs at 50°C. Unbound probes were washed at 35°C for 15 min, and a ligation reagent was introduced to join the two probe ends that annealed adjacently on the RNA (30 min at 42°C). The ligation produces a circular probe molecule, which is then subjected to enzymatic rolling circle amplification (RCA) to generate many copies of the gene-specific barcode for each detected transcript. The amplification was conducted as instructed with an enhancement reaction for 2 hours at 4°C, and the RCA for 1.5 hrs at 30°C, followed by a post-amplification wash in TE buffer.

value: Lung

value: formalin-fixed paraffin


title: ROI 33, Patient 5, Lymph node, MPR

description: Library name: ROI 33


title: unstim_dmso 2

description: Library name: S2


title: Granuloma at 90 days_1


title: ROI 31, Patient 5, Lymph node, MPR

description: Library name: ROI 31


title: unstim_dmso 1

description: Library name: S1


title: ROI 30, Patient 5, Primary tumor bed, MPR

description: Library name: ROI 30


title: Granuloma at 60 days_2


title: ROI 29, Patient 5, Primary tumor bed, MPR

description: Library name: ROI 29


title: B cells, stimulated A943931, rep5

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

country: France

institute: INSERM

description: Library name: FARNEB-5-4_S20

data_processing:
After quality checking with fastQC, sequencing adapters were trimmed with cutadapt (v3.6) and reads were aligned to GRCh38 (GCA_000001405.15) with bwa-mem2 and duplicates were filtered using samblaster (v0.1.26).
Chromatin accessibility peaks were called running MACS2 (v2.2.7.1) on tagmentation sites extended by 75 bp in each direction, with the –nolambda parameter. Peaks were post-processed as previously described (Corces et al., Science, 2018, PMID:  30361341) to enforce a consistent 500-bp width and to resolve overlaps. Peak maps were built according to Corces et al., 2018, retaining peaks overlapped by at least two distinct samples. Peaks were annotated with the Rgb (v1.7.4) R package (Mareschal et al ;, Bioinformatics, 2014) using Ensembl Genes 106 annotation.
Downstream analysis was performed with R4.1.3. Differential accessibility was analyzed with edgeR (v3.36.0) after filtering for low covered peaks, retaining 55785 ATAC-seq peaks. Putative TF differential binding was tested with chromVAR (v1.16.0) using motifmatchr (v1.16.0) and chromVARmotifs (v0.2.0).
Assembly: GRCh38
Supplementary files format and content: peak_table.txt: tab delimited file, annotated list of peaks
Supplementary files format and content: count_matrix_raw.txt: tab delimited file, matrix of raw read counts (line = peaks, coumns = samples)

source_name: Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from blood donors (Etablissement Français du Sang; code CIRI2) by density-gradient centrifugation over Ficoll (lymphocyte separation medium) at 1800 rpm, for 30 minutes at room temperature, with no brake applied. B cells were isolated using Human REAlease CD19 MicroBead kit and MiniMACS Separation Columns following the manufacturer’ instructions. Purified CD19+ B cells were seeded into a 48-well plate at a density of 106 cells per ml in complete RPMI 1640 medium, supplemented with GlutaMAX, 10% heat-inactivated FCS, 100 U/ml penicillin, 100 μg/ml streptomycin, and then stimulated with 5 μg/mL CpG-B ODN2006 and 10 μg/mL anti-Human IgG + IgM (H+L).

extract_protocol:
Ten thousand live cells were used for each transposition reaction, lyzed, permeabilized and tagmented as described in Corces et al., Nature Genetics 2016 (PMID: 27526324)
ATAC-seq libraries were generated according to the FAST-ATAC protocol (Corces et al., Nature Genetics, 2016, PMID: 27526324) with few changes.  The number of PCR amplification cycles was standardized to 13. The libraries were quantified by qPCR using Library Quantification Primer plus KAPA SYBR FAST and pooled at 1 nM. Samples were sequenced using single-index paired-end (75+75 bp) reads on an Illumina® NextSeq 500 instrument in high-output mode.

treatment_protocol: Purified CD19+ B cells were mock-treated with DMSO or treated with the molecules of interest. Purified CD19+ B cells were as well stimulated through the different receptors and co-receptors separately or on the combination of BCR and CD40 or BCR and TLR9 stimulations and simultaneously treated with the H4R antagonist A943931. CD40 activation was induced by adding 200 ng/mL CD40 ligand and 66 ng/mL anti-tag HA. BCR stimulation alone was performed using 20 μg/mL anti-Human IgG + IgM (H+L).

value: Blood

value: Primary B cells


title: ROI 28, Patient 5, Primary tumor bed, MPR

description: Library name: ROI 28


title: Granuloma at 60 days_1


title: ROI 27, Patient 4, Lymph node, MPR

description: Library name: ROI 27


title: B cells, stimulated DMSO, rep5

description: Library name: FARNEB-5-3_S19

value: DMSO


title: ROI 25, Patient 4, Lymph node, MPR

description: Library name: ROI 25


title: B cells, unstimulated A943931, rep5

description: Library name: FARNEB-5-2_S18


title: ROI 24, Patient 4, Primary tumor bed, MPR

description: Library name: ROI 24


title: Granuloma at 30 days_2


title: ROI 32, Patient 5, Lymph node, MPR

description: Library name: ROI 32


title: ROI 23, Patient 4, Primary tumor bed, MPR

description: Library name: ROI 23


title: B cells, unstimulated DMSO, rep5

description: Library name: FARNEB-5-1_S17


title: ROI 22, Patient 4, Primary tumor bed, MPR

description: Library name: ROI 22


title: Granuloma at 30 days_1


title: KrasG12D+Twist1 overexpression Late,rep6

status: Public on Jun 30 2026

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

description:
Library name: PGRT_4-6M_PDAC6
Column name in raw_count_all.txt:PGRT_4-6M_PDAC6

data_processing:
reads passed QC  are aligned to humann  reference hg38 using aligner HiSat (HISAT2-2.1.0)
read counts were estimated using htseq (2.1.0)
ERCC normalization and batch effect correction is done using RUVseq(1.38.0)
Differential expression analysis is conducted using DESeq2(1.44.0)
Assembly: hg38
Supplementary files format and content: tab-delimited files included the raw counts for each sample.

source_name: Pancreas

growth_protocol: The mice were housed in controlled temperature, humidity, and scheduled light and dark cycles, in groups of no more than five per cage. Food and water were freely available to animals. Cohort age-(>3-5 weeks) and sex-matched mice with the genotypes: (i) Pdx1-Cre (P)/ROSA26-LSL-rtTA-IRES-GFP (G)/LSL-KrasG12D (R) (or PGR) mice; and (ii) Pdx1-Cre/ROSA26-LSL-rtTA-IRESGFP/Twist1-tetO-Luc (T) (or PGT) mice; and (iii) Pdx1-Cre/ROSA26-LSL-rtTA-IRES-GFP/LSL-KrasG12D/Twist1-tetO-Luc (or PGRT) were used in this study. Gene expression in the mouse pancreas was induced using the Pdx1 (Pancreatic and duodenal homeobox 1) promoter-Cre (P) allele to specifically express the Cre recombinase in pancreatic ductal epithelium leading to the stable expression of the KrasG12D oncogene (R) and rtTA-IRES-GFP (G) alleles. Twist1 expression used a reverse tetracycline-controlled transactivator (rtTA), which is knocked in within Rosa26 locus. Doxycycline (DOX) (2 mg/mL in drinking water to 3.4-5 weeks old mice) was added for the temporal gene expression of Twist1. The animals were followed for the  pancreatic cancer symptoms and necropsy was performed to collect the tissues for further analysis. Mice age was indicated in the figure legends for the progression of cancer in genotypes (PGR and PGRT).

extract_protocol:
Total RNA from each sample was extracted using TRIzol Reagent and qc was done through a NanoDrop (Thermo Fisher Scientific Inc.) and agarose gel (1%).
To prepare the library, 1µg of total RNA was used. The libraries of cDNA were prepared using TruSeq sample preparation kit and enriched for mRNA with rRNA depletion and with ERCC spike-in

value: Pancreas

value: KrasG12D+Twist1 overexpression Late


title: tumor tissue derived from FFPE synovial sarcoma sample AYA9

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Library name: AYA9

data_processing:
Raw sequencing data underwent quality assessment using FastQC. High-quality reads were aligned to the human reference genome (hg38) using the STAR aligner (v2.7.10a). Gene-level quantification was performed with featureCounts (v1.6.4) to obtain raw read counts. For gene expression analysis, we applied the voom/limma pipeline. Genes with fewer than 10 reads in more than 95% of samples were excluded to reduce background noise. Normalization was conducted using the trimmed mean of M-values (TMM) method to account for differences in library size and reduce technical variability. The data were then transformed using voom, which converts raw counts into log2 counts per million (log2-CPM) and assigns precision weights to each observation. Differential expression analysis was performed using these transformed values, and P values were adjusted for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR) method. Differential expressed protein coding genes were selected at 0.05 adjusted p-value and 1.5 fold change cut off values.
Assembly: hg18
Supplementary files format and content: compressed FASTQ file obtained from each strand sequencing for all the samples

source_name: cancer tissue

extract_protocol:
Total RNA was extracted after the manually microdissection of neoplastic cells from tumor-representative FFPE  8–10 µm thick sections using the Maxwell® RSC RNA FFPE Kit (Cat: AS1440, Promega Corporation, Madultison, WI, USA) on a semi-automated Maxwell® RSC extractor (Promega) and following the manufacturer’s instructions
Libraries for RNAseq were performed using Illumina Stranded Total RNA Prep with Ribo-ZeroTM Plus (Cat: 20040525, Illumina, San Diego, CA, USA) according to the manufacturer's protocol. Final libraries with optimal quality and quantity criteria, assessed by D1000 Screen tape kit (Agilent Technologies) and Qubit® dsDNA High Sensitivity Assay Kit (Thermofisher) were run on NextSeq550 sequencer (Illumina)

