title: NSC-male-wt_rep3

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

description: Library name: NSC-male-wt_rep3

data_processing:
RNA-seq reads were trimmed for adapter and low quality sequences using TrimGalore! v0.4.4, before mapping onto the GRCm38 mouse genome reference with HISAT2 v2.0.5 (Kim et al., 2015), in paired-end mode and disabling soft-clipping. Because the samples have 129/SvJ maternal alleles and either Cast/EiJ or C57BL/6 paternal alleles (except the paternal X that is only Cast), we prepared N-masked versions of the genome using SNPsplit v0.3.2. For autosomal gene expression analysis, both 129/SvJ and Cast/EiJ SNPs are N-masked. For X-linked expression analysis, we used a dual-hybrid genome prepared with SNPsplit. Alignments specific to the C57BL/6, 129/SvJ and Cast/EiJ alleles were separated using SNPsplit v0.3.2 in paired-end mode.
Gene counts were obtained in R 3.5.1 (R Development Core Team, 2019) from the split and non-split bam files with the featureCounts function from the Rsubread package (1.32.1 Liao et al., 2014; Liao et al., 2019), provided with the GRCm38.90 GTF annotation downloaded from Ensembl, and ignoring multi-mapping or multi-overlapping reads.
For analysis of global expression changes, total (non-haplotyped) counts were normalized in edgeR v3.24.0 (Robinson et al., 2010; McCarthy et al., 2012) with the TMM method (Robinson and Oshlack, 2010). Genes were defined as expressed and retained for differential expression analysis if they had at least one count per million (cpm) in at least a third of the libraries. Differential expression analysis was performed with likelihood ratio tests. P-values were corrected with the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Differential expression results were visualized with Glimma 1.10.0 (Su et al., 2017), with differential expression cut-offs of adjusted p-value<0.05. Plots were generated in R with the ggplot2 (Wickham, 2016), cowplot (Wilke, 2019), ggbeeswarm (Clarke and Sherrill-Mix, 2017), and ggrepel (Slowikowski, 2019) packages.
For allele-specific analysis of autosomal imprinted genes, we genotyped samples as previously (Wanigasuriya et al. 2019), fitting a recursive partition tree with the rpart function (R Development Core Team, 2019; Therneau and Atkinson, 2019; Breiman et al., 1984) to the proportion of Cast/EiJ or C57BL/6 reads in each 100 kb bin tiling the genome, with options minsplit = 4, cp = 0.05. We compiled a list of all 316 known mouse imprinted genes and kept genes with at least 20 haplotyped counts in at least 2 samples per genotype. To determine whether these genes were imprinted in the neural stem cells, we then fitted a logistic regression with the glm function from the stats package (R Development Core Team, 2019) on the maternal and paternal counts for each gene in the wild-type samples and retained the genes with an absolute log-ratio of expression greater than or equal to log(1.5). A betabinomial test (from the aod package, Lesnoff & Lancelot 20212) was performed for each gene to assess for differences in parental expression ratios between wild-types and mutants. The p-values were corrected with the Benjamini-Hochberg method.
We compiled a list of all 316 known mouse imprinted genes and kept genes with at least 20 haplotyped counts in at least 2 samples per genotype. To determine whether these genes were imprinted in the neural stem cells, we then fitted a logistic regression with the glm function from the stats package (R Development Core Team, 2019) on the maternal and paternal counts for each gene in the wild-type samples and retained the genes with an absolute log-ratio of expression greater than or equal to log(1.5). A betabinomial test (from the aod package, Lesnoff & Lancelot 20212) was performed for each gene to assess for differences in parental expression ratios between wild-types and mutants. The p-values were corrected with the Benjamini-Hochberg method. To investigate the effect of the E147A Smchd1 mutation on X chromosome inactivation in females, we used edgeR’s paired-sample design (Chen et al., 2017) with common dispersion to model the maternal (Xa) and paternal (Xi) counts as a function of genotype. We tested the effect of genotype with a likelihood ratio test. The p-values were corrected with the Benjamini-Hochberg method. We used the criteria of 5% false discovery rate (FDR).
Assembly: mm10/GRCm38
Supplementary files format and content: tab-separated files of gene counts from the Ensemble GRCm38 v90 release. The table includes both total counts (non-haplotyped) and haplotyped counts (129/Cast) for allele-specific analysis of the X chromosome for each female sample

source_name: Neural Stem Cells

growth_protocol: Generation of Neural Stem Cells Neural stem cells were generated exactly as we have previously described (Chen et al., PNAS 2015; Jansz et al., NSMB 2018; Jansz et al. Cell Rep 2018). In brief, we set up timed matings, and dissected embryos at embryonic day 14.5. The cortices of each embryo were dissociated and grown as an adherent monolayer on laminin coated tissue culture treated plates. Their growth media was NeuroCult NSC Basal Medium (mouse) with NeuroCult Proliferation Supplement (Stem Cell Technologies), with the addition of recombinant human EGF (20 ng/mL) and recombinant human basic FGF (20ng/mL, both from Stem Cell Technologies).  Neural stem cell samples for RNA sequencing To enable us to assess the X inactivation status in neural stem cell populations, we created neural stem cells from embryos that were Smchd1GFP-E147A/+; XistdeltaA/+ or Smchd1+/+; XistdeltaA/+ for females, or Smchd1GFP-E147A/+; XY or Smchd1+/+; XY for males. In addition to the genetic changes, the animals were all F1, derived from a Castaneus father mated with a mother that was 129/C57 F1. Therefore, all Castaneus alleles were of paternal origin, and for the X inactivation the XistdeltaA allele ensured that the Castaneus X was always the inactive X chromosome. This approach allowed allele-specific analysis of the RNA sequencing data

extract_protocol:
RNA was extracted using the Zymo quick-RNA miniprep kit according to manufacturer’s instructions
Libraries were prepared using the Illumina TruSeq V2 stranded mRNA sample preparation kits from 500 ng total RNA as per manufacturer’s instructions. Fragments above 200 bp were size-selected and cleaned up using AMPure XP magnetic beads. Final cDNA libraries were quantified using D1000 tape on the TapeStation (4200, Agilent Technologies) for sequencing on the Illumina Nextseq500 platform using 80 bp, paired-end reads.

value: Neural Stem Cells

value: SMCHD1 +/+

value: Male

tag: litter


title: cr-endosperm.sRNA.nrpd1 / nrpd1.replicate1

status: Public on Feb 02 2026

type: SRA

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description:
Library name: endo_pol_x_pol_rep1
Capsella rubella nrpd1 scion grafteing to nrpd1 root: endosperm of the grafting plants

library_source: transcriptomic

data_processing:
Adapters were removed from the reads using Cutadapt, and the resulting 18–30 bp long reads were selected. Reads belonging to chloroplast, mitochondria, and structural noncoding RNAs (tRNAs, snRNAs, rRNAs, or snoRNAs) were removed using Bowtie (-v 1). The remaining reads were mapped to the eight chromosome scaffolds of the Capsella genome v.1.0 build.
Assembly: Capsella rubella v1.0  (also listed as 183) http://www.phytozome.org/dataUsagePolicy.php?org=Org_Crubella
Supplementary files format and content: Unique small RNAs (between 18-25 nts) and their accumulation number (raw reads) are represented in a two column format file: <unique_smallRNA> <number_of_raw_reads>.<length_nts>

molecule: total RNA

organism: Capsella rubella

source_name: endosperm

growth_protocol: Seeds were sterilized with 70% EtOH, rinsed with distilled water, and sown on half-strength Murashige and Skoog (MS) medium with 1% sucrose. Seeds were stratified for two days in the dark at 4°C and then transferred to a growth chamber with a long-day photoperiod (16h of light / 8h of dark, 22°C, 50% humidity) for two weeks. Seedlings were then transferred to soil and grown under long-day conditions in the phytotron under 16h of light at 21 °C and 8h of darkness at 18°C with a light intensity of 150 µE and 70% humidity.

extract_protocol:
Total RNA was extracted using mirVanaTM miRNA isolation Kit, small RNA was extracted by gel size selection of 10~40 nt
sRNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (E7300). Final libraries were purified from a size selection of bands of about 150bp on a 6% polyacrylamide gel. Two biological replicates were used for anther, pollen, and endosperm samples, three biological replicates were used for root samples

treatment_protocol: For endosperm and pollen, sample were collected from the scion of grafted plants as indicated genotypes.

tag: tissue

value: endosperm

tag: genotype

value: nrpd1(Cr1Gr1) / nrpd1(Cr1Gr1)

tag: treatment

value: grafting (scion/root)


title: NSC-male-wt_rep1

description: Library name: NSC-male-wt_rep1

molecule: polyA RNA

organism: Mus musculus

tag: cell type

tag: Sex


title: NSC-male-E147A_rep3

description: Library name: NSC-male-E147A_rep3

value: SMCHD1 E147A/+


title: cr-anther.sRNA. rdr6-2.replicate2

description:
Library name: ant_jz134_rdr6_rep3
Capsella rubella rdr6-2 anther

source_name: anther

value: anther

value: rdr6-2 (Cr1GR1)


title: Alzheimer's Disease, PTP1B +/+, rep2

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

country: USA

institute: Cold Spring Harbor Laboratory

description:
Library name: AD4
10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing reads were demultiplexed with matrices using 10X Genomics' Cell Ranger mkfastq software v6.0.0.
Reads were aligned to the mouse reference genome GCRm38 GENCODE vM23 using Ensembl 98 annotations (i.e. prebuilt Cell Ranger reference mm10-2020-A, 10X Genomics, https://www.10xgenomics.com/support/software/cell-ranger/downloads/cr-ref-build-steps#mouse-ref-2020-a) using Cell Ranger v7.1.0 and default settings (which includes assigning uniquely mapping intronic reads to their parent gene in the count matrix).
Ambient RNA was subtracted using Cellbender 0.3.0 (https://github.com/broadinstitute/CellBender). Potential doublets/multiplets were removed with scDblFinder v 1.24.0 (https://github.com/plger/scDblFinder)
Seurat version 5.1.0 was used for normalization, dimensionality reduction, clustering and projection. Dimensionality reduction was conducted with PCA and UMAP (30 PCs), and graph-based clustering identified major cell populations, which were then manually annotated based on marker gene expression. Cell types were assigned to clusters based on differential expression of a curated list of marker genes.  A microglial subset was further isolated, re-processed, and sub-clustered to profile specific microglial states.
Assembly: GRCm38
Supplementary files format and content: Integrated Seurat objects containing 3' cell/gene count matrices corrected for ambient RNA contamination using Cellbender. Clustering, cell-type annotations, and dimensionality reduction coordinates (PCA,UMAP), and SCTransform-adjusted matrix included in object.
Supplementary files format and content: Seurat .RDS objects for all viable cells and for in silico-filtered microglial cells provided

source_name: Brain

extract_protocol:
FACS-based viability enrichment and single-cell library preparation were carried out at the Cold Spring Harbor Laboratory Single-Cell Biology Shared Resource. Prior to FACS, Single-cell suspensions were washed by centrifugation at 4°C, 600xg in a swinging bucket rotor, and resuspended in 1X PBS with 0.04% BSA, and stained with SytoxBlue dead cell stain (ThermoFisher #S34857). Viable, intact cells were sorted using a Sony SH800 sorter on a 70um chip into PBS/BSA, pelleted as above and resuspended at 1,000 cells/μL.
Single-cell RNA sequencing was performed using 10X Genomics NextGEM v3.1 3' Gene Expression kits by the Cold Spring Harbor Laboratory Single-Cell Biology Shared Resource. Cells were loaded into a 10x Genomics Chromium X instrument and libraries prepared according to the manufacturer’s instructions. Unique dual-indexed libraries were paired end sequenced using the Illumina NextSeq2000 sequencing system with 28x10x10x90bp reads to a mean depth of ~50,000 reads per cell.

