title: scRNA-seq+ TCR-seq+BCR-seq (Multiplexed Samples S25A-S48A, S25B-S48B)

description:
Library name: S2_WTA_CKDL220029865-1A_HLJMMDSX5
BD Rhapsody
VDIBD2024.rds

data_processing:
Fastq files were processed using BD's Rhapsody analysis pipeline on the Seven Bridges Platform using default parameters and the human reference genome, GRCh38-PhiX-gencodev29 to generate raw cell by gene matrices.
Assembly: Human GRCh38-PhiX-gencodev29
Supplementary files format and content: Merged scRNA-eq Seurat Object in RDS format
Supplementary files format and content: Immune Repetoire (TCR and BCR) in AIRR format

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated from whole blood. In brief, blood samples (5-10 mL) were poured into Accuspin tubes (Sigma-Aldrich, Catalog No. A2055) layered with Ficoll (GE Healthcare, Catalog No. 14-1440-03,) and centrifuged to generate a buffy coat layer. PBMCs were isolated from the buffy coat layer, concentrated, and placed in Gibco Recovery™ Cell Culture Freezing Medium (Catalog No. 12648010). Samples were kept in Mr. Frosty containers in -80C freezer and subsequently stored in liquid nitrogen until downstream experiments. The BD® Human Single-Cell Multiplexing Kit (Catalog No. 633781) was used to multiplex PBMCs from each patient in batches of 12 patients. About 5,000-10,000 multiplexed PBMCs from each patient were loaded into the BD Rhapsody™ Cartridge (BD Biosciences, Catalog No. 633733).
Single-cell capture, barcoding, lysis, and cDNA synthesis were performed with the BD Rhapsody™ Express Single-Cell Analysis System according to the manufacturer's instructions. Paired TCR/BCR Full Length (BD Rhapsody™ TCR/BCR Amplification Kit, Catalog No. 665345) and mRNA Whole Transcriptome Analysis (WTA) (BD Rhapsody™ WTA Amplification Kit, Catalog No. 633801) libraries were indexed according to manufacturer’s instructions. Libraries were sequenced using the NovaSeq X Plus sequencer at a depth of 25,000 reads for WTA and 5,000 reads per cell for TCR and BCR.

value: Blood

value: Peripheral blood mononuclear cells


title: Mouse thoracic spinal cord snATAC-seq_biol_rep1_tech_rep3

status: Public on Feb 16 2026

type: SRA

city: Dallas

first: Allan-Hermann

last: Pool

state: TX

address: 6000 Harry Hines Blvd

department: Department of Neuroscience, Peter O'Donnell Brain Institute, Department of Anesthesia and Pain Management

country: USA

institute: University of Texas Southwestern Medical Center

description:
Library name: AT01C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds

library_source: genomic single cell

data_processing:
Raw sequencing reads were demultiplexed, aligned, and a count matrix was generated using CellRanger Arc (v2.0.2) using the Mouse mm10 (GENCODE vM23/Ensembl98) reference transcriptome with – include introns parameter specified.
Assembly: GENCODE vM23/Ensembl98
Supplementary files format and content: Summary RDS files containing gene expression data were generated with Seurat v5

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse thoracic spinal cord

extract_protocol:
8-week old male and female mice were anesthetized with isoflurane and decapitated. Vertebral column was rapidly dissected out and transferred to ice-cold carbogenated (95% O2 and 5% CO2) NMDG-HEPES-ACSF (93 mM NMDG, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 10 mM MgSO4, 1 mM CaCl2, 1 mM kynurenic-acid Na salt, 5 mM Na-ascorbate, 2 mM thiourea and 3 mM Na-pyruvate, pH adjusted to 7.4, osmolarity ranging 300–310 mOsm). Cervical, thoracic, lumbar or sacral segments of the spinal cord were microdissected out and cut into small 1 mm2 size pieces. Microdissected spinal cord pieces were transferred to a Kimble Dounce tissue-grinder containing 750 microL of Lysis Buffer (0.1% Triton-X100, 320 mM sucrose, 10 mM Tris-HCl – pH=7.4, 3mM MgCl2, 10 mM NaCl, 0.5% RNAse free BSA, 1% Kollidon VA64, 1mM dithiotreitol, 0.1 U/microL Roche Protector RNAse inhibitor in DNAse/RNAse free ddH2O). Tissue was homogenized with 5 strokes with loose pestle and 15 strokes with tight pestle and resulting nuclear suspension was strained with a 40 micron cell strainer and washed with 1.25 mL of Nuclear Buffer (320 mM sucrose, 10 mM Tris-HCl – pH=7.4, 3 mM MgCl2, 10 mM NaCl, 0.5% RNAse free BSA, 1% Kollidon VA64, 1mM dithiotreitol, 0.1 U/microL Roche Protector RNAse inhibitor in DNAse/RNAse free ddH2O). Cell suspension is layered onto 12 mL of 1M sucrose cushion (1M sucrose, 10 mM pH=7.4, Tris-HCl (pH=7.4), 3 mM MgCl2, 10 mM NaCl, 0.5% RNAse free BSA, 1% Kollidon VA64, 1mM dithiotreitol, 0.1 U/microL Roche Protector RNAse inhibitor in DNAse/RNAse free ddH2O) in a 5 mL Oakridge tube. The latter are centrifuged at 500g for 5 min at 4C in a spin-out-rotor. The sucrose cushion is decanted and pure nuclei are resuspended in 300 µL of nuclear buffer containing 10 µg/mL 7-AAD and 1:100 custom conjugated anti-NeuN-Alexa647 antibody (Biolegend #608452). The nuclei are incubated for 15 min at 4C. Thereafter, nuclei are spun down at 500g for 5 minutes and washed twice with 3 mL of nucleus buffer and resuspended in 1 mL of nucleus buffer. The resulting nucleus suspension is FACS sorted to enrich for NeuN/7-AAD double positive cells (neurons). The neuronal nuclei are concentrated with CUTANA ConA beads per manufacturer’s protocol and resuspended in 1x Nucleus Buffer from 10x Genomics with resulting nuclear suspension loaded to the 10x Genomics microfluidic chip and processed per manufacturer’s protocol.
Single-nucleus suspensions were processed on a 10X Chromium Xi instrument using the Chromium Next GEM Single Cell Multiome Reagent Bundle (#100028) following the manufacturers protocol. The resulting sequencing libraries were sequenced on a Novaseq X platform (PE 150 bp). Libraries were sequenced to a minimum depth of 50,000 reads per nucleus.

tag: tissue

value: Mouse thoracic spinal cord

tag: genotype


title: CCseq_LLR36_sae2Dndt80Drec114-8D_6h_rep1

city: Brighton

first: Jon

middle: Alexander

last: Harper

address: School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

description: Library name: MATa/alpha ho::LYS2/_, lys2/_, ura3/_, arg4-nsp/_, leu2::hisG/_, his4X::LEU2/_, nuc1::LEU2/_, sae2∆::KanMX4/_, ndt80∆::LEU2/_, rec114-8D::hphMX4/_ rep1

library_source: genomic

data_processing:
FASTQ reads were aligned to the reference genome (SacCer3H4L2; which includes the HIS4::LEU2 and leu2::hisG loci inserted into the Cer3 S. cerevisiae genome build as described in Gittens 2019) via Bowtie2, using TermMapper as previously described in Gittens 2019 (https://github.com/Neale-Lab/terminalMapper) Assembly: SacCer3H4L2 which includes the HIS4::LEU2 and leu2::hisG loci inserted into the Cer3 R64 S. cerevisiae genome build Supplementary files format and content: Sparse table of positions (Pos) of read frequencies of 5' ends of Read 1 molecules mapping to the top (Watson) and bottom (Crick) strand of each chromosome (Chrom) of the reference genome Library strategy: CC-seq
Assembly: SacCer3H4L2 which includes the HIS4::LEU2 and leu2::hisG loci inserted into the Cer3 R64 S. cerevisiae genome build
Supplementary files format and content: FASTQ paired reads

organism: Saccharomyces cerevisiae

growth_protocol: For meiosis induction, a single colony was inoculated in 4mL of YPD medium (1% yeast extract, 2% peptone, 2% glucose supplemented with 0.5 mM adenine and 0.4 mM uracil) and incubated at 30 °C, 250 rpm for a day to reach saturation, then diluted to OD600 of 0.2 in a volume of 200 mL of either YPA (1% yeast extract, 2% peptone, 1% potassium acetate) or SPS (0.5% yeast extract, 1% peptone, 0.67% Yeast Nitrogen Base without amino acids, 1% potassium acetate, 0.05M Potassium Hydrogen phthalate, 0.001% Antifoam 204) pre-sporulation medium. Cultures were incubated at 30 °C, 250 rpm for 14–16 hours, then washed and resuspended in 200 mL pre-warmed SPM sporulation medium (2% potassium acetate supplemented with diluted amino acids) and incubated at 30°C, 250rpm for the duration of the time course.

extract_protocol:
Protein-DNA Covalent-Complex Mapping (CC-seq) in yeast followed a method previously described (Gittens 2019). Briefly, meiotic cell samples are chilled and frozen at -20˚C for at least 8 hours, then thawed and spheroplasted (in 1 M sorbitol, 50 mM NaHPO4, 10 mM EDTA, 30 min at 37˚C), fixed in 70% ice-cold ethanol, collected by centrifugation, dried briefly, then lysed in STE (2% SDS, 0.5 M Tris, 10 mM EDTA). Genomic DNA was extracted via Phenol/Chloroform/IAA extraction (25:24:1 ratio) at room temperature, with aqueous material carefully collected, precipitated with ethanol, washed, dried, then resuspended in 1xTE buffer (10 mM Tris/1 mM EDTA). Total genomic DNA was sonicated to <500 bp average length using a Covaris M220 before equilibrating to a final concentration of 0.3 M NaCl, 0.1% TritonX100, 0.05% Sarkosyl. Covalent complexes were enriched on silica columns (Qiagen) via centrifugation, washed with TEN solution (10 mM Tris / 1 mM EDTA / 0.3 M NaCl), before eluted with TES buffer (10 mM Tris / 1 mM EDTA / 1% SDS). Samples were treated with Proteinase K at 50˚C, and purified by ethanol precipitation.
DNA ends were filled and repaired using NEB Ultra II end-repair module (NEB #E7645), with adapters ligated sequentially to the sonicated, then blocked, ends with recombinant TDP2 treatment in between these steps to remove the 5-phosphotyrosyl-linked Spo11 peptide. Ampure bead cleanups were used to facilitate sequential reactions. PCR-amplified libraries were quantified on a Bioanalyser and appropriately diluted and multiplexed for deep sequencing (Illumina MiSeq 2x75 bp).

treatment_protocol: 50 mL of culture was taken at t = 6 hours. Samples were centrifuged at 3000 x g for 5 minutes, supernatant discarded and pellet frozen at -20 °C until use.

tag: cell line

tag: cell type

value: Meiotic

tag: treatment

value: 6 hour


title: scRNA-seq+ TCR-seq+BCR-seq (Multiplexed Samples S1A-S24A, S1B-S24B)

city: Jacksonville

first: John

last: Gubatan

state: FL

address: Mayo Clinic Mangurian Building 5220, 4500 San Pablo Rd

institute: Mayo Clinic Florida

description:
Library name: S1_WTA_CKDL220029861-1A_HLJMMDSX5
BD Rhapsody
VDIBD2024.rds