value: soft tissue

value: synovial sarcoma


title: ROI 21, Patient 3, Lymph node, MPR

description: Library name: ROI 21

value: Non-small cell lung cancer, Lymph node


title: B cells, stimulated A943931, rep4

description: Library name: FARNEB-4-4_S16


title: ROI 20, Patient 3, Lymph node, MPR

description: Library name: ROI 20


title: WT-infected mice_1

description:
Library name: WT_1
10X Genomics

library_source: transcriptomic single cell

data_processing:
Initial identification of cell types was performed using Over Representation Analysis 60 using canonical marker lists from previous studies in lung or established databases. Subsetting and re-clustering was performed to enhance identification of different cell types. At this stage a few small clusters that expressed markers from two or more cell types were eliminated. Based on this initial analysis, a hierarchical ontology of cell types was constructed (Supplementary Table S1). Use of a hierarchical approach reduces the possibility of misclassification by relying on multiple choice points in the classification tree before assignment of cell type. A total of several distinct cell types were identified in this analysis although not all cell types were found in every experimental condition.
Assembly: Mouse mm10
Supplementary files format and content: Mus musculus
Supplementary files format and content: Count matrices (barcodes.tsv,features.tsv and matrix.mtx)

extract_protocol:
Lung granulomas and/or lung tissue were rapidly dissected and immediately homogenized. Large granulomas were cut into smaller pieces on ice in the buffer using spring scissors before dounce homogenization. The homogenates were filtered (40 µm Flowmi filters, Bel-Art) and pelleted by centrifugation at 500 g for 5 minutes at 4C. The nuclei pellets were resuspended in homogenization buffer with 25% iodixanol (OptiPrep™ Density Gradient Medium, Millipore Sigma), and single nuclei were purified on an iodixanol gradient (25%-30%-40%) by centrifugation at 2,200 g for 20 minutes at 4C without brake. A 120µl aliquot containing nuclei was taken at the interface between the 30% and the 40% iodixanol layers. Nuclei concentrations were determined using a Countess 2FL and Trypan Blue staining. The nuclei suspensions were used directly for single-nucleus capture in the 10x Genomics Chromium iX. Single nuclei RNA-sequencing was performed using a Chromium Next GEM Single Cell 5' Reagent Kit, v2 on a Chromium iX, according to the manufacturer’s instructions. Briefly, single nuclei suspensions, gel beads, and partitioning oil were loaded onto a Chromium NextGEM K Chip, for a target recovery of up to 10,000 nuclei per sample. The chip was loaded into a Chromium iX (10X Genomics) and single nuclei were captured in Gel Bead-In-Emulsions (GEMs).
Reverse transcription was performed in a PCR cycler, and the cDNA was collected using Recovery Agent (10X Genomics), purified with DynaBeads MyOne Silane beads (10X Genomics), amplified with PCR for 13 cycles, and further purified with SPRISelect reagent (Beckman Coulter). Quality control and quantification of the amplified cDNA was performed on a Tapestation 4200 (Agilent) using D5000 High Sensitivity ScreenTapes (Agilent, 5067-5592). 5’ single nuclei RNA-seq libraries were generated using 50ng of the amplified cDNA. After fragmentation, end-repair, A-tailing and size selection purification, the cDNA was ligated with Illumina adaptors and subsequently purified with SPRISelect reagent. Libraries were amplified and barcoded by PCR with dual index oligonucleotides from the Chromium Dual Index TT Set A kit (10X Genomics), for a total of 15 PCR cycles. The final PCR products were subjected to double-sided size selection with SPRISelect beads (0.6x and 0.8x). The library fragment size distribution was analyzed on the Agilent 4200 Tapestation, and library yields and concentrations were determined by qPCR using the KAPA Illumina Library Quantification PCR kit (Roche Diagnostics). Sequencing of the libraries (min. depth: 20,000 paired reads/nucleus) was performed on an Illumina NovaSeq instrument operated by a commercial provider, with the following paired-end sequencing settings: Read1, 151 cycles; i7 index, 10 cycles; i5 index, 10 cycles; Read2, 151 cycles.

value: Lung cells


title: ROI 75, Patient 13, Primary tumor bed, NMPR

description: Library name: ROI 75


title: ROI 19, Patient 3, Lymph node, MPR

description: Library name: ROI 19


title: WT-infected mice_2


title: B cells, stimulated DMSO, rep4

description: Library name: FARNEB-4-3_S15


title: ROI 26, Patient 4, Lymph node, MPR

description: Library name: ROI 26


title: ROI 18, Patient 3, Primary tumor bed, MPR

description: Library name: ROI 18


title: Granuloma at 30 days_3


title: WT-infected mice_1


title: B cells, unstimulated A943931, rep4

description: Library name: FARNEB-4-2_S14


title: ROI 17, Patient 3, Primary tumor bed, MPR

description: Library name: ROI 17


title: ROI 16, Patient 3, Primary tumor bed, MPR

description: Library name: ROI 16


title: ROI 15, Patient 2, Primary tumor bed, MPR

description: Library name: ROI 15


title: Uninfected mice_2


title: ROI 65, Patient 11, Primary tumor bed, MPR

description: Library name: ROI 65


title: B cells, unstimulated DMSO, rep4

description: Library name: FARNEB-4-1_S13


title: ROI 14, Patient 2, Primary tumor bed, MPR

description: Library name: ROI 14


title: ROI 60, Patient 10, Primary tumor bed, MPR

description: Library name: ROI 60


title: Uninfected mice_1


title: B cells, stimulated A943931, rep3

description: Library name: FARNEB-3-4_S12


title: ROI 13, Patient 2, Primary tumor bed, MPR

description: Library name: ROI 13


title: ROI 12, Patient 2, Primary tumor bed, MPR

description: Library name: ROI 12


title: day0died_10

city: Tokyo

first: Riho

last: Saito

address: 7-3-1 Hongo Bunkyo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: University of Tokyo

description: Library name: Sample46

data_processing:
Sequences were mapped to the mouse reference genome (mm10) with the use of STAR (v 2.7.10a). Raw read counts of each gene was calculated using featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: csv file includes raw read counts for each sample

source_name: Lethal group

extract_protocol:
Approximately 150 µl of blood was collected from the tail artery into a tube containing 100 µl of 50 mM EDTA-2K in PBS. The red blood cells were lysed with ACK lysing buffer (Thermo, A1049201). Cells were incubated at 4°C for 15 min firstly with anti-CXCR2 antibody (1:50, clone SA044G4, BioLegend, 149304) and subsequently with anti-PE microbeads (1:100, Miltenyi Biotec, 130-048-801). Subsequently, cells were subjected to Magnetic Activated Cell Sorting (MACS) (Miltenyi Biotec) and magnetically retained cells were eluted from the MS column and collected by centrifugation for 5 min at 400 x g/4°C. Total RNA was isolated from isolated with the use of RNAiso Plus reagent (Takara).
RNA libraries were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer’s protocols.
Sequencing was carried out on a DNBSEQ-G400RS platform with 100 bp single-end reads. Adaptor sequences were converted into the DNBSEQ format using the MGIEasy Universal Library Conversion Kit (App-A) (MGI).

treatment_protocol: Blood was sampled from 8 weeks old C57B6J WT male mice. After the sampling, they received intranasal vesicular stomatitis virus infection with 1.0 x 10^7 PFU in 50μl PBS under 5% isoflurane anesthesia. Their survival and body weight were monitored for 14 days. Mice lost more than 30% of body weight at the time of the infection or survived over 14 days after the infection was euthanized for humane endpoint.

value: CXCR2+ cells

value: C57B6J WT

value: Sampled before VSV (New Jersey) intranasal infection


title: B cells, stimulated DMSO, rep3

description: Library name: FARNEB-3-3_S11


title: ROI 11, Patient 2, Primary tumor bed, MPR

description: Library name: ROI 11

value: Non-small cell lung cancer, Primary tumor bed


title: ROI 10, Patient 2, Primary tumor bed, MPR

description: Library name: ROI 10


title: day0died_9

description: Library name: Sample45


title: ROI 9, Patient 1, Lymph node, MPR

description: Library name: ROI 9


title: B cells, unstimulated A943931, rep3

description: Library name: FARNEB-3-2_S10


title: E13.5-Cramp1-WT-DNA-nanopore

value: E13.5d Liver

value: Cramp1 heterozygote


title: ROI 8, Patient 1, Lymph node, MPR

description: Library name: ROI 8


title: day0died_8

description: Library name: Sample44


title: ROI 7, Patient 1, Lymph node, MPR

description: Library name: ROI 7


title: combo_belinostat 20

description: Library name: S20

value: intestine

value: fibroblast


title: ROI 6, Patient 1, Primary tumor bed, MPR

description: Library name: ROI 6


title: day0died_7

description: Library name: Sample43

value: Blood


title: B cells, unstimulated DMSO, rep3

description: Library name: FARNEB-3-1_S9

value: Primary B cells


title: ROI 5, Patient 1, Primary tumor bed, MPR

description: Library name: ROI 5


title: B cells, stimulated A943931, rep2

description: Library name: FARNEB-2-4_S8


title: ROI 4, Patient 1, Primary tumor bed, MPR

description: Library name: ROI 4


title: day0died_6

description: Library name: Sample42


title: A3_Patient_2_Region _1`

value: lung

value: FFPE


title: ROI 3, Patient 1, Primary tumor bed, MPR

description: Library name: ROI 3


title: B cells, stimulated DMSO, rep2

description: Library name: FARNEB-2-3_S7

value: DMSO


title: ROI 2, Patient 1, Primary tumor bed, MPR

description: Library name: ROI 2


title: day0died_5

description: Library name: Sample41


title: ROI 1, Patient 1, Primary tumor bed, MPR

description: Library name: ROI 1


title: B cells, unstimulated A943931, rep2

description: Library name: FARNEB-2-2_S6


title: CON3 control neuron

city: Cleveland

first: Tian

last: Liu

state: Ohio

address: 2103 Cornell Road

department: Pathology

institute: Case Western Reserve University

description:
Library name: CON3
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.

data_processing:
Sequencing reads were aligned to the human reference genome using Bismark.
Duplicate reads were removed prior to downstream analysis.
Methylation calls were extracted using the Bismark methylation extractor.
CpG methylation levels were calculated for each sample.
Differential methylation analysis (DML, DMR, and CpG-level analysis) was performed by Azenta.
Assembly: GRCh38
Supplementary files format and content: Processed data include Bismark methylation call files (*.bismark.cov.gz) and CpG methylation tables (*.txt.gz), containing genomic coordinates and CpG methylation levels.
Supplementary files format and content: Additional processed files include differential methylation results, including differentially methylated CpGs (DM), loci (DML), and regions (DMR).  Summary analysis reports are provided as HTML files.