value: Dissociated single cells

value: Brain

tag: strain

value: C57BL/6; APP/PS1;PTP1B+/+

tag: age

value: 13 mo


title: OPC_4AP_ctrl-1

city: Edinburgh

first: Tim

last: Czopka

address: 49 Little France Crescent

department: Institute of Neuroscience and Cardiovascular Research

country: United Kingdom

institute: The University of Edinburgh

description: Library name: OPC_4AP_ctrl-1_lib1

data_processing:
The “Demultiplex QIAseq UPX 3’ reads” tool of the CLC Genomics Workbench 22.0.2 was used to demultiplex the raw sequencing reads according to the sample indices. The “Quantify QIAseq UPX 3’ workflow” was used to process the demultiplexed sequencing reads with default settings.
Assembly: Zebrafish genome GRCz11
Supplementary files format and content: Processed data files are .csv tables containing chromosome, region complement, expression value, TPM, RPKM, Exons, Gene ID, Gene Length, ensembl ID, Biotype, unique gene reads, total gene reads, annotated transcripts, uniquely identified transcripts, exon length, unique exon reads, total exon reads, ratio of unique to total, unique exon-exon reads, total exon-exon reads, unique exon reads, total exon reads, ratio of intron to total gene reads.

organism: Danio rerio

source_name: oligodendrocyte precursor cell

extract_protocol:
RNA was extracted using the RNeasy micro UCP kit (QIAGEN), as per kit instructions
The library preparation was done using the QIAseq UPX 3'™ Transcriptome Kit (QIAGEN). A total of 1ng or 4ng purified RNA was converted into cDNA NGS libraries.

value: oligodendrocyte precursor cell

value: 4AP control


title: cr-endosperm.sRNA.nrpd1 / nrpd1.replicate2

description:
Library name: endo_pol_x_pol_rep2
Capsella rubella nrpd1 scion grafteing to nrpd1 root: endosperm of the grafting plants


title: cr-endosperm.sRNA.nrpd1 / wt.replicate2

description:
Library name: endo_pol_x_wt_rep2
Capsella rubella nrpd1 scion grafteing to wt root: endosperm of the grafting plants

value: nrpd1(Cr1Gr1) / wt(Cr1Gr1)


title: hybrid_juvenile_male_litter#2_individual#2

city: Madrid

first: Lena

last: Arévalo

state: Madrid

address: Avda. Puerta de Hierro, 18

department: Animal Reproduction

country: Spain

institute: INIA-CSIC

description: Library name: J2_2

data_processing:
Quality control, trimming of raw sequencing reads, filtering and mapping were performed as described in Arévalo et al. (2021). To improve comparability, all samples (Dom, Spret, and hybrid) were mapped to a pseudo-hybrid genome, generated using the genome preparation tool of the program SNPsplit (Krueger and Andrews 2016). Briefly, SNPs from both Dom (WSB/EiJ) and Spret (SPRET/EiJ) relative to the mouse genome (GRCm38.89) available from the Ensembl FTP server (ftp://ftp.ensembl.org) were introduced into the mouse genome. SNPs between Dom and Spret were then N-masked to allow mapping of both Dom- and Spret-derived reads. We randomly downsampled all alignment files to the same number of reads (~40 million reads) using SAMtools 0.1.19 (Li et al. 2009). For analysis of allele specific expression (ASE) in hybrids we used SNPsplit to split the hybrid alignment files, separating reads originating from the Spret and Dom alleles. Reads that were unassignable (did not overlap SNPs between WSB/EiJ and SPRET/EiJ) or contained conflicting or non-informative (polymorphic) SNPs were removed. On average, 69% of mapped RNAseq reads were assignable, 26% unassignable and 5% conflicting.
Transcript quantification and annotation was done using StringTie 1.3.3 (Pertea et al. 2015). Mouse genome annotation information (GRCm38.89) was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org). We used the python script (preDE.py) included in the StringTie package to prepare gene-level count matrices for analysis of differential expression (DE; Table 1) and ASE in DESeq2 1.16.1 (Love et al. 2014). Pseudogenes were removed from the count matrices based on “biotype” annotation information extracted from Biomart (R-package biomaRt, Durinck et al. 2005). Low counts were removed by the independent filtering process implemented in DESeq2 (Bourgon et al. 2010). The adjusted p-value (Benjamini-Hochberg method) cutoff was set at ≤ 0.05. Following the recommendations of Love et al. (2014; see also Vallejos et al. 2016; Schurch et al. 2016), we chose an absolute log2 fold change (LFC) cutoff of ≥ 0.5 (1.41 times higher or lower expression) for standard DE analysis.
Assembly: GRCm38.89 (with N-masked SNPs between WSB/EiJ) and Spret (SPRET/EiJ))
Supplementary files format and content: tab delimited file including DEseq-normalized read counts for all samples

organism: Mus musculus domesticus x Mus spretus

source_name: murine hypothalamus

extract_protocol:
Total RNA was extracted from hypothalamus tissue using the AllPrep RNA/DNA Mini Kit (Qiagen), and was stored at -80°C until sequencing.
Illumina library preparation was done at the sequencing facility (Novogene, Sacramento, CA) using the NEB Next Ultra RNA library prep kit for Illumina.  Individual libraries were sequenced on the Illumina HiSeq 4000 platform, producing >40 million, 150bp paired-end reads per sample.

treatment_protocol: Mice used in this study were maintained on a 12:12 light:dark cycle with lights on at 9:00 AM and were provided with 5001 Rodent Diet (LabDiet, Brentwood, MO, U.S.A.) and water ad lib. All animal procedures were approved by the Oklahoma State University IACUC under protocol #141-AS. M. m. domesticus (hereafter, Dom) was represented by the wild-derived inbred strain WSB/EiJ (Jackson Laboratory) and M. spretus (hereafter, Spret) was represented by the wild-derived inbred strain SFM/Pas (Montpellier Wild Mice Genetic Repository). We conducted three crosses, Dom x Dom, Dom x Spret, Spret x Spret (female listed first). For embryonic tissue collections we used timed mating to establish embryonic age ±24h as described previously (Arévalo and Campbell 2020; Arévalo et al. 2021). Pregnant females (n=5/cross) were euthanized by cervical dislocation between 10:00 and 11:00 AM on embryonic day 17-18 (e17.5).  Tissues (maternal brain, embryo heads, placentas) were collected into RNAlater (Thermo Fisher, USA), kept at 4°C overnight to allow RNAlater perfusion, and stored at -20°C until processing. Embryo sex was determined by PCR for the Y-linked gene, Zfy1, and the hypothalamus was dissected from 1 female and 1 male embryo per litter per genotype with the exception of one all-male hybrid litter (n=5 males/genotype, n=5 Dom females, n=5 Spret females, n=4 hybrid females).  Brains from juvenile and adult animals were collected into RNAlater at day 21 (average 21.3, SD 0.73, n=5/sex/genotype), and day 71 (average 70.9, SD 2.09, n=5/sex/genotype), respectively. The hypothalamus was dissected and stored at -20°C in RNAlater until processing. Adult animals were sexually naïve and singly housed for at least 24h prior to euthanasia.

value: murine hypothalamus

tag: developmental stage

value: juvenile

value: male

value: M. m. domesticus/M. spretus hybrid


title: hybrid_juvenile_female_litter#1_individual#2

description: Library name: J1_2

value: female


title: NSC-male-wt_rep2

description: Library name: NSC-male-wt_rep2

value: Neural Stem Cells

value: SMCHD1 +/+

value: Male


title: Alzheimer's Disease, PTP1B -/-, rep1

description:
Library name: KO7
10x Genomics

value: C57BL/6; APP/PS1;PTP1B-/-


title: hybrid_juvenile_female_litter#2_individual#1

description: Library name: J2_1


title: NSC-male-E147A_rep2

description: Library name: NSC-male-E147A_rep2

value: SMCHD1 E147A/+


title: cr-anther.sRNA. rdr6-2.replicate1

description:
Library name: ant_jz134_rdr6_rep2
Capsella rubella rdr6-2 anther

value: anther

value: rdr6-2 (Cr1GR1)


title: Alzheimer's Disease, PTP1B -/-, rep2

description:
Library name: KO8
10x Genomics

value: Dissociated single cells

value: Brain


title: cr-anther.sRNA.rdr6-1.replicate2

description:
Library name: ant_jz127_rdr6_rep3
Capsella rubella rdr6-1 anther

value: rdr6-1 (Cr1GR1)


title: NSC-male-E147A_rep1

description: Library name: NSC-male-E147A_rep1


title: hybrid_juvenile_male_litter#1_individual#1

description: Library name: J1_1


title: HNSC.100, untreated wild type cells, 3

city: Ulm

first: Estera

middle: Anna

last: Jeruzalska

address: James-Franck-Ring N27

department: Institute of Pharmaceutical Biotechnology

country: Germany

institute: Ulm University

description: Library name: Sample HNSC_3

data_processing:
adapter removal using Cutadapt tool (Galaxy version 4.8)
trimming the sequence end using Trimmomatic tool (Galaxy version 0.39)
reads mapping using RNA Star tool (Galaxy version 2.7.11a) with setting: paired-end, lenght 50 nt per read, MAPQ = 60 without WASP filtering
read counting using htseq-count (galaxy version 2.0.9)
measurement of gene expression using featureCounts (Galaxy version 2.08)
Assembly: human genome GRCh38.14 version 46 (https://www.gencodegenes.org/)
Supplementary files format and content: tabular type of data including counts for each transcript in the sample

organism: Homo sapiens

growth_protocol: collected 1 Mio cells per sample, cells were cultivated in DMEM/F12 medium with supplements

extract_protocol:
total RNA isolation using High Pure RNA isolation kit (Roche)
mRNA isolation using NEBNext Poly(A) mRNA magnetic isolation module
cDNA synthesis and library prep using NEBNext Ultra II Directional RNA Library Prep for Illumina, 60 bp paired-end sequencing with 30-35 million reads per sample

treatment_protocol: untreated

tag: cell line

value: neural stem cell

value: WT

value: untreated


title: Alzheimer's Disease, PTP1B +/+, rep1

description:
Library name: AD3
10x Genomics

value: C57BL/6; APP/PS1;PTP1B+/+

value: 13 mo


title: NSC-female-wt_rep2

description: Library name: NSC-female-wt_rep2

value: Female


title: hybrid_adult_male_litter#19_individual#2

description: Library name: A19_2

value: murine hypothalamus

value: adult

value: male

value: M. m. domesticus/M. spretus hybrid


title: cr-anther.sRNA.wt.replicate2

description:
Library name: ant_wt_rep3
Capsella rubella wt anther


title: HNSC.100, untreated wild type cells, 4

description: Library name: Sample HNSC_4


title: hybrid_adult_female_litter#19_individual#1

description: Library name: A19_1

value: female


title: NSC-female-E147A_rep2

description: Library name: NSC-female-E147A_rep2

value: Neural Stem Cells

value: SMCHD1 E147A/+


title: hybrid_adult_male_litter#15_individual#2

description: Library name: A15_2


title: cr-anther.sRNA.rdr6-1.replicate1

description:
Library name: ant_jz127_rdr6_rep2
Capsella rubella rdr6-1 anther

value: anther


title: NSC-female-wt_rep1

description: Library name: NSC-female-wt_rep1

value: SMCHD1 +/+


title: hybrid_adult_female_litter#15_individual#1

description: Library name: A15_1


title: cr-microspore.RNAseq.nrpd1 / wt.replicate2

description:
Library name: micro_pol_x_wt_rep2
Capsella rubella nrpd1 scion grafteing to wt root: microspore of the grafting plants

data_processing:
For each replicate, the reads were quality trimmed using Trimmomatic and mapped to the Capsella genome v. 1.0 (Phytozome) using HISAT2 with default parameters. Raw counts of transcripts were estimated using HTSeq and Transcripts Per Kilobase Million (TPM) were estimated using StringTie.
Assembly: Capsella rubella v1.0  (also listed as 183) http://www.phytozome.org/dataUsagePolicy.php?org=Org_Crubella
Supplementary files format and content: expression levels (TPM) are shown for genes in the chromosome-like first eight scaffolds of the Capsella rubella genome for each condition and replicate.

source_name: microspore

extract_protocol:
RNA was extracted with Direct-zol RNA Miniprep Kit according to manufacturer’s instruction.
RNA Seq library was prepared with NEBNext Poly(A)mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra RNA LibraryPrep Kit for Illumina (E7530). For each analyzed genotype there were two biological replicates. Libraries were sequenced on HiSeqX in a 150 bp paired-end mode.