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

treatment_protocol: Patients with established inflammatory bowel disease (ulcerative colitis or Crohn’s disease) were screened and invited to participate in vitamin D prospective study at Stanford University (IRB 60958) and the University of Copenhagen (IRB 2021-1696). Patients who met inclusion criteria (adult patients (18 years or older) with inflammatory bowel disease (ulcerative colitis or Crohn's disease), low serum vitamin D (25(OH)D ≤ 25 ng/mL, not on vitamin D supplementation at time of recruitment, no prior bowel resections, no antibiotic use in past 3 months) were enrolled. Patients who had prior bowel surgeries (colectomy, small bowel resections), renal dysfunction, history of hypercalcemia, history of HIV (human immunodeficiency virus), history of IgA deficiency, history of common variable immunodeficiency (CVID), or current or recent C. diff infection were excluded from study. All patients provided consent in accordance with Institutional Review Board guidance for each institution as noted above. At the time of enrollment (week 0), patients had blood and stool samples collected. Patients were then treated with 50,000 units of oral vitamin D (ergocalciferol) once per week for 12 weeks. Blood and stool samples were collected at the end of study (week 12). C-reactive protein and fecal calprotectin were measured from week 0 and week 12 blood and stool samples, respectively. Disease activity scores (partial Mayo score for ulcerative colitis, Harvey Bradshaw Index for Crohn’s disease), quality of life scores (short inflammatory bowel disease questionnaire/SIBDQ) were collected at week 0 and week 12.


title: IgA-Seq Sample IgA21A

description:
Library name: IgA21A
Novogene
IGASEQ.rds

library_source: other

data_processing:
Analyses of 16S rRNA data were performed using the Quantitative Insights into Microbial Ecology (QIIME) 2 (http://qiime.org), an open-source bioinformatics pipeline for performing analysis of microbiome sequence data as previously described (Boylen et al., 201960).  Briefly, raw sequencing data were demultiplexed using unique barcodes assigned to each sample and then denoised using Dada2 as previously described (Callahan et al., 2016).  Remaining reads were then clustered into Operational Taxonomic Units (OTUs) using Greengenes v13-8 as a reference set to assign taxonomy to each OTU
Assembly: Greengenes v13-8 reference
Supplementary files format and content: Merged IGA-SEQ Phyloseq obejct, Merged IGG-SEQ Phyloseq obejct,
Library strategy: 16S rRNA-seq

molecule: other

source_name: Stool

extract_protocol:
Frozen stool (200 mg) samples from each patient were thawed and dissolved in 1 mL of phosphate buffered saline (Invitrogen, Catalog No. Catalog No. AM9624). Stool was resuspended in 1 mL of 5 mM N-acetyl-cysteine (Thermo Scientific Chemicals, Catalog No. 616-91-1) to break disulfide bonds in mucus and release bacterial cells and then passed through 100 uM filters and centrifuged. The resulting stool pellets were resuspended in 1 mL of PBS and divided into four fractions for downstream experiments (bacterial FACS, whole microbiome 16S, IgA-Seq, and IgG-Seq). For bacterial FACS, stool cell pellets were centrifuged and resuspended in PBS and stained with 1:10,000 SYBR Green (Sigma Aldrich) at room temperature in dark for 20 minutes. Cell pellets were subsequently centrifuged, resuspended in PBS, and stained with 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) and 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Cell pellets were centrifuged and resuspended in FACS buffer and 1:50 Fc block was to each sample and incubated at room temperature for 10 minutes. Bacterial cell pellets were then centrifuged and resuspended in FACS buffer. FACS was used to quantify the proportion of SYBR green positive (live bacterial cells) that were IgA-APC+, IgG-PE+, and IgA+IgG+ double positives.Stool pellets from each patient were processed as previously described. Bacterial cell pellets were resuspended in PBS and separate stool fractions were stained with either 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) or 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Bacterial cell pellets were centrifuged and then washed with MACS buffer.  Anti-PE MicroBeads (Miltenyi Biotec, Catalog No. 130-090-855) were added to IgG fraction and Anti-APC MicroBeads (Miltenyi Biotec, Catalog No. 130-048-801) to IgA fraction. Bacterial cell pellets were then centrifuged, resuspended in MACS buffer, and placed onto OctoMACS™ Separator (Miltenyi Biotec, Catalog No. 130-042-108) columns for magnetic separation. IgA and IgG-bound bacterial fractions were then collected for each sample. Purity of IgA-bound and IgG-bound gut bacteria were above 90% for all samples included in downstream analyses.
DNA from bacterial cell pellets from IgA-bound, IgG-bound, and unfractionated (whole gut microbiome) samples were isolated using the PureLink™ Microbiome DNA Purification Kit (Catalog No. A29790) per manufacturer’s instructions. Bacterial 16S sequencing of the V4 and V5 regions (primer 515F/sequence GTGCCAGCMGCCGCGGTAA, primer 907R/sequence CCGTCAATTCCTTTGAGTTT) were performed at Novogene using 2x250 sequencing on an Illumina MiSeq.

value: Stool

value: Pre-vitamin D


title: Healthy male control

city: Bydgoszcz

first: Katarzyna

last: Bilińska

address: M.Skłodowskiej-Curie 9

country: Poland

institute: Nicolaus Copernicus University

description:
Library name: WP_K2
KvsControl_expression_exons.xlsx

library_source: transcriptomic

data_processing:
Illumina NovaSeq X Plus software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence by fastp v 0.23.2. Then, for gene-level analysis, RNA-seq reads were aligned to the reference genome (GRCh38, GENCODE v49 primary assembly annotation) using hisat2 v2.1.1, while Star v2.7.11 was used for exon-level analysis.
For gene-level differential expression analysis, statistical testing was performed using Cuffdiff v2.2.1.  For exon-level analysis, annotation preparation was carried out using dexseq_prepare_annotation.py from the DEXSeq package. The reference annotation file was converted to GFF format, with flattened exon-counting bins, which were then used for exon-level differential usage analysis.
For exon-level analysis, read counting was done with the dexseq_count.py Python script (from the DEXSeq package) for each sample alignment file and collapsed exon counting bins. Test for differential exon usage was performed with DEXSeq R package v 1.54.1.
Assembly: GRCh38
Supplementary files format and content: For each pair of samples (control vs. case), the differential expression values such as fold change and p-value are computed at gene level.

molecule: polyA RNA

source_name: whole blood

extract_protocol:
Total RNA was isolated from whole blood using TRIzol Reagent according to the manufacturer’s instructions. The concentration and purity of extracted RNA which was measured using NanoDrop spectrophotometer and Qubit fluorimeter.
The library was prepared at the Genomics Laboratory of the Institute of Bioorganic Chemistry, Polish Academy of Sciences (Poznań, Poland) using the KAPA RNA HyperPrep Kit with RiboErase (Roche) and KAPA Unique Dual-Indexed Adapter Kit (15 μM) according to the manufacturer’s instructions. Libraries were sequenced on Illumina NovaSeq X Plus platform.

value: whole blood

tag: Sex

value: male

tag: condition

value: Healthy


title: Mouse thoracic spinal cord snRNA-seq_biol_rep1_tech_rep3

description:
Library name: AT01C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds

molecule: nuclear RNA


title: IgA-Seq Sample IgA20A

description:
Library name: IgA20A
Novogene
IGASEQ.rds


title: Healthy female control

description:
Library name: KB_K1
KvsControl_expression_exons.xlsx

value: female


title: MN1> GFP [Replicate2]

city: San Francisco

first: Daniel

last: Karmelic

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: Library name: Control_2

data_processing:
Raw reads were first processed with flexbar version 3.5.0 (https://github.com/seqan/flexbar) to remove adapters specific to the NEBNext library prep, using parameters as described in https://github.com/nebiolabs/nebnext-single-cell-rna-seq.
The reads were then processed with HTStream v.1.1.0 (https://ibest.github.io/HTStream/) to perform data QA/QC, remove Illumina adapter contamination, PCR duplicates, and low-quality bases/sequences.
The trimmed reads were aligned to the Drosophila melanogaster genome v.BDGP6.22 (http://ensembl.org/Drosophila_melanogaster/Info/Annotation) with annotation release version using the aligner STAR v. 2.7.0e (Dobin et al., 2013) to generate raw counts per gene. On average, 93.7% of the trimmed reads aligned to the Drosophila genome, and 80% of the trimmed reads uniquely aligned to an annotated Drosophila gene.
Prior to analysis, genes with fewer than 5 counts per million reads in all samples were filtered, leaving 8598 genes.
Differential expression analyses were conducted using limma-voom in R (limma version 3.40.6, edgeR version 3.26.7, R 3.6.1).
Assembly: Drosophila melanogaster genome v.BDGP6.22 (http://ensembl.org/Drosophila_melanogaster/Info/Annotation)
Supplementary files format and content: Excel spreadsheet with raw counts for each Sample

organism: Drosophila melanogaster

source_name: larva VNC MN1-Ib motoneurons

extract_protocol:
Individual motoneurons were visualized by driving the expression of membrane-bound GFP (MN1-Ib-GAL4, UASmCD8:GFP) in 3rd-instar larvae. To obtain the cytoplasmic content of the cell, whole-cell tight-seal patch-clamp was used. Whole-cell configuration was established with leak currents less than 100pA. The cytoplasmic content of the cell was gently aspirated by applying negative pressure to the patch-pipette. The individual motoneuron was then pulled from the tissue while visually confirming the GFP fluorescent signal at the tip of the pipette. Immediately after, the pipette tip was immersed in a test tube containing the Cell Lysis Buffer and RNAse inhibitor medium and the pipette tip was broken by gently touching the tube wall. The content of the pipette tip was ejected by applying positive pressure. Each reaction contained 4-8 pooled motoneurons.
The Low Input RNA: cDNA Synthesis, Amplification and Library Generation kit from NEB (New England Biolabs Inc.) was used to isolate, reverse-transcribe the RNA and prepare the libraries for sequencing. Following the reverse transcription and template switching, the cDNA was amplified by PCR. Amplified cDNA was cleaned using SPRI beads. The quality and quantity of the amplified cDNA were assessed by Bioanalyzer (Agilent Technologies Inc.). After fragmentation and adaptor ligation, adaptor-ligated DNA was enriched with i7 primer and universal primer by PCR-amplification. Amplified libraries were quality checked by Bioanalyzer with High Sensitivity DNA chips (Agilent Technologies Inc.) and the quantity was measured by Qubit fluorometer (ThermoFisher Scientific). Barcoded libraries were sequenced using an Illumina HiSeq 4000 at 100bp paired-end reads in the Center for Advanced Technology genomic facility at UCSF.