source_name: fibroblast-converted neuron

growth_protocol: Directly reprogrammed human neurons were cultured under standard neuronal culture conditions.

extract_protocol:
Genomic DNA was extracted from directly reprogrammed human neurons using a standard DNA extraction method.
DNA methylation libraries were prepared using the NEBNext Enzymatic Methyl-seq (EM-seq) kit according to the manufacturer’s instructions.

treatment_protocol: Cells were subjected to CHCHD10-WT overexpression prior to DNA methylation analysis.

value: fibroblast-converted neuron

value: control


title: B cells, unstimulated DMSO, rep2

description: Library name: FARNEB-2-1_S5


title: CON2 control neuron

description:
Library name: CON2
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.


title: day0died_4

description: Library name: Sample40


title: day0died_3

description: Library name: Sample39


title: CON1 control neuron

description:
Library name: CON1
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.


title: B cells, stimulated A943931, rep1

description: Library name: FARNEB-1-4_S4


title: ADD10-4 CHCHD10-WT neuron

description:
Library name: ADD10-4
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.

value: CHCHD10-WT overexpression


title: ADD10-3 CHCHD10-WT neuron

description:
Library name: ADD10-3
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.


title: CON4 control neuron

description:
Library name: CON4
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.


title: day0died_2

description: Library name: Sample38


title: A0_Patient_1_Region _1


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 1 biological replicate 3

city: Vancouver

first: Luis

middle: M.

last: Silva

state: British Columbia

address: 2212 Main Mall

department: Department of Zoology

country: Canada

institute: The University of British Columbia

description:
Library name: L13
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 1, biological replicate 3; column name in processed expression matrix: L13

data_processing:
Demultiplexing was performed with bcl2fastq2 v2.20.
Adapters and low-quality bases were removed with Cutadapt, reads shorter than 40 nt were discarded, and reads mapping to rRNA were removed with fastq_screen. Filtered reads were aligned to a concatenated Anopheles gambiae and Vavraia culicis reference using STAR. Gene-level counts were obtained with htseq-count.
Assembly: Anopheles gambiae assembly GCA_943734735.2 and Vavraia culicis floridensis assembly GCA_000192795.1
Supplementary files format and content: File_S9_data1.txt: tab-delimited processed host gene expression matrix for all 48 samples, with gene identifiers, sample expression values and gene annotation columns.

molecule: polyA RNA

organism: Anopheles gambiae

source_name: whole adult female mosquito

growth_protocol: Anopheles gambiae Kisumu larvae were reared under standard insectary conditions at 26 ± 1 °C, 70 ± 5% relative humidity and a 12 h light:12 h dark cycle. Freshly hatched larvae were reared at 50 larvae in 80 ml distilled water and fed daily with fish food. Adult females were maintained with constant access to 6% sucrose solution.

extract_protocol:
Total RNA was extracted from independent pools of 10 adult females using the Qiagen RNeasy Universal Plus kit. Adults were homogenized in QIAzol reagent with stainless steel beads, genomic DNA was removed according to the manufacturer protocol, and RNA was eluted in nuclease-free water.
RNA quality was assessed on an Agilent Fragment Analyzer. Libraries were prepared from 250 ng total RNA per sample using the Illumina Stranded mRNA Prep kit with unique dual indices and sequenced as 150 bp single-end reads on an Illumina NovaSeq 6000 platform.

treatment_protocol: On day 2 of larval development, mosquitoes were exposed to 10,000 Vavraia culicis spores per larva from the relevant parasite lineage. Treatments were uninfected controls, an unselected reference parasite lineage, five early-selected parasite lineages and five late-selected parasite lineages. Adult females were sampled on day 10 of adulthood, when infections were chronic and sporulating.

value: whole adult female mosquito

value: Kisumu


title: B cells, stimulated DMSO, rep1

description: Library name: FARNEB-1-3_S3


title: ADD10-2 CHCHD10-WT neuron

description:
Library name: ADD10-2
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.


title: Shoot,2,5-D,24hours,rep2

city: Saijo

first: Theint

last: Thida

state: 広島県

address: 2081-1, Joy Seven, room no. 213

department: Hiroshima University

institute: Hiroshima University

description:
Library name: Sample4
Shoot_Proceed_Data.txt

data_processing:
HISAT2 v2.0.4
Assembly: GCF_000001735.4
Supplementary files format and content: txt files include TPM values for each Sample

organism: Arabidopsis thaliana

source_name: Shoot

growth_protocol: 100 µM of 2,5-dimethylpyrazine volatile and sterilized water (control) applied to the paper disc.  After 14 days of co-cultivation in the I-plate, shoots and roots from plants were harvested.

extract_protocol:
RNA was harvested using RNA Extraction Kit Mini. 100 ng of total RNA was used for the construction of sequencing libraries.
DNBSEQ Fast RNA Library Prep Set is paired with DNBSEQ UDB Primers Adapter Kit for library construction.

treatment_protocol: Arabidopsis plants were treated with 100 µM of 2,5-D, along with a control group treated with water,  for 24 hours

tag: ecotype

value: Shoot

value: WT

tag: time


title: ROI 118, Patient 21, Primary tumor bed, NMPR

description: Library name: ROI 118

value: Non-small cell lung cancer, Primary tumor bed


title: ADD10-1 CHCHD10-WT neuron

description:
Library name: ADD10-1
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.


title: AD4 AD neuron

description:
Library name: AD4
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.

value: AD


title: day0survived_10

description: Library name: Sample10

source_name: Survival group

value: CXCR2+ cells

value: C57B6J WT

value: Sampled before VSV (New Jersey) intranasal infection


title: day0died_1

description: Library name: Sample37

value: Blood


title: B cells, unstimulated A943931, rep1

description: Library name: FARNEB-1-2_S2

value: Primary B cells


title: ROI 117, Patient 21, Primary tumor bed, NMPR

description: Library name: ROI 117


title: B cells, unstimulated DMSO, rep1

description: Library name: FARNEB-1-1_S1


title: A3_Patient_1_Region _3

value: lung


title: AD3 AD neuron

description:
Library name: AD3
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.


title: AD2 AD neuron

description:
Library name: AD2
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.


title: AD1 AD neuron

description:
Library name: AD1
Processed DNA methylation data are provided at the study level as supplementary files; raw FASTQ files are unavailable.


title: ROI 38, Patient 6, Lymph node, MPR

description: Library name: ROI 38

value: Non-small cell lung cancer, Lymph node


title: shwhite-RNAseq-Rep2

description: bynGal4_sh-white_VS_sh-crm-4F8_pupa4d_HG_RNAseq_rep1and2_transposon.csv

data_processing:
The expression of genes and transposons was analyzed and quantified by piPipes.
Assembly: dm6 and Drosophila TE consensus sequence for fruitfly; mm10 and repBase sequence for mouse.
Supplementary files format and content: csv

organism: Drosophila melanogaster

source_name: pupa 4d hindgut

extract_protocol:
Total RNA was extracted by using TRIzol Reagent (Invitrogen, CAT#: 15596018) and precipitated by isopropanol. 10µg of total RNA was treated with DNase and then purified by RNA Clean & Concentrator-5 (Zymo research, CAT#: R1016).
One µg of purified RNA was used for RNA-Seq library preparation by utilizing TruSeq Stranded Total RNA Library Prep kit (Illumina, CAT#: 20020596).

value: pupa 4d hindgut

value: sh-white


title: 9-SEL120-3-8H

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

description: Library name: 9-SEL120-3-8H

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations and taking account a reverse strand orientation.
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and the RNeasy MinElute Cleanup Kit.
cDNA libraries were prepared from total RNA using a PolyA selection and were further amplified for sequencing.

value: acute myeloid leukemia cells


title: day0survived_9

description: Library name: Sample9


title: 8-SEL120-2-8H

description: Library name: 8-SEL120-2-8H


title: 7-SEL120-1-8H

description: Library name: 7-SEL120-1-8H


title: shcrm-RNAseq-Rep2


title: day0survived_8

description: Library name: Sample8


title: 6-874-3-8H

description: Library name: 6-874-3-8H


title: shwhite-RNAseq-Rep1


title: 5-874-2-8H

description: Library name: 5-874-2-8H


title: day0survived_6

description: Library name: Sample6


title: 4-874-1-8H

description: Library name: 4-874-1-8H


title: shcrm-RNAseq-Rep1


title: day0survived_5

description: Library name: Sample5


title: 2-DMSO-2-8H

description: Library name: 2-DMSO-2-8H

value: DMSO


title: dcramp1-GFP-L3-Input-rep1

description: 20230603_crm-GFP-L3-ChIP_k1_chip-input.bw

data_processing:
Adapters were trimmed via cutadapt (v 4.1) with parameters -e 0.1 -O 3 -m 55 --quality-cutoff 25, then using bowtie2 with default parameters aligned reads to dm6 and TE sequences.  Functions “view” and “sort” of samtools (v 1.9) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further deduplicated by picard (v2.18.7) and converted to bed files by the bedtools (v2.25.0) bamToBed command. BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig.
Assembly: dm6; Drosophila TE consensus sequence
Supplementary files format and content: bigwig

source_name: Larva3 hindgut

extract_protocol:
Tissues were dissected in ice-cold PBS and fixed in 1.8% PFA. Samples were sonicated and protein-DNA complexes were immunoprecipitated. DNA was purified by using Phenol/Chloroform and precipitated by using ethanol.
Libraries for ChIP-Seq were prepared by using TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, CAT#: TD502/TD503). The libraries were purified by RNAClean XP beads and sent to Novogene for quality control and sequencing.