treatment_protocol: Microspore was extracted from the scion of grafted plants

value: microspore

value: nrpd1(Cr1GR1) / wt(Cr1GR1)

value: grafting


title: HNSC.100, untreated wild type cells, 1

description: Library name: Sample HNSC_1

value: neural stem cell

value: WT


title: cr-anther.sRNA.wt.replicate1

description:
Library name: ant_wt_rep1
Capsella rubella wt anther


title: HD with NFKB1 variant introduced 6 hr culture with LPS_R3

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: Library name: S47

data_processing:
Reads were mapped to GRCh38
Counts per gene were summarized using the featureCounts function from the subread package
edgeR package was used to import and filter the counts
Differential expression using MAST models
The limma package with its voom method, namely, linear modelling and empirical Bayes moderation was used to test differential expression (moderate t-test). P-values were adjusted for multiple testing using Benjamini-Hochberg correction (false discovery rate-adjusted p-value; FDR). Differentially expressed genes for each comparison were visualized using Glimma package, and FDR<0.05 was set as the threshold for determining significant differential gene expression. Enrichment analyses were carried out using Fgsea package.
Assembly: GRCh38
Supplementary files format and content: Tab separated file having raw read count for each sample in singular file

source_name: iPSC-derived

growth_protocol: iPSC-derived monocytes cultured for 4 weeks

extract_protocol:
RNeasy Micro Kit (Qiagen) as per manufacturer's protocol.
RNA libraries were prepared using the NEB Ultra Express Kit with Poly-A selection.

treatment_protocol: Cultured in presence of absence of LPS for 18 hours

value: iPSC-derived

value: monocyte

value: NFKB1 variant

value: cell culture with LPS

tag: batch

value: same


title: HNSC.100, untreated wild type cells, 2

description: Library name: Sample HNSC_2

value: untreated


title: hybrid_adult_female_litter#13_individual#1

description: Library name: A13_1

value: murine hypothalamus

value: adult

value: M. m. domesticus/M. spretus hybrid


title: cr-microspore.RNAseq.nrpd1 / nrpd1.replicate2

description:
Library name: micro_pol_x_pol_rep2
Capsella rubella nrpd1 scion grafteing to nrpd1 root: microspore of the grafting plants

value: nrpd1(Cr1GR1) / nrpd1(Cr1GR1)


title: HD with NFKB1 variant introduced 6 hr culture with LPS_R2

description: Library name: S46


title: Xenium, output-XETG00113__0010699__Region_3__20240621__170414

type: RNA

city: St Louis

first: Junedh

last: Amrute

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

hyb_protocol: NOT PROVIDED; REQUESTED

scan_protocol: NOT PROVIDED; REQUESTED

data_processing: Methods Amrute et al, 2025; REQUESTED

label: not provided

source_name: human coronary artery

label_protocol: FFPE blocks and sectioned and the 10x Genomics Xenium In Situ Gene Expression with Cell Segmentation Staining User Guide protocol (10x Genomics, Protocol number CG000749) used for sample (#1000661; #1000460; #1000487. 10x Genomics). 17 regions were analyzed.

extract_protocol: Xenium in situ: A custom gene panel was designed (Supplementary Table 4) based on the CITE-seq reference map and combined with the Xenium Human Multi-Tissue and Cancer Panel (#1000626, 10x Genomics).

value: human coronary artery


title: NSC-female-E147A_rep1

description: Library name: NSC-female-E147A_rep1

value: Neural Stem Cells

value: SMCHD1 E147A/+

value: Female


title: HD with NFKB1 variant introduced 6 hr culture with LPS_R1

description: Library name: S45


title: cr-microspore.RNAseq.nrpd1 / nrpd1.replicate1

description:
Library name: micro_pol_x_pol_rep1
Capsella rubella nrpd1 scion grafteing to nrpd1 root: microspore of the grafting plants

value: microspore

value: grafting


title: PyMT-driven orthotopic xenograft tissue microarray

city: Bethesda

first: Lisbeth

last: Berrueta

state: MD

address: 30 Convent drive, 5th floor room 532

institute: NIDCR/NIH

description: 20 Stretch and 20 No Stretch mammary xenograft tumor samples.

data_processing:
Xenium data was analyzed with the Seurat R package. Initial QC analysis revealed poor staining in 20 (10 Stretch, 10 No Stretch) of the 40 tissues and were removed by the Seurat’s crop() function from downstream analyses. Group metadata was added to cell-based coordinate locations and cells featuring less than 100 Xenium counts were removed from subsequent analysis. The total number of cells remaining was 19,9087. Expression levels were normalized using the SCTransform() function and PCA, clustering and UMAP embeddings were computed using the first 30 dimensions and default parameters. Optimal clustering resolution was determined by the Clustree R package.
To identify cell populations, we performed clustering and cell type annotation based on canonical markers and then downsampled each condition to have equal number of cells (66013 cells per group). We computed total number of cells per cell type and per tissue section (10 Stretch, 10 No-Stretch) and analyzed this table by the scCODA method which aims to identify changes in compositional parameters  as previously described [37]

label: Xenium probe set

source_name: mammary tumor

label_protocol: Xenium probe set

growth_protocol: Met-1 cell lines were cultured in DMEM supplemented with 10% FBS, 1% penicillin and streptomycin, and 1% L-glutamine (Gibco) and maintained at 37°C with 5% CO2. For injections: Six-week-old FVB mice underwent bilateral tumor cell injection. Single tumor cell suspensions (Met-1 or GFP-Met-1) were prepared in a mixture containing 40% Geltrex  and 60% DMEM. A total of 0.020X106 tumor cells in 100 µl were injected subcutaneously, bilaterally on the back, at the third mammary fat pad

extract_protocol: tissue preparation protocol: Tissue was fixed using PFA and  FfPA

treatment_protocol: Animals were No stretch or stretch during 10 minutes twice a day, actively or under anesthesia (once a day). For ex vivo experiments: gels were stretched twice a day using 23% amplitude

value: mammary tumor

tag: tissue preservation method

value: FFPE

value: Stretch and No Stretch

value: FVB-Met 1 orthotopic injection


title: HD with NFKB1 variant introduced 6 hr culture with LPS_R4

description: Library name: S48

value: iPSC-derived

value: monocyte

value: NFKB1 variant

value: cell culture with LPS


title: cr-microspore.RNAseq.wt / wt.replicate2

description:
Library name: micro_wt_x_wt_rep2
Capsella rubella wt scion grafteing to wt root: microspore of the grafting plants

value: wt(Cr1GR1) / wt(Cr1GR1)


title: hybrid_adult_female_litter#12_individual#2

description: Library name: A12_2

value: murine hypothalamus

value: adult

value: female

value: M. m. domesticus/M. spretus hybrid


title: cr-microspore.RNAseq.nrpd1 / wt.replicate1

description:
Library name: micro_pol_x_wt_rep1
Capsella rubella nrpd1 scion grafteing to wt root: microspore of the grafting plants

value: nrpd1(Cr1GR1) / wt(Cr1GR1)


title: Xenium, output-XETG00113__0010699__Region_2__20240621__170414

value: human coronary artery


title: hybrid_adult_male_litter#14_individual#1

description: Library name: A14_1

value: male


title: hybrid_adult_male_litter#12_individual#1

description: Library name: A12_1


title: cr-microspore.RNAseq.wt / wt.replicate1

description:
Library name: micro_wt_x_wt_rep1
Capsella rubella wt scion grafteing to wt root: microspore of the grafting plants

value: microspore

value: grafting


title: HD with NFKB1 variant introduced 4 hr culture with LPS_R3

description: Library name: S43

value: same


title: hybrid_adult_male_litter#10_individual#1

description: Library name: A10_1


title: hybrid_adult_female_litter#11_individual#1

description: Library name: A11_1


title: Xenium, output-XETG00113__0010641__Region_5__20240628__212431


title: HD with NFKB1 variant introduced 4 hr culture with LPS_R2

description: Library name: S42


title: cr-leaf.BSseq.nrpd1 / wt.replicate2

description:
Library name: leaf_pol_x_wt_rep2
Capsella rubella nrpd1 scion grafting to wt root: leaf of the grafting plants

library_source: genomic

data_processing:
The 150-bp-long pair-end reads were quality trimmed by removing the first five bases from the 5’ end and the last 15 bases from the 3’ end using Trim Galore. Reads were mapped to the Capsella rubella v1.0 reference genome in paired-end mode (–score_min L, 0, 0.6) using Bismark v0.16.3. Mapped reads were deduplicated and cytosine methylation values calculated using the Bismark Methylation Extractor
Assembly: Capsella rubella v1.0  (also listed as 183) http://www.phytozome.org/dataUsagePolicy.php?org=Org_Crubella
Supplementary files format and content: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format: <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>

molecule: genomic DNA

source_name: leaf

growth_protocol: Seeds were sterilized with 70% EtOH, rinsed with distilled water, and sown on half-strength Murashige and Skoog (MS) medium with 1% sucrose. Seeds were stratified for two days in the dark at 4°C and then transferred to a growth chamber with a long-day photoperiod (16h of light / 8h of dark, 22°C, 50% humidity). Hypocotyl grafting was conducted 3 days after germination.  Seedlings were then transferred to soil and grown under long-day conditions in the phytotron under 16h of light at 21 °C and 8h of darkness at 18°C with a light intensity of 150 µE and 70% humidity.

extract_protocol:
Samples were stored at -80 °C and then used for isolation of genomic DNA with DNeasy Plant Mini Kit (Qiagen).
Bisulfite libraries were prepared with the Accel-NGS Methyl-Seq DNA Library Kit from Illumina (Cat No. 30096, Swift), and the sequencing was performed at Novogene (Hongkong, China) on a NovaSeq 6000 platform in 150-bp paired-end mode

treatment_protocol: Pollen, microspore, and leaves were collected from grafted plants, and seedling leaves were collected from the progeny of grafted plants.

value: leaf

value: grafting (scion/root)


title: EP.YSGr [Yun.Yp.12]

city: Houston

first: Nourhan

last: Abdelfattah

state: TX

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

data_processing:
Bulk RNA-seq analysis was carried out using the in-house pipeline at The Jackson Laboratory. Trimmomatic (version 0.33) was used to remove adapters and also leading and trailing low quality bases. Reads fewer than 36 bases long were discarded. Reads with more than 50% low-quality bases overall were filtered out, and the remaining high-quality reads were then used for expression estimation. Alignment estimation of gene expression levels using the EM algorithm for paired-end read data was performed using RSEM (v1.2.12 RRID:SCR_013027). RSEM uses bowtie2 (RRID:SCR_016368) as an aligner to align the mapped reads against the mm10 reference genome. Data quality control was performed using Picard (v1.95- RRID:SCR_006525) and bamtools (RRID:SCR_015987) to obtain general alignment statistics from the BAM file. The read counts estimated for each gene by RSEM were given as input to the R package edgeR (v3.30.3-RRID:SCR_012802) for differential expression analysis.
Assembly: mm10
Supplementary files format and content: comma separated file containig the log2CPM values for all samples

source_name: MB

extract_protocol:
RNA was isolated  from tumor tissue using the standard Triazol protocol.
Whole RNA was sent to BGI for library prep and sequencing on the BGISEQ-500 platform

value: MB

value: Female


title: HD with NFKB1 variant introduced 4 hr culture with LPS_R1

description: Library name: S41

value: iPSC-derived

value: monocyte

value: NFKB1 variant


title: HD with NFKB1 variant introduced 0 hr culture with LPS_R4

description: Library name: S40

value: cell culture with LPS


title: Xenium, output-XETG00113__0010641__Region_2__20240628__212431


title: EP.YSGr [Yun.Yp.11]


title: cr-leaf.BSseq.nrpd1 / nrpd1.replicate2

description:
Library name: leaf_pol_x_pol_rep2
Capsella rubella nrpd1 scion grafting to nrpd1 root: leaf of the grafting plants

value: nrpd1(Cr1GR1) / nrpd1(Cr1GR1)


title: Xenium, output-XETG00113__0010699__Region_1__20240621__170414


title: HD with NFKB1 variant introduced 0 hr culture with LPS_R3

description: Library name: S39


title: EP.YSGr [Yun.Yp.9]

value: Male


title: Xenium, output-XETG00113__0010641__Region_4__20240628__212431


title: EP.YSGr [Yun.Yp.10]


title: cr-leaf.BSseq.nrpd1 / nrpd1.replicate1

description:
Library name: leaf_pol_x_pol_rep1
Capsella rubella nrpd1 scion grafting to nrpd1 root: leaf of the grafting plants