value: larva VNC MN1-Ib motoneurons

value: MN1> GFP


title: MN1> GFP [Replicate3]

description: Library name: Control_3


title: Mouse thoracic spinal cord snATAC-seq_biol_rep1_tech_rep2

description:
Library name: AT01B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA19A

description:
Library name: IgA19A
Novogene
IGASEQ.rds


title: MN1> GFP [Replicate1]

description: Library name: Control_1


title: MN1> GFP, Shal_RNAi [Replicate3]

description: Library name: Shal_RNAi_3

value: MN1> GFP, Shal_RNAi


title: IgA-Seq Sample IgA18A

description:
Library name: IgA18A
Novogene
IGASEQ.rds


title: Affected male 2nd

description:
Library name: K3
KvsControl_expression_exons.xlsx

value: Affected


title: Carrier female

description:
Library name: K4
KvsControl_expression_exons.xlsx

value: Carrier


title: Mouse thoracic spinal cord snATAC-seq_biol_rep1_tech_rep1

description:
Library name: AT01A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mouse thoracic spinal cord snRNA-seq_biol_rep1_tech_rep2

description:
Library name: AT01B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA17A

description:
Library name: IgA17A
Novogene
IGASEQ.rds


title: Affected male 1st

description:
Library name: K1
KvsControl_expression_exons.xlsx


title: MN1> GFP, Shal_RNAi [Replicate2]

description: Library name: Shal_RNAi_2


title: IgA-Seq Sample IgA16A

description:
Library name: IgA16A
Novogene
IGASEQ.rds


title: HEK293 TurboID-noNES pulldown 3

city: Atlanta

first: Christina

last: Ramelow

address: 615 Michael St RM 375

institute: Emory University

description:
Library name: Sample 74
/home/ec2-user/23238R-11-14_S23_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt

data_processing:
Global sequencing of 40 million paired-end reads per sample was completed using the Illumina-based platform at Admera Health. FASTQ files were evaluated for quality using FastQC and then mapped to the mouse genome, GRCm38 (mm10), or GRCh38, human genome (hg38), using the Spliced Transcripts Alignment to a Reference (STAR) (for mRNA-seq) or Bowtie 2 (for smRNA-seq) aligners with the paired-end option. The featureCounts package was used to generate a raw counts data matrix from mapped reads. Lowly abundant transcripts across all samples (average count value ≤ 10) were filtered out. After generating the filtered, raw counts data matrices, we used DESeq2 to normalize the matrices and perform differential gene ex-pression-based statistics.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file that includes raw counts for each sample.

growth_protocol: Mouse microglia BV2 cells were cultured in 0.2 µm vacuum filter sterilized Dulbecco’s Modified Eagle Medium (DMEM) supplemented with high glucose and L-glutamine containing 1% penicillin-streptomycin, and 10% fetal bovine serum. BV2 cells were incubated in 100 mm cell culture dish at 37°C and 5% CO2 until reaching 80-90% confluency. Cells were treated with 100 ng/mL of LPS for 48 h and 200 µM of biotin for 24 h during the second day of LPS treatment. Human embryonic kidney 293 cells (HEK293) were cultured in DMEM containing 1% penicillin-streptomycin and 10% fetal bovine serum. HEK293 cells were incubated in 6-well cul-ture dishes in the same condition as the BV2 cells described above. At 30% confluency, HEK293 cells were infected with 3 µL of the two LVs generated (TurboID-NES, viral titer: 3.9x108 IU/mL or TurboID-noNES, viral titer: 1.7x109 IU/mL). LV-containing media was removed after 3 days, and successful infection was determined by cellular GFP signal using the ECHO Revolve fluores-cence microscope (Echo, USA) prior to lysis. HEK293 cells were grown to 80-90% confluency cells before biotin treatment (200 µM for 24 h). The 48 h LPS and 24 h biotin treatment paradigms were used to model similar treatment and labeling kinetics for in vivo SPARO studies.

extract_protocol:
After protein enrichment using streptavidin and A/B beads, RNA was extracted from the beads and bulk/g;obal cell or bulk cortical lysates using a miRNeasy Mini Kit (Qiagen Inc., 217004) following the manufacturer’s instructions. 1-3 ug of total RNA was used to generate cDNA libraries.
The SMART-Seq® v4 PLUS Kit (Takara Bio) was used following the manufacturer’s protocol. For small RNA-sequencing library preparation, a QIAseq miRNA NGS kit (Qiagen, 331565) was used.

treatment_protocol: BV2 cells were treated with 100 ng/mL of lipopolysaccharide (LPS) for 48 h and 200 mM of biotin for 24 h during the second day of LPS treatment. All mice were given tamoxifen (75 mg/kg) intraperitoneally (i.p.) for 5 days at 6 weeks of age and allowed 3 weeks of Cre recombination. After Cre recombination, TurboID mice were given water supplemented with biotin (37.5 mg/L) for 2 weeks until euthanasia at 3-4 months of age. RiboTag mice were euthanized at 2.5 months of age. For astrocyte-TurboID LPS studies, systemic LPS at 0.75mg/kg/dose x 5 days was given via i.p. injection during the first week of biotin water supplementation. Mice from each cohort were anesthetized using ketamine/xylazine (ketamine 87.5 mg/kg, xylazine 12.5 mg/kg) followed by transcardial perfusion with ice-cold PBS.

value: embryonic kidney epithelial

value: TurboID knockin

tag: batch


title: Mouse thoracic spinal cord snRNA-seq_biol_rep1_tech_rep1

description:
Library name: AT01A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: MN1> GFP, Shal_RNAi [Replicate1]

description: Library name: Shal_RNAi_1


title: HEK293 TurboID-noNES pulldown 2

description:
Library name: Sample 73
/home/ec2-user/23238R-11-13_S22_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt


title: Mouse cervical spinal cord snATAC-seq_biol_rep3_tech_rep3

description:
Library name: AC05C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds

source_name: Mouse cervical spinal cord

value: Mouse cervical spinal cord


title: IgA-Seq Sample IgA15A

description:
Library name: IgA15A
Novogene
IGASEQ.rds


title: MN1> GFP, Notch RNAi, Shal_RNAi [Replicate3]

description: Library name: Notch_Shal_RNAi_3

value: MN1> GFP, Notch RNAi, Shal_RNAi


title: Mouse cervical spinal cord snRNA-seq_biol_rep3_tech_rep3

description:
Library name: AC05C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: HEK293 TurboID-noNES pulldown 1

description:
Library name: Sample 72
/home/ec2-user/23238R-11-12_S21_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt


title: Mouse cervical spinal cord snATAC-seq_biol_rep3_tech_rep2

description:
Library name: AC05B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA13A

description:
Library name: IgA13A
Novogene
IGASEQ.rds


title: MN1> GFP, Notch RNAi, Shal_RNAi [Replicate2]

description: Library name: Notch_Shal_RNAi_2


title: HEK293 TurboID-NES pulldown 3

description:
Library name: Sample 71
/home/ec2-user/23238R-11-11_S20_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt


title: MN1> GFP, Notch RNAi, Shal_RNAi [Replicate1]

description: Library name: Notch_Shal_RNAi_1


title: HEK293 TurboID-NES pulldown 2

description:
Library name: Sample 70
/home/ec2-user/23238R-11-10_S19_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt


title: IgA-Seq Sample IgA12A

description:
Library name: IgA12A
Novogene
IGASEQ.rds


title: Mouse cervical spinal cord snATAC-seq_biol_rep3_tech_rep1

description:
Library name: AC05A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: HEK293 TurboID-NES pulldown 1

description:
Library name: Sample 69
/home/ec2-user/23238R-11-09_S18_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt


title: Mouse cervical spinal cord snRNA-seq_biol_rep3_tech_rep2

description:
Library name: AC05B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: MN1> GFP, Notch RNAi [Replicate3]

description: Library name: Notch_RNAi_3

value: MN1> GFP, Notch RNAi


title: IgA-Seq Sample IgA11A

description:
Library name: IgA11A
Novogene
IGASEQ.rds


title: Mouse cervical spinal cord snRNA-seq_biol_rep3_tech_rep1

description:
Library name: AC05A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: MN1> GFP, Notch RNAi [Replicate4]

description: Library name: Notch_RNAi_4


title: IgA-Seq Sample IgA10A

description:
Library name: IgA10A
Novogene
IGASEQ.rds


title: HEK293 pulldown 3

description:
Library name: Sample 68
/home/ec2-user/23238R-11-08_S1_L004_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt

value: WT


title: IgA-Seq Sample IgA9A

description:
Library name: IgA9A
Novogene
IGASEQ.rds

value: Stool


title: MN1> GFP, Notch RNAi [Replicate1]

description: Library name: Notch_RNAi_1


title: MN1> GFP, Notch RNAi [Replicate2]

description: Library name: Notch_RNAi_2


title: Mouse cervical spinal cord snRNA-seq_biol_rep2_tech_rep3

description:
Library name: AC04C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: OVSAHO_6

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: Pennsylvania

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

description: Library name: A18

data_processing:
Completed by Novogene
R studio (2023.12.0+369) and R packages ggplot2 (3.4.4),
pheatmap (1.0.12),
biomaRT (2.58.2),
clusterProfiler (4.10.0), org.Hs.eg.db (3.18.0), and AnnotationDbi (1.64.1)
Assembly: hg38
Supplementary files format and content: The processed .tsv file is a tab-delimited text file containing structured data.

source_name: Ovarian

growth_protocol: Cells were grown in 10% RPMI media

extract_protocol:
Trizol
Completed by Novogene

treatment_protocol: 3 uM vorinostat for 48 hours

value: Ovarian

value: OVSAHO

value: Ovarian Cancer

value: Vorinostat


title: Mouse cervical spinal cord snATAC-seq_biol_rep2_tech_rep2

description:
Library name: AC04B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: Mouse cervical spinal cord snATAC-seq_biol_rep2_tech_rep3

description:
Library name: AC04C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: HEK293 pulldown 1

description:
Library name: Sample 66
/home/ec2-user/23238R-11-06_S16_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt

value: female


title: HEK293 TurboID-noNES global 1

description:
Library name: Sample 65
/home/ec2-user/23238R-11-05_S15_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt


title: IgA-Seq Sample IgA7A

description:
Library name: IgA7A
Novogene
IGASEQ.rds

value: Pre-vitamin D


title: HEK293 pulldown 2

description:
Library name: Sample 67
/home/ec2-user/23238R-11-07_S17_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt


title: Mouse cervical spinal cord snRNA-seq_biol_rep2_tech_rep2

description:
Library name: AC04B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA8A

description:
Library name: IgA8A
Novogene
IGASEQ.rds


title: OVSAHO_4

description: Library name: A16


title: OVSAHO_5

description: Library name: A17

value: DMSO


title: IgA-Seq Sample IgA6A

description:
Library name: IgA6A
Novogene
IGASEQ.rds


title: HEK293 TurboID-NES global 1

description:
Library name: Sample 64
/home/ec2-user/23238R-11-04_S14_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt


title: Mouse cervical spinal cord snATAC-seq_biol_rep2_tech_rep1

description:
Library name: AC04A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: HEK293 global replicate 3

description:
Library name: Sample 63
/home/ec2-user/23238R-11-03_S13_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt


title: IgA-Seq Sample IgA5A

description:
Library name: IgA5A
Novogene
IGASEQ.rds


title: Mouse cervical spinal cord snRNA-seq_biol_rep2_tech_rep1

description:
Library name: AC04A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: OVSAHO_3