value: Larva3 hindgut

tag: chip antibody

value: dCramp1-GFP knock-in


title: day0survived_4

description: Library name: Sample4


title: dcramp1-GFP-L3-ChIP-rep1

value: GFP (CAT#:ab290)


title: 16-SEL120-1-24H

description: Library name: 16-SEL120-1-24H

value: WT


title: day0survived_3

description: Library name: Sample3


title: sh-white-H3K9me3-Input-rep2

source_name: Pupa 4d hindgut

value: Pupa 4d hindgut


title: day0survived_2

description: Library name: Sample2


title: 15-874-3-24H

description: Library name: 15-874-3-24H


title: sh-white-H3K9me3-ChIP-rep2


title: day0survived_1

description: Library name: Sample1


title: 13-874-1-24H

description: Library name: 13-874-1-24H


title: 12-DMSO-3-24H

description: Library name: 12-DMSO-3-24H


title: sh-crm-H3K9me3-Input-rep2


title: day1died_10

description: Library name: Sample46

extract_protocol:
Approximately 150 µl of blood was collected from the tail artery into a tube containing 100 µl of 50 mM EDTA-2K in PBS. The red blood cells were lysed with ACK lysing buffer (Thermo, A1049201). Cells were incubated at 4°C for 15 min firstly with anti-CXCR2 antibody (1:50, clone SA044G4, BioLegend, 149304) and subsequently with anti-PE microbeads (1:100, Miltenyi Biotec, 130-048-801). Subsequently, cells were subjected to Magnetic Activated Cell Sorting (MACS) (Miltenyi Biotec) and magnetically retained cells were eluted from the MS column and collected by centrifugation for 5 min at 400 x g/4°C. Total RNA was isolated from isolated with the use of RNAiso Plus reagent (Takara).
RNA libraries were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer’s protocols.
Sequencing was carried out on an Illumina NextSeq 2000 platform with paired-end 36 bp reads or on a DNBSEQ-G400RS platform with 100 bp single-end reads. For DNBSEQ-G400RS sequencing, adaptor sequences were converted into the DNBSEQ format using the MGIEasy Universal Library Conversion Kit (App-A) (MGI).

treatment_protocol: 8 weeks old C57B6J WT male mice received intranasal vesicular stomatitis virus infection with 1.0 x 10^7 PFU in 50μl PBS under 5% isoflurane anesthesia. Their survival and body weight were monitored for 14 days. Mice lost more than 30% of body weight at the time of the infection or survived over 14 days after the infection was euthanized for humane endpoint.

value: VSV (New Jersey) intranasal infection

tag: group

value: Lethal group


title: sh-crm-H3K9me3-ChIP-rep2


title: Rep12

city: houston

first: Suresh

last: Satpati

state: Texas

address: 1901 east road scrb4

department: GENOMIC MEDICINE

institute: MD ANDERSON CANCER CENTER

description: Library name: Sample12

data_processing:
All data were processed using fastqc
bwa
dmrseq
Assembly: hg38
Supplementary files format and content: bismark,cov.gz

extract_protocol:
The genomic DNA from treated cells was isolated using the QIAamp DNA Kit (Qiagen, Germantown, MD). Briefly, cells were lysed with proteinase K in lysis buffer from the kit and incubated at 56 °C for 10min. DNA was then extracted with ethanol and purified using the spin column from the kit. The isolated DNA was dissolved into the AE buffer from kit and subjected to RRBS.
Reduced Representation Bisulfite Sequencing (RRBS). We applied RRBS (Meissner, Mikkelsen et al. 2008, Gu, Smith et al. 2011) to evaluate CpG DNA methylation genome wide. Libraries were prepared from genomic DNA using Ovationâ RRBS Methyl-Seq Kit (Tecan Trading AG, Switzerland) at the MDACC Epigenomics Profiling Core. In brief, 100 ng of genomic DNA was digested with MspI restriction enzyme, and Illumina-compatible cytosine-methylated adaptor were ligated to the enzyme-digested DNA. Following repair and bisulfite-conversion, library preparation was done by PCR amplification. Libraries were quantitated using Qubit 4 Fluorometer (ThermoFisher Scientific, Waltham, MA) and further evaluated using a 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA). Pooled libraries were sequenced on an Illumina NovaSeq 6000 instrument as 76-bp single-end reads, at the MDACC Advanced Technology Genomics Core

value: AML

value: TP53 wild type

value: control


title: day1died_9

description: Library name: Sample45

value: Blood

value: CXCR2+ cells

value: C57B6J WT


title: sh-white-H3K9me3-Input-rep1


title: Rep11

description: Library name: Sample11

value: NTX-301 high dose


title: Rep10

description: Library name: Sample10


title: day1died_8

description: Library name: Sample44


title: Rep9

description: Library name: Sample9


title: Rep8

description: Library name: Sample8


title: day1died_7

description: Library name: Sample43


title: Rep7

description: Library name: Sample7


title: sh-crm-H3K9me3-Input-rep1


title: Rep6

description: Library name: Sample6


title: day1died_6

description: Library name: Sample42


title: Rep5

description: Library name: Sample5


title: Rep4

description: Library name: Sample4


title: day1died_5

description: Library name: Sample41


title: sh-crm-H3K9me3-ChIP-rep1


title: Rep3

description: Library name: Sample3

value: TP53 knockout


title: sh-white-H3K36me2-Input-rep2

value: sh-white


title: Rep2

description: Library name: Sample2


title: day1died_4

description: Library name: Sample40


title: Rep1

description: Library name: Sample1


title: sh-white-H3K36me2-ChIP-rep2


title: day1died_3

description: Library name: Sample39


title: FFA scalp scRNA-seq – FFA010

city: New York

first: Juan

last: Ruano

address: 1230 York ave

institute: Rockefeller University

description:
Library name: FFA010
Frontal fibrosing alopecia scalp biopsy

data_processing:
Raw sequencing reads were demultiplexed, aligned and quantified using Cell Ranger (10x Genomics).
Reads were aligned to the human reference genome (GRCh38).
Filtered feature-barcode matrices were generated for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Processed data consist of Cell Ranger filtered feature-barcode matrices (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) and quality control summary files.

source_name: scalp skin

extract_protocol:
Scalp skin biopsies were enzymatically and mechanically dissociated to generate single-cell suspensions according to standard protocols.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3′ Library Prep Kit following the manufacturer’s instructions.

value: scalp skin

value: single cell


title: day1died_2

description: Library name: Sample38


title: FFA scalp scRNA-seq – FFA005

description:
Library name: FFA005
Frontal fibrosing alopecia scalp biopsy


title: Control scalp scRNA-seq – CON267

description:
Library name: CON267
Control scalp skin biopsy


title: sh-crm-H3K36me2-ChIP-rep2


title: day1died_1

description: Library name: Sample37


title: Control scalp scRNA-seq – CON265

description:
Library name: CON265
Control scalp skin biopsy


title: Control scalp scRNA-seq – CON256

description:
Library name: CON256
Control scalp skin biopsy


title: sh-white-H3K36me2-ChIP-rep1


title: Anakinra, PBS, c

city: La Jolla

first: Jared

middle: S

last: Simmons

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

description: Library name: ana_pbs_c

data_processing:
Cell Ranger (10X Genomics) with default parameters was used to perform sample demultiplexing, barcode processing, alignment to the mm10 reference genome, and gene counting
Assembly: mm10
Supplementary files format and content: _barcodes.tsv.gz barcodes in tab-separated values files for each sample (scRNA-seq)
Supplementary files format and content: _features.tsv.gz gene symbols in tab-separated values files for each sample (scRNA-seq)
Supplementary files format and content: _matrix.mtx.gz counts matrices in matrix files for each sample (scRNA-seq)
Supplementary files format and content: bulk_filtered_counts.txt filtered count matrix by gene symbol (rows) and sample (columns) (RNA-seq)

source_name: human preadipocyte

extract_protocol:
Single-cell suspensions generated from mouse skin
10X Genomics Chromium GEM-X Single Cell 3'

value: human preadipocyte

value: wild type

tag: treatment 1

value: 24h Anakinra

tag: treatment 2

value: 4h KC-CM


title: Anakinra, PBS, b

description: Library name: ana_pbs_b


title: sh-crm-H3K36me2-Input-rep1

value: Pupa 4d hindgut


title: Anakinra, PBS, a

description: Library name: ana_pbs_a


title: day1survived_7

description: Library name: Sample7

value: VSV (New Jersey) intranasal infection

value: Survival group


title: Anakinra, KC-CM, c

description: Library name: ana_dial_c

value: 24h PBS


title: sh-crm-H3K36me2-ChIP-rep1


title: Anakinra, KC-CM, b

description: Library name: ana_dial_b


title: day1survived_6

description: Library name: Sample6


title: Total_RNA_TM_replica2

city: Heidelberg

first: Mykola

last: Roiuk

address: Im Neuenheimer Feld 580

department: Signal Transduction in Cancer and Metabolism

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Library name: Total_RNA_TM_replica2_438652

data_processing:
for footprints only: removal of of adaptors and randomized nucleotides.
The reads aligning to tRNA or rRNA were removed using bowtie2.
Remaining reads were mapped to the human transcriptome (Ensemble transcript assembly 94) and genome (hg38) using BBMap software, with multiple mapping allowed
The reads mapping to the coding sequences were quantified with lab-based software written in C (https://github.com/aurelioteleman/Teleman-Lab).
To enable to comparison between samples reads were normalised to the library depth, and rpkm values were quantified.
Assembly: Assembly: hg38
Supplementary files format and content: Supplementary files format and content: The processed data file contains raw reads for each of the samples. The reads are not normalised to the library depth. Reads mapped to the coding sequence were counted in Ribosome profiling libraries and total RNA for ribosome profiling samples.

source_name: epithelial cells

extract_protocol:
Total RNA was extracted with Qiagene Rneasy Kit. Ribosomal footprints were extracted from the monosomal fraction after RNaseI digestion via the size selection. rRNA depletion samples were depleted with Illumina rRNA depletion kit (discontinued)
Libraries from total RNA samples were prepared using the Illumina TruSeq Stranded library preparation kit. Ribosomal footprints were converted into libraries with the use of Next-Flex small RNA v.4 kit protocol.