title: HD with NFKB1 variant introduced 0 hr culture with LPS_R1

description: Library name: S37


title: Xenium, output-XETG00113__0010641__Region_3__20240628__212431


title: HD with NFKB1 variant introduced 0 hr culture with LPS_R2

description: Library name: S38


title: Xenium, output-XETG00113__0010641__Region_1__20240628__212431


title: EP.YSGr [Yun.Yp.8]


title: cr-leaf.BSseq.wt / wt.replicate2

description:
Library name: leaf_wt_x_wt_rep2
Capsella rubella wt scion grafting to wt root: leaf of the grafting plants

value: wt(Cr1GR1) / wt(Cr1GR1)


title: cr-leaf.BSseq.wt / wt.replicate1

description:
Library name: leaf_wt_x_wt_rep1
Capsella rubella wt scion grafting to wt root: leaf of the grafting plants


title: cr-leaf.BSseq.nrpd1 / wt.replicate1

description:
Library name: leaf_pol_x_wt_rep1
Capsella rubella nrpd1 scion grafting to wt root: leaf of the grafting plants

value: nrpd1(Cr1GR1) / wt(Cr1GR1)


title: HD 6 hr culture with LPS_R4

description: Library name: S36

value: wildtype


title: Xenium, output-XETG00113__0005113__Region_1__20240628__212431

value: human coronary artery


title: EP.YSGr [Yun.Yp.7]


title: cr-microspore.BSseq.nrpd1 / wt.replicate1

description:
Library name: micro_pol_x_wt_rep1
Capsella rubella nrpd1 scion grafting to wt root: microspore of the grafting plants

value: microspore


title: HD 6 hr culture with LPS_R3

description: Library name: S35


title: Xenium, output-XETG00113__0005113__Region_3__20240628__212431


title: Xenium, output-XETG00113__0005113__Region_2__20240628__212431


title: cr-microspore.BSseq.nrpd1 / nrpd1.replicate2

description:
Library name: micro_pol_x_pol_rep2
Capsella rubella nrpd1 scion grafting to nrpd1 root: microspore of the grafting plants


title: cr-microspore.BSseq.nrpd1 / wt.replicate2

description:
Library name: micro_pol_x_wt_rep2
Capsella rubella nrpd1 scion grafting to wt root: microspore of the grafting plants


title: Xenium, output-XETG00113__0005092__Region_6__20240621__170414


title: HD 6 hr culture with LPS_R2

description: Library name: S34


title: Xenium, output-XETG00113__0005092__Region_5__20240621__170414


title: EP.SG [Yun.Yp.5]


title: cr-microspore.BSseq.nrpd1 / nrpd1.replicate1

description:
Library name: micro_pol_x_pol_rep1
Capsella rubella nrpd1 scion grafting to nrpd1 root: microspore of the grafting plants


title: EP.SG [Yun.Yp.4]


title: HD 6 hr culture with LPS_R1

description: Library name: S33


title: EP.SG [Yun.Yp.2]


title: EP.SG [Yun.Yp.3]


title: Xenium, output-XETG00113__0005092__Region_4__20240621__170414


title: Xenium, output-XETG00113__0005092__Region_3__20240621__170414


title: Xenium, output-XETG00113__0005092__Region_2__20240621__170414


title: HD 4 hr culture with LPS_R3

description: Library name: S31


title: EP.SG [Yun.Yp.6]


title: HD 4 hr culture with LPS_R2

description: Library name: S30


title: cr-microspore.BSseq.wt / wt.replicate2

description:
Library name: micro_wt_x_wt_rep2
Capsella rubella wt scion grafting to wt root: microspore of the grafting plants


title: EP.SG [Yun.Yp.1]


title: HD with NFKB1 variant introduced 4 hr culture with LPS_R4

description: Library name: S44


title: cr-pollen.BSseq.nrpd1 / wt.replicate2

description:
Library name: pollen_pol_x_wt_rep2
Capsella rubella nrpd1 scion grafting to wt root: pollen of the grafting plants

source_name: pollen

value: pollen


title: HD 4 hr culture with LPS_R1

description: Library name: S29

value: same


title: Xenium, output-XETG00113__0005092__Region_1__20240621__170414


title: cr-microspore.BSseq.wt / wt.replicate1

description:
Library name: micro_wt_x_wt_rep1
Capsella rubella wt scion grafting to wt root: microspore of the grafting plants


title: HD 4 hr culture with LPS_R4

description: Library name: S32


title: R2 cartilage rep2

city: Bunkyo-ku, Tokyo

first: Hisatoshi

last: Ishikura

state: Japan

department: Orthopaedic

country: Japan

institute: University of Tokyo

description: cartilage.csv

data_processing:
BGISEQ
The sequencing reads containing low-quality, adaptor-polluted and high content of unknown base reads were removed before downstream analyses
After reads filtering, we mapped clean reads to reference genome using HISAT2.
Genome_build: mm10
Supplementary files format and content: comma-delimited text files include FPKM values for each Sample

source_name: cartilage

extract_protocol:
Synovium or Cartilage was removed and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard BGI protocols

value: cartilage

tag: intervention


title: cr-pollen.BSseq.nrpd1 / nrpd1.replicate2

description:
Library name: pollen_pol_x_pol_rep2
Capsella rubella nrpd1 scion grafting to nrpd1 root: pollen of the grafting plants

value: grafting (scion/root)


title: R2 cartilage rep1

description: cartilage.csv


title: HD 0 hr culture with LPS_R4

description: Library name: S28


title: HD 0 hr culture with LPS_R3

description: Library name: S27


title: cr-pollen.BSseq.nrpd1 / nrpd1.replicate1

description:
Library name: pollen_pol_x_pol_rep1
Capsella rubella nrpd1 scion grafting to nrpd1 root: pollen of the grafting plants


title: P. tabuliformis stage 3

city: Shanghai

first: Tao

last: Jin

address: Handan Rd. 220

country: China

institute: Fudan University

description:
Library name: PT_s3
Fresh frozen Spatial transcriptome sequencing

data_processing:
Sequences were aligned to corresponding genome to gene expression count using BSTMatrix's default settings
Raw sequencing data were processed using BSTMatrix to generate matrix files
Assembly: gigadb(GB)/ DRYAD(GM)/ NGBdb(PT, CP)
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: barcodes_pos.tsv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: he.tif: image of tissue
Library strategy: Spatial Transcriptomics

organism: Pinus tabuliformis

source_name: ovules

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10μm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with BMK S1000 Gene Expression Slides

value: ovules


title: R1 cartilage rep2

description: cartilage.csv


title: cr-pollen.BSseq.nrpd1 / wt.replicate1

description:
Library name: pollen_pol_x_wt_rep1
Capsella rubella nrpd1 scion grafting to wt root: pollen of the grafting plants


title: P. tabuliformis stage 2

description:
Library name: PT_s2
Fresh frozen Spatial transcriptome sequencing


title: R1 cartilage rep1

description: cartilage.csv


title: P. tabuliformis stage 1

description:
Library name: PT_s1
Fresh frozen Spatial transcriptome sequencing


title: cr-pollen.BSseq.wt / wt.replicate2

description:
Library name: pollen_wt_x_wt_rep2
Capsella rubella wt scion grafting to wt root: pollen of the grafting plants


title: MMS D28 cartilage rep2

description: cartilage.csv

value: MMS D28


title: cr-pollen.BSseq.wt / wt.replicate1

description:
Library name: pollen_wt_x_wt_rep1
Capsella rubella wt scion grafting to wt root: pollen of the grafting plants


title: VEC

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

description:
Library name: VEC
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 with --expect-cells=5000 --nosecondary commands.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Single-cell suspensions from lung tissue were collected. FACS-sorted cells were gated on CD45+ live cells. Sorted cells from 5 mice were combined and were washed with PBS, and cell numbers and viabilities were assessed by trypan blue staining. The 10,000 cells isolated from the lung were used for scRNA-seq library prep.
scRNA-seq library prep was  following the protocol from 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits V2.

value: Lung

value: CD45+ cells

value: VEC


title: 4II

description:
Library name: 4II
10x Genomics


title: Il12b-3

description:
Library name: Sample_OT1-9_374_203
Bulk RNA-seq

data_processing:
FASTQ files were aligned to the mouse genome reference version gencode.vM32 by STAR 2.7.10b. Reads mapped to each gene were counted using --quantMode GeneCounts in STAR.
Assembly: gencode.vM33
Supplementary files format and content: tab-delimited text files include read counts, tpm for each Sample

source_name: OT-I T Cells

extract_protocol:
RNA was  extracted by TRIZOL. The RNA sequencing library was prepared using the NEBNext rRNA Depletion Kit v2 and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina
RNA-seq

value: OT-I T Cells

tag: sample group


title: CVID with NFKB1 variant corrected 6 hr culture with LPS_R4

description: Library name: S24

value: iPSC-derived

value: monocyte

value: cell culture with LPS


title: CVID with NFKB1 variant corrected 6 hr culture with LPS_R3

description: Library name: S23


title: HD 0 hr culture with LPS_R1

description: Library name: S25


title: MMS D28 cartilage rep1

description: cartilage.csv


title: cr-seedling.BSseq.nrpd1 / wt.replicate1

description:
Library name: seedling_pol_x_wt_rep1
Capsella rubella nrpd1 scion grafting to wt root: seedling of the grafting progeny

source_name: seedling leaf

value: seedling leaf

value: nrpd1(Cr1GR1) / wt(Cr1GR1)


title: HD 0 hr culture with LPS_R2

description: Library name: S26

value: wildtype


title: cr-seedling.BSseq.nrpd1 / nrpd1.replicate2

description:
Library name: seedling_pol_x_pol_rep2
Capsella rubella nrpd1 scion grafting to nrpd1 root:  seedling of the grafting progeny

value: nrpd1(Cr1GR1) / nrpd1(Cr1GR1)


title: CVID with NFKB1 variant corrected 6 hr culture with LPS_R2

description: Library name: S22


title: cr-seedling.BSseq.nrpd1 / wt.replicate2

description:
Library name: seedling_pol_x_wt_rep2
Capsella rubella nrpd1 scion grafting to wt root: seedling of the grafting progeny


title: MMS D14 cartilage rep1

description: cartilage.csv

value: MMS D14


title: Il12b-2

description:
Library name: Sample_OT1-8_291_286
Bulk RNA-seq


title: cr-seedling.BSseq.nrpd1 / nrpd1.replicate1

description:
Library name: seedling_pol_x_pol_rep1
Capsella rubella nrpd1 scion grafting to nrpd1 root:  seedling of the grafting progeny


title: Il12b-1

description:
Library name: Sample_OT1-7_303_274
Bulk RNA-seq


title: CVID with NFKB1 variant corrected 6 hr culture with LPS_R1

description: Library name: S21

value: same


title: 41bbl-3

description:
Library name: Sample_OT1-6_315_262
Bulk RNA-seq


title: MMS D14 cartilage rep2

description: cartilage.csv

value: cartilage


title: cr-seedling.BSseq.wt / wt.replicate2

description:
Library name: seedling_wt_x_wt_rep2
Capsella rubella wt scion grafting to wt root: seedling of the grafting progeny

value: wt(Cr1GR1) / wt(Cr1GR1)

value: grafting (scion/root)


title: MMS D7 cartilage rep1

description: cartilage.csv

value: MMS D7


title: 41bbl-2

description:
Library name: Sample_OT1-5_327_250
Bulk RNA-seq


title: CVID with NFKB1 variant corrected 4 hr culture with LPS_R4

description: Library name: S20


title: MMS D7 cartilage rep2

description: cartilage.csv


title: CVID with NFKB1 variant corrected 4 hr culture with LPS_R3

description: Library name: S19


title: cr-seedling.BSseq.wt / wt.replicate1

description:
Library name: seedling_wt_x_wt_rep1
Capsella rubella wt scion grafting to wt root: seedling of the grafting progeny


title: MMS D3 cartilage rep2

description: cartilage.csv

value: MMS D3


title: CVID with NFKB1 variant corrected 4 hr culture with LPS_R2

description: Library name: S18


title: Vec-3

description:
Library name: Sample_OT1-3_351_226
Bulk RNA-seq

value: Vec


title: Control cartilage rep2

description: cartilage.csv

value: Control


title: C. panzhihuaensis stage 1

description:
Library name: CP_s1
Fresh frozen Spatial transcriptome sequencing

organism: Cycas panzhihuaensis

value: ovules


title: MMS D3 cartilage rep1

description: cartilage.csv


title: 41bbl-1

description:
Library name: Sample_OT1-4_339_238
Bulk RNA-seq

value: OT-I T Cells


title: CVID with NFKB1 variant corrected 4 hr culture with LPS_R1

description: Library name: S17

value: iPSC-derived

value: monocyte


title: Vec-2

description:
Library name: Sample_OT1-2_363_214
Bulk RNA-seq


title: CVID with NFKB1 variant corrected 0 hr culture with LPS_R4

description: Library name: S16

value: cell culture with LPS


title: G. montanum stage 2

description:
Library name: GM_s2
Fresh frozen Spatial transcriptome sequencing

organism: Gnetum montanum


title: Control cartilage rep1

description: cartilage.csv


title: Vec-1

description:
Library name: Sample_OT1-1_375_202
Bulk RNA-seq


title: CVID with NFKB1 variant corrected 0 hr culture with LPS_R2

description: Library name: S14


title: Treated Tumor- HER2 DC1+aSEMA4D #3

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

description: Immunology

hyb_protocol: The CodeSet of each NanoString panel was hybridized to approximately 100 ng of RNA according to the manufacturer's protocol and the bound probes were immobilized to cartridge on the nCounter PrepStation following the vendor protocol.