description: Library name: A15


title: OVSAHO_2

description: Library name: A14


title: IgA-Seq Sample IgA4A

description:
Library name: IgA4A
Novogene
IGASEQ.rds


title: HEK293 global replicate 1

description:
Library name: Sample 61
/home/ec2-user/23238R-11-01_S11_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt


title: HEK293 global replicate 2

description:
Library name: Sample 62
/home/ec2-user/23238R-11-02_S12_L008_Aligned.sortedByCoord.out.bam
HEK293_feature_counts.txt


title: Mouse cervical spinal cord snATAC-seq_biol_rep1_tech_rep3

description:
Library name: AC03C-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: OVSAHO_1

description: Library name: A13


title: Mouse cervical spinal cord snATAC-seq_biol_rep1_tech_rep2

description:
Library name: AC03B-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA1A

description:
Library name: IgA1A
Novogene
IGASEQ.rds


title: IgA-Seq Sample IgA2A

description:
Library name: IgA2A
Novogene
IGASEQ.rds


title: S340_4

description: Library name: A11


title: CK17-208

city: Madison

first: Huy

last: Dinh

state: WI

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

description: Library name: CK17-208

data_processing:
FASTQ outputs from 10X Visium FFPE samples were mapped and pre-processed using SpaceRanger (v1.3.1, 10X Genomics) using the Human Transcriptome Probe set v1.
Assembly: 10X Genomics Human Transcriptome Probe set v1/
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and coordinates specifying spots

source_name: Oral Cavity

extract_protocol:
FFPE tissue slices were mounted on the 10X Visium capture area with four samples per Visium slide. Mounted samples were incubated, deparaffinized, stained with hematoxylin and eosin (H&E), imaged, and decrosslinked according to manufacturer recommendations by the UW SMPH TRIPath lab
Library construction and sequencing were performed by the Gene Expression Center (GEC) at the University of Wisconsin-Madison Biotechnology Center.

value: Oral Cavity

tag: subject status

value: head and neck cancer patient sample

tag: response status

value: Non-Responder


title: Mouse cervical spinal cord snRNA-seq_biol_rep1_tech_rep3

description:
Library name: AC03C-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: IgA-Seq Sample IgA3A

description:
Library name: IgA3A
Novogene
IGASEQ.rds


title: S340_3

description: Library name: A10


title: Mouse cervical spinal cord snRNA-seq_biol_rep1_tech_rep2

description:
Library name: AC03B-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: CK17-129-4

description: Library name: CK17-129-4

source_name: Oropharynx

value: Oropharynx

value: Responder


title: S340_2

description: Library name: A9


title: circH siR + LPS_4hr_2

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hanover Medical School

description: Library name: N1425

data_processing:
Sequencing was performed on the Illumina Hiseq2000 with 2 × 76 sequencing length.Fastq files were aligned to the Mus musculus genome reference (GRCm38.p6; release M18).Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool Version 2.11.40.2) with default settings.
Assembly: mm10 (GRCm38.p6; release M18)
Supplementary files format and content: tabular file of normalized read counts

extract_protocol:
Samples for RNA-seq were 1 μg in 10 μl, as assessed by the Agilent Bioanalyzer for RNA integrity, prior to library preparation. Digested RNA was purified with standard RNA Phenol/Chloroform/Isoamylic alcohol extraction (RNeasy Mini kit).
300ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs).

value: circH siR + LPS


title: CK17-159-2

description: Library name: CK17-159-2


title: circH siR + LPS_4hr_3

description: Library name: N1426


title: S340_1

description: Library name: A7


title: Mouse cervical spinal cord snRNA-seq_biol_rep1_tech_rep1

description:
Library name: AC03A-GEX
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds

value: Mouse cervical spinal cord


title: circH siR + LPS_4hr_1

description: Library name: N1424


title: Mouse cervical spinal cord snATAC-seq_biol_rep1_tech_rep1

description:
Library name: AC03A-ATAC
P56_glutamatergic_multiome.rds
P56_gabaergic_multiome.rds
P56_cholinergic_multiome.rds


title: S412_4

description: Library name: A5


title: Mouse lumbar spinal cord snRNA-seq_experiment2

description: Library name: Scord2_GEX

source_name: Mouse Lumbar Spinal Cord (L1-L5)

extract_protocol:
8-week old male and female mice were anesthetized with isoflurane and decapitated. Vertebral column was rapidly dissected out and transferred to ice-cold carbogenated (95% O2 and 5% CO2) NMDG-HEPES-ACSF (93 mM NMDG, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 10 mM MgSO4, 1 mM CaCl2, 1 mM kynurenic-acid Na salt, 5 mM Na-ascorbate, 2 mM thiourea and 3 mM Na-pyruvate, pH adjusted to 7.4, osmolarity ranging 300–310 mOsm). L1-L5 lumbar spinal cords were microdissected out and cut into small 1 mm2 size pieces. Microdissected spinal cord pieces were transferred to a Kimble Dounce tissue-grinder containing 750 microL of Lysis Buffer (0.1% Triton-X100, 320 mM sucrose, 10 mM Tris-HCl – pH=7.4, 3mM MgCl2, 10 mM NaCl, 0.5% RNAse free BSA, 1% Kollidon VA64, 1mM dithiotreitol, 0.1 U/microL Roche Protector RNAse inhibitor in DNAse/RNAse free ddH2O). Tissue was homogenized with 5 strokes with loose pestle and 15 strokes with tight pestle and resulting nuclear suspension was strained with a 40 micron cell strainer and washed with 1.25 mL of Nuclear Buffer (320 mM sucrose, 10 mM Tris-HCl – pH=7.4, 3 mM MgCl2, 10 mM NaCl, 0.5% RNAse free BSA, 1% Kollidon VA64, 1mM dithiotreitol, 0.1 U/microL Roche Protector RNAse inhibitor in DNAse/RNAse free ddH2O). Cell suspension is layered onto 12 mL of 1M sucrose cushion (1M sucrose, 10 mM pH=7.4, Tris-HCl (pH=7.4), 3 mM MgCl2, 10 mM NaCl, 0.5% RNAse free BSA, 1% Kollidon VA64, 1mM dithiotreitol, 0.1 U/microL Roche Protector RNAse inhibitor in DNAse/RNAse free ddH2O) in a 5 mL Oakridge tube. The latter are centrifuged at 500g for 5 min at 4C in a spin-out-rotor. The sucrose cushion is decanted and pure nuclei are resuspended in 300 µL of nuclear buffer containing 10 µg/mL 7-AAD and 1:100 custom conjugated anti-NeuN-Alexa647 antibody (Biolegend #608452). The nuclei are incubated for 15 min at 4C. Thereafter, nuclei are spun down at 500g for 5 minutes and washed twice with 3 mL of nucleus buffer and resuspended in 1 mL of nucleus buffer. The resulting nucleus suspension is FACS sorted to enrich for NeuN/7-AAD double positive cells (neurons). The neuronal nuclei are concentrated with CUTANA ConA beads per manufacturer’s protocol and resuspended in 1x Nucleus Buffer from 10x Genomics with resulting nuclear suspension loaded to the 10x Genomics microfluidic chip and processed per manufacturer’s protocol.
Single-nucleus suspensions were processed on a 10X Chromium Xi instrument using the Chromium Next GEM Single Cell Multiome Reagent Bundle (#100028) following the manufacturers protocol. The resulting sequencing libraries were sequenced on a Novaseq X platform (PE 150 bp). Libraries were sequenced to a minimum depth of 50,000 reads per nucleus.

value: Mouse Lumbar Spinal Cord (L1-L5)


title: S412_3

description: Library name: A4


title: CK17-12-E6

description: Library name: CK17-12-E6


title: Mouse lumbar spinal cord snATAC-seq_experiment2

description: Library name: Scord2_ATAC


title: CK17-19

description: Library name: CK17-19


title: CK17-25

description: Library name: CK17-25

source_name: Nasal Cavity

value: Nasal Cavity


title: CK17-7

description: Library name: CK17-7


title: ctrl siR + LPS 4hr_3

description: Library name: N1420

value: ctrl siR + LPS 4hr


title: S412_2

description: Library name: A3

value: Ovarian


title: CK17-5

description: Library name: CK17-5


title: ctrl siR + LPS 4hr_1

description: Library name: N1418


title: ctrl siR + LPS 4hr_2

description: Library name: N1419


title: Root cells, Mock2

status: Public on Feb 15 2026

city: Ann arbor

first: Ping

last: He

state: Michigan

address: 1105 N. University Ave

institute: University of Michigan

description:
Library name: Sample4
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: TAIR10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Seeds were sterilized, maintained for two days at 4 degree in the dark, and germinated on agar plates containing Murashige and Skoog medium (1/2 MS) with 0.5% sucrose, 0.8% agar, and 2.5 mM MES at pH 5.7, in a growth room at 23 degree, 85 μE m-2s-1 light with a 12-hr light/12-hr dark photoperiod. Seeds were grown vertically on agar plates.

extract_protocol:
Roots of seven-day-old seedlings were cut approximately one centimeter from their tips, broadly diced with a scalpel blade, and then incubated in protoplast isolation solution (1.5% cellulase R10, 1.2% cellulase RS, 0.2% macerozyme R10, and 0.15% pectinase, in 600 mM mannitol, 2 mM MES hydrate, 10 mM KCl, 2 mM CaCl2, 2 mM MgCl2, and 0.1% BSA, pH 5.7) for 2.5 hr at 20°C on an orbital shaker set at 60 revolutions/min. The individual elicitor was applied 30 min before cutting the roots of the seedlings and was also added to the protoplast solution. Protoplasts were filtered through 40 μm cell strainers and centrifuged at 300 g for 3 mins. The supernatant was gently removed, and the pellet resuspended in 10 ml of 8% mannitol solution. This wash procedure was repeated again; the protoplasts were centrifuged again and resuspended in ∼500 μl of 8% mannitol solution.
Single-cell RNA-seq libraries were prepared from fresh protoplasts according to the 10x Genomics Single Cell 3’ Reagent Kit v3 protocol (10x Genomics, USA). For each sample, 10,000 cells were loaded in the 10x Genomics Chromium single-cell microfluidics device with the aim of capturing 7,000 cells. 11 cycles were used for cDNA amplification, as well as for final PCR amplification of the adapter-ligated libraries. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent, USA), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina. The scRNA-seq library sequencing was performed on the NextSeq platform (Illumina, USA).

treatment_protocol: The individual elicitor was applied 30 min before cutting the roots of the seedlings and was also added to the protoplast solution for another 2.5h.