value: epithelial cells

value: HeLa

value: an immortal human epithelial cell line

value: wt

value: 1 µg/ml treatment with tunicamycin for 2 hours


title: day1survived_5

description: Library name: Sample5

value: Blood

value: CXCR2+ cells

value: C57B6J WT


title: Total_RNA_TM_replica1

description: Library name: Total_RNA_TM_replica1_438665


title: PBS, KC-CM, a

description: Library name: pbs_dial_a

value: 4h PBS


title: day1survived_4

description: Library name: Sample4


title: PBS, PBS, c

description: Library name: pbs_pbs_c

value: human preadipocyte


title: Total_RNA_DMSO_replica2

description: Library name: Total_RNA_DMSO_replica2_438663

value: DMSO treatment for 2 hours


title: PBS, PBS, b

description: Library name: pbs_pbs_b

value: wild type


title: P2 cerebellar cells, Tead1/2 mutant1, ATACSeq

city: Memphis

first: Xinwei

last: Cao

state: TN

address: 62 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description:
Library name: Tead_Mutant1_ATACSeq
Genome-wide chromatin accessibility of TEAD Mutant1

data_processing:
TrimGalore v0.6.3 was used to trim bulk RNA-seq reads prior to alignment against GRCm38.p6 with STAR v2.7.9a (Gencode M22) and quantification with RSEM v1.3.3. Differential expression was tested with limma-voom (limma v3.42.2, R v4.1.0) on TMM-normalized counts from genes with CPM > 0.1 in at least one condition. For scRNA-seq (Parse Evercode WT), FASTQs were processed with Parse Trailmaker (mm10), and cells passing QC (≥800 UMIs, <5% mitochondrial reads) were retained after doublet removal. Seurat v4.4.0 was used for log-normalization, variable feature selection (2,000 VST features), PCA, and Leiden clustering on 20 PCs without batch correction. ATAC-seq reads were trimmed with Trim-Galore v0.4.4/cutadapt (Q20, first 15 bp removed), aligned with BWA-MEM v0.7.17, and deduplicated with fq2bam v3.0.0.6. Only fragments <2 kb were used; bigWigs were built from 80 bp fragment centers normalized to 20M fragments (UCSC tools v4). Per-sample peaks from MACS2 v2.1.1 were merged across replicates, and differential accessibility was tested with ComBat-seq + edgeR TMM + limma-voom. CUT&RUN reads were trimmed with Trim-Galore v0.4.4/cutadapt (Q20), aligned with bwa aln/samse v0.7.12, and duplicate-marked with biobambam2 v2.0.87. Fragments <2 kb were retained for bigWig generation (80 bp fragment centers, 10M fragment normalization, UCSC tools v4). Narrow peaks for TFs were called with MACS2 v2.1.1 and broad peaks for histone marks with SICER v1.1.
Assembly: Mouse mm10
Supplementary files format and content: Tab separated values files, bigwig files, comma separated values files and matrix files

source_name: Cerebelleum

extract_protocol:
For Bulk RNA-seq, P2 mouse cerebella were dissected from individual pups in cold PBS and immediately processed for total RNA extraction. For scRNA-seq, P7 cerebella were dissected from individual pups (one cerebellum per sample, no pooling) and dissociated into a single-cell suspension with a papain-based kit (Miltenyi Biotec 130-094-802); 1 × 10⁶ cells per animal were fixed with the Parse Biosciences Evercode Fixation v3 kit (ECWT3300), slow-frozen in a Mr. Frosty container, and stored at −80 °C until library preparation. For ATAC-seq, P2 cerebella were dissected in cold PBS and nuclei isolated by brief lysis in cold ATAC lysis buffer prior to Tn5 tagmentation. For CUT&RUN, P2 cerebella were dissected in cold PBS, dissociated into a single-cell/nuclei suspension, immobilized on Concanavalin A–coated magnetic beads, and processed for antibody incubation and pAG-MNase digestion.
For Bulk RNA-seq, total RNA was isolated from P2 cerebella using the Direct-zol RNA MiniPrep kit (Zymo Research #R2052), and sequencing libraries were prepared with the Illumina Stranded Total RNA Prep library kit (Illumina #20040529) according to the manufacturer's instructions. For scRNA-seq, fixed cells were thawed and loaded onto the Parse Biosciences Evercode WT v3 kit, then processed through split-pool combinatorial barcoding per the manufacturer's protocol with a target recovery of ~100,000 cells. For ATAC-seq, nuclei isolated from P2 cerebella were tagmented with the Tn5 transposase using the ATAC-seq kit (Active Motif 53150) and libraries were prepared according to the manufacturer's instructions. For CUT&RUN, cells/nuclei from P2 cerebella were bound to Concanavalin A–coated magnetic beads and incubated at room temperature for 4 h with antibodies against TEAD1, HA (for INSM1 in Insm1^HA/HA^ tissue), KDM1A, H3K4me3, H3K27me3, or H3K27ac, or rabbit IgG as a negative control; chromatin was digested by Ca²⁺-activated pAG-MNase, released fragments purified, and libraries prepared. CUT&RUN libraries were prepared using the NEBNext Ultra II kit (NEB #E7103) with modifications as in https://dx.doi.org/10.17504/protocols.io.bagaibse. Library size and quality for all assays were assessed on an Agilent TapeStation/ Bioanalyzer prior to sequencing.

value: Cerebelleum

value: Atoh1Cre;Tead1fl/fl; ;Tead2fl/fl


title: PBS, PBS, a

description: Library name: pbs_pbs_a


title: Ccd18-Co, OSM 4

city: Cambridge

first: Simon

last: Koplev

address: Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way

institute: University of Cambridge

description: Library name: Sample:48

data_processing:
MACS2 peak calling.
Assembly: TxDb.Hsapiens.UCSC.hg38.knownGene
Supplementary files format and content: Raw peak counts, .tsv format.

source_name: intestine

extract_protocol:
For chromatin accessibility profiling of bulk cell populations (Ccd18-Co intestinal fibroblasts), the Omni-ATAC protocol was followed for nuclei isolation and library preparation was followed. Briefly, fibroblasts were collected by trypsin-based detachment and pelleted by centrifugation. After confirming viability of > 95% (Trypan blue hemacytometer), nuclei were isolated by incubating cells for 3 minutes on ice in nuclei isolation buffer containing 0.1% NP-40, 0.1% Tween20 and 0.01% Digitonin. Following washes, nuclei were transposed (Illumina Nextera Tn5 transposase contained in #FC-121-1030) for 30minutes at 37C with 1000rpm mixing.
Transposed DNA fragments were isolated using Qiagen MinElute PCR Purification Kit (#28004) and pre-amplified for 5 cycles using NEBNext High Fidelity 2x PCR Master Mix (#M0541) and Illumina Nextera primers (#FC-121-1030). At this stage, the additionally required amplification cycles were determined by SYBR green (Invitrogen #S7563) based quantitative PCR. After amplification for additional cycles (between 3-6), amplified DNA was cleaned up using Qiagen MinElute kit and quantified using KAPA absolute quantification kit (Roche #07960166001). Resulting libraries were quality-controlled on an Agilent TapeStation 4200 using High Sensitivity DNA Screen Tape analysis D1000 (Agilent #5067-5584). Libraries were then pooled and size selected using Ampure XP beads (Beckman # A63880), before re-quantification by TapeStation and adjustment to 2.8 pM and sequencing on an Illumina NovaSeq6000.

treatment_protocol: Ccd-18Co were seeded at 25,000 cells in 200ul of full growth medium in 48-well format tissue culture plates. After attachment, cells were stimulated with cytokines in serum-free medium (10ng/ml for each cytokine, except IL-1B 0.1ng/ml). Cellular extracts were prepared immediately after stimulation period.

value: intestine

value: fibroblast


title: day1survived_2

description: Library name: Sample2

value: VSV (New Jersey) intranasal infection

value: Survival group


title: day0survived_7

description: Library name: Sample7

value: Sampled before VSV (New Jersey) intranasal infection


title: Ccd18-Co, OSM 3

description: Library name: Sample:47


title: 3-DMSO-3-8H

description: Library name: 3-DMSO-3-8H

value: acute myeloid leukemia cells

value: WT

value: DMSO


title: 18-SEL120-3-24H

description: Library name: 18-SEL120-3-24H

value: Blood


title: 17-SEL120-2-24H

description: Library name: 17-SEL120-2-24H


title: 1-DMSO-1-8H

description: Library name: 1-DMSO-1-8H


title: Riboseq_TM_rRNA_depleted_replica2

description: Library name: Riboseq_TM_rRNA_depleted_replica2_438648

value: epithelial cells

value: HeLa

value: an immortal human epithelial cell line

value: wt

value: 1 µg/ml treatment with tunicamycin for 2 hours


title: Ccd18-Co, OSM 2

description: Library name: Sample:46


title: day1survived_3

description: Library name: Sample3

value: CXCR2+ cells

value: C57B6J WT


title: 14-874-2-24H

description: Library name: 14-874-2-24H


title: day1survived_1

description: Library name: Sample1


title: 11-DMSO-2-24H

description: Library name: 11-DMSO-2-24H


title: Ccd18-Co, OSM 1

description: Library name: Sample:45


title: 10-DMSO-1-24H

description: Library name: 10-DMSO-1-24H


title: Riboseq_TM_rRNA_depleted_replica1

description: Library name: Riboseq_TM_rRNA_depleted_replica1_438661


title: Ccd18-Co, TNF 4

description: Library name: Sample:44


title: clone68_7

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

description:
Library name: 366723
SMART-Seq v3

data_processing:
Alignment was performed using STAR (v.2.7.9a) on GRCm39 and Gencode vM27 with STAR parameters: --outFilterMultimapNmax 1, --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical, --outFilterScoreMinOverLread 0.22, --outFilterMatchNminOverLread 0.22. Note that we only used the R2 reads from paired end sequencing for this analysis. Reads in exonic and intronic regions (Gencode vM27) were counted using the aligned bam files produced by STAR and summarizeOverlaps (GenomicAlignments v1.40.0, R v4.4.0) with singleEnd=TRUE, mode = "IntersectionNotEmpty", ignore.strand = T, inter.feature = T parameters.
Assembly: GRCm39
Supplementary files format and content: Matrix in csv format with columns corresponding to cells and rows to genes. One file for exonic and one file for intronic reads is given.