scan_protocol: Each cartridge was scanned on the NanoString Digital Analyzer at 555 fields of view (FOV).

data_processing:
Gene expression data was analysed using nSolver™ Analysis Software version 4.0 from NanoString Technologies (NanoString Technologies, WA, USA).
Default parameters were used for QC. Normalizations were done by using selected housekeeping genes with low CV at different data ranges.
Selected house keeping genes are as follows: GPL30557 (Cog7,Oaz1,Sap130,Sdha,Ubb); GPL31165 (Alas1,Eef1g,Eif2b4,Nubp1,Oaz1,Polr1b);GPL32407 (Alas1,Eef1g,Gapdh,G6pdx,Oaz1,Ppia); GPL32728 (Abcf1,G6pdx,Eef1g,Polr1b,Hprt,Sdha).
Differential expression was analyzed using Limma package.

source_name: Soft Tissue

label_protocol: Not applicable

growth_protocol: TUBO tumor cell lines were cultured in standard complete media before injected into BALB/c mice

extract_protocol: Mice were euthanized at the same timepoint and the tumors were dissected. Tumor samples were flash frozen in liquid nitrogen, then stored at -80C before RNA sequencing

treatment_protocol: TUBO bearing mice were treated with a combination of spmaphorin4D blocking antibody and intratumoral dendritic cell therapy for 3 weeks before analysis

tag: gender

value: Female

value: BALB/c

tag: tissue type

value: Tumor


title: CVID with NFKB1 variant corrected 0 hr culture with LPS_R3

description: Library name: S15

value: wildtype


title: R2 synovium rep3

description: synovium.csv

source_name: synovium

value: synovium


title: R2 synovium rep2

description: synovium.csv


title: G. montanum stage 3

description:
Library name: GM_s3
Fresh frozen Spatial transcriptome sequencing


title: CVID with NFKB1 variant corrected 0 hr culture with LPS_R1

description: Library name: S13

value: same


title: 4II-2

description:
Library name: Sample_OT1-14_314_263
Bulk RNA-seq


title: R2 synovium rep1

description: synovium.csv


title: R1 synovium rep3

description: synovium.csv


title: G. montanum stage 1

description:
Library name: GM_s1
Fresh frozen Spatial transcriptome sequencing


title: 4II-1

description:
Library name: Sample_OT1-13_326_251
Bulk RNA-seq


title: Treated Tumor- HER2 DC1+aSEMA4D #1

description: Immunology


title: Treated Tumor- HER2 DC1+aSEMA4D #2

description: Immunology


title: Ifng-3

description:
Library name: Sample_OT1-12_338_239
Bulk RNA-seq

value: Ifng


title: 4II-3

description:
Library name: Sample_OT1-15_302_275
Bulk RNA-seq


title: Ifng-2

description:
Library name: Sample_OT1-11_350_227
Bulk RNA-seq


title: R1 synovium rep2

description: synovium.csv


title: Treated Tumor- anti-Semaphorin4D #2

description: Immunology


title: Treated Tumor- anti-Semaphorin4D #1

description: Immunology


title: CVID with NFKB1 variant uncorrected 6 hr culture with LPS_R3

description: Library name: S11

value: NFKB1 variant


title: CVID with NFKB1 variant uncorrected 6 hr culture with LPS_R4

description: Library name: S12


title: CVID with NFKB1 variant uncorrected 6 hr culture with LPS_R2

description: Library name: S10


title: Ifng-1

description:
Library name: Sample_OT1-10_362_215
Bulk RNA-seq


title: CVID with NFKB1 variant uncorrected 6 hr culture with LPS_R1

description: Library name: S9


title: MMS D14 synovium rep3

description: synovium.csv

value: MMS D14


title: CVID with NFKB1 variant uncorrected 4 hr culture with LPS_R4

description: Library name: S8


title: Treated Tumor- HER2 DC1 Treatment #2

description: Immunology


title: MMS D14 synovium rep2

description: synovium.csv


title: R1 synovium rep1

description: synovium.csv


title: Treated Tumor- HER2 DC1 Treatmen #1

description: Immunology


title: E0771-LUNG-4

description:
Library name: E0771-LUNG-4
gRNA profile

library_source: other

data_processing:
Raw single-end fastq read files were filtered and demultiplexed using Cutadapt. Raw fastq read files were then trimmed to the 20 bp sgRNA spacer sequences. The 20 bp sgRNA spacer sequences from each demulitplexed sample were mapped the sgRNA spacers to the mSAM library using Bowtie 1.1.2: bowtie -v 2 --suppress 4,5,6,7 --chunkmbs 2000 –best. Using the resultant mapping output, we quantitated the number of reads that had mapped to each sgRNA within the library.
Assembly: GRCm39
Supplementary files format and content: read counts for each Sample; the sgRNA sequence in the second column
Library strategy: CRISPR Screen

molecule: other

extract_protocol:
The genomic DNA was extracted Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8.0), Proteinase K and RNase A. DNA was precipitated by isopropanol.
The sgRNA library readout was performed using a two-step PCR strategy, where the first PCR includes enough genomic DNA to preserve full library complexity and the second PCR adds appropriate sequencing adapters to the products from the first PCR.


title: Treated Tumor- Untreated Control #2

description: Immunology


title: CVID with NFKB1 variant uncorrected 4 hr culture with LPS_R3

description: Library name: S7


title: E0771-LUNG-5

description:
Library name: E0771-LUNG-5
gRNA profile


title: MMS D14 synovium rep1

description: synovium.csv


title: E0771-LUNG-3

description:
Library name: E0771-LUNG-3
gRNA profile


title: Untreated Tumor- HER2 DC1+aSEMA4D #3

description: Immunology


title: Treated Tumor- Untreated Control #1

description: Immunology


title: MMS D7 synovium rep3

description: synovium.csv

value: MMS D7


title: E0771-LUNG-2

description:
Library name: E0771-LUNG-2
gRNA profile


title: MMS D7 synovium rep1

description: synovium.csv


title: MMS D7 synovium rep2

description: synovium.csv


title: CVID with NFKB1 variant uncorrected 4 hr culture with LPS_R1

description: Library name: S5


title: CVID with NFKB1 variant uncorrected 4 hr culture with LPS_R2

description: Library name: S6


title: E0771-LUNG-1

description:
Library name: E0771-LUNG-1
gRNA profile


title: CVID with NFKB1 variant uncorrected 0 hr culture with LPS_R4

description: Library name: S4


title: Untreated Tumor- HER2 DC1+aSEMA4D #2

description: Immunology


title: E0771-2

description:
Library name: E0771-2
gRNA profile


title: CVID with NFKB1 variant uncorrected 0 hr culture with LPS_R3

description: Library name: S3


title: E0771-1

description:
Library name: E0771-1
gRNA profile


title: Untreated Tumor- anti-Semaphorin4D #2

description: Immunology


title: Untreated Tumor- HER2 DC1+aSEMA4D #1

description: Immunology


title: MMS D3 synovium rep2

description: synovium.csv

value: MMS D3


title: CVID with NFKB1 variant uncorrected 0 hr culture with LPS_R2

description: Library name: S2


title: Untreated Tumor- anti-Semaphorin4D #1

description: Immunology


title: TC_MLN_RANK, HTO

city: New York

first: Chrysothemis

last: Brown

state: NY

address: 417 East 68th Street

department: Immunology Program, Sloan Kettering Institute

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: TC_MLN_RANK_HTO
HTO library

data_processing:
For sample demultiplexing, HTO sequencing data were aligned to the HTO barcodes, and UMIs were counted for each cell using CITE-seq-Count. Using a two-component Kmeans algorithm, we partitioned logged HTO counts into two distributions: background noise (lower mean) and positive tags (larger mean). Each droplet was then assigned to its source sample based on tags in the positive signal component. We classified droplets with multiple assignments as doublets and those with a single assignment as singlets. This analysis was performed using SHARP v0.1.1. scRNA-seq and HTO FASTQ files were aligned to mm10 (Cell Ranger mouse reference genome mm10-2020-A) and HTO barcodes were counted and demultiplexed using Cell Ranger v8.0.0 multi to generate RNA and HTO count matrices for each sample. Each sample was further demultiplexed based on HTO counts using HTODemux function in Seurat v4.4.0. RNA count matrices for individual samples were first merged into a single count matrix. Barcodes classified as singlets from HTO demultiplexing were further filtered based on the number of RNA-seq transcripts (>1,800), the number of detected genes (>600), and the fraction of mitochondrial transcripts (<8%). Finally, any genes detected in <2 cells in the scRNA-seq data were discarded.
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output files: TC_MLN_RANK-gex_matrix.mtx.gz, TC_MLN_RANK-gex_features.tsv.gz, TC_MLN_RANK-gex_barcodes.tsv.gz
Supplementary files format and content: Outpus files for hashtag: TC_MLN_RANK-hto_matrix.mtx.gz, TC_MLN_RANK-hto_features.tsv.gz, TC_MLN_RANK-hto_barcodes.tsv.gz
Supplementary files format and content: Analysis results from Scanpy including pheno_louvain clusters, Celltype annotations, WT_vs_CRE annotations and UMAP

molecule: protein

source_name: mesenteric lymph node

extract_protocol:
RORgt+CXCR6–MHCII+ cells were FACS-isolated from mLN of 2-week-old (P16) RorcVenusTnfrsf11afl/fl (n = 4 biological replicates) and RorcVenusRorgtcreTnfrsf11afl/fl mice (n = 6 biological replicates). Lymph nodes were processed as outlined above. Each biological replicate single cell suspension was hashtagged with BioLegend TotalSeq-B Hashtag antibodies. Live, Lin(TCRb, TCRgd, CD19, NK1.1, SiglecFhi)–CD64–Ly6C–CD90.2+MHCII+RORgt(Venus)+CXCR6– cells were then sort purified. Cells were sorted into cRPMI-20% FBS before being pelleted and resuspended in cRPMI-2% FBS. scRNA-Seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X Genomics) following the user guide manual for 3′ v3.1. In brief, cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 2% BSA to a final concentration of 700–1,300 cells per ml. Cell viability was confirmed to be >80% by 0.2% (w/v) Trypan Blue staining (Countess II).
Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken, and cDNA was purified using Dynabeads MyOne SILANE followed by PCR amplification as per manufacturer’s instructions. ~10,000 cells were targeted. Samples were multiplexed on one lane of 10X Chromium using HashTag Oligonucleotides (HTO) following a previously published protocol88. Libraries were sequenced on an Illumina Novaseq X with standard dual indexing and demultiplexing.