value: Root

value: Mock


title: Root cells, SCOOP10

description:
Library name: Sample6
10x Genomics


title: Mouse lumbar spinal cord snATAC-seq_experiment1

description: Library name: Scord1_ATAC


title: Root cells, Pep1

description:
Library name: Sample3
10x Genomics


title: Mouse lumbar spinal cord snRNA-seq_experiment1

description: Library name: Scord1_GEX


title: Root cells, flg22

description:
Library name: Sample2
10x Genomics


title: Root cells, Chitin

description:
Library name: Sample5
10x Genomics

value: Chitin


title: Root cells, SCREW1

description:
Library name: Sample7
10x Genomics


title: Root cells, Mock1

description:
Library name: Sample1
10x Genomics


title: left ventricular, ZSHLF, rep 3

city: Jinan

first: Xiaolin

last: Wu

address: No. 4655, Daxue Road, Changqing District, Jinan, Shandong Province

country: China

institute: Shandong University of Traditional Chinese Medicine

data_processing:
The sequencing data generated by the Illumina NextSeq 500 is raw sequencing data.
Raw sequencing data goes through quality control (QC) to assess whether the sequencing data can be used for subsequent data analysis.
After QC, the trimmed data generated by the pretreatment and filtering step (removing the linker sequence and too short fragment in Read) was compared to the reference genome, and the statistical analysis of the comparison results was carried out to determine whether the comparison results could be used for subsequent data analysis.
Raw reads were normalized by calculated CPM value.
Assembly: miRBase22
Supplementary files format and content: the cpm value of detected miRNA for each sample

organism: Rattus norvegicus

source_name: left ventricular

extract_protocol:
Total RNA was extracted from the left ventricular using TRI Reagent (Sigma T9429) and Nanodrop 1000 was used for RNA quantification and quality assurance.
RNA samples from different groups were mixed for subsequent cDNA library construction. The library construction process mainly includes the following steps: connecting the 3′ end and the 5′ linker, reverse transcription into cDNA, and then performing PCR amplification, size selection of 135-155 bp PCR amplified fragments. DNA fragments in libraries were denatured with 0.1 M NaOH to yield single-stranded DNA.

tag: strain

value: spontaneously hypertensive rat (SHR)

value: left ventricular

value: WT

value: male

tag: age

value: 16 weeks old

value: Chinese herbal medicine Zishen Huoluo formula (ZSHLF)

tag: time

value: 4 weeks


title: left ventricular, ZSHLF, rep 2


title: left ventricular, ZSHLF, rep 1


title: left ventricular, WKY, rep 2

value: Wistar-Kyoto

value: normal saline (NS)


title: left ventricular, WKY, rep 3


title: left ventricular, WKY, rep 1


title: left ventricular, SHR, rep 3


title: left ventricular, SHR, rep 2


title: left ventricular, SHR, rep 1


title: long-read, nascent RNA, KCL, 45min, biol rep 1

city: New Haven

first: Paulina

last: Podszywalow-Bartnicka

state: CT

address: 333 Cedar Street

department: Department of Molecular Biophysics and Biochemistry

institute: Yale University

description: Library name: LRS_KCL45min_1

data_processing:
The data analysis pipeline encompassed pre-processing using modules Cutadapt to trim the adapters, Minimap2 for read alignment, and UMICollapse for deduplication. Custom-made scripts were used to filter poly(A)+ reads, filter and separate categories of reads according to the alignment region, calculating gene readthrough transcription index, and other downstream analyses. Pre-processing steps and custom scripts to filter poly(A)+ reads were consolidated in Snakemake. The code used for data analysis is available at https://github.com/NeugebauerLab/Cancer-stress.
Assembly: GRCh38.p14
Supplementary files format and content: For each sample, the LRS_readthroughCounts.txt contains the number of reads per gene that aligned to the last exon and the downstream of gene region (readthrough). This is an output of a custom-made notebook (splicingANDreadthrough) that calculates the readthrough transcription index of poly(A)-filtered reads (*_polyA_filtered_polyAfiltered_sorted_unique_no_splicing_int.bed), a result of the Snakemake pipeline.

growth_protocol: Cells were cultured in suspension, in 175cm2 flasks, RPMI1640 media supplemented with 10% FBS heat inactivated, Pen/Strep; in the atmosphere of 5% CO2 at 37oC.

extract_protocol:
Cell fractionation, nascent RNA isolation, polyA-RNA and rRNA depletion, and library preparation steps were performed following the protocol described by Reimer K, Neugebauer K, Curr Prot 2020 (PMID: 33440169). Following cell fractionation, RNA was isolated from the chromatin after Trizol/chloroform extraction using RNAeasy Mini Kit (including on-column treatment with RNAse-free DNAse). Then poly(A)+ RNA was depleted using DynaBeads mRNA Direct Micro Purification kit, followed by rRNA depletion using RiboMinus Eukaryote Kit v2. and ligation of a 3’end adapter to each nascent RNA.
Libraries for PacBio sequencing were prepared following the protocol described by Reimer K, Neugebauer K, Curr Prot 2020 (PMID: 33440169). After poly(A)+ RNA and rRNA depletion steps, a 3’end DNA adapter with UMI was ligated to each nascent RNA. The PacBio HiFi library for SMARTER/Advantage2 PCR amplified cDNA size selected for fragments longer than 500nt was prepared using SMRTbell Express Template Prep Kit 2.0 from PacBio following the manufacturer’s instructions.

treatment_protocol: Cells were seeded a day before the addition of treatment. To induce hyperosmotic shock 110mM KCl was added to the media. Imatinib was pre-diluted in growth media and added to the cell culture at 1uM, and JTE-607 at 5uM. Nascent RNA was isolated from cells treated for 45min with KCl, 1h or 18h with IM, or 1h with JTE.

value: KCLfor 45min


title: long-read, nascent RNA, KCL, 45min, biol rep 2

description: Library name: LRS_KCL45min_2

value: KCL for 45min


title: long-read, nascent RNA, JTE, 1h, biol rep 2

description: Library name: LRS_JTE1h_2

value: JTE for 1h


title: long-read, nascent RNA, JTE, 1h, biol rep 1

description: Library name: LRS_JTE1h_1


title: long-read, nascent RNA, untreated, biol rep 1

description: Library name: LRS_CTRL_1

value: untreated


title: L-3

city: Nantong

first: Chen

last: Chen

state: Jiangsu Province

address: Qixiu Road,Nantong,226001,Jiangsu,China

institute: Nantong university

description:
Library name: Sample9
L-2_tpm

data_processing:
1. Raw data processing:    - Sequencing was performed on the Illumina NovaSeq 6000 platform, generating paired - end reads in FASTQ format.    - Raw reads were first subjected to quality control using FastQC v0.11.9 to assess the quality metrics such as base quality, GC content, and adapter contamination. Reads with low - quality bases (Phred score < 20) and adapter sequences were trimmed using Trimmomatic v0.39 with the following parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36. 2. Read alignment:    - The trimmed reads were aligned to the Homo sapiens GRCh38 reference genome using HISAT2 v2.2.1 with the gene annotation file from GENCODE v38.    - The alignment was performed with the default parameters of HISAT2, except for --rna - strandness RF to account for the stranded library preparation. 3. Gene expression quantification:    - Gene expression levels were quantified as fragments per kilobase of exon per million mapped reads (FPKM) using StringTie v2.1.4. StringTie was run with the --rf option to be consistent with the stranded library. 4. Differential expression analysis:    - Differential expression analysis was performed using DESeq2 v1.32.0. Genes with an adjusted p - value < 0.05 and a fold - change > 2 were considered as differentially expressed genes. 5. Batch effect correction:    - Batch effects were corrected using the ComBat function in the sva R package to remove potential batch - related variations.
Assembly: Mus musculus, GRCm39
Supplementary files format and content: The processed data files are in TSV format. The main file named 'gene_expression_matrix.tsv' contains a gene expression matrix. The first column lists the Ensembl gene IDs, followed by columns representing different samples (Sample1, Sample2, ..., SampleN). The values in each cell are the FPKM (fragments per kilobase of exon per million mapped reads) values, which represent the normalized gene expression levels. Another file named 'diff_expression_results.tsv' shows the results of differential expression analysis. It has columns for gene ID, log2 fold change, p - value, adjusted p - value, and base mean as described above.

source_name: primary cell

extract_protocol:
1. Sample source: Mouse spinal meninges tissue 2. Sample status: Freshly collected primary cell samples without special treatment 3. Extraction reagents and materials     - Lysis buffer: TRIzol reagent (Invitrogen, Cat. No. 15596026)     - Chloroform (Sigma - Aldrich, Cat. No. C2432)     - Isopropanol (Sigma - Aldrich, Cat. No. I9516)     - 75% ethanol (self - made, prepared with RNase - free water and absolute ethanol)     - RNase - free water (Qiagen, Cat. No. 129114) 4. Extraction steps     - Sample lysis: Take approximately 300 ul of cell, add 1 ml of TRIzol reagent, homogenize on ice for 2 - 3 minutes using a homogenizer, and then let it stand at room temperature for 5 minutes.     - Phase separation: Add 0.2 ml of chloroform, vortex vigorously for 15 seconds, let it stand at room temperature for 2 - 3 minutes, and then centrifuge at 12,000 rpm for 15 minutes at 4°C.     - RNA precipitation: Transfer the upper aqueous phase to a new tube, add 0.5 ml of isopropanol, let it stand at room temperature for 10 minutes, and then centrifuge at 12,000 rpm for 10 minutes at 4°C.     - RNA washing: Discard the supernatant, add 1 ml of 75% ethanol, gently invert the tube to mix well, centrifuge at 7,500 rpm for 5 minutes at 4°C, discard the supernatant, and repeat the washing step once.     - RNA dissolution: Air - dry the RNA pellet at room temperature for 5 - 10 minutes, add 50 μl of RNase - free water, and incubate at 55 - 60°C for 10 minutes. 5. Quality control     - RNA concentration measurement: Measured using Nanodrop 2000, and the RNA concentration was 500 ng/μl.     - RNA integrity detection: Detected by Agilent Bioanalyzer, and the RIN value of RNA was 8.5.
1. Starting materials:     - RNA input amount: 1 μg of total RNA     - RNA quality: RIN value of 8.0 2. Library construction kit:     - Kit name: Illumina TruSeq Stranded Total RNA Library Prep Kit     - Manufacturer: Illumina     - Product number: RS - 122 - 2201 3. Main experimental steps:     - RNA fragmentation:         - Fragmentation method: Chemical fragmentation using magnesium ions at high temperature         - Fragmentation conditions: Fragmentation at 94°C for 8 minutes     - Reverse transcription:         - Reverse transcriptase: SuperScript III Reverse Transcriptase (Invitrogen)         - Primer type: Random primers         - Reaction conditions: Reverse transcription at 50°C for 60 minutes     - Adapter ligation:         - Adapter type: Illumina TruSeq adapters         - Ligase: T4 DNA Ligase (NEB)         - Ligation conditions: Ligation at 20°C for 15 minutes     - PCR amplification:         - PCR primers: Universal primers provided by Illumina         - PCR enzyme: Phusion High - Fidelity DNA Polymerase (NEB)         - Number of amplification cycles: 12 cycles         - Amplification conditions: Denaturation at 98°C for 10 seconds, annealing at 65°C for 30 seconds, extension at 72°C for 30 seconds 4. Quality control:     - Library concentration measurement: Measured by Qubit fluorescence quantification, the library concentration was 20 nM     - Library size distribution detection: Detected by Agilent Bioanalyzer, the average library size was 350 bp

value: spinal cord

value: fibroblast


title: long-read, nascent RNA, KCL, 45min, biol rep 3

description: Library name: LRS_KCL45min_3


title: L-1

description:
Library name: Sample7
L-1_tpm


title: hapo_newborn_cordblood_A0192

type: genomic

city: Chicago

first: Jami

middle: L

last: Josefson

state: Illinois

address: 225 E Chicago Avenue

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

hyb_protocol: Genome-wide methylation profiling was conducted with the Infinium MethylationEPIC BeadChip version 1.0 (Illumina, Inc., San Diego, California) array, which interrogates > 850,000 CpG sites at singlenucleotide resolution