source_name: cerebral organoid

growth_protocol: mESCs were plated at high density so that colonies covered approximately half of the well area after 2 days of incubation. Medium was changed 1-2 hours prior to dissociation with StemPro Accutase (Thermo Fisher Scientific) or CTS TrypLE (Thermo Fisher Scientific) for 5 min at 37°C. Cells were counted with an automated cell counter, and were only used if >90% of cells were alive based on Trypan blue staining (Thermo Fisher Scientific). mESCs were centrifuged for 5 min at 200 x g, resuspended in Solution 1, and plated at a density of 3500 cells/microwell in a 24w-Aggrewell plate (Stem Cell Technologies). Solution 1 contained G-MEM (Thermo Fisher Scientific), 10% knockout serum replacement (Thermo Fisher Scientific), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin and WNT inhibitor (3 µM, IWR1, Sigma). No SMAD inhibitors were used as they were not required to direct cortical differentiation in mouse. Embryoid bodies were generated by day (D) 1, which were then transferred to 10 cm dishes with fresh Solution 1 and 2% growth factor-reduced Matrigel (Corning). On D5, organoids were gently pipetted to remove Matrigel and Solution 2 was added, containing DMEM/F12 (Thermo Fisher Scientific), 1% N2 supplement (Thermo Fisher Scientific), 0.1 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin, 1% chemically defined lipid concentrate (Thermo Fisher Scientific), and heparin (1 mg/ml; Sigma). On D7, organoids were transferred to 6-well plates and placed on an orbital shaker at low speed (50 r.p.m.) to prevent organoid fusion. From D9, organoids were grown in medium containing a 50:50 mix of DMEM/F12 and Neurobasal (Thermo Fisher Scientific), 0.5% N2, 1% B27 (Thermo Fisher Scientific), 0.5 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml pen/strep, 1% chemically defined lipid concentrate, and 50 mM 2-mercaptoethanol. Throughout the protocol medium was replaced as necessary every 2-3 days, and orbital shaker speed was increased after D9 (80 r.p.m.). Fused organoids and/or organoids that failed to grow were discarded throughout the procedure. Standard cell culture conditions (37°C with 5% CO2) were applied throughout all procedures.

extract_protocol:
Organoids with MADM clones induced at D13 were collected at D20 for MADM-CloneSeq. The sample collection steps for MADM-CloneSeq were adapted from previously published protocols (PMID: 38968076). Organoids were kept in cell culture membrane (Millicell) in oxygenated (95% O2, 5% CO2) artificial cerebrospinal fluid (ACSF) containing (in mM): 118 NaCl, 2.5 KCl, 1.25 NaH2PO4, 1.5 MgSO4, 1 CaCl2, 10 Glucose, 3 Myo-inositol, 30 Sucrose, 30 NaHCO3 prepared   with ultra-distilled water; pH=7.4, at 35C, until sample collection. All work surface and equipment were cleaned using RNase away solution (Thermo Fisher Scientific) prior to experiments. Single organoids were transferred to a LNscope 240XY miscroscope (Luigs & Neumann) and superfused with ACSF at a rate of 0.5 ml/min at room temperature. Individual clones were visualized under a 20x objective and by using ImageJ software. To observe red or green fluorescence, light was emitted from a LED light source (CoolLED, Andover, UK). Glass pipettes (B150-86-10, Sutter Instrument, Novato, CA) previously autoclaved, were pulled using a P-1000 pipette puller (Sutter Instrument) to generate pipettes with an opening of around 3-5ym. Before use, each pipette was filled with 3.5yl of pipette solution which consisted of RNase inhibitor (Takara, 1.95%) in RNase-free PBS (Invitrogen) filtered through a 0.22mm filter. Red or green fluorescent neurons were approached with the pipette under positive pressure to avoid tissue contamination of the pipette tip. When contact with cell membrane was made, tight seal formation was achieved under IR/DIC visualization. The complete aspiration of the cell body was immediately performed by applying a gentle and steady suction while monitoring under fluorescence and typically takes 5-10 s. The negative pressure was removed immediately once the target cell was collected and the pipette was carefully withdrawn from the acute slice to avoid contamination. The content of each pipette was directly transferred into individual PCR tubes and kept at -80C until cDNA library preparation.
cDNA libraries for individual MADM-CloneSeq cells were were prepared using Smart-seq3 protocol (PMID 32518404) in 3 batches (96well plates).

treatment_protocol: Stock solutions of 4-hydroxytamoxifen (4-OHT, Sigma) were generated by dilution in 100% ethanol to a concentration 1000-fold greater (20-80 µM) than the working solution. A concentration of 60 nM 4-OHT was used for D13. If 4-OHT treatment occurred on a day without medium change, medium was removed from wells containing organoids to be treated and placed in a tube, 4-OHT was added, and medium was added back to wells. After 24 h, medium was completely replaced and organoids were washed 1x with PBS.

value: cerebral organoid

tag: plate

tag: cloneid

tag: color

value: G

tag: clone type

value: N

tag: clone size


title: Ccd18-Co, TNF 3

description: Library name: Sample:43

tag: tissue

value: intestine

tag: cell line

value: fibroblast


title: sh-white-H3K9me3-ChIP-rep1

city: Shanghai

first: Yu

last: Liang

address: Yueyang Road 320

institute: CEMCS, CAS

value: Pupa 4d hindgut

tag: genotype

value: sh-white


title: Riboseq_TM_replica2

description: Library name: Riboseq_TM_replica2_438646

tag: cell type

tag: treatment


title: clone68_6

description:
Library name: 366722
SMART-Seq v3


title: Ccd18-Co, TNF 1

description: Library name: Sample:41


title: Ccd18-Co, TNF 2

description: Library name: Sample:42


title: Ccd18-Co, TGFB1 4

description: Library name: Sample:40


title: clone68_5

description:
Library name: 366721
SMART-Seq v3


title: Riboseq_TM_replica1

description: Library name: Riboseq_TM_replica1_438659


title: Ccd18-Co, TGFB1 3

description: Library name: Sample:39


title: Riboseq_DMSO_rRNA_depleted_replica2

description: Library name: Riboseq_DMSO_rRNA_depleted_replica2_438644

value: DMSO treatment for 2 hours


title: Total_RNA_DMSO_replica1

description: Library name: Total_RNA_DMSO_replica1_438650


title: clone68_4

description:
Library name: 366720
SMART-Seq v3

value: R


title: Ccd18-Co, TGFB1 1

description: Library name: Sample:37


title: Riboseq_DMSO_rRNA_depleted_replica1

description: Library name: Riboseq_DMSO_rRNA_depleted_replica1_438655


title: Ccd18-Co, IFNG 4

description: Library name: Sample:36


title: Ccd18-Co, TGFB1 2

description: Library name: Sample:38


title: clone68_3

description:
Library name: 366719
SMART-Seq v3


title: Ccd18-Co, IFNG 3

description: Library name: Sample:35


title: Ccd18-Co, IFNG 2

description: Library name: Sample:34


title: Riboseq_DMSO_replica2

description: Library name: Riboseq_DMSO_replica2_438657


title: FFA scalp scRNA-seq – FFA007

description:
Library name: FFA007
Frontal fibrosing alopecia scalp biopsy

value: scalp skin

value: single cell

tag: batch


title: FFA scalp scRNA-seq – FFA011

description:
Library name: FFA011
Frontal fibrosing alopecia scalp biopsy


title: sh-crm-H3K36me2-Input-rep2


title: clone68_2

description:
Library name: 366718
SMART-Seq v3


title: Ccd18-Co, IFNG 1

description: Library name: Sample:33


title: Riboseq_DMSO_replica1

description: Library name: Riboseq_DMSO_replica1_438642

value: epithelial cells

value: HeLa


title: clone68_1

description:
Library name: 366717
SMART-Seq v3


title: Ccd18-Co, IFNA 4

description: Library name: Sample:32


title: Sorted CD3+ T cells in hPBMC, treated 14 days with D2L3(TB4), rep4

city: 달성군

first: Jun-Kook

last: Park

state: 대구광역시

address: 대구광역시 테크노북로

country: South Korea

institute: DGIST

description: Library name: D2L3_4

data_processing:
The raw sequencing data were processed by performing quality control using FastQC. Adapter sequences and low-quality reads were trimmed using bbduk, and the resulting clean reads were aligned to the reference genome using Bowtie2. Read quantification was conducted using Bedtools, followed by normalization with the TMM+CPM method using EdgeR. Data mining and graphical visualization were carried out using ExDEGA (Ebiogen Inc., Gangseo-gu, Seoul, South Korea). Differential expression analysis and data visualization, including heatmaps and volcano plots, were conducted using ExDEGA software (Ebiogen Inc., Gangseo-gu, Seoul, South Korea).
Assembly: GRCh38
Supplementary files format and content: A XLSX with fold change, normalized data, raw data, etc

source_name: CD3+ T cells from hPBMC

extract_protocol:
HPBMCs were cultured in the presence of TB4 (500 nM) or IL-7 (1 nM) for 14 days. CD3⁺ T cells were then isolated by flow cytometric sorting using anti -CD3-PerCP-Cy5.5 antibody (300429; BioLegend, San Diego, CA, USA) on an LSR Fortessa III flow cytometer (BD Biosciences, San Jose, CA, USA). Total RNA was extracted from the sorted CD3⁺ T cells using the QIAzol Lysis Reagent (79306; QIAGEN, Hilden, North Rhine-Westphalia, Germany). RNA integrity was assessed using the Agilent TapeStation 4000 system (Agilent Technologies, Amstelveen, The Netherlands), and RNA concentration was measured using the ND-2000 Spectrophotometer (Thermo Fisher Scientific, DE, USA).
For both control and treated samples, sequencing libraries were constructed using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen, Inc., Vienna, Austria) according to the manufacturer’s instructions. Briefly, total RNA was reverse-transcribed using an oligo-dT primer containing an Illumina-compatible sequence at its 5′ end. After RNA template degradation, second-strand synthesis was initiated using a random primer that included a 5′ Illumina-compatible linker. The resulting double-stranded libraries were purified using magnetic beads to remove all reaction components and were subsequently amplified to incorporate the full set of adapter sequences required for cluster generation. The finished libraries were further purified from PCR components, and high-throughput sequencing was performed on an Illumina NextSeq 550 platform, generating single-end 75 bp reads.