value: mesenteric lymph node

value: RORgt+CXCR6-MHCII+ cells


title: Untreated Tumor- HER2 DC1 Treatment #2

description: Immunology


title: TC_MLN_RANK, GEX

description:
Library name: TC_MLN_RANK_mRNA
GEX (3' mRNA) library


title: Negative control, day 118

city: Vestec

first: Zuzana

last: Matusova

address: Prumyslova 595

department: Laboratory of Glial Biology and Omics Technologies

country: Czech Republic

institute: Institute of Biotechnology of the Czech Academy of Sciences

description: Library name: Neg_d118

data_processing:
The data were processed with 10x Genomics software CellRanger (v9.0.1). Genome alignment was performed with Chromium Human Transcriptome Probe Set v1.0.1 GRCh38 2020 A. Count matrixes with raw data were filtered with EmptyDrops (DropletUtils R package v1.26.0, Lun et al. (2019)), with FDR <= 0.01, to remove empty droplets, yielding consistently ~16.5k cells per sample and ~17.5k genes per sample.
The data were further processed using R programming language (v4.4.2, R Core Team (2024)) and the Seurat package (v5.2.1, Hao et al. (2023)). The data from all samples were merged, LogNormalized, scaled, and SCTransformed within the Seurat pipeline.
Quality control (QC) and filtering included identification of doublets with DoubletFinder (v2.0.4, McGinnis et al. (2019), estimated doublet rate set to 8% according to 10x recommendation) and removal of cells with less than 1700 genes (keeping nFeature > 1700). After these QC steps, the dataset contained 60,405 cells and 18,121 genes.
Assembly: GRCh38 2020 A
Supplementary files format and content: Data pre-processed in CellRanger are provided as barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz for each sample. These data went though the Seurat analysis pipeline, including their quality control and filtering. The resulting seurat_object.rds, all samples in one, is provided and should contain gene counts, normalized gene counts, SCT assay, and metadata information per cell. SampleID column in metadata corresponds to library name.

source_name: cerebral organoid culture

extract_protocol:
Single-cell suspensions from brain organoids were fixed and processed with Chromium Fixed RNA Profiling Reagent Kit (10x Genomics, Pleasanton, CA) according to the manufacturer’s instructions, using the Next GEM protocol.
The library was amplified in 10 indexing PCR cycles. The concentration and quality of the libraries were measured using Qubit dsDNA HS Assay Kit (Invitrogen) and Fragment Analyzer HS NGS Fragment Kit (#DNF-474, Agilent). The libraries were sequenced in paired-end dual indexing mode with NextSeq 2000 (P3 chemistry, 138 cycles). Cell-specific 10x GEM Barcodes (16 bp) and molecule-specific UMIs (12 bp) were contained within Read 1 (28 bp), and target sequence was contained within Read 2 (90 bp).

treatment_protocol: Organoids were exposed to the conditioned medium derived from endothelial cell culture (HCMEC/D3) since day 50 in culture until harvesting for scRNAseq. Control medium was clean DMEM/F12.

value: cerebral organoid culture

value: WT

tag: time point

value: day 118

value: CTRL


title: MMS D3 synovium rep3

description: synovium.csv


title: MMS D3 synovium rep1

description: synovium.csv


title: Control synovium rep3

description: synovium.csv

value: Control


title: TC, SS3

description:
Library name: TC_mRNA
GEX of TC from Smart-seq3

data_processing:
Smart-seq3 FASTQ files from individual wells were combined into single FASTQ files. Non-demultiplexed Smart-seq3 FASTQ files were aligned to the mouse reference genome (GRCm38.p6 from GENCODE release M25) and counted using zUMIs v2.9.7e with STAR v2.7.11a. Plates 5 and 6 were not included in downstream analysis due to low QC metrics. The barcodes were filtered based on the number of RNA-seq transcripts (>1,500), the number of detected genes (>1,000), and the fraction of mitochondrial transcripts (<5%). Any genes detected in <2 cells were discarded. In total, 1,260 cells remained with a median library size of 16,606 from 27,543 genes.
Assembly: mm10
Supplementary files format and content: Raw read count matrix from zUMIs
Supplementary files format and content: Information on each cell barcode in the raw read count matrix including tissue, cell type, and corresponding fastq files
Supplementary files format and content: Analysis results including clustering, cell type annotations, and UMAP for QC-filtered cells

source_name: mLN, pLN, LI

extract_protocol:
Single cell suspensions from mLN of 2-week-old (P17) RorcVenus mice were depleted of TCRb, TCRgd, CD19, B220, NK1.1, and Ly6G+ cells via staining with biotinylated antibodies followed by magnetic bead (Dynabeads M-280 streptavidin; Invitrogen) negative selection. Live, Lin(TCRb, TCRgd CD19, B220, NK1.1, Ly6G, SiglecFhi)–CD88–Ly6C–MHCII+RORgt(Venus)+CXCR6– or Lin–CD88–Ly6C–MHCII+RORgt(Venus)–NCAM1+ cells were then sorted into single wells.  Cells were also stained for EpCAM, CD11c, CD11b, CCR6 and NRP1 for acquisition of index sorting information on cell surface expression. Cells were sorted into 3 µL Lysis Master Mix consisting of PEG 8000, Triton X-100, dNTPs, Oligo dT30VN, and RNase Inhibitor in 384-well plates.
First-strand cDNA synthesis was done using Maxima H Minus Reverse Transcriptase (ThermoFisher catalog # EP0751) according to the manufacturer’s protocol using a custom template-switch oligo in a 2 µM final concentration. cDNA was amplified for 23 cycles using KAPA HiFi HotStart ReadyMix (Kapa Biosystems KK2601) and cleaned up using aMPure XP beads (Beckman Coulter catalog # A63882) at a 0.6X ratio. Full-length cDNA was tagmented using Tn5 (Illumina catalog # 20034198) for 10 minutes at 55°C and libraries were prepared with the Nextera XT DNA Library Preparation Kit (Illumina catalog # FC-131-1024) in a total volume of 6.25 µL with 12 cycles of PCR. Indexed libraries were pooled by volume according to plate quadrant and cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 0.8X ratio. Pools were sequenced on a NovaSeq X in a PE100 run using the NovaSeq X 10B Reagent Kit (Illumina).  An average of 551 thousand paired reads were generated per cell.

value: mLN, pLN, LI

value: RORgt+CXCR6-MHCII+, RORgt-MHCII+NCAM1+


title: Conditioned medium, day 118

description: Library name: D3cm_d118

value: CMED


title: TCp, HTO

description:
Library name: TCp_HTO
HTO from 10x Flex

data_processing:
scRNA-seq and HTO FASTQ files were aligned to mm10 (Cell Ranger mouse reference genome mm10-2020-A) and HTO barcodes and were counted and demultiplexed using Cell Ranger v8.0.0 multi to generate RNA and HTO count matrices for each sample. Each sample was further demultiplexed based on HTO counts using HTODemux function in Seurat v4.4.0. Two samples (Flex_15 and Flex_16) formed a separate TC analysis and were not included in the downstream analysis. RNA count matrices for individual samples were first merged into a single count matrix. Next, barcodes classified as singlets from HTO demultiplexing were further filtered based on the number of RNA-seq transcripts (>1,000 and <60,000), the number of detected genes (>500 and <8,000), and the fraction of mitochondrial transcripts (<10%). Finally, any genes detected in <2 cells in the scRNA-seq data were discarded. After clustering (described in  Dimensionality reduction, cell clustering, and visualization ) and analysis of QC metrics and differentially expressed genes, we identified 10 minor contaminant or low QC clusters (fibroblast: cluster 54, hepatocyte: cluster 62, osteoclast: cluster 56, mixed/undefined: 42, 49, 59, low quality: clusters 25, 44, 57, 61) which were excluded from downstream analyses. In total, 101,192 cells remained, with a median scRNA-seq library-size of 10,314 from 17,330 genes.
Assembly: mm10
Supplementary files format and content: CellRanger output files from each demultiplexed sample
Supplementary files format and content: Analysis results including clustering, cell type annotations, and UMAP for QC-filtered cells
Library strategy: CITE-seq

source_name: mesenteric anlagen, fetal liver, bone marrow, mesenteric lymph node, liver

extract_protocol:
mLN and liver from P7 RorcVenus-creERT2 mice (n = 9); mesenteric anlagen, fetal liver, and fetal bone marrow from E17.5-18.5 RorcVenus-creERT2 mice (n = 25); mLN, liver, and bone marrow from P7 Il7rcreR26lsl-tdTomato mice  (n = 4), and mesenteric anlagen, fetal liver, and fetal bone marrow from E17.5-18.5 Il7rcreR26lsl-tdTomato mice (n = 9) were processed for Flex scRNA-seq analysis of progenitors (Supplemental Table 1). Fetal liver, liver, fetal bone marrow and bone marrow were depleted of lineage (TCRb, TCRgd, CD19, B220, NK1.1, Ter-119, Ly-6G, CD3e)+ cells via staining with biotinylated antibodies followed by magnetic bead (Dynabeads M-280 streptavidin; Invitrogen) negative selection. Cells were incubated with anti-CD16/32 and extracellular antigens were stained for 30 minutes at room temperature in sorting buffer (2% FBS, 2mM EDTA, in PBS) and labeled with BioLegend TotalSeq-C Hashtag antibodies. Cells were washed and resuspended in cRPMI with SYTOX blue (Invitrogen) for exclusion of dead cells. Cells were sorted as per Extended Data Fig. 3a into 500ml of Fixation Buffer (4% Formaldehyde, 1X Conc. Fix and Perm Buffer – 10x Genomics PN2000517). Cells were fixed for 16-20h at 4°C. To stop the fixation, cells were spun down at 850 rcf for 5 min at room temperature and quenched with 500ml of Quenching Buffer (1X Conc. Quench Buffer – 10x Genomics PN-2000516). Preparations were then processed by adding 0.1 volumes of Enhancer (10x Genomics PN2000482) and 10% glycerol for storage at -80°C.  Samples were then thawed at room temperature, centrifuged at 850 rcf for 5 min and resuspended in 1 mL 0.5X PBS – 0.02% BSA. Cell concentration and viability were assessed by 0.2% (w/v) Trypan Blue staining (Countess II).
Cells were processed per hybridization according to the 10X protocol. Hybridizations were set up in 80 mL of hybridization mix with 20 mL of Human or Mouse WTA probes (10x Genomics PN-2000510 or PN-2000718) and 4 mL of Antibody Multiplexing Barcode (10x Genomics PN-2000917- 2000932). Hybridizations were performed at 42°C for 16-24h. After hybridization samples were diluted in Post-Hyb Wash Buffer and measured by 0.2% (w/v) Trypan Blue staining (Countess II). For each experiment, we pooled an equal number of cells from each hybridization to have an equal contribution per sample. Pooled cells were then washed 3 times in Post-Hyb Wash Buffer for 10 min at 42°C, resuspended in Post-Hyb Resuspension Buffer, filtered through a Miltenyi Biotec 30 mm filter, and measured with the cell counter to determine the amount required for the Chromium X run. GEM encapsulation was performed according to the 10X Genomics protocol. After loading the Chip Q and running it on the Chromium X, GEMs were recovered and processed as indicated by 10X Genomics. Post-processing, the product was pre-amplified and indexed to construct the sequencing library. All libraries were sequenced on an Illumina Novaseq X with standard dual indexing and demultiplexing.

value: hematopoietic cells


title: Untreated Tumor- Untreated Control #2

description: Immunology

value: Female

value: BALB/c

value: Tumor


title: CVID with NFKB1 variant uncorrected 0 hr culture with LPS_R1

description: Library name: S1

source_name: iPSC-derived

value: iPSC-derived

value: monocyte

value: NFKB1 variant

value: cell culture with LPS

value: same


title: Untreated Tumor- Untreated Control #1

description: Immunology


title: c. elegans, young adult, scaffold:agar, rep3

status: Public on Feb 01 2026

city: Montreal

first: Michael

last: Hendricks

state: QC

address: 1205 Avenue Docteur Penfield

country: Canada

institute: McGill University

description:
Library name: Sample 12
column name in counts.txt: ./aligned/NS.1961.004.UDP0044_i7---UDP0044_i5.Tis002017_RNA_sorted.bam

data_processing:
Sequencing reads were cleaned and aligned to the C. elegans reference genome using a custom Linux shell script. Quality control of raw sequencing data was performed using FastQC (v0.11.9) and MultiQC (v1.12) (Andrews, 2010; Ewels et al., 2016). Reads were trimmed using Trimmomatic (v0.39) to remove low-quality bases and potential adapter contamination (Bolger et al., 2014). Specifically, the first 10 bases were removed from the 5' end of each read to mitigate potential priming biases, and a sliding window quality trimming was performed (window size 4, required quality 15). Trimmed reads shorter than 36 bp were discarded. The trimmed high-quality reads were then aligned to the C. elegans reference genome (WBcel235) using HISAT2 (v2.2.1) with default parameters (Kim et al., 2019). Post-alignment, a minimal filtering step was performed to remove a small number of malformed alignment entries (31 out of 161,930,474 total entries). The resulting alignments were converted to BAM format, sorted, and indexed using SAMtools (v1.13) (Danecek et al., 02 2021). Gene-level quantification was performed using featureCounts (v2.0.3) against the Ensembl gene annotation (release 104) (Liao et al., 2014).
Assembly: C. elegans reference genome WBcel235
Supplementary files format and content: tab-delimited text file with raw counts per sample

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: For 3D decellularized fruit tissue scaffold conditions see https://doi.org/10.1002/cpz1.288

extract_protocol:
The RNA was isolated using the RNeasy Plus Universal Mini kit. Total RNA was quantified and its integrity was assessed using 5K / RNA / Charge Variant Assay LabChip and RNA Assay Reagent Kit (Perkin Elmer).
Libraries were generated from 250 ng of total RNA as following: mRNA enrichment and library preparation were performed using the Illumina Stranded mRNA Prep Kit (Illumina), as per the manufacturer’s recommendations. Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a LabChip GX II (PerkinElmer) instrument. The libraries were normalized and pooled and then denatured in 0.02N NaOH and neutralized using HT1 buffer. The pool was loaded at 200pM on a Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.

value: whole body

value: N2 WT

value: Sequencing day 2


title: Control synovium rep2

description: synovium.csv

value: synovium


title: Control synovium rep1

description: synovium.csv

value: Control


title: TCp, GEX

description:
Library name: TCp_mRNA
GEX from 10x Flex

value: mesenteric anlagen, fetal liver, bone marrow, mesenteric lymph node, liver


title: Conditioned medium, day 64

description: Library name: D3cm_d64

value: cerebral organoid culture

value: WT

value: day 64


title: Negative control, day 64

description: Library name: Neg_d64

value: CTRL


title: Untreated Tumor- HER2 DC1 Treatmen #1

description: Immunology

value: Female

value: BALB/c


title: c. elegans, young adult, agar:scaffold, rep3

description:
Library name: Sample 8
column name in counts.txt: ./aligned/NS.1961.004.UDP0037_i7---UDP0037_i5.Tis002013_RNA_sorted.bam


title: c. elegans, young adult, scaffold:scaffold, rep3

description:
Library name: Sample 10
column name in counts.txt: ./aligned/NS.1961.004.UDP0039_i7---UDP0039_i5.Tis002015_RNA_sorted.bam


title: c. elegans, young adult, scaffold:agar, rep2

description:
Library name: Sample 11
column name in counts.txt: ./aligned/NS.1961.004.UDP0040_i7---UDP0040_i5.Tis002016_RNA_sorted.bam


title: c. elegans, young adult, scaffold:agar, rep1

description:
Library name: Sample 4
column name in counts.txt: ./aligned/NS.1961.004.UDP0033_i7---UDP0033_i5.D1_sorted.bam

value: Sequencing day 1


title: c. elegans, young adult, scaffold:scaffold, rep2

description:
Library name: Sample 9
column name in counts.txt: ./aligned/NS.1961.004.UDP0038_i7---UDP0038_i5.Tis002014_RNA_sorted.bam


title: c. elegans, young adult, agar:agar, rep2

description:
Library name: Sample 5
column name in counts.txt: ./aligned/NS.1961.004.UDP0034_i7---UDP0034_i5.Tis002010_RNA_sorted.bam


title: c. elegans, young adult, agar:scaffold, rep2

description:
Library name: Sample 7
column name in counts.txt: ./aligned/NS.1961.004.UDP0036_i7---UDP0036_i5.Tis002012_RNA_sorted.bam


title: c. elegans, young adult, agar:agar, rep3

description:
Library name: Sample 6
column name in counts.txt: ./aligned/NS.1961.004.UDP0035_i7---UDP0035_i5.Tis002011_RNA_sorted.bam


title: c. elegans, young adult, agar:scaffold, rep1

description:
Library name: Sample 2
column name in counts.txt: ./aligned/NS.1961.004.UDP0031_i7---UDP0031_i5.B1_sorted.bam


title: c. elegans, young adult, scaffold:scaffold, rep1

description:
Library name: Sample 3
column name in counts.txt: ./aligned/NS.1961.004.UDP0032_i7---UDP0032_i5.C1_sorted.bam


title: c. elegans, young adult, agar:agar, rep1

description:
Library name: Sample 1
column name in counts.txt: ./aligned/NS.1961.004.UDP0030_i7---UDP0030_i5.A1_sorted.bam


title: lin-39p::RFP unc-3 MNs rep 3

city: Nashville

first: David

middle: M

last: Miller III

state: Tennessee

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
Library name: Sample 3
10X Genomics

data_processing:
Demultiplexing, barcode processing, read mapping and gene counting were performed using CellRanger v6.1.1
Base calling was performed with Real-Time Analysis software (RTA, version 2.4.11; Illumina).
FASTQ files were processed using the 10X Genomics Cell Ranger software (version 6.1.1) using a custom reference genome from Wormbase release WS273 that incorporated extended 3’ UTR regions for several specific genes.
We distinguished cells from empty droplets using the emptydrops algorithm from the DropletUtils R package, then corrected for background RNA using SoupX. Quality control metrics were generated with the scater R package. These steps were performed on the gene by barcode matrix from CellRanger for each sample independently.
Background corrected datasets were converted into monocle3 cell_data_set objects and combined into one dataset in monocle3. Monocle3 was used for dimensionality reduction (PCA followed by UMAP) and plotting.
Assembly: Custom 3' UTR extended genome reference built from WS273, available as supplemental file.
Supplementary files format and content: all_cells.mtx [gene by barcode matrix for all cells]
Supplementary files format and content: all_cells_cell_metadata.csv [comma-separated values file featuring metadata for all cells (including barcode, percent of UMIs from mitochondria, Size factor, number of genes expressed, UMAP coordinates, cluster, experiment ID, Cell type, strain, and anatomical class)]
Supplementary files format and content: all_cells_gene_metadata.csv [comma-separated values file featuring metadata for all genes (gene IDs, gene symbols, and number of cells in which gene was detected)]
Supplementary files format and content: MN_subset.mtx [gene by barcode matrix for ventral cord motor neurons]
Supplementary files format and content: MN_subset_cell_metadata.csv [comm-separated values file featuring metadata for ventral nerve cord motor neurons (including barcode, percent of UMIs from mitochondria, Size factor, number of genes expressed, UMAP coordinates, cluster, experiment ID, Cell type, strain, and anatomical class)]
Supplementary files format and content: MN_subset_gene_metadta.csv [comma-separated values file featuring metadata for all genes found in ventral cord motor neurons (gene IDs, gene symbols, and number of cells in which gene was detected)]

source_name: Motor neurons

growth_protocol: Worms were grown on 8P nutrient agar plates (150 mm) seeded with E. coli strain NA22. To obtain synchronized cultures of day 1 adult stage animals, adult hermaphrodites were treated with hypochlorite to isolate embryos, which were then incubated in M9 buffer at room temperature for 16 hours to hatch and arrest at L1 stage. L1 animals were then grown on NA22-seeded plates for 62-65 hours. Young adults were further isolated by size exclusion using a 35 µm nylon mesh. Worms were washed off plates with M9 then placed on a 35 µm nylon mesh suspended over M9 containing NA22 bacteria for 25 minutes.

extract_protocol:
KRA547 worms were collected and washed twice. 250 uL pellets of worms were incubated in 500 uL of SDS-DTT buffer (20 mM HEPES, 0.25% SDS, 200 mM DTT, 3% sucrose, pH 8.0) for 6 minutes, then washed 5 times in egg buffer (25 mM HEPES pH 7.3, 118 mM NaCl, 48 mM KCl, 2mM CaCl2, 2mM MgCl2). Worms were then incubated in 500 uL of cold active protease (10 mg/mL in egg buffer, Protease from Bacillus licheniformis, Sigma-Aldrich P4860, with DNAse I 35 U/mL) for 35 minutes at 4 C. During the protease incubations, solutions were triturated by pipetting through a P1000 pipette tip for four sets of 80 repetitions Digestions were quenched by addition of 750 uL of L-15 media supplemented with 10% FBS. Cells and worm debris were pelleted by centrifugation (530 rcf for 5 minutes at 4 C), and then resuspended in 1 mL L-15-10. Cells were separated from worm debris by centrifugation for 2 minutes at 100 rcf at 4 C. The supernatant was collected and filtered through the 35-micron strainer cap of a 5 mL FACS tube (Falcon 352235) The pellet was resuspended a second time in 1 mL of L-15-10, spun at 100 rcf for 2 min at 4 C, and the supernatant was collected and filtered into the same FACS tube to combine with the first extraction. Fluorescently labeled motor neurons were isolated using FACS on a BD FACSAria III equipped with a 70-micron nozzle. GFP+ cells were collected into L-15 media with 33% FBS.
Young adult worms remaining on the mesh were collected into M9 and centrifuged at 150 relative centrifugal force (rcf) for 2.5 minutes. Worms were transferred to a 1.6 mL centrifuge tube and centrifuged at 16,000 rcf for 1 minute to form 250 uL pellets. Worm pellets were then treated with 500 µL of SDS-DTT solution (20 mM HEPES, 0.25% SDS, 200 mM DTT, 3% sucrose, pH 8.0) for 6 minutes. Following SDS-DTT treatment, worms were washed five times (each wash: dilute with 1 mL egg buffer, centrifuge at 16,000 rcf for 30 seconds). Worms were then digested in cold-active protease (10 mg/mL, Protease from Bacillus licheniformis, Sigma-Aldrich P4860, with DNAse I 35 U/mL) in egg buffer for 35 minutes at 4°C. Cells were kept at 4°C from protease incubation through all subsequent procedures. During the protease incubations, solutions were triturated by pipetting through a P1000 pipette tip for four sets of 80 repetitions. Dissociation efficiency was monitored at 5-minute intervals with a fluorescence dissecting scope. Digestions were stopped by adding 750 µL L-15 media supplemented with 10% fetal bovine serum (L-15-10). Cells were then centrifuged at 530 rcf for 5 minutes at 4°C. The pellet was resuspended in 1 mL L-15-10, and individual cells were separated from whole worms and debris by centrifuging at 100 rcf for 2 minutes at 4°C. The supernatant was filtered through a 35-micron strainer cap into a 5 mL collection tube (Falcon 352235). The pellet was resuspended a second time, centrifuged (100 rcf for 2 minutes at 4°C), and the resulting supernatant was added to the collection tube. For higher sorting efficiency, samples were diluted with an additional 1 mL of L-15-10. Single-cell suspensions of both genotypes were sorted simultaneously on two BD FACSAria™ III cell sorters faceted with 70-micron diameter nozzles. DAPI was added to the samples (final concentration of 1 µg/mL) to label dead /dying cells. Cells were sorted for three hours under the “4-way Purity” mask into 1.5 mL microcentrifuge tubes containing 200 uL L-15-33 (L-15 medium with 33% fetal bovine serum) and subsequently centrifuged (1200 rcf for 12 minutes at 4°C).
Libraries were prepared using P/N 1000075, 1000073, and 120262 following the manufacturer's protocol. Illumina NovaSeq 6000 with 150 bp paired end reads was used for library sequencing

value: Motor neurons

value: young adult

tag: synchronization protocol

value: L1 arrest + mesh synchronization


title: lin-39p::RFP unc-3 MNs rep 2

description:
Library name: Sample 2
10X Genomics

tag: tissue


title: UFM1-2

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

description: Library name: UFM1-2

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the Caenorhabditis elegans transcriptome and genome version WBcel235 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01.
Normalization and differential expression analysis were performed using the DESeq2 package. Genes with a sum of counts less than 10 over all samples were filtered out, then size factors and dispersion were calculated. The normalized counts were further batch corrected for the effect of the 2 repeats of the biological procedure
Assembly: WBcel235, with annotations from Ensembl release 106
Supplementary files format and content: DESeq2_raw_norm_bcor_EV_UFA1.xlsx
Supplementary files format and content: excel table with raw counts, DESeq2 normalized counts and batch corrected + normalized counts, per gene (rows) per sample(column)

source_name: pool of whole worms

growth_protocol: Synchronized CL2006 worms were grown from hatching on EV bacteria or on bacteria that express ufm-1 RNAi at 20C. The worms were washed and transferred onto new plates every day to remove progeny.