scan_protocol: BeadChips were scanned with an Illumina iScan

data_processing:
minfi package in R environment (version 1.40.0)
processed value definition: M values transformed from beta (HAPO_GA_illumina_methylation.xlsx linked to the Series record)

label: Cy3, Cy5

source_name: newborn cordblood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from whole blood that was stored at -80 C and was quantified with the Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts)

value: Male

value: cord clood

tag: developmental stage

value: newborn

value: whole blood cells


title: T-3

description:
Library name: Sample6
T-3_tpm


title: long-read, nascent RNA, JTE, 1h, biol rep 3

description: Library name: LRS_JTE1h_3


title: T-2

description:
Library name: Sample5
T-2_tpm


title: T-1

description:
Library name: Sample4
T-1_tpm


title: long-read, nascent RNA, untreated, biol rep 3

description: Library name: LRS_CTRL_3


title: C-3

description:
Library name: Sample3
C-3_tpm


title: C-1

description:
Library name: Sample1
C-1_tpm


title: VB1_SCLC

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description:
Library name: VB1
FFPE Spatial Transcriptome Sequencing, 10X Visium

data_processing:
spaceranger-2.0.1
Assembly: GRCh38-2020-A
Supplementary files format and content: Processed results from spaceranger, including count matrix and image.
Library strategy: Spatial Transcriptomics

source_name: SCLC

growth_protocol: FFPE H&E-stained tissues of SCLC patient samples

extract_protocol:
tissues were subject to pathology review to assess tissue quality, structural preservation, cellular viability, tumor content, inflammation, fibrosis, and necrosis. Samples were excluded based on small tissue size, low cellularity, or extensive necrosis. 50 um scrolls of suitable tissue were subjected to RNA quality control using an Agilent RNA ScreenTape System, and samples with DV200 greater than 50% were selected. If necessary, regions of interest (ROIs) were then selected based on the criteria mentioned, and marked on H&E images for subsequent tissue sectioning and mounting on Visium slides. Tissues were sectioned under RNAse-free conditions at 5 um thickness placed in the capture areas Visium Spatial Gene Expression slides (10X Genomics).
The spatial gene expression slide was processed according to the manufacturer’s protocols for spatial profiling of FFPE tissue (CG000409_Demonstrated_Protocol_VisiumSpatialFFPE). In short, following sectioning, Visium slide mounting, deparaffinization, and H&E staining, brightfield morphology images were obtained with a Nikon Eclipse 80i microscope equipped with automated motorized stage (Proscan) at 20x resolution. The images were stitched together with the Nikon IS Elements software (Nikon) and exported as tiff files. Tissues were decrosslinked, and the released RNAs from the tissue were reverse transcribed into complimentary DNA by priming to the spatial barcoded primers on the glass in the presence of template switching oligo. After second strand synthesis, a denaturation step released the cDNAs, which were then amplified with 16-20 cycles of PCR amplification. Finally, indexed sequencing-ready, spatial gene expression libraries were constructed according to the manufacturer’s protocol. The libraries were pooled together to generate upwards of 25,000 read pairs per spatial spot and sequenced on Illumina NovaSeq sequencers with S1 and SP kits and the settings: read 1, 28 cycles; read 2, 90 cycles; index 1, 10 cycles; index 2, 10 cycles.

value: SCLC


title: VA2_SCLC

description:
Library name: VA2
FFPE Spatial Transcriptome Sequencing, 10X Visium


title: VA1_SCLC

description:
Library name: VA1
FFPE Spatial Transcriptome Sequencing, 10X Visium


title: DynaMITE-cGAMP-monocyte

description:
Library name: MN4
10x Genomics

data_processing:
Raw sequencing reads were processed using the 10x Genomics CellRanger bioinformatics pipeline v7.2 and filtered feature matrices were exported as .mtx files with barcodes and features .tsv files. Cell ranger counts matrix of four conditions (w/ or w/o cGAMP and w/ or w/o Monocyte) were integrated as Seurat objects in Seurat 5 (5.0.1) and Seurat wrapper (0.3.4) in R (4.3.2). Low-quality cells and doublets were removed from the following downstream analysis according to the number of genes (less than 200 and more than 7000) and mitochondria percentage (less than 20%) and scDblFinder, respectively. After QC, a total number of analyzing cells was reduced from 36,668 cells to 24,482 cells in all conditions.
Assembly: Human hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: HUVEC, HLFB, CORL47, NK cells, monocyte

growth_protocol: Microphysiological immune tumor environment (MITE) models were generated by using a PDMS-based microfluidic device, containing a microvascular network (MVN) formed by HUVEC and HLF cells surrounding SCLC cancer spheroids. HUVEC and HLF with 4 U/ml thrombin from bovine plasma (Millipore Sigma) were combined with cell densities of 24x106/ml HUVECs and 8x106/ml HLF in cold vascular medium (Vasculife, Lifeline). Cell suspensions were mixed 1:1 volume ratio with 6 mg/ml fibrinogen (Millipore Sigma) and sequentially resuspended with 1x106/ml CORL47 spheroids (previously generated in ULA plate for 24h) mixture by mixing spheroids at 1:0.5 volume ratio with HUVEC and HLF. After injection, MITE devices were incubated for 15 min at 37 °C in humidity chambers, then hydrated with culture media (Vasculife with 10% FBS) and supplemented with 50 ng/ml VEGF (Peprotech), and refreshed daily. After 6 days, PBMC-derived NK cells (2x105 cells/ml) and monocytes (2x105 cells/ml) were perfused through the vascularized MITE model for 15 minutes using Vasculife with IL-2 (300 U/ml, without hydrocortisone supplement)

extract_protocol:
Dynamic single-cell RNAseq (DynaMITE-seq) : Component cells of the MITE devices were extracted from the devices for single-cell RNA sequencing following enzymatic digestion of collagen-hydrogel gel. First, MITE devices were incubated for 30 min with a solution of digestive enzymes comprising 100 U/mL collagenase type IV (Life Technologies) and enzymes from the human tumor dissociation kit (Miltenyi Biotec). Devices were then washed with 0.25% trypsin-EDTA (Thermo Fisher Scientific) for 5 mins and cells were collected by washing the device twice with Vasculife with 10% FBS.
Single cell suspensions were loaded onto a 10X Chromium instrument (10X Genomics) per the manufacturer’s instructions. Single-cell RNA libraries were generated using the Chromium Single Cell 5’ Library Construction (10X Genomics) per user guide. Quality control of the completed libraries was performed using the Bioanalyzer High Sensitivity DNA Kit (Agilent) and then sequenced using the Illumina NextSeq 500 platform.

treatment_protocol: 1 ug/ml of 2’,3’-cGAMP (STING agonist) or untreated

value: HUVEC, HLFB, CORL47, NK cells, monocyte

value: Endothelial cells, fibroblast, cancer cells, nk cells, monocyte

value: WT


title: DynaMITE-cGAMP

description:
Library name: MN2
10x Genomics

source_name: HUVEC, HLFB, CORL47, NK cells

value: HUVEC, HLFB, CORL47, NK cells

value: Endothelial cells, fibroblast, cancer cells, nk cells


title: DynaMITE-control-monocyte

description:
Library name: MN3
10x Genomics


title: DynaMITE-control

description:
Library name: MN1
10x Genomics


title: HCT116/CMV-OS Tir1 Rad21-mAID-mClover EfIa- H3.3-Halo, Non-treated 4

city: Cleveland

first: Le

last: Xiong

address: 9620 Carnegie Ave N Bldg

institute: Cleveland Clinic

description:
Library name: Sample 6
Illumina NovaSeq X

data_processing:
Paired-end 150 bp reads were collected for each samples and Nextera Transposase adapter sequence was removed using Cutadapt (Martin, 2011). Bowtie2 (Langmead and Salzberg, 2012) was used to align reads to the human genome assembly hg38 with the ‘--local’ and ‘--no-discordant’ options. SAMtools (Li et al., 2009) was used to remove alignments with MAPQ smaller than 7 and only proper pairs were kept. MACS2 (Zhang et al., 2008) was used to call  peaks with options: -f BAMPE -g hs -q 0.0001. Peaks for untreated samples were merged to generate consensus peak annotation.
Assembly: hg38
Supplementary files format and content: bigWig, Narrowpeak, Concensus peak

extract_protocol:
ATAC-seq (Buenrostro et al. 2015),Nextera Tn5 enzyme-NEBNext High fidelity master mix
ATAC-seq was performed as described (Buenrostro et al., 2015). HCT116 cells were harvested using trypsin. Nuclear isolation of 5 × 10^4 cells was followed by treatment with Nextera Tn5 enzyme for 30 min at 37°C with 1000 RPM shaking. PCR amplification of the samples was performed using Nextera primers 1 and 2 and NEBNext High fidelity master mix for 12 cycles. Libraries were purified ZYMO DCC5 spin column. Sequencing of libraries was performed on an Illumina NovaSeq X Plus.

value: Human colorectal cancer

value: non-treated


title: HCT116/CMV-OS Tir1 Rad21-mAID-mClover EfIa- H3.3-Halo, Non-treated 3

description:
Library name: Sample 5
Illumina NovaSeq X


title: HCT116/CMV-OS Tir1 Rad21-mAID-mClover EfIa- H3.3-Halo, Non-treated 1

description:
Library name: Sample 1
Illumina NovaSeq X


title: HCT116/CMV-OS Tir1 Rad21-mAID-mClover EfIa- H3.3-Halo, 5-Ph IAA, Sample 2

description:
Library name: Sample 4
Illumina NovaSeq X

value: 5-Ph IAA


title: HCT116/CMV-OS Tir1 Rad21-mAID-mClover EfIa- H3.3-Halo, 5-Ph IAA, Sample 1

description:
Library name: Sample 3
Illumina NovaSeq X


title: H69EZ-GV HLA positive 1

description:
Library name: H69EZ-GV HLA positive 1
H69EZ-G1_HLA_pos_1_NM8114_S82

data_processing:
Reads were aligned to human reference genome using STAR and quantified using HTSeq.
Assembly: hg38
Supplementary files format and content: Gene Expression count matrix

growth_protocol: Human SCLC cell lines H69 and H69EZ-GV were cultured in RPMI-1640 ATCC modification (Thermo Fisher Scientific) containing 10% FBS (Gemini Bio-products), 1X penicillin/streptomycin (Thermo Fisher Scientific), and prophylactic Plasmocin (2.5 ug/mL; Invivogen).

extract_protocol:
For cell line comparison, RNA was isolated directly from duplicate or triplicate samples with the Qiagen (Hilden, Germany) RNeasy isolation kit (Cat# 8028) using on-column DNAse digestion. RNA libraries were prepared from 250 ng total RNA using the Illumina Exome Capture kit per manufacturer’s instructions. RNA-sequencing (RNA-seq) was performed per the standard protocols at the Dana-Farber Molecular Biology Core Facilities with Illumina NextSeq 500 instrument. Data quality controls and replicate correlation were evaluated using VIPER software package.
RNA libraries were prepared from 250 ng total RNA using the Illumina Exome Capture kit per manufacturer’s instructions. RNA-sequencing (RNA-seq) was performed per the standard protocols at the Dana-Farber Molecular Biology Core Facilities with Illumina NextSeq 500 instrument.