value: CD3+ T cells from hPBMC


title: Ccd18-Co, IFNA 2

description: Library name: Sample:30


title: clone67_3

description:
Library name: 366716
SMART-Seq v3

value: SN


title: Sorted CD3+ T cells in hPBMC, treated 14 days with D2L3(TB4), rep3

description: Library name: D2L3_3


title: Ccd18-Co, IFNA 1

description: Library name: Sample:29


title: Ccd18-Co, IL22 3

description: Library name: Sample:27


title: Sorted CD3+ T cells in hPBMC, treated 14 days with D2L3(TB4), rep2

description: Library name: D2L3_2


title: Ccd18-Co, IL22 2

description: Library name: Sample:26


title: clone67_1

description:
Library name: 366714
SMART-Seq v3


title: Ccd18-Co, IL22 4

description: Library name: Sample:28


title: Ccd18-Co, IL22 1

description: Library name: Sample:25


title: clone67_2

description:
Library name: 366715
SMART-Seq v3


title: Sorted CD3+ T cells in hPBMC, treated 14 days with D2L3(TB4), rep1

description: Library name: D2L3_1


title: Ccd18-Co, IL17A 3

description: Library name: Sample:23


title: Sorted CD3+ T cells in hPBMC, treated 14 days with IL-7, rep4

description: Library name: IL7_4


title: clone66_4

description:
Library name: 366712
SMART-Seq v3


title: Ccd18-Co, IL17A 2

description: Library name: Sample:22


title: Sorted CD3+ T cells in hPBMC, treated 14 days with IL-7, rep3

description: Library name: IL7_3


title: Ccd18-Co, IL13 2

description: Library name: Sample:18


title: Ccd18-Co, IL13 1

description: Library name: Sample:17


title: Sorted CD3+ T cells in hPBMC, treated 14 days with IL-7, rep1

description: Library name: IL7_1


title: Ccd18-Co, IL6 4

description: Library name: Sample:16


title: clone66_2

description:
Library name: 366710
SMART-Seq v3


title: clone66_1

description:
Library name: 366709
SMART-Seq v3


title: Ccd18-Co, IL6 3

description: Library name: Sample:15


title: Sorted CD3+ T cells in hPBMC, treated 14 days with PBS, rep4

description: Library name: PBS4

value: PBS


title: Ccd18-Co, IL6 2

description: Library name: Sample:14


title: Ccd18-Co, IL1B 4

description: Library name: Sample:12


title: clone65_3

description:
Library name: 366707
SMART-Seq v3


title: Sorted CD3+ T cells in hPBMC, treated 14 days with PBS, rep2

description: Library name: PBS_2


title: Ccd18-Co, IL1B 2

description: Library name: Sample:10


title: clone65_2

description:
Library name: 366706
SMART-Seq v3


title: Ccd18-Co, IL1B 1

description: Library name: Sample:9


title: Sorted CD3+ T cells in hPBMC, treated 14 days with PBS, rep1

description: Library name: PBS_1


title: Ccd18-Co, unstimulated 4

description: Library name: Sample:4


title: clone65_1

description:
Library name: 366705
SMART-Seq v3


title: Ccd18-Co, unstimulated 3

description: Library name: Sample:3


title: Ccd18-Co, unstimulated 2

description: Library name: Sample:2


title: clone64_3

description:
Library name: 366704
SMART-Seq v3


title: Ccd18-Co, unstimulated 1

description: Library name: Sample:1


title: Si30 cells at P3, replicate 1

city: Guangzhou

first: Jiangfan

address: Xiaoguwei Street

institute: South China University of Technology

description:
Library name: Si30-P3-1
Si30 cells at passage P3

data_processing:
Raw FASTQ data were quality controlled using FastQC and filtered using Cutadapt to remove adapters and low-quality reads (Q<20, length <75 bp).
Clean reads were aligned to the human reference genome (GRCh38) using HISAT2.
Gene expression was quantified using Cufflinks/Cuffdiff to obtain read counts and FPKM values.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Gene count matrices are provided in CSV format for P0 and P1-P3 samples
Supplementary files format and content: FPKM expression matrices are also provided in CSV format for the same samples, with identical structure

source_name: cervical cancer

growth_protocol: HeLa cells were cultured in standard DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA quality was assessed by agarose gel electrophoresis and RNA integrity number (RIN).
RNA sequencing libraries were prepared using standard Illumina TruSeq RNA library preparation kits following the manufacturer's protocol, including mRNA enrichment, fragmentation, cDNA synthesis, end repair, adaptor ligation, and PCR amplification.

treatment_protocol: Cells were subjected to cryosilicification treatment using Si20 or Si30 conditions. Native cells without cryosilicification treatment were used as controls. Samples were collected at early response stage (P0, 0 h and 6 h) and after passaging (P1–P3).

value: cervical cancer

value: Hela

value: epithelial-like cervical cancer cell

value: cryosilicification with Si30

tag: passage


title: CD45-EPCAM- stromal cells_110614

description: Library name: Tissue 20

library_source: genomic single cell

data_processing:
Processing of scATAC-seq data were performed from 10x CellRanger Arrow files with the default ArchR pipeline. Doublet scores were computed with the number of neighbouring cell criteria set at k=10 with the ‘UMAP’ method and ‘tf-logidf’ term frequency-inverse document frequency (TF-IDF) normalization. Doublette cells were excluded by the filterDoublet function with parameters cutEnrich=1 and filterRatio=1, in addition to requiring DoubletScore ≤ 30.
Assembly: GRCh38
Supplementary files format and content: .h5ad format of peak counts

extract_protocol:
Surgical specimens were cleaned up by dissection, and the external muscle layer removed after whole thickness samples were taken for pathology/spatial work. Remaining mucosa and submucosa was minced using surgical scissors and scalpel blades, after removal of bulk epithelial cells by two washes in PBS containing antibiotics (penicillin/streptomycin, amphotericin B, gentamicin, ciprofloxacin) and 5 mM EDTA (Sigma-Aldrich). Minced tissue was then subjected to multiple rounds of digestion in RPMI 1640 medium, 5 mM HEPES, antibiotics as above and 1 mg/ml of Collagenase A and DNase I (Sigma-Aldrich). After 30 min, digestion supernatant containing cells was removed, filtered through a cell strainer, spun down and resuspended in 10 ml of PBS containing 5% bovine serum albumin (BSA) and 5 mM EDTA. Remaining tissue was then topped up with fresh digestion medium until no more cells were liberated. Single-cell suspensions obtained from tissue digests were blocked in PBS 5% BSA containing human anti-Fc block (Miltenyi) stained for FACS analysis or sorting with Fixable Viability Dye eFluor 780 (eBioscience, 1:1,000), DAPI (Invitrogen, 1:50,000) and antibodies (all from Biolegend, except anti-PDPN: clone NZ-1.3 from eBioscience) in PBS with 5% BSA and 5 mM EDTA for 20 min on ice. After washing in the same buffer, cells were sorted on a BD Aria III (100-µm nozzle) for the EPCAM-CD45- stromal fraction. Sorted fractions were immediately processed for 10x single-cell analysis.
Samples were processed according to 10X Chromium Next GEM Single Cell ATAC kit manufacturer's instructions and sequenced on a NovaSeq 6000

value: intestine

value: stromal


title: CD45-EPCAM- stromal cells_110375

description: Library name: Tissue 12


title: Si20 cells at P3, replicate 2

description:
Library name: Si20-P3-2
Si20 cells at passage P3

value: cryosilicification with Si20


title: CD8+ T Cells, Sham or 6Gy, no infection or infected 7dpi

city: Washington

first: Henghong

last: Li

state: DC

address: 3700 Reservoir Rd. NW

department: Oncology

institute: Georgetown University

description:
Library name: Library D2
10X Genomics

data_processing:
The demultiplexing, barcode processing and gene counting were made using Cell Ranger software v7.1.0
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD8+ T Cells

extract_protocol:
Cells were recovered in phenol red free RPMI1640 complete medium (1% L-Glutamine, 5% HEPES, 1% NEAA, 1% Sodium Pyruvate, 50 μM 2-ME, and 0.1% Gentamicin) with 10% fetal bovine serum, and then subjected to red blood cell lysis in ACK lysis buffer. The reaction was neutralized with RPMI1640 complete medium and washed with RPMI1640 complete medium twice. Cell pellets were resuspended in RPMI1640 complete medium for T cell purification. Total CD8+ T cell purifications were performed using the MojoSort Mouse CD8 T Cell Isolation Kit (BioLegend) following manufacturer’s guidelines.
Library construction was performed according to the manufacturers instructions (single cell Chromium Fixed RNA Profiling Reagent Kit for Multiplexed Samples protocol, 10X Genomics)

treatment_protocol: Irradiation and/or Listeria monocytogenes infection

tag: strain

value: CD8+ T Cells


title: Si30 cells at P3, replicate 2

description:
Library name: Si30-P3-2
Si30 cells at passage P3


title: CD45-EPCAM- stromal cells_110373

description: Library name: Tissue 11


title: clone64_1

description:
Library name: 366702
SMART-Seq v3

value: cerebral organoid


title: 7F2, eCLIP, Input, AD Int 4

city: Gainesville

first: John

last: Koren

state: FL

address: 1275 Center Dr

institute: University of Florida

description:
Library name: A20-001 Input
7F2 eCLIP

data_processing:
Eclipse's proprietary analysis pipeline (v1). UMIs were pruned from read sequences using umi_tools (v1.1.1). Next, 3' adapters were trimmed from reads using cutadapt (v3.2). Reads were then mapped to a custom database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the hg38 genome using STAR (v2.7.7a). PCR duplicates were removed using umi_tools (v1.1.1). For each peak, IP versus input fold enrichments and p-values were calculated. Peaks were annotated using transcript information from GENCODE v41 with the following priority hierarchy to define the final annotation of overlapping features: protein coding transcript (CDS, UTRs, intron), followed by non-coding transcripts (exon, intron).
Assembly: Human (hg38)
Supplementary files format and content: excel filss with gene ID, ensemble ID, -log10(P-value), Log2 Fold Change, and feature
Library strategy: iCLIP

source_name: Hippocampus

extract_protocol:
Frozen human hippocampal samples tissue was disrupted by cryogrinder and UV crosslinked at 400 mJoules/cm2 with 254 nm radiation
Van Nostrand, E.L., et al., Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol, 2017. 1648: p. 177-200.