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (MACHEREY-NAGEL; 740955) according to the manufacturer instructions.
PolyA-selection, mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1µg was used for the library construction; library was eluted in 20µl of elution buffer. All DNA samples libraries were pooled to 10nM sample. Multiplex samples Pool were loaded on NovaSeq 6000 (Illumina), using NovaSeq 6000 SP Reagent Kit v1.5 100 cycles (cat# 20028401), with 122 cycles
Single End 122bp length

treatment_protocol: The worms were grown for two generations on EV bacteria or on bacteria that expressed ufm-1 RNAi at 20C.  Four independent sets of the experiment were collected (for instance EV1, EV2, EV3 and EV4). Total RNA was extracted from 6 days old worms and sent for RNA-sequencing.

value: pool of whole worms

value: second generation, grown to day 6 of adulthood

tag: genotype

value: dvIs2 [pCL12(unc-54/human Abeta peptide 1-42 minigene) + rol-6(su1006)]

value: qrown on ufm-1 RNAi


title: lin-39p::RFP unc-3 MNs rep 1

description:
Library name: Sample 1
10X Genomics


title: UFM1-3

description: Library name: UFM1-3

tag: treatment


title: EV-4

description: Library name: EV-4

tag: cell type

value: qrown on ev


title: EV-3

description: Library name: EV-3


title: EV-2

description: Library name: EV-2


title: EV-1

description: Library name: EV-1


title: HAP1_wt_1

type: genomic

city: Chicago

first: Gemma

last: Carvill

state: IL

address: 303 E Chicago, Ward 9-183

department: Neurology

institute: Northwestern University

description:
exon21-B4
208397930005_R07C01

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Human Methylation Epic arrays using standard Illumina Protocols

scan_protocol: Arrays were imaged using a BeadArray Reader (iScan) using standard recommended Illumina settings

data_processing:
Betas and p-values for all samples were generated using the Sesame R package (version 1.24.0) with default parameters
*processed value definition: Beta and p-value for each probe

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: gDNA was extracted from frozen cell pellets using the Invitrogen Purelink DNA mini kit (K182002)

value: wildtype


title: HAP1_path_8

description:
exon21_A2
208779790099_R07C01

value: pathogenic


title: HAP1_path_3

description:
exon16_B1
208779790099_R01C01


title: HAP1_path_5

description:
exon16_B3
208779790099_R03C01


title: HAP1_path_9

description:
exon21_B5
208779790099_R08C01


title: HAP1_path_2

description:
exon21-D3
208397930005_R08C01


title: HAP1_path_6

description:
exon16_C4
208779790099_R05C01


title: UFM1-1

description: Library name: UFM1-1


title: HAP1_path_4

description:
exon16_B2
208779790099_R02C01


title: HAP1_benign_3

description:
exon37-C3
208397930005_R03C01

value: benign


title: HAP1_wt_2

description:
exon16_B5
208779790099_R04C01


title: HAP1_benign_4

description:
exon37-D1
208397930005_R04C01


title: HAP1_benign_2

description:
exon37-B5
208397930005_R02C01


title: HAP1_benign_1

description:
exon37-A5
208397930005_R01C01


title: HAP1_path_1

description:
exon37-D2
208397930005_R05C01


title: HAP1_benign_5

description:
exon37-D3
208397930005_R06C01


title: HAP1_path_7

description:
exon16_C6
208779790099_R06C01


title: BALF immune cells, 3 hours 1.5 ppm Ozone-exposed

city: Raleigh,

first: Yogesh

last: Saini

state: NC

address: 1060 William Moore Drive

department: Population Health and Pathobiology

institute: NCSU

description:
Library name: O3_1.5 ppm
10X genomics

data_processing:
Raw data were demultiplexed, mapped and unique transcripts were counted using the Cell Ranger pipeline (cellranger-8.0.0) and GRCm39 mouse genome (10X genomics, Pleasanton, CA)
Assembly: GRCm39 (mouse mm39)
Supplementary files format and content: tab-separated value files and matrix files

extract_protocol:
mice were anesthetized via intraperitoneal injection of 2,2,2-tribromoethanol (Millipore Sigma, Burlington, MA). Midline laparotomy was performed to expose and severe inferior vena cava for exsanguination. Thereafter, thoracotomy was performed to expose the lung and trachea. The left main stem bronchus was ligated, and the right lung lobes were lavaged with a calculated volume of ice-cold Dulbecco’s Phosphate Buffered Saline (DPBS) (Corning, Manassas, VA). The retrieved bronchoalveolar lavage fluid (BALF) was centrifuged at 500 x g for 5 min at 4°C. To maximize the recovery of airspace immune cells, further lavages were performed to collect an additional 5 ml of BALF. The remaining portion of the immune cells from the first lavage and the additional 5 ml lavage of 3-4 mice per group were pooled and centrifuged at 500 x g for 5 min at 4°C. The supernatant was removed, and the cell pellet was resuspended in 500 ml of fresh DPBS. The washing process was repeated one more time. After the last wash, the BALF was centrifuged at 500 x g for 5 min at 4°C, the supernatant was removed, and the cell pellet was resuspended in DPBS with 1% Fetal Bovine Serum (FBS). The concentration of BALF immune cells was adjusted to 2000 cells/ml. Samples were submitted to the Advance Analytics Core at the University of North Carolina at Chapel Hill (UNC) School of Medicine for library construction and sequencing.
BALF immune cells collected from C57BL/6J mice were stained with acridine orange and propidium iodide and assessed for viability and concentration using the LUNA-FX7 dual fluorescence cell counter (Logos Biosystems, Annandale, VA), and loaded into a Chromium Next GEM Chip G (10X genomics, Pleasanton, CA) to generate gel-beads in emulsions. Barcoded sequencing libraries were conducted following the instruction manual of the Chromium Single Cell 3’ Reagent Kit v3.1 (10X genomics, Pleasanton, CA). Single-cell libraries were sequenced using NovaSeq X Plus (Admera Health, South Plainfield, NJ).

treatment_protocol: Filtered Air or Ozone exposure (1 ppm, 1.5 ppm ) for 3 hours

value: Lung

value: BALF immune cells

value: WT

value: 1.5 ppm Ozone exposed for 3 hours


title: IL1215_9_F_resub_1_Pool

city: Eugene

first: John

last: Postlethwait

state: OR

address: 1210 University Of Oregon

department: Biology

institute: University of Oregon

description:
Library name: 9_F_resub_1_Pool
IL1215_9_F_resub_1_Pool

data_processing:
Base calling via Bases2Fastq
Adapter clipping with Trimmomatic with the following parameters: "ILLUMINACLIP:/home/msistaff/public/CHURP_Deps/v1/db/all_illumina_adapters.fa:4:15:7:2:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:18"
Trimmed reads were aligned to the reference genome with HISAT2.
Duplicate reads based on alignment position were marked with SAMTools.
Cleaned and name-sorted alignments were processed with the featureCounts tool from the subread package in a strand-specific manner to give the processed data file in this submission.
Assembly: GRCm39
Supplementary files format and content: Gene expression Count Matrix: Maurice_subread_counts_gene_symbol.tsv

source_name: CD8 T cells

growth_protocol: Cells were isolated and cultured in RP10 media for 24 hours.

extract_protocol:
Cells were sorted into RLT buffer plus beta-mercaptoethanol and frozen at -80°C. RNA was extracted using Zymo Research Quick-RNA MicroPrep with gDNA digestion.
Watchmaker Stranded mRNA kit

treatment_protocol: Cells were exposed to cytokines (100ng/mL) and/or agonist peptide (SIINFEKL; 1µM) at start of culture. Stimuli included mock, mock+IL-4, IL-12/15, IL-12/15+IL-4, IL-12/15/18, IL-12/15/18+IL-4, SIINFEKL, SIINFEKL+IL-4.

value: CD8 T cells


title: IL1215_7_8_pool

description:
Library name: 7_8_pool
IL1215_7_8_pool


title: IL4_6_D_resub_1_pool

description:
Library name: 6_D_resub_1_pool
IL4_6_D_resub_1_pool


title: Mock_3_B_resub_1_pool

description:
Library name: 3_B_resub_1_pool
Mock_3_B_resub_1_pool

value: Mock


title: BALF immune cells, 3 hours Filtered Air exposed

description:
Library name: FA
10X genomics

value: Filtered Air exposed for 3 hours


title: BALF immune cells, 3 hours 1 ppm Ozone-exposed

description:
Library name: O3_1 ppm
10X genomics

value: 1 ppm Ozone exposed for 3 hours


title: Mock_1_2_pool

description:
Library name: 1_2_pool
Mock_1_2_pool


title: OVA_21_N_resub_1_Pool

description:
Library name: 21_N_resub_1_Pool
OVA_21_N_resub_1_Pool

value: OVA


title: IL4_OVA_22_23_pool

description:
Library name: 22_23_pool
IL4_OVA_22_23_pool


title: IL121518_15_J_resub_1_pool

description:
Library name: 15_J_resub_1_pool
IL121518_15_J_resub_1_pool


title: IL4_IL1215_12_H_resub_1_pool

description:
Library name: 12_H_resub_1_pool
IL4_IL1215_12_H_resub_1_pool


title: IL4_IL121518_18_L_resub_1_pool

description:
Library name: 18_L_resub_1_pool
IL4_IL121518_18_L_resub_1_pool


title: IL4_IL121518_16_17_pool

description:
Library name: 16_17_pool
IL4_IL121518_16_17_pool


title: IL4_4_5_pool

description:
Library name: 4_5_pool
IL4_4_5_pool


title: OVA_19_20_pool

description:
Library name: 19_20_pool
OVA_19_20_pool


title: IL4_IL121518_K_resub_1

description:
Library name: K_resub_1
IL4_IL121518_K_resub_1


title: IL4_OVA_24_P_resub_1_pool

description:
Library name: 24_P_resub_1_pool
IL4_OVA_24_P_resub_1_pool


title: IL4_IL1215_10_11_pool

description:
Library name: 10_11_pool
IL4_IL1215_10_11_pool


title: IL4_IL1215_G_resub_1

description:
Library name: G_resub_1
IL4_IL1215_G_resub_1


title: IL4_OVA_O_resub_1

description:
Library name: O_resub_1
IL4_OVA_O_resub_1


title: Mock_A_resub_1

description:
Library name: A_resub_1
Mock_A_resub_1


title: IL121518_I_resub_1

description:
Library name: I_resub_1
IL121518_I_resub_1


title: OVA_M_resub_1

description:
Library name: M_resub_1
OVA_M_resub_1


title: Streptococcus parasagnuinis , bacterial cells, OD600 0.8, 2 mM of Nitrite treatment, bio rep 1

city: Birmingham

first: Sara

middle: Elizabeth

last: Edmonds

state: AL

address: 1720 2nd Ave South, BBRB 744

department: Microbiology

institute: University of Alabama at Birmingham

description: Library name: Sample 4

data_processing:
Intermediate RNA Analysis was performed at SeqCenter (Pittsburg, PA), specifically sequencing was done on a NovaSeq 6000 giving 2x51bp reads.
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.0.3).
Assembly: Read mapping was performed with HISAT2 (v2.2.0). Read quantification was performed using Subread’s featureCounts (v2.0.1) functionality. Read counts loaded into R (v4.0.2) and were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (cpm). Differential expression analysis was performed using edgeR’s (v1.14.5) exact test for differences between two groups of negative-binomial counts with an estimated dispersion value of .1.
Supplementary files format and content: The file “All Quantified Genes.tsv” contains the results of the qlfTest for all genes in addition to the normalized counts per million.
Supplementary files format and content: The file “Differentially Expressed Genes.tsv” is a subset of the aforementioned file with |logFC| > 1 and p < .05.

organism: Streptococcus parasanguinis FW213

source_name: Gram-positive Bacteria

growth_protocol: Overnight cultures of S. parasanguinis were subcultured in Todd Hewitt Broth (+/- 2 mM Nitrite) and harvested at a to an optical density of 0.8 at an absorbance of 600nm (OD600 0.8). Cultures were grown in three biological replicates at 37°C with 5% CO2.

extract_protocol:
RNA was extracted utilizing the Direct-zol RNA Miniprep (Zymo Research, Cat: R2052). Samples were DNAse treated with Invitrogen DNAse (RNAse free).
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

value: Gram-positive Bacteria

value: 2 mM of Nitrite


title: IL121518_13_14_pool

description:
Library name: 13_14_pool
IL121518_13_14_pool