treatment_protocol: For H69EZ-GV derivation, H69 cells were treated with EZH2 inhibitor (GSK126, 5mM; Cayman Chemical Company) for 6 d. On day 3, EZH2 inhibitor was replenished, and cells were additionally treated with Vorinostat (1 mM; Selleckchem).  After 3 days, treated or control cells were thoroughly washed twice in PBS (Thermo Fisher Scientific) and all cells recultured in cell culture medium without drug. Cultures were routinely passaged as necessary and were examined daily for the emergence of adherent populations.

value: HLA positive


title: H69EZ-GV HLA positive 2

description:
Library name: H69EZ-GV HLA positive 2
H69EZ-G1_HLA_pos_2_NM8114_S83


title: HCT116/CMV-OS Tir1 Rad21-mAID-mClover EfIa- H3.3-Halo, Non-treated 2

description:
Library name: Sample 2
Illumina NovaSeq X


title: H69EZ-GV HLA negative 2

description:
Library name: H69EZ-GV HLA negative 2
H69EZ-G1_HLA_neg_2_NM8114_S81

value: HLA negative


title: BIHi264-A, 5d, DMSO 1

city: Berlin

first: Christian

last: Schinke

address: Charitéplatz 1

institute: Charité Universitätsmedizin Berlin

description:
Library name: CS04_38-5d-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points

data_processing:
Computational Methods. RNA Seq reads were mapped to human genome (GRCh38.p7) with STAR-version 2.7.3a [95] using the default parameters. Reads were assigned to genes with featureCounts version 2.0.0 [96] with the following parameters: -t exon -g gene_id -s 0 -p, gene annotation - Gencode GRCh38/v25. The differential expression analysis was carried out with DESeq2-version 1.32.0 [97] using the default parameters. We kept genes that have at least 5 reads in at least 3 samples. Gene set enrichment analysis was carried out with R/tmod package version 0.50.07 using MSigDB gene sets [98].
Assembly: GRCh38/v25
Supplementary files format and content: export_raw_counts.00_202501_All_lines_contrasts_full.PTX_vs_DMSO_ID0.all.csv: contains all raw counts of the iPSC-DSN cell lines BIHi005-A, BIHi263-A, BIHi264-A, BIHi272-A, BIHi273-A that were treated with DMSO or paclitaxel.//export_raw_counts.all_Timecourse.csv: contains all raw counts for the different time points of iPSC-DSN BIHi264-A treated with paclitaxel or DMSO.//00_202501_All_lines_contrasts_full.PTX_vs_DMSO_ID0.xlsx: contains differential expression analyses of paclitaxel vs. DMSO treated iPSC-DSN with pooled data of the 5 iPSC-DSN cell lines mentioned above.//01_contrasts_full.2h_PTX_vs_DMSO_ID1.xlsx, 02_contrasts_full.6h_PTX_vs_DMSO_ID2.xlsx, 03_contrast.12h_PTX_vs_DMSO_ID3.andTPMs, 04_contrast.24h_PTX_vs_DMSO_ID4.andTPMs.xls, 05_contrasts_full.48h_PTX_vs_DMSO_ID5.xlsx, 06_contrasts_full.72h_PTX_vs_DMSO_ID0.xlsx and 07_contrasts_full.5d_PTX_vs_DMSO_ID6.xlsx are the differential expression analyses tables of iPSC-DSN BIHi264-A treated with paclitaxel or DMSO for the respective time points mentioned in the tables.
Supplementary files format and content: see above

source_name: iPSC-DSN

growth_protocol: iPSC lines Experiments from this study were conducted in sensory neurons derived from five different iPSC lines, s.c. BIHi263-A, BIHi264-A, BIHi272-A, BIHi273-A (all female, ClinicalTrials identifier NCT02753036; ethics approval at Charité [EA4/069/14], referenced in [32]) and the established reference stem cell line BIHi005-A (male donor, https://hpscreg.eu/cell-line/BIHi005-A). Written informed consent was obtained from all individuals prior to sample acquisition. iPSC were reprogrammed from peripheral mononuclear blood cells (PBMC) or dermal fibroblasts (only BIHi005-A) using Sendai viral vectors, according to established protocols [90-92]. iPSC were tested for the absence of the reprogramming vector with immunofluorescence staining for pluripotency markers, in-vitro directed differentiation into the three germ layers, karyotyping using SNP arrays and g banding and absence of mycoplasma contamination [90, 91]. iPSC were maintained on growth factor reduced Geltrex (Gibco) in E8 media, which was exchanged daily. Cells were enzymatically clump-passaged every 2-4 days when >70% confluency was reached using EDTA (UltraPure™ 0.5 M EDTA, Thermo Fisher). Sensory neuron differentiation and maintenance Differentiation was performed as described previously [30] according to the protocol of Chambers et al. [26] with modification in media formulations according to the s.c. P2 protocol by Schwartzentruber et al. [93]. In brief, >70% confluent clump-passaged iPSCs were single-cell seeded at a density between 200.000-400.000/well into 6-well plates (Falcon) coated with growth factor reduced Geltrex (Gibco) and cultivated in E8 media until 70-80% confluency was achieved, which usually required 48 to 72h. On day 0, neural induction was commenced by replacing E8 media with Knockout Serum Replacement Media (500ml DMEM-KO [Gibco]) supplemented with 130ml CTS KnockOut SR XenoFree Medium (Gibco), 1x MEM-Non-essential Amino Acid Solution (Sigma), 1x Glutamax (Gibco) and 0.01mM β-Mercapto-ethanol (Gibco) containing the two small molecule inhibitors ‘2i’: 100 nM LDN-193189 (Sigma) and 10 µM SB-431542 (Peprotech) to drive neuroectoderm differentiation. On day 2, ‘3i’ consisting of 3 µM CHIR99021 (Sigma), 10µM DAPT (Sigma) and 10 µM SU5402 (Sigma) were added to promote neural crest specification. On day 4, N2B27 media (500ml Neurobasal-Medium [Gibco], 5ml of N-2 (100x) supplement [Gibco], 10ml of B27-supplement (50x) without Vitamin A [Gibco], 1x Glutamax and 0.01mM β-Mercapto-ethanol [Sigma]) was progressively phased in. From day 6 onwards, ‘2i’ addition was ceased but ‘3i’ continued to be added until Day 11. On day 11, iPSC-DSN were reseeded using TrypLe select (Gibco) for dissociation and resuspended in N2B27 maintenance media containing 10 μM ROCK inhibitor, at densities of 48.000/well into geltrex-coated 96-well plates for cell viability/cytotoxicity assays and MTT live assays, 1mio/well into 6-well plates for transcriptomic, proteomic and lipidomic experiments, 30.000cells/well in 48-well MEA plates for electrophysiological assessment, 100.000/well in 8-chamber-slides (ibidi) for calcium imaging or staining and in a droplet at 50.000-100.000cells/well onto coverslips for patch-clamp experiments. ROCK inhibitor containing N2B27 media was removed 24h after reseeding and replaced with N2B27 supplemented with BDNF, GDNF, βNGF and NT3 (all at 25 ng/ml, Peprotech). On day 14, cells were treated with 1 µg/ml Mitomycin C (Sigma) for 2h to eliminate few dividing non-neuronal cells. From day 14 onwards, 1x Pen/Strep (Gibco) was also supplemented. iPSC-DSN were maturated for at least 4 more weeks for viability assays (>d40), at least 40 more days for stainings, calcium imaging and patch-clamp experiments (>d50) and 50 more days for multi-electrode-arrays, transcriptome and proteome analyses (>d60) for relative functional maturity [27]. Half media change was performed every 3-4 days with N2B27 supplemented with BDNF, GDNF, βNGF and NT3 (all at 25ng/ml, Peprotech; summary of differentiation timeline in Suppl. Fig. 7). For references, please refer to our CDDis manuscript.

extract_protocol:
RNA was harvested with the Aurum™ Total RNA Mini Kit according to manufacturers’ instructions.
RNA sequencing was performed by Brooks Life Sciences Genewiz® with PolyA selection for RNA removal, 2x150 bp sequencing configuration and 20-30 million reads per sample. RNA Library Preparation and NovaSeq Sequencing by AzentaLifeSciences Genewiz: RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies) and RNA integrity was checked with an RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies). RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB, Ipswich). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First-strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies), and quantified by using Qubit 4.0 Fluorometer (Invitrogen). The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and basecalling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was tolerated for index sequence identification.

treatment_protocol: Compound preparation Paclitaxel (Adipogen) was dissolved in the appropriate amount of DMSO to reach a 6mM stock solution, which was further diluted in N2B27 media to reach the final concentrations 100pM, 1nM, 10nM, 100nM, 1µM and 10µM. Concentrations of the vehicles were adapted to the amount of DMSO in which the highest paclitaxel dosage was dissolved, e.g., 1/600 DMSO for cell viability experiments (as paclitaxel concentrations reached a maximum of 10µM for viability curve calculation), or 1/60.000 for RNA sequencing, proteomic and lipidomic experiments (paclitaxel concentration of 100nM). All solutions were prepared on the day of experimentation. Cell viability and cytotoxicity assays For the calculation of cell viability, RealTime-Glo™ MT Cell Viability Assays (Promega) were performed in white wall, clear bottom 96-well imaging plates (Greiner), according to the manufacturers’ instructions. Luminescence intensities were measured every 12 hours up to 108 h using the Berthold TriStar LB 941 luminescence reader, with Mikrowin Software, and all values were background subtracted and normalized to the individual well baseline and vehicle control [94].

value: iPSC-DSN

value: Maturation more than 60d

value: Wildtype

value: Batch 1


title: Hi-C S-phase,  MATa cells, replicate 2

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

country: France

institute: ENS Lyon

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function with mapping quality set to 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz) with the HML, HMR, MAT, and the rDNA repeated regions masked.
Supplementary files format and content: Hi-C and unfiltered ssHi-C contact data in cooler format binned at 1kb

growth_protocol: Cells were grown to exponential phase in YP-lactate media containing galactose. For synchronization in G1, cells growin in YP-lactate were treated with alpha-factor for 3 hours. For S-phase cells, G1-arrested cells were washed and released in YP-lactate media containing auxin for 20 minutes. The same protocol was used for depletion of Cdc45-AID and Scc1-AID in S-phase. For cells arrested in mitosis,G1-arrested cells were released in YP-lactate media containing nocodazole for 4 hours. For cells arrested in metaphase upon activation of the DNA damage checkpoint, G1-arrested cells were released in YP-lactate media containing galactose to induce the expression of the HO gene under control of the pGAL1 promoter. It triggers formation of an unrepairable break on chr. V, and samples are collected at 2 and 4 hours post-G1 release. For break induction at MAT, exponential cultures grown in YP-lactate were supplemented to induce expression of the HO gene.

extract_protocol:
Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm.
Hi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells.
DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions.