value: Hippocampus

value: ApoE 3/3


title: CD45-EPCAM- stromal cells_110501

description: Library name: Tissue 15


title: Si20 cells at P3, replicate 1

description:
Library name: Si20-P3-1
Si20 cells at passage P3


title: CD45-EPCAM- stromal cells_113395

description: Library name: Tissue 23


title: clone63_4

description:
Library name: 366701
SMART-Seq v3

value: G

value: N


title: 7F2, eCLIP, Input, AD Int 2

description:
Library name: A15-011 Input
7F2 eCLIP


title: Native cells at P3,  replicate 2

description:
Library name: Native-P3-2
Native cells at passage P3

value: No cryosilicification


title: CD8+ T Cells, sham or 3Gy, no infection or infected 4dpi or 7dpi

description:
Library name: Library D1
10X Genomics


title: CD45-EPCAM- stromal cells_113394

description: Library name: Tissue 22


title: CD45-EPCAM- stromal cells_110458

description: Library name: Tissue 14


title: clone64_2

description:
Library name: 366703
SMART-Seq v3


title: clone63_3

description:
Library name: 366700
SMART-Seq v3


title: CD45-EPCAM- stromal cells_110457

description: Library name: Tissue 13


title: Native cells at P3,  replicate 1

description:
Library name: Native-P3-1
Native cells at passage P3


title: clone63_2

description:
Library name: 366699
SMART-Seq v3


title: Ccd18-Co, IFNA 3

description: Library name: Sample:31

value: fibroblast


title: CD45-EPCAM- stromal cells_110560

description: Library name: Tissue 19


title: Si30 cells at P2, replicate 2

description:
Library name: Si30-P2-2
Si30 cells at passage P2


title: CD45-EPCAM- stromal cells_110615

description: Library name: Tissue 21


title: CD45-EPCAM- stromal cells_110559

description: Library name: Tissue 18


title: clone63_1

description:
Library name: 366698
SMART-Seq v3


title: CD45-EPCAM- stromal cells_110543

description: Library name: Tissue 16


title: Si30 cells at P2, replicate 1

description:
Library name: Si30-P2-1
Si30 cells at passage P2


title: Ccd18-Co, IL17A 4

description: Library name: Sample:24


title: CD45-EPCAM- stromal cells, 110615

description: Library name: Tissue 21

data_processing:
Sequences were aligned to GRCh38 with CellRanger using STAR. scRNA-seq doublets were identified with Scrublet and excluded if p<0.5 (BH corrected) or Scrublet score > 0.3. Ribosomal, mitochondrial, and ‘hb’ genes were excluded by string matching. For cell quality control (QC), standard metrics were calculated for: read counts, number of unique genes, percent top-50, along with percentages of mitochondrial, ribosomal, and hb reads per cell. To threshold each QC metric, outliers were detected by fitting univariate 10-component Gaussian mixture models to each observed distribution, using pseudo log-transformed values for count data. Cells were excluded requiring >60% of cells to pass according to the auto_qc_filter() function in the scanpy_scripts package.
Assembly: GRCh38
Supplementary files format and content: .h5ad format

extract_protocol:
Surgical specimens were cleaned up by dissection, and the external muscle layer removed after whole thickness samples were taken for pathology/spatial work. Remaining mucosa and submucosa was minced using surgical scissors and scalpel blades, after removal of bulk epithelial cells by two washes in PBS containing antibiotics (penicillin/streptomycin, amphotericin B, gentamicin, ciprofloxacin) and 5 mM EDTA (Sigma-Aldrich). Minced tissue was then subjected to multiple rounds of digestion in RPMI 1640 medium, 5 mM HEPES, antibiotics as above and 1 mg/ml of Collagenase A and DNase I (Sigma-Aldrich). After 30 min, digestion supernatant containing cells was removed, filtered through a cell strainer, spun down and resuspended in 10 ml of PBS containing 5% bovine serum albumin (BSA) and 5 mM EDTA. Remaining tissue was then topped up with fresh digestion medium until no more cells were liberated. Single-cell suspensions obtained from tissue digests were blocked in PBS 5% BSA containing human anti-Fc block (Miltenyi) stained for FACS analysis or sorting with Fixable Viability Dye eFluor 780 (eBioscience, 1:1,000), DAPI (Invitrogen, 1:50,000) and antibodies (all from Biolegend, except anti-PDPN: clone NZ-1.3 from eBioscience) in PBS with 5% BSA and 5 mM EDTA for 20 min on ice. After washing in the same buffer, cells were sorted on a BD Aria III (100-µm nozzle) for the EPCAM-CD45- stromal fraction. Sorted fractions were immediately processed for 10x single-cell analysis.
Samples were processed according to 10X GEX 3' manufacturer's instructions and sequenced on a NovaSeq 6000


title: CD45-EPCAM- stromal cells_110544

description: Library name: Tissue 17


title: clone66_5

description:
Library name: 366713
SMART-Seq v3


title: clone62_6

description:
Library name: 366697
SMART-Seq v3

value: SN


title: Si20 cells at P2, replicate 2

description:
Library name: Si20-P2-2
Si20 cells at passage P2


title: CD45-EPCAM- stromal cells, 110614

description: Library name: Tissue 20


title: Ccd18-Co, IL13 4

description: Library name: Sample:20


title: Ccd18-Co, IL17A 1

description: Library name: Sample:21


title: clone62_5

description:
Library name: 366696
SMART-Seq v3


title: CD45-EPCAM- stromal cells, 110375

description: Library name: Tissue 12


title: Si20 cells at P2, replicate 1

description:
Library name: Si20-P2-1
Si20 cells at passage P2


title: Ccd18-Co, IL13 3

description: Library name: Sample:19


title: clone66_3

description:
Library name: 366711
SMART-Seq v3


title: Sorted CD3+ T cells in hPBMC, treated 14 days with IL-7, rep2

description: Library name: IL7_2

value: CD3+ T cells from hPBMC


title: clone62_4

description:
Library name: 366695
SMART-Seq v3


title: CD45-EPCAM- stromal cells, 113395

description: Library name: Tissue 23


title: CD45-EPCAM- stromal cells, 110501

description: Library name: Tissue 15


title: Native cells at P2,  replicate 2

description:
Library name: Native-P2-2
Native cells at passage P2

value: cervical cancer


title: clone62_3

description:
Library name: 366694
SMART-Seq v3

value: R


title: CD45-EPCAM- stromal cells, 113394

description: Library name: Tissue 22


title: CD45-EPCAM- stromal cells, 110373

description: Library name: Tissue 11


title: Native cells at P2,  replicate 1

description:
Library name: Native-P2-1
Native cells at passage P2

value: Hela

value: epithelial-like cervical cancer cell


title: CD45-EPCAM- stromal cells, 110458

description: Library name: Tissue 14

value: intestine


title: clone62_2

description:
Library name: 366693
SMART-Seq v3


title: CD45-EPCAM- stromal cells, 110457

description: Library name: Tissue 13

value: stromal


title: Si30 cells at P1, replicate 2

description:
Library name: Si30-P1-2
Si30 cells at passage P1

value: cryosilicification with Si30


title: clone62_1

description:
Library name: 366692
SMART-Seq v3


title: CD45-EPCAM- stromal cells, 110559

description: Library name: Tissue 18


title: CD45-EPCAM- stromal cells, 110560

description: Library name: Tissue 19


title: Si30 cells at P1, replicate 1

description:
Library name: Si30-P1-1
Si30 cells at passage P1


title: CD45-EPCAM- stromal cells, 110544

description: Library name: Tissue 17


title: clone61_5

description:
Library name: 366691
SMART-Seq v3


title: Si20 cells at P1, replicate 2

description:
Library name: Si20-P1-2
Si20 cells at passage P1

value: cryosilicification with Si20


title: CD45-EPCAM- stromal cells, 110543

description: Library name: Tissue 16


title: OSM 4

description: Library name: Sample:48

data_processing:
Resulting .fastq raw files were quality checked using FASTQC v. 0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MULTIQC v. 1.14. (https://github.com/MultiQC/MultiQC), before quantification using KALLISTO (https://github.com/pachterlab/kallisto) v. 0.48.0 with default settings. Processing of raw files was run in a Python virtual (v. 3.10.8) environment using CGATcore v. 12.2.0 pipeline framework (https://doi.org/10.12688/f1000research.18674.2).
Assembly: hg38
Supplementary files format and content: matrix of kallisto unnormalised counts for all samples (.csv)

extract_protocol:
RNA was isolated using the Qiagen RNeasey Mini kit (Qiagen #74104) or Zymo Quick-RNA 96 kits (ZymoResearch #R-1052) with the optional on-column DNA digestion step. Isolates from cell cultures were prepared by direct lysis in RNA lysis buffer, followed by RNA isolation with the Zymo RNA extraction kits including on-column DNase treatment. Isolated RNA was stored at –80C until further processing or shipped to service providers.
Libraries were prepared according to manufacturer's instructions, using NEBNext Ultra II RNA Library Prep Kit for Illumnia. Resulting libraries were sequenced on an Illumina NovaSeq6000.


title: Ccd18-Co, IL6 1

description: Library name: Sample:13


title: Sorted CD3+ T cells in hPBMC, treated 14 days with PBS, rep3

description: Library name: PBS3

value: PBS


title: clone65_4

description:
Library name: 366708
SMART-Seq v3

value: cerebral organoid


title: clone61_4

description:
Library name: 366690
SMART-Seq v3


title: OSM 3

description: Library name: Sample:47


title: Si20 cells at P1, replicate 1

description:
Library name: Si20-P1-1
Si20 cells at passage P1


title: OSM 2

description: Library name: Sample:46


title: clone61_3

description:
Library name: 366689
SMART-Seq v3


title: Ccd18-Co, IL1B 3

description: Library name: Sample:11


title: OSM 1

description: Library name: Sample:45


title: Native cells at P1,  replicate 2

description:
Library name: Native-P1-2
Native cells at passage P1


title: clone61_2

description:
Library name: 366688
SMART-Seq v3


title: TNF 3

description: Library name: Sample:43


title: Native cells at P1,  replicate 1

description:
Library name: Native-P1-1
Native cells at passage P1


title: TNF 2

description: Library name: Sample:42


title: TNF 1

description: Library name: Sample:41


title: clone61_1

description:
Library name: 366687
SMART-Seq v3


title: TGFB1 4

description: Library name: Sample:40


title: clone60_1

description:
Library name: 366686
SMART-Seq v3


title: TGFB1 3

description: Library name: Sample:39