treatment_protocol: ~1.5x10^9 cells were crosslinked with 3% formaldehyde for 30 minutes at 120 rpm at room temperature, followed by quenching with 330 mM glycine for 30 minutes at 120 rpm.

value: MATa-inc, ura3::LY-HOcs, lys2::LY, can1::HIS3-LY-Pad, trp1::GAL-HO-hphMX, his3::OsTIR1-9Myc::HIS3, ade2-1, leu2-3,112, RAD5

value: Auxin


title: H69EZ-GV HLA negative 1

description:
Library name: H69EZ-GV HLA negative 1
H69EZ-G1_HLA_neg_1_NM8114_S80

value: SCLC


title: BIHi264-A, 5d, DMSO 2

description:
Library name: CS04_41-5d-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 72h, paclitaxel 1

description:
Library name: CS04_32-72h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points

value: Paclitaxel 100 nM, 72h


title: BIHi264-A, 5d, paclitaxel 3

description:
Library name: CS04_40-5d-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points

value: Paclitaxel 100 nM, 5d


title: BIHi264-A, 48h, paclitaxel 3

description:
Library name: CS04_29-48h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points

value: Paclitaxel 100 nM, 48h


title: BIHi264-A, 48h, DMSO 3

description:
Library name: CS04_30-48h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 5d, paclitaxel 2

description:
Library name: CS04_39-5d-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 72h, DMSO 3

description:
Library name: CS04_36-72h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 5d, paclitaxel 1

description:
Library name: CS04_37-5d-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 72h, paclitaxel 3

description:
Library name: CS04_35-72h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 48h, paclitaxel 1

description:
Library name: CS04_26-48h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 48h, DMSO 1

description:
Library name: CS04_25-48h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 72h, paclitaxel 2

description:
Library name: CS04_34-72h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 72h, DMSO 2

description:
Library name: CS04_33-72h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 24h, DMSO 2

description:
Library name: CS04_22-24h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 48h, paclitaxel 2

description:
Library name: CS04_28-48h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 24h, paclitaxel 1

description:
Library name: CS04_20-24h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points

value: Paclitaxel 100 nM, 24h


title: BIHi264-A, 72h, DMSO 1

description:
Library name: CS04_31-72h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 24h, DMSO 1

description:
Library name: CS04_19-24h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 48h, DMSO 2

description:
Library name: CS04_27-48h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 24h, paclitaxel 3

description:
Library name: CS04_23-24h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 24h, DMSO 3

description:
Library name: CS04_24-24h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 12h, DMSO 3

description:
Library name: CS04_18-12h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 24h, paclitaxel 2

description:
Library name: CS04_21-24h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 12h, paclitaxel 2

description:
Library name: CS04_15-12h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points

value: Paclitaxel 100 nM, 12h


title: BIHi264-A, 12h, paclitaxel 3

description:
Library name: CS04_17-12h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 6h, DMSO 2

description:
Library name: CS04_10-6h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 12h, DMSO 2

description:
Library name: CS04_16-12h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 6h, DMSO 1

description:
Library name: CS04_8-6h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 12h, DMSO 1

description:
Library name: CS04_14-12h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 6h, paclitaxel 2

description:
Library name: CS04_9-6h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points

value: Paclitaxel 100 nM, 6h


title: BIHi264-A, 6h, paclitaxel 3

description:
Library name: CS04_11-6h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 6h, DMSO 3

description:
Library name: CS04_12-6h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 6h, paclitaxel 1

description:
Library name: CS04_7-6h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 12h, paclitaxel 1

description:
Library name: CS04_13-12h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 2h, paclitaxel 3

description:
Library name: CS04_6-2h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points

value: Paclitaxel 100 nM, 2h


title: BIHi264-A, 2h, DMSO 1

description:
Library name: CS04_2-2h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 2h, paclitaxel 2

description:
Library name: CS04_4-2h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 2h, DMSO 3

description:
Library name: CS04_5-2h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 2h, DMSO 2

description:
Library name: CS04_3-2h-DMSO
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi264-A, 2h, paclitaxel 1

description:
Library name: CS04_1-2h-PTX
RNA Seq data of iPSC-DSN BIHi264-A, paclitaxel vs. DMSO - different time points


title: BIHi273-A, paclitaxel 3

description:
Library name: p273_9_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO

value: Maturation more than 55d


title: BIHi273-A, DMSO 3

description:
Library name: p273_9_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi273-A, paclitaxel 1

description:
Library name: p273_7_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi273-A, DMSO 1

description:
Library name: p273_7_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi273-A, paclitaxel 2

description:
Library name: p273_8_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi273-A, DMSO 2

description:
Library name: p273_8_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: IH2

city: Houston

first: Akdes

last: Serin Harmanci

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: 25031-01Q2-02
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hippocampus

extract_protocol:
Mouse gliomas were dissociated into single cells. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3. RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.
Library was performed according to the manufacter’s instructions (Single Cell 3' v3 or Single Cell 3' v4, 10X Genomics).

value: hippocampus


title: IH3

description:
Library name: 25031-01-02
10X Genomics


title: IH1

description:
Library name: 25031-01Q2-01
10X Genomics


title: BIHi272-A, paclitaxel 3

description:
Library name: p272_12_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi272-A, paclitaxel 2

description:
Library name: p272_11_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: IgA-Seq Sample IgA14A

city: Jacksonville

first: John

last: Gubatan

institute: Mayo Clinic Florida

description:
Library name: IgA14A
Novogene
IGASEQ.rds

data_processing:
Analyses of 16S rRNA data were performed using the Quantitative Insights into Microbial Ecology (QIIME) 2 (http://qiime.org), an open-source bioinformatics pipeline for performing analysis of microbiome sequence data as previously described (Boylen et al., 201960).  Briefly, raw sequencing data were demultiplexed using unique barcodes assigned to each sample and then denoised using Dada2 as previously described (Callahan et al., 2016).  Remaining reads were then clustered into Operational Taxonomic Units (OTUs) using Greengenes v13-8 as a reference set to assign taxonomy to each OTU
Assembly: Greengenes v13-8 reference
Supplementary files format and content: Merged IGA-SEQ Phyloseq obejct, Merged IGG-SEQ Phyloseq obejct,
Library strategy: 16S rRNA-seq

source_name: Stool

extract_protocol:
Frozen stool (200 mg) samples from each patient were thawed and dissolved in 1 mL of phosphate buffered saline (Invitrogen, Catalog No. Catalog No. AM9624). Stool was resuspended in 1 mL of 5 mM N-acetyl-cysteine (Thermo Scientific Chemicals, Catalog No. 616-91-1) to break disulfide bonds in mucus and release bacterial cells and then passed through 100 uM filters and centrifuged. The resulting stool pellets were resuspended in 1 mL of PBS and divided into four fractions for downstream experiments (bacterial FACS, whole microbiome 16S, IgA-Seq, and IgG-Seq). For bacterial FACS, stool cell pellets were centrifuged and resuspended in PBS and stained with 1:10,000 SYBR Green (Sigma Aldrich) at room temperature in dark for 20 minutes. Cell pellets were subsequently centrifuged, resuspended in PBS, and stained with 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) and 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Cell pellets were centrifuged and resuspended in FACS buffer and 1:50 Fc block was to each sample and incubated at room temperature for 10 minutes. Bacterial cell pellets were then centrifuged and resuspended in FACS buffer. FACS was used to quantify the proportion of SYBR green positive (live bacterial cells) that were IgA-APC+, IgG-PE+, and IgA+IgG+ double positives.Stool pellets from each patient were processed as previously described. Bacterial cell pellets were resuspended in PBS and separate stool fractions were stained with either 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) or 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Bacterial cell pellets were centrifuged and then washed with MACS buffer.  Anti-PE MicroBeads (Miltenyi Biotec, Catalog No. 130-090-855) were added to IgG fraction and Anti-APC MicroBeads (Miltenyi Biotec, Catalog No. 130-048-801) to IgA fraction. Bacterial cell pellets were then centrifuged, resuspended in MACS buffer, and placed onto OctoMACS™ Separator (Miltenyi Biotec, Catalog No. 130-042-108) columns for magnetic separation. IgA and IgG-bound bacterial fractions were then collected for each sample. Purity of IgA-bound and IgG-bound gut bacteria were above 90% for all samples included in downstream analyses.
DNA from bacterial cell pellets from IgA-bound, IgG-bound, and unfractionated (whole gut microbiome) samples were isolated using the PureLink™ Microbiome DNA Purification Kit (Catalog No. A29790) per manufacturer’s instructions. Bacterial 16S sequencing of the V4 and V5 regions (primer 515F/sequence GTGCCAGCMGCCGCGGTAA, primer 907R/sequence CCGTCAATTCCTTTGAGTTT) were performed at Novogene using 2x250 sequencing on an Illumina MiSeq.

value: Stool

value: Pre-vitamin D


title: control3

description:
Library name: 25031-01Q1-02
10X Genomics


title: BIHi272-A, DMSO 3

description:
Library name: p272_12_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO

value: iPSC-DSN


title: BIHi272-A, paclitaxel 1

description:
Library name: p272_10_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO

value: Wildtype


title: control 2

description:
Library name: 25031-01Q1-01
10X Genomics


title: BIHi272-A, DMSO 1

description:
Library name: p272_10_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO

value: Batch 1


title: control 1

description:
Library name: 25031-01-01
10X Genomics


title: mES_5GEx_1K

city: Memphis

first: Brian

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
The raw sequencing data from the Illumina sequencer was de-multiplexed and processed using Cell Ranger v6.0.0 (10X Genomics) pipeline
FASTQ files were generated with a command ‘cellranger mkfastq’. The mapping of raw reads to mm10 mouse genome and generating count matrices of cell and unique molecular identifier (UMI) barcodes was performed with ‘cellranger count’
The resulted filtered feature-barcode matrices from Cell Ranger pipeline were futher analyzed with Seurat v4.1.0 in R v4.0.2
Assembly: mm10
Supplementary files format and content: filtered feature-barcode matrices stored in the Market Exchange Format (MEX)

growth_protocol: mESC V6.5 cells are male cells derived from a C57BL/6(F) x 129/sv(M) cross. All cell lines were cultured in 2i + LIF medium.

extract_protocol:
Cell cultures at the growths of log phase were collected and checked for cell number and viability using TC20 automated counter (Bio-Rad). Samples with >90 % viability were processed to prepare single cell suspensions and diluted into target numbers plus multiplet rate (1000 cells plus 0.8 % per library).
Single cell RNA sequencing libraries were generated using the Chromium Next GEM Single Cell 5’ Kit v2 (10x Genomics), following the manufacturer’s manual. Briefly, single cell suspensions were loaded on the chromium controller to capture single cell gel beads and then to perform in-droplet reactions of barcoding followed by the amplification of full-length cDNAs. Sequencing libraries were constructed by sequential ligation reactions of kit-provided adaptor oligos and then dual indexes to enzymatically fragmented cDNAs. The resulting cDNA libraries were purified with solid-phase reversible immobilization SPIRI beads (Beckman) and checked on a BioAnalyzer High sensitivity chip (Agilent) and a Qubit fluorometer (InVitrogen) for DNA concentrations and size distributions, respectively.

value: emborynic stem cells


title: BIHi272-A, DMSO 2

description:
Library name: p272_11_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO