title: AAV_d14_3

status: Public on May 16 2025

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

institute: University of Michigan

description: Library name: Sample 23

data_processing:
For non-multiplexed samples, gene expression count matrices were generated using the count command from Cell Ranger v8.0.0 with the --include-introns=true argument, aligning reads to the GRCm39 mouse reference genome. For multiplexed samples labeled with CellPlex Cell Multiplexing Oligos (CMOs), count matrices were generated using the multi command in Cell Ranger v8.0.0, following the 10x Genomics guidelines for CMO demultiplexing. Default parameters were used unless otherwise specified.
Assembly: GRCm39
Supplementary files format and content: barcodes, features, and mtx files

source_name: Skeletal Muscle

extract_protocol:
Tibialis anterior muscles were harvested, minced, and nuclei were isolated using two approaches: (1) Dounce homogenization in Miltenyi Nuclei Extraction Buffer with RNase inhibitor, followed by filtration and centrifugation; or (2) the 10X Genomics Chromium Nuclei Isolation Kit, following the manufacturer’s protocol for frozen tissues. In both methods, nuclei were resuspended in wash buffer containing BSA and RNase inhibitor. Nuclei quality and counts were assessed by trypan blue exclusion with a hemocytometer or automated fluorescence-based cell counting. All steps were performed on ice or at 4°C to preserve RNA integrity.
Single-nucleus RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3' Gene Expression v3.1 chemistry. Nuclei were loaded onto a Chromium Controller to create gel bead-in-emulsions (GEMs) for barcoding and reverse transcription. Libraries were constructed following the manufacturer’s protocol, either using the Standard or High-Throughput workflows. Some samples were multiplexed using 10x Genomics CellPlex Cell Multiplexing Oligos (CMOs) according to the CellPlex Protocol #1. Final libraries were sequenced on an Illumina NovaSeq X platform using a 2 × 150 bp configuration, targeting a depth of 50,000 reads per nucleus.

value: Skeletal Muscle

value: Skeletal muscle cells

value: AAV + 14 days post sciatic nerve crush

tag: library type

value: mRNA


title: EAE Control 03

status: Public on Jun 12 2025

type: SRA

city: Mainz

first: Neuroimmunology

last: Mainz

address: Langenbeckstr. 1

department: Neurology

country: Germany

institute: University Medical Center of the Johannes Gutenberg University Mainz

library_source: transcriptomic

data_processing:
The raw sequencing reads (30 mio 150 PE reads per sample) of Illumina’s NovaSeq 6000 (Novogene; Cambridge, UK) were preprocessed according to the Illumina standard protocol.
Sequence reads were trimmed for adapter sequences and further processed using Qiagen’s software CLC Genomics Workbench (v21.0.5 with CLC’s default settings for RNA-Seq analysis).
Reads were aligned to GRCm38 genome. Unique gene counts from the CLC workbench were used to perform statistical differential expression analysis with DESeq2 (Love et al., 2014). Gene ontology analysis was performed for genes with adjusted p-values under 0.05 using clusterProfiler and DOSE (Yu et al., 2015). Network plots were generated with Enrichplot (Yu et al., 2015). Heatmaps were generated using the pheatmap R package (Kolde, 2019). Volcano plots were created with the ggplot2 (Wickham, 2016) and ggrepel (Slowikowski, 2021) R packages. The database org.Mm.eg.db was used for annotating genes (Carlson, 2019).
Unique gene counts from the CLC workbench were used to perform statistical differential expression analysis with DESeq2 (Love et al., 2014). Gene ontology analysis was performed for genes with adjusted p-values under 0.05 using clusterProfiler and DOSE (Yu et al., 2015).
Network plots were generated with Enrichplot (Yu et al., 2015). Heatmaps were generated using the pheatmap R package (Kolde, 2019). Volcano plots were created with the ggplot2 (Wickham, 2016) and ggrepel (Slowikowski, 2021) R packages. The database org.Mm.eg.db was used for annotating genes (Carlson, 2019).
Assembly: GRCm38
Supplementary files format and content: DESeq 2 output

molecule: total RNA

organism: Mus musculus

source_name: inguinal lymph node

extract_protocol:
RNA was purified immediately after with the RNeasy Plus Micro Kit according to the manufacturer’s protocol (Qiagen). RNA was quantified with a Qubit 2.0 fluorometer (Invitrogen) and the quality was assessed on a Bioanalyzer 2100 (Agilent) using a RNA 6000 Pico chip (Agilent). Samples with an RNA integrity number (RIN) of > 9 were used for library preparation.
Barcoded mRNA-seq cDNA libraries were prepared from 100 ng of total RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual with a final amplification of 12 PCR cycles. Quantity was assessed using Invitrogen’s Qubit HS assay kit and library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay.

treatment_protocol: Inguinal lymph nodes were isolated on day 3 after EAE induction from 3 SJL mice therapeutically treated with perampanel as well as 3 control mice. Lymph nodes were meshed through a 100-µm cell strainer in order to create a single-cell suspension.

tag: tissue

value: inguinal lymph node

tag: cell line

value: primary tissue

tag: cell type

value: Lymphocytes

tag: genotype

value: SJL

tag: treatment

value: Control


title: AAV_d0_3

city: Ann Arbor

country: USA

description: Library name: Sample 21

library_source: transcriptomic single cell

molecule: nuclear RNA

value: AAV uninjured


title: EAE Control and  Perampanel Tag 01-06

data_processing:
Resulting raw data was preprocessed according to the Illumina standard protocol and transcript alignment, counting and demultiplexing was performed using the BD Rhapsody WTA analysis pipeline yielding 8,300 so-called putative cells overall with a mean of 88,500 aligned reads per cell. The outputs of the BD Rhapsody WTA Analysis Pipeline were used for single-cell downstream analysis.
Single-cell gene expression analysis and visualization were carried out using Seurat (Hao et al., 2021). High-quality cells with at least 500 UMIs, 250 genes, log10 genes per UMI over 0.8, and mitochondrial ratios under 20 percent were retrieved for further analysis. In addition, only genes expressed in more than 10 cells were kept.
After the log normalization, dimensionality reduction was carried out with 500 variable features and 50 principal components. The UMAP clusters were defined using the Louvain algorithm with multilevel refinement. The clusters were assigned to the different cell types using the gene markers. Cell type-specific differentially expressed genes were statistically identified using DESeq2 (Love et al., 2014).
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

extract_protocol:
Inguinal lymph nodes were isolated on day 3 after EAE induction from 3 SJL mice therapeutically treated with perampanel as well as 3 control mice. Lymph nodes were meshed through a 100-µm cell strainer in order to create a single-cell suspension.
Single-cell capturing, isolation of RNA and synthesis of cDNA was performed according to the BD Rhapsody Single-Cell Analysis System (BD Rhapsody) following the manufacturer’s guidelines. Each sample was tagged with a unique sample tag in order to allow multiplexing of samples on the same cartridge.  Whole transcriptome libraries and sample tag libraries were prepared using BD WTA Amplification Kit (BD Rhapsody) with random primers followed by amplification and insertion of sequencing adaptors following the BD Rhapsody System mRNA WTA and Sample Tag Library Preparation Protocol (BD Biosciences). Quality and quantity of cDNA libraries was checked on a Bioanalyzer2100 (Agilent) and sequencing (150 PE reads aiming on 100,000 raw reads /cell) was performed on a NovaSeq 6000 (Illumina) at Novogene (Cambridge; UK).


title: AAV_d0_4

description: Library name: Sample 19


title: EAE Control 01


title: EAE Control 02


title: AAV_d14_2

description: Library name: Sample 16


title: aged_d14_1

description: Library name: Sample 8

value: 7 days post sciatic nerve crush


title: PBS_d0_1

description: Library name: Sample 10

value: Saline uninjured


title: young_d0_3

description: Library name: Sample 4

value: young uninjured


title: PBS_d14_3

description: Library name: Sample 22

value: PBS + 14 days post sciatic nerve crush


title: young_d14_308; young_d14_309 (GEX)

description:
Library name: Sample 3_GEX
young_d14_309_barcodes.tsv.gz
young_d14_309_features.tsv.gz
young_d14_309_matrix.mtx.gz
young_d14_308_barcodes.tsv.gz
young_d14_308_features.tsv.gz
young_d14_308_matrix.mtx.gz

value: 14 days post sciatic nerve crush


title: AAV_d14_1

description: Library name: Sample 14


title: PBS_d0_3

description: Library name: Sample 20


title: embryo E7.5 rep1

status: Public on Jun 19 2025

city: nanjing

first: yi

last: yang

address: sipailou 2

country: China

institute: southeast university

description: Library name: Sample 1

data_processing:
Sequencing reads were processed with the SAW workflow (https://github.com/BGIResearch/SAW), which encompasses several critical steps: mRNA spatial location restoration, data filtering, mRNA genome alignment, gene region annotation, MID correction, expression matrix generation, and tissue region extraction. These Clean Reads were mapped to the NCBI-referenced genome using STAR (v2.5.3).
Assembly: GRCm38
Supplementary files format and content: h5ad; gene expression matrix where the rows are genes and columns are single cells

molecule: polyA RNA

source_name: Whole embryo

extract_protocol:
Stereo-seq
Briefly, following cryosection, tissue sections are mounted on Stereo-seq chips, incubated at 37°C, and fixed with 20°C methanol. The chips underwent ssDNA staining and imaging with a Nikon Ti-7 Eclipse microscope. Tissue permeabilization was performed with 0.1% pepsin in HCl buffer, followed by washing with SSC buffer containing RNAase Inhibitor. Captured mRNA was reverse transcribed at 42°C. Post in situ reverse transcription, the chips were treated with tissue removal buffer and then washed. cDNA was released from the chips using a cDNA Release Mix at 55°C, followed by fragmentation, amplification, and purification to produce a DNBs library.

value: Whole embryo

value: WT


title: young_d7_306; young_d7_307 (GEX)

description:
Library name: Sample 2_GEX
young_d7_307_barcodes.tsv.gz
young_d7_307_features.tsv.gz
young_d7_307_matrix.mtx.gz
young_d7_306_barcodes.tsv.gz
young_d7_306_features.tsv.gz
young_d7_306_matrix.mtx.gz

value: Skeletal Muscle


title: PBS_d14_2

description: Library name: Sample 17

value: Skeletal muscle cells


title: FaTTy rep4

status: Public on Apr 30 2025

city: Roslin

first: F. Xavier

last: Donadeu

address: Easter Bush

country: United Kingdom

institute: University of edinburgh

description:
NovaSeq 2x150 bp sequencing
FaTTy_D

data_processing:
Raw sequence data converted to fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software
Trimming for adapters and poor quality reads was performed using Trimmomatic v0.36
Mapping performed using STAR aligner v2.5.2b
Gene hit counts calculated using feature Counts from the Subread package v1.5.2
Differential expression analysis performed using DESeq2 v1.16.1
Assembly: Sscrofa10.2
Supplementary files format and content: raw_counts: comma separated values containing raw reads, Ensembl ID, and associated hgnc symbols where applicable for each sample

organism: Sus scrofa

source_name: FaTTy

growth_protocol: Cells were obtained from a subcutaneous adipose tissue sample and grown in high glucose DMEM with 10% FBS, 1% penicillin/streptomycin, and 5ng/ul human basic fibroblast growth factor at 39C and 5% CO2

extract_protocol:
RNA was extracted from confluent wells using TRIzol/BCP and an RNeasy Mini kit (Qiagen)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufaturer's instructions

value: FaTTy

value: Immortalised Mesenchymal Stem Cell


title: PBS_d14_1

description: Library name: Sample 15

value: mRNA


title: PBS_d0_4

description: Library name: Sample 18


title: young_301; young_308 (GEX)

description:
Library name: Sample 1_GEX
young_308_barcodes.tsv.gz
young_308_features.tsv.gz
young_308_matrix.mtx.gz
young_301_barcodes.tsv.gz
young_301_features.tsv.gz
young_301_matrix.mtx.gz


title: FaTTy rep1

description:
NovaSeq 2x150 bp sequencing
FaTTy_A


title: PBS_d0_2

description: Library name: Sample 12


title: young_d7_2

description: Library name: Sample 9


title: aged_d7_1

description: Library name: Sample 7


title: AAV_d0_1

description: Library name: Sample 11


title: MSC rep3

description:
NovaSeq 2x150 bp sequencing
MSC_C

source_name: MSC

value: MSC

value: Mesenchymal Stem Cell


title: wq7

description: Library name: Sample 5

value: aged uninjured


title: aged_d0_2

description: Library name: Sample 6


title: MSC rep2

description:
NovaSeq 2x150 bp sequencing
MSC_B


title: 832/13 cells, Tovar MPRA library, cDNA rep 3

status: Public on Apr 27 2025

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

data_processing:
We processed MPRA sequencing data using a custom pipeline that quantifies barcode counts while accounting for possible sequencing errors. We identified reads with the barcode sequence and trimmed constant sequences using cutadapt v4.3. We used UMI-tools v1.1.2 to identify and cluster UMIs, then used starcode-umi to cluster UMI-barcode and perform deduplication (Zorita et al. 2015; Smith et al. 2017). Finally, we used starcode to cluster and count barcodes.
Assembly: hg19
Supplementary files format and content: "tovar_library_counts.txt" is a tab-delimited text file containing the barcode sequences, the RNA counts for the five replicates and DNA counts for the input sample. "tovar_library_barcode_pairing.txt" is a tab-delimited text file containing the oligo IDs and barcode pairing of each element tested in the MPRA library. "tovar_library_annotations.txt" is a tab-delimited text file containing the oligo IDs and hg38 coordinates of each element tested in the MPRA library along with information about overlapping motifs.
Library strategy: MPRA amplicon library

organism: Rattus norvegicus

extract_protocol:
We electroporated 30 ug of plasmid into 30 million 832/13 rat insulinoma cells for each biological replicate. We lysed cells 24 hours later with Buffer RLT Plus and isolated total RNA with the Qiagen RNeasy Midi Kit.
We reverse transcribed 30 ug of DNAse I-treated total RNA using SuperScript IV. We performed a cDNA amplification PCR and sample indexing with all cDNA made.

value: Insulinoma


title: young_301; young_308 (CMO)

description:
Library name: Sample 1_CMO
young_308_barcodes.tsv.gz
young_308_features.tsv.gz
young_308_matrix.mtx.gz
young_301_barcodes.tsv.gz
young_301_features.tsv.gz
young_301_matrix.mtx.gz

library_source: other

molecule: other

value: CMO

tag: cmo


title: AAV_d0_2

description: Library name: Sample 13

value: AAV uninjured


title: young_d7_306; young_d7_307 (CMO)

description:
Library name: Sample 2_CMO
young_d7_307_barcodes.tsv.gz
young_d7_307_features.tsv.gz
young_d7_307_matrix.mtx.gz
young_d7_306_barcodes.tsv.gz
young_d7_306_features.tsv.gz
young_d7_306_matrix.mtx.gz

value: 7 days post sciatic nerve crush


title: young_d14_308; young_d14_309 (CMO)

description:
Library name: Sample 3_CMO
young_d14_309_barcodes.tsv.gz
young_d14_309_features.tsv.gz
young_d14_309_matrix.mtx.gz
young_d14_308_barcodes.tsv.gz
young_d14_308_features.tsv.gz
young_d14_308_matrix.mtx.gz


title: 832/13 cells, Tovar MPRA library, plasmid input

description: input

library_source: genomic

molecule: genomic DNA

organism: synthetic construct

source_name: synthetic construct

value: synthetic construct


title: Interactions, Rywal, roots, inoculated_PS-216_YFP_218_mKate_2h_46

status: Public on Apr 24 2025

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS871

data_processing:
filtering low quality reads (--quality 20) and trimming Ns (--trim-n) using Trim Galore
mapping filtered reads to reference potato genome using STAR v2.7.5c (parameters: --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.02 --quantTranscriptomeBan Singleend --outFilterType BySJout --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 10000 --alignMatesGapMax 10000)
generating raw counts table
taxonomic classification of reads using Centrifuge v1.0.4. Due to significant contamination observed in sample BS472, we have made the decision to exclude this sample from subsequent analysis.
differential expression analysis in R: filter genes with low expression, TMM normalization using edgeR v3.26.8 package, export of TMM normalized values using function cpm(log=TRUE, prior.count=0.5)
Assembly: Solanum tuberosum DM v4.04, GTF with merged PGSC and ITAG gene model annotations (https://doi.org/10.15490/fairdomhub.1.datafile.3408.1)
Supplementary files format and content: tab-delimited text files with raw count values and TMM-normalized count values for each Sample

organism: Solanum tuberosum

source_name: roots

growth_protocol: Potato plants cv. Rywal were grown in stem node tissue culture for two to four weeks after in-vitro micropropagation under controlled environmental conditions (22±2°C in the light and 19±2°C in the dark with 70–90 μmol/m2/s2 radiation with OSRAM L 58 W/77 FLUORA lamps and a 16-h photoperiod) as previously described by Lukan et al., 2022 (https://doi.org/10.1093/hr/uhac147).

extract_protocol:
Total RNA was isolated from roots and shoots by RNeasy Plant Mini Kit (Qiagen) and treated with RNA Clean & Concentrator-5, including DNase treatment (Zymo Research).
Poly-A selection and strand-specific Illumina RNA-Seq library preparation was performed by Novogene Ltd. using their standard procedure.

treatment_protocol: For 'Monocultures' experiment, plants were added to bacterial culture after the culture reached 107 CFU/ml and were incubated for 2 or 26 h. For 'Interactions' experiment, when two strains were used, bacterial cultures were mixed in the ratio of 1:1 and roots were incubated for 2 h. In both experiments, plant shoots were not in contact with the bacterial culture. Noninoculated plants were incubated in media for the same time.

value: roots

tag: experiment group

value: Interactions

tag: plantno

tag: cultivar

value: Rywal

value: inoculated

value: PS-216-YFP & PS-218-mKate

tag: timeafterbiofilmformation


title: Interactions, Rywal, roots, inoculated_PS-216_YFP_218_mKate_2h_47

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS872


title: FaTTy rep3

description:
NovaSeq 2x150 bp sequencing
FaTTy_C


title: MSC rep4

description:
NovaSeq 2x150 bp sequencing
MSC_D

value: WT


title: MSC rep1

description:
NovaSeq 2x150 bp sequencing
MSC_A


title: Interactions, Rywal, roots, inoculated_PS-218_YFP_218_mKate_2h_37

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS862

value: PS-218-YFP & PS-218-mKate


title: FaTTy rep2

description:
NovaSeq 2x150 bp sequencing
FaTTy_B

value: FaTTy

value: Immortalised Mesenchymal Stem Cell


title: Interactions, Rywal, roots, inoculated_PS-218_2h_mKate_32

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS857


title: Interactions, Rywal, roots, inoculated_PS-218_2h_mKate_31

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS856


title: Interactions, Rywal, roots, inoculated_PS-216_YFP_218_mKate_2h_45

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS870


title: Interactions, Rywal, roots, inoculated_PS-218_YFP_218_mKate_2h_39

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS864


title: Interactions, Rywal, roots, inoculated_PS-216_YFP_218_mKate_2h_48

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS873


title: Interactions, Rywal, roots, inoculated_PS-216_2h_YFP_23

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS848


title: Interactions, Rywal, roots, inoculated_PS-218_YFP_218_mKate_2h_40

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS865


title: Interactions, Rywal, roots, inoculated_PS-218_YFP_218_mKate_2h_38

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS863


title: Interactions, Rywal, roots, inoculated_PS-218_2h_mKate_30

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS855


title: Interactions, Rywal, roots, inoculated_PS-216_2h_YFP_22

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS847


title: Interactions, Rywal, roots, noninoculated_2h_8

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS833

value: noninoculated


title: Interactions, Rywal, roots, inoculated_PS-216_2h_YFP_24

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS849


title: Interactions, Rywal, roots, inoculated_PS-218_2h_YFP_15

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS840


title: Monocultures, Rywal, shoots, inoculated_PS-218-YFP_26h_236

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS485

source_name: shoots

value: shoots

value: Monocultures


title: Interactions, Rywal, roots, inoculated_PS-218_2h_YFP_14

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS839


title: Interactions, Rywal, roots, noninoculated_2h_7

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS832


title: Interactions, Rywal, roots, noninoculated_2h_5

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS830


title: Interactions, Rywal, roots, noninoculated_2h_6

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS831


title: Monocultures, Rywal, shoots, inoculated_PS-218-YFP_26h_237

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS486


title: Monocultures, Rywal, shoots, inoculated_PS-218-YFP_26h_235

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS484


title: Monocultures, Rywal, shoots, inoculated_PS-216-YFP_26h_233

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS482


title: Monocultures, Rywal, shoots, noninoculated_26h_229

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS478


title: Monocultures, Rywal, roots, inoculated_PS-218-YFP_26h_236

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS473


title: Monocultures, Rywal, shoots, inoculated_PS-216-YFP_26h_230

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS479


title: Monocultures, Rywal, shoots, inoculated_PS-216-YFP_26h_231

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS480


title: Monocultures, Rywal, shoots, inoculated_PS-218-YFP_26h_234

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS483


title: Monocultures, Rywal, shoots, noninoculated_26h_226

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS475


title: Monocultures, Rywal, roots, inoculated_PS-216-YFP_26h_233

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS470


title: Monocultures, Rywal, roots, inoculated_PS-218-YFP_26h_235

description: Due to significant contamination observed in sample BS472, we have made the decision to exclude this sample from subsequent analysis.


title: Monocultures, Rywal, roots, noninoculated_26h_227

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS464


title: Monocultures, Rywal, roots, inoculated_PS-218-YFP_26h_237

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS474


title: Monocultures, Rywal, shoots, inoculated_PS-216-YFP_26h_232

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS481


title: Monocultures, Rywal, roots, inoculated_PS-216-YFP_26h_231

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS468


title: Monocultures, Rywal, roots, inoculated_PS-216-YFP_26h_232

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS469


title: Monocultures, Rywal, roots, noninoculated_26h_228

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS465


title: Monocultures, Rywal, roots, inoculated_PS-218-YFP_26h_234

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS471


title: Monocultures, Rywal, shoots, noninoculated_26h_227

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS476


title: Monocultures, Rywal, roots, inoculated_PS-218-YFP_2h_217

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS454


title: Monocultures, Rywal, roots, inoculated_PS-216-YFP_2h_211

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS448


title: Monocultures, Rywal, shoots, noninoculated_26h_228

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS477


title: Monocultures, Rywal, roots, noninoculated_26h_229

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS466


title: Monocultures, Rywal, roots, inoculated_PS-216-YFP_2h_213

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS450


title: Monocultures, Rywal, roots, inoculated_PS-218-YFP_2h_215

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS452


title: Monocultures, Rywal, roots, inoculated_PS-218-YFP_2h_214

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS451


title: VML +AICAR

status: Public on Jan 31 2025

description:
Library name: Sample 1
10X Genomics

data_processing:
The `count` command from CellRanger v8.0.0 (10X Genomics) was used with the `--include-introns` argument set to `true`, aligning reads to the GRCm39 genome build.
Assembly: GRCm39
Supplementary files format and content: Filtered features, barcodes, count matrices (h5 format)

source_name: Skeletal muscle

extract_protocol:
Bilateral 3mm biopsy punch defects were administered to the quadriceps muscles of (12-16-week-old) C57BL/6 mice. Mice were treated with AICAR and vehicle loaded synthetic protein nano particles (SPNPs) at the site of injury on days 1, 4, and 7 days post injury. At 8 days post injury, mice were humanely euthanized, quadriceps extracted and pooled according to treatment. After tissues were manually homogenized with scissors, they were digested into single cell suspensions for 1h at 37°C using 2 mg/ml collagenase II and 2.5 U/ml dispase II. The enzymatic reaction was stopped using 10% heat inactivated FBS with 5 mM EDTA and passed through a 70 mm strainer. Samples were centrifuged for 10 min at 300g, and resuspended in red blood cell lysis buffer for 2 min at room temperature. After washing, suspension was stained with DAPI and sorted by FACs to remove debris and dead cells (DAPI positive). Sorted cells were then labeled with 10x genomics cell multiplexing oligos (one per treatment) and then analyzed by single cell RNA sequencing.
Library preparation and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan. Cells were loaded into the 10X Genomics chromium single cell controller for each sample and captured into nanoliter-scale gel bead-in-emulsions. cDNAs were prepared using the single cell protocol as per manufacturer’s instructions.

value: Skeletal muscle

value: Mononucleated single cells

value: C57BL/6J (WT)

value: AICAR


title: Monocultures, Rywal, roots, noninoculated_2h_207

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS444


title: Monocultures, Rywal, roots, noninoculated_2h_208

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS445


title: Monocultures, Rywal, roots, inoculated_PS-218-YFP_2h_216

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS453


title: Monocultures, Rywal, roots, inoculated_PS-216-YFP_26h_230

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS467


title: Monocultures, Rywal, roots, noninoculated_26h_226

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS463


title: PBMCs, scRNA-seq, sublibrary 14

status: Public on Jan 30 2025

city: Stanford

first: Leslie

last: Chan

state: CA

address: 300 Pasteur Dr Bldg S131, Grant

institute: Stanford University

data_processing:
ParseBiosciences-Pipeline.1.0.3p was used to identify barcodes, align sequencing reads, assign transcript counts to genes, and generate a cell-by-gene count matrix
After running each sublibrary through the pipeline, the outputs of each sublibrary were combined into a single dataset
Assembly: Custom genome containing the human genome (HG38) and the annotated Wuhan-Hu-1 SARS-CoV-2 reference sequence (NC_045512.2)
Supplementary files format and content: .mtx file containing expression matrix

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
PBMCs were fixed using Parse fixation reagents, frozen at -80°C for less than 6 months, and prepped according to Parse Evercode WT Mega v2 protocol. In this combinatorial split pool barcoding process, samples were first loaded into a 96-well plate and underwent reverse transcription with barcoded primers, pooled, split and barcoded again, followed by cell lysis using Parse reagents.
According to Parse Evercode WT Mega v2 protocol. First, cDNA was amplified, then underwent fragmentation, adaptor ligation, sublibrary index PCR, and double-sided size selection. Sequencing was performed on a NovaSeq S4 instrument (Illumina; Chan Zuckerberg Biohub). The read structure was paired-end with i7 index, i5 index, and the 4th barcode (6bp) that tags each sublibrary acting as a standard Illumina index.

value: Peripheral blood

value: Cryopreserved PBMCs

tag: participant group

value: Pooled PBMCs


title: Monocultures, Rywal, roots, inoculated_PS-216-YFP_2h_212

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS449

value: roots

value: Rywal


title: PBMCs, scRNA-seq, sublibrary 15


title: PBMCs, scRNA-seq, sublibrary 13


title: VML +Vehicle

description:
Library name: Sample 2
10X Genomics

value: Control


title: Monocultures, Rywal, roots, inoculated_PS-216-YFP_2h_210

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS447

value: inoculated


title: Monocultures, Rywal, roots, noninoculated_2h_209

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS446


title: PBMCs, scRNA-seq, sublibrary 11


title: PBMCs, scRNA-seq, sublibrary 10


title: Monocultures, Rywal, roots, noninoculated_2h_206

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS443


title: PBMCs, scRNA-seq, sublibrary 8


title: PBMCs, scRNA-seq, sublibrary 6


title: PBMCs, scRNA-seq, sublibrary 7


title: PBMCs, scRNA-seq, sublibrary 16


title: PBMCs, scRNA-seq, sublibrary 9


title: PBMCs, scRNA-seq, sublibrary 5


title: PBMCs, scRNA-seq, sublibrary 12


title: PBMCs, scRNA-seq, sublibrary 1


title: sample302_GCB-DLBCL-NOS-MYC-R

status: Public on Jan 15 2025

city: Warsaw

first: Michalina

last: Zajdel

address: Roentgena 5

department: Department of Experimental Oncology

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology

data_processing:
Raw sequencing results were analysed in Torrent Suite (version 5.6), including sequence reading, truncation of adapter sequences and assignment of reads to the correct samples.
Unmapped BAM files were converted to fastq files using the bamToFastq script from the BEDTools package (version 2.225).
NGS reads were mapped to the human genome (hg19) using the BWA software (version 0.7.17).
Reads included in the miRBase database (version 21), and new microRNAs were counted with the miRDeep2 application (version 2.0.1.2).
Assembly: hg19
Supplementary files format and content: Comma-delimited CSV file includes a matrix of raw counts

source_name: GCB-DLBCL-NOS-MYC-R

extract_protocol:
Total RNA containing microRNA fraction was isolated using Trizol
The concentration of miRNA in total RNA was estimated with a Bioanalyser (Agilent 2100) using the Agilent Small RNA Kit. MicroRNA libraries were prepared using the Ion Total RNA-seq Kit v2 for Small RNA Libraries reagent kit (Thermo Fisher Scientific) according to the manufacturer's procedure.

value: GCB-DLBCL-NOS-MYC-R

value: cell aspirates of tumours obtained by fine-needle aspiration biopsy


title: sample35_GCB-DLBCL-NOS-MYC-R


title: sample755_GCB-DLBCL-NOS-MYC-R


title: PBMCs, scRNA-seq, sublibrary 4


title: sample1263_GCB-DLBCL-NOS-MYC-R


title: sample763_GCB-DLBCL-NOS

source_name: GCB-DLBCL-NOS

value: GCB-DLBCL-NOS


title: PBMCs, scRNA-seq, sublibrary 2


title: sample758_GCB-DLBCL-NOS


title: sample466_GCB-DLBCL-NOS-MYC-R


title: sample123_BL

source_name: BL

value: BL


title: sample751_GCB-DLBCL-NOS-MYC-R


title: sample71_BL


title: sample610_HGBCL-11q


title: sample762_GCB-DLBCL-NOS


title: PBMCs, scRNA-seq, sublibrary 3


title: sample402_HGBCL-11q


title: sample289_HGBCL-11q


title: sample611_BL


title: sample165_BL


title: sample752_BL


title: sample115_BL


title: sample351_GCB-DLBCL-NOS-MYC-R


title: 207675480016_R12C01

status: Public on Dec 13 2024

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.

label: Cy5 and Cy3

source_name: Human primary cell DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from 30-70 mg of tissue or 5.0 x 10^6 cells for cell lines using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol. DNA was quantified using a Qubit 4 Fluorometer (Invitrogen).

value: Blood R315218

tag: modification

value: Illumina Alpha Test (Blood)


title: sample452_BL


title: sample441_HGBCL-11q


title: 207675480016_R13C01

value: Blood R315185


title: 207675480016_R11C01

value: Blood R315141


title: sample753_BL


title: 207675480016_R15C01


title: 207675480016_R08C01

value: Blood R311882


title: 207675480016_R14C01

value: Blood R315178


title: 207675480016_R07C01

value: Blood R315134


title: 207675480016_R01C01

value: Blood R315165


title: 207675480016_R03C01


title: 207675480016_R02C01

value: Blood R315166


title: 207675480016_R04C01


title: sample339_HGBCL-11q


title: 207675480015_R14C03

value: Blood R315182


title: 207675480015_R13C03

value: Blood R315184


title: 207675480016_R05C01


title: 207675480016_R16C01


title: 207675480015_R13C02

value: Blood R315174


title: 207675480015_R16C02

value: Blood R315151


title: 207675480015_R15C02


title: 207675480015_R14C02


title: 207675480016_R10C01


title: 207675480015_R11C02

value: Blood R315220


title: 207675480015_R11C03

value: Blood R315212


title: 207675480016_R09C01


title: 207675480015_R12C02

value: Blood R315203


title: 207675480015_R15C01

value: Blood R311874


title: 207675480015_R12C03

value: Blood R315215


title: 207675480015_R13C01

value: Illumina Alpha Test (Blood)


title: 207675480015_R10C01

value: Blood R315145


title: 207675480015_R09C03


title: 207675480015_R10C03


title: 207675480015_R10C02


title: 207675480015_R15C03


title: 207675480015_R16C01

value: Blood R315156


title: sample185_HGBCL-11q

value: cell aspirates of tumours obtained by fine-needle aspiration biopsy


title: 207675480015_R16C03


title: 207675480015_R08C03

value: Blood R315158


title: 207675480015_R08C01

value: Blood R315222


title: 207675480015_R11C01

value: Blood R315194


title: 207675480016_R06C01

value: Blood R311882


title: 207675480015_R04C02

value: Blood R315140


title: 207675480015_R14C01


title: 207675480015_R12C01


title: 207675480015_R09C02


title: 207675480015_R07C03

value: Blood R315159


title: 207675480015_R06C01


title: 207675480015_R04C03

value: Blood R315139


title: 207675480015_R09C01


title: 207675480015_R02C03


title: 207675480015_R08C02

value: Blood R315172


title: 207675480015_R07C01

value: Blood R311895


title: 207675480015_R01C03

value: Blood R315213


title: 207675480015_R05C01


title: 207854510108_R16C02

value: Thymus

tag: age

tag: Sex

value: F

value: 8. Tissue-specific 5hmC


title: 207675480015_R01C02

value: Blood R315146

value: Illumina Alpha Test (Blood)


title: 207854510108_R16C01

value: Testis

value: M


title: 207675480015_R03C02


title: 207675480015_R06C03

value: Blood R315158


title: 207675480015_R05C02

value: Blood R315181


title: 207675480015_R07C02


title: 207675480015_R04C01

value: Blood R311886


title: 207675480015_R02C02


title: 207854510108_R14C02


title: 207675480015_R06C02


title: 207675480015_R01C01

value: Blood R311861


title: 207854510108_R15C03

value: Liver


title: 207854510108_R16C03

value: Lung


title: 207854510108_R13C01

value: Heart


title: 207675480015_R03C01


title: 207675480015_R05C03

value: Blood R315159


title: 207854510108_R15C02

value: Ovary


title: 207675480015_R02C01


title: 207854510108_R12C02

value: Spleen


title: 207854510108_R13C03


title: 207854510108_R11C03

value: Placenta


title: 207854510108_R14C01


title: 207854510108_R15C01


title: 207854510108_R12C03

value: Eye


title: 207854510108_R09C03

value: F

value: 8. Tissue-specific 5hmC


title: 207854510108_R11C01


title: 207854510108_R14C03

value: Bladder


title: 207854510108_R10C03


title: 207854510108_R12C01

value: Testis


title: 207854510108_R10C01

value: M


title: 207854510108_R10C02


title: 207854510108_R11C02


title: 207675480015_R03C03

value: Blood R315213

value: Illumina Alpha Test (Blood)


title: 207854510108_R09C02


title: 207854510108_R13C02


title: 207854510108_R08C03

value: Colon


title: 207854510108_R09C01


title: 207854510108_R08C01


title: 207854510108_R07C02


title: 207854510108_R08C02

value: Stomach


title: 207854510108_R07C03


title: 207854510108_R07C01

value: Thyroid


title: 207854510108_R06C03


title: 207854510108_R06C02

value: Trachea


title: 207854510108_R05C03


title: 207854510108_R04C02


title: 207854510108_R05C02


title: 207854510108_R04C03

value: Liver


title: 207854510108_R02C03


title: 207854510108_R03C02


title: 207854510108_R02C01

value: Heart


title: 207854510108_R03C03


title: 207854510026_R16C02

value: Esophagus


title: 207854510026_R15C03

value: Thymus


title: 207854510026_R16C01

value: Lung


title: 207854510108_R01C03


title: 207854510108_R01C01

value: 0a. Additional control


title: 207854510026_R15C02

value: Lymph Node

value: F


title: 207854510108_R01C02

value: Bladder

value: 8. Tissue-specific 5hmC


title: 207854510108_R03C01


title: 207854510026_R14C01

value: M


title: 207854510026_R14C03

value: Adrenal


title: 207854510026_R13C03


title: 207854510108_R05C01


title: 207854510026_R13C02

value: Kidney


title: 207854510108_R06C01

value: Testis


title: 207854510026_R13C01

value: Larynx


title: 207854510108_R04C01

value: Spinal Cord


title: 207854510026_R12C03


title: 207854510026_R12C01

value: Stomach


title: 207854510026_R12C02


title: 207854510026_R11C02


title: 207854510108_R02C02

value: Trachea


title: 207854510026_R10C01


title: 207854510026_R11C03

value: Prostate


title: 207854510026_R10C02

value: Esophagus


title: 207854510026_R16C03


title: 207854510026_R15C01

value: Spleen


title: 207854510026_R10C03


title: 207854510026_R11C01


title: 207854510026_R08C01


title: 207854510026_R09C01


title: 207854510026_R07C02


title: 207854510026_R07C01


title: 207854510026_R06C03


title: 207854510026_R09C02


title: 207854510026_R09C03


title: 207854510026_R14C02


title: 207854510026_R06C02


title: 207854510026_R07C03


title: 207854510026_R06C01


title: 207854510026_R08C03


title: 207854510026_R05C01


title: 207854510026_R05C02


title: 207854510026_R05C03


title: 207854510026_R08C02


title: 207854510026_R04C03

value: Thymus


title: 207854510026_R04C01


title: 207854510026_R04C02


title: 207854510026_R03C03


title: 207854510026_R02C01


title: 207854510120_R16C03

value: 5. Tissue-specific methylation


title: 207854510026_R01C03


title: 207854510026_R02C03


title: 207854510026_R02C02

value: Lymph Node


title: 207854510026_R01C02

value: Lung


title: 207854510026_R03C01

value: Heart

value: F

value: 0a. Additional control


title: 207854510120_R15C02


title: 207854510120_R16C02


title: 207854510120_R13C03

value: M


title: 207854510026_R01C01


title: 207854510120_R14C01


title: 207854510120_R13C01


title: 207854510120_R14C03

value: Adrenal


title: 207854510120_R13C02

value: Kidney


title: 207854510120_R14C02


title: 207854510120_R15C03


title: 207854510120_R15C01


title: 207854510120_R12C02


title: 207854510120_R16C01


title: 207854510120_R12C01


title: 207854510120_R11C02


title: 207854510026_R03C02

value: 8. Tissue-specific 5hmC


title: 207854510120_R10C03


title: 207854510120_R10C02


title: 207854510120_R11C01

value: Larynx


title: 207854510120_R09C02


title: 207854510120_R08C03


title: 207854510120_R09C03


title: 207854510120_R09C01


title: 207854510120_R10C01

value: Stomach


title: 207854510120_R08C01


title: 207854510120_R11C03


title: 207854510120_R05C02


title: 207854510120_R07C02


title: 207854510120_R08C02


title: 207854510120_R07C03


title: 207854510120_R12C03


title: 207854510120_R06C01


title: 207854510120_R04C03


title: 207854510120_R07C01


title: 207854510120_R05C03


title: 207854510120_R04C02


title: 207854510120_R06C02


title: 207854510120_R04C01


title: 207854510120_R02C03


title: 207854510120_R02C02


title: 207854510120_R03C02


title: 207854510120_R03C03

value: Trachea


title: 207854510120_R02C01


title: 207854510120_R06C03


title: 207854510120_R03C01

source_name: Human cell line DNA


title: 207854510120_R01C01


title: 207854510120_R01C03


title: 207854510094_R16C02


title: 207854510094_R14C03

value: Bladder


title: 207854510094_R15C02

value: Ovary


title: 207854510094_R14C02


title: 207854510094_R15C03

value: Liver


title: 207854510094_R11C03

value: Placenta


title: 207854510094_R16C03

value: 5. Tissue-specific methylation


title: 207854510094_R12C02

value: Spleen


title: 207854510120_R05C01


title: 207854510094_R11C01


title: 207854510120_R01C02

value: Lung


title: 207854510094_R16C01

value: Testis


title: 207854510094_R13C01

value: Heart


title: 207854510094_R13C02

value: F


title: 207854510094_R13C03

value: M


title: 207854510094_R09C02


title: 207854510094_R15C01


title: 207854510094_R10C01


title: 207854510094_R10C02


title: 207854510094_R12C01


title: 207854510094_R07C01

value: Thyroid


title: 207854510094_R08C01


title: 207854510094_R05C02


title: 207854510094_R09C03


title: 207854510094_R08C02


title: 207854510094_R12C03

value: Eye


title: 207854510094_R07C03


title: 207854510094_R08C03

value: Colon


title: 207854510094_R10C03


title: 207854510094_R06C02


title: 207854510094_R05C03


title: 207854510094_R04C02


title: 207854510094_R05C01


title: 207854510094_R03C02


title: 207854510094_R09C01


title: 207854510094_R14C01


title: 207854510094_R11C02


title: 207854510094_R07C02


title: 207854510094_R02C03


title: 207854510094_R04C03


title: 207854510094_R06C03


title: 207854510094_R06C01


title: 207854510094_R03C01


title: 207854510094_R01C01


title: 207854510094_R01C02


title: 207854510094_R03C03


title: 207854510094_R04C01

value: Spinal Cord


title: 207854510094_R02C02


title: pair2, inter, 20% CICI, rep2

status: Public on Dec 11 2024

city: State College

first: Yi

last: Li

address: 406 SOUTH FREAR, UNIVERSITY PARK

institute: Penn State University

description: Library name: pair2_20_rep2

data_processing:
Next generation sequencing was performed on NextSeq 2000, and 100 million of  50 bp paired-end reads were generated for each replicate. Hi-C data analysis was performed with HiC-pro (version 3.1.0), cooler(version 0.10.0), cooltools (version 0.7.0) and HiCExplorer (version 3.7.2).
Assembly: sacCer3
Supplementary files format and content: cool files

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in 200 mL SCD-Met medium until OD660 reached 0.3.

extract_protocol:
Standard method was used to perform Hi-C and extract DNA.
Hi-C libraries were prepared with NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: To arrest cells in the G1 phase, 80 µM alpha-factor (Zymo, Y1001) was added to the culture for a total of 2.5 hours. During the final hour of this incubation, 1 ng/µL rapamycin was added to induce CICI. DMSO was added in the control group instead. After 1 hour of rapamycin treatment, cells were harvested for imaging analysis and Hi-C measurement.

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::966175_LacO, Chr4::1166682_TetO

value: 20% CICI cell + 80% DMSO cell


title: pair1, intra, 50% CICI, rep2

description: Library name: pair1_50_rep2

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr15::793958_TetO

value: 50% CICI cell + 50% DMSO cell


title: pair2, inter, 10% CICI, rep2

description: Library name: pair2_10_rep2

value: 10% CICI  cell + 90% DMSO cell


title: pair2, inter, 50% CICI, rep1

description: Library name: pair2_50_rep1


title: pair2, inter, 10% CICI, rep1

description: Library name: pair2_10_rep1


title: pair2, inter, 50% CICI, rep2

description: Library name: pair2_50_rep2


title: pair2, inter, 20% CICI, rep1

description: Library name: pair2_20_rep1


title: pair1, intra, 10% CICI, rep2

description: Library name: pair1_10_rep2


title: 207854510094_R01C03


title: pair2, inter, 100% CICI, rep2

description: Library name: pair2_100_rep2

value: 100% CICI cell + 0% DMSO cell


title: pair2, inter, 0% CICI, rep2

description: Library name: pair2_0_rep2

value: 0% CICI  cell + 100% DMSO cell


title: pair2, inter, 0% CICI, rep1

description: Library name: pair2_0_rep1


title: pair1, intra, 100% CICI, rep1

description: Library name: pair1_100_rep1


title: pair1, intra, 20% CICI, rep2

description: Library name: pair1_20_rep2


title: pair1, intra, 100% CICI, rep2

description: Library name: pair1_100_rep2


title: pair1, intra, 0% CICI, rep2

description: Library name: pair1_0_rep2


title: Basal cells from normal donor 4

status: Public on Nov 18 2024

city: Glendale

first: Crystal

last: Marconett

address: 1856 Kirkby Rd

department: Translational Genomics

institute: Keck School of Medicine

data_processing:
Raw FASTQ files underwent quality control analysis using FASTQC. Adapter sequences were then trimmed from raw FASTQ reads using AdapterTrimmer. Reads were then filtered to remove those of low quality. Retained reads had a quality score of >30 per base for at least 90% of the read.
Reads were then aligned to the Hg38 genome with STAR aligner (PMC3530905) using the Ensembl v110 (July 2023 release) transcriptome build.
Counts per gene per sample were then used for calculating differential expression analysis in DeSeq2 (PMID: 25516281) in R
Preprocessing of raw ATACseq data to generate clean read files was performed as was done for the RNA samples. Cleaned ATACseq reads were aligned to the hg38 genome using bwa aligner (PMID: 19451168).
Peak enrichment was subsequently calculated using the GenRich peak caller (Gaspar, John M. "Genrich: detecting sites of genomic enrichment."GitHub repository. GitHub(2018)) using the intrinsic background of the sample. Peaks were then annotated to nearest-neighbor genes using the annotatepeaks.pl function in HOMER (PMID: 20513432), which also binned peaks into categories relative to the genomic structures they occurred in (eg; promoter, enhancer, etc).
Assembly: Hg38
Supplementary files format and content: Bulk RNAseq table of counts in .CSV format
Supplementary files format and content: GenRich narrowpeak genomic files

source_name: Lung Basal cells

growth_protocol: Remnant human transplant lungs were obtained in compliance with Institutional Review Board-approved protocols for the use of human source material in research (HS-07-00660) and processed within 3 days of death

extract_protocol:
Lung parenchyma was macrodissected to a depth of > 2mm in order to isolate alveolar tissue. The visceral pleura was removed using forceps, and alveolar tissue was then minced to fine pieces with scissors. Tissue was then washed in 50:50 DMEM/F12 media, which is a 50:50 mixture of DME-F12 (#D64421, Sigma) and DMEM High Glucose (#21063, GIBCO) supplemented with 1% penicillin/streptomycin (), 0.1% Gentamycin (#G1272, Sigma), and 1% Fungizone (A2411, Sigma). Following overnight incubation, the tissue was again minced briefly using a razor blade and resuspended in HBSS media without Ca2+ or Mg2+ supplemented with 13U/mL of elastase (#LS002280, Worthington) for 30min at 37C. Cells were filtered through a gauze mesh and then through a 100um filter, then pelleted and resuspended in 50:50 DMEM/F12 media and applied to a Percoll density gradient centrifugation, followed by IgG panning (#I4506, Sigma). Magnetic-activated sorting with Epcam+ beads (Miltenyi Biotec #130-061-101) and FcR blocking (Biotec #130-059-901) was then performed, followed by separation using LS columns (Miltenyi Biotec #130-042-401). Following separation, Cells were counted using trypan blue to measure viability. After counting, cells were fixed in 4% paraformaldehyde (PFA) for 10 minutes, washed with Phosphate Buffered Saline (1xPBS), resuspended in PBS for each cytospin. Cytospins were prepared using EZ single cytofunnels (#1439045, Thermo Fisher Scientific) and a Shandon CytoSpin III cytocentrifuge (GMI, Ramsey, Minnesota). Cytospin slides were stored at -20°C until use.
For RNA, 6 million AT2 or basal cells were frozen into a pellet and stored at -80C. RNA was extracted using the Aurum Total RNA Mini kit (# 7326820, BioRad, Hercules CA) according to manufacturer guidelines. 2 ug of total RNA then underwent bulk RNA library preparation with PolyA selection performed by Genewiz (now Azenta, Burlington MA). Samples were barcoded using Illumina adapters to allow for multiplexed sequencing. For ATAC, between 5-50 K of freshly isolated AT2 cells were placed in 0.1 to 0.25 mL of ATAC lysis buffer (AM1) and immediately processed for ATAC library generation using the Active Motif ATACseq kit (#53150, Carlsbad CA) according to manufacturer guidelines. Nextera i7 dual indexing primers were used for library construction as listed in Table 1. Integration of indexing primers was performed with the Tn5 enzymes listed in Table 1. The Benchmark Scientific H5000-H MultiTherm shaker was used to ensure uniformity in library construction. The Agilent 4200 Tape Station system was used for assessment of ATAC fragment quality throughout library construction
Bulk RNA paired end sequencing and bulk AT2 ATAC paired end sequencing was performed at Genewiz, using an Illumina HiSeq at 2x150 bp. RNAseq was performed using single index chemistry, whereas ATACseq was performed using dual-index chemistry.

value: Lung Basal cells

tag: disease state

value: Normal

value: Basal


title: pair1, intra, 0% CICI, rep1

description: Library name: pair1_0_rep1


title: pair2, inter, 100% CICI, rep1

description: Library name: pair2_100_rep1


title: Alveolar Epithelial Type 2 cells from normal donor 3, ATAC-seq

source_name: Lung AT2 cells

extract_protocol:
Lung parenchyma was macrodissected to a depth of > 2mm in order to isolate alveolar tissue. The visceral pleura was removed using forceps, and alveolar tissue was then minced to fine pieces with scissors. Tissue was then washed in 50:50 DMEM/F12 media, which is a 50:50 mixture of DME-F12 (#D64421, Sigma) and DMEM High Glucose (#21063, GIBCO) supplemented with 1% penicillin/streptomycin (), 0.1% Gentamycin (#G1272, Sigma), and 1% Fungizone (A2411, Sigma). Following overnight incubation, the tissue was again minced briefly using a razor blade and resuspended in HBSS media without Ca2+ or Mg2+ supplemented with 13U/mL of elastase (#LS002280, Worthington) for 30min at 37C. Cells were filtered through a gauze mesh and then through a 100um filter, then pelleted and resuspended in 50:50 DMEM/F12 media and applied to a Percoll density gradient centrifugation, followed by IgG panning (#I4506, Sigma). Magnetic-activated sorting with Epcam+ beads (Miltenyi Biotec #130-061-101) and FcR blocking (Biotec #130-059-901) was then performed, followed by separation using LS columns (Miltenyi Biotec #130-042-401). Following separation, Cells were counted using trypan blue to measure viability. After counting, cells were fixed in 4% paraformaldehyde (PFA) for 10 minutes, washed with Phosphate Buffered Saline (1xPBS), resuspended in PBS for each cytospin. Cytospins were prepared using EZ single cytofunnels (#1439045, Thermo Fisher Scientific) and a Shandon CytoSpin III cytocentrifuge (GMI, Ramsey, Minnesota). Cytospin slides were stored at -20°C until use.
For RNA, 6 million AT2 cells were frozen into a pellet and stored at -80C. RNA was extracted using the Aurum Total RNA Mini kit (# 7326820, BioRad, Hercules CA) according to manufacturer guidelines. 2 ug of total RNA then underwent bulk RNA library preparation with PolyA selection performed by Genewiz (now Azenta, Burlington MA). Samples were barcoded using Illumina adapters to allow for multiplexed sequencing. For ATAC, between 5-50 K of freshly isolated AT2 cells were placed in 0.1 to 0.25 mL of ATAC lysis buffer (AM1) and immediately processed for ATAC library generation using the Active Motif ATACseq kit (#53150, Carlsbad CA) according to manufacturer guidelines. Nextera i7 dual indexing primers were used for library construction as listed in Table 1. Integration of indexing primers was performed with the Tn5 enzymes listed in Table 1. The Benchmark Scientific H5000-H MultiTherm shaker was used to ensure uniformity in library construction. The Agilent 4200 Tape Station system was used for assessment of ATAC fragment quality throughout library construction
Bulk RNA paired end sequencing and bulk AT2 ATAC paired end sequencing was performed at Genewiz, using an Illumina HiSeq at 2x150 bp. RNAseq was performed using single index chemistry, whereas ATACseq was performed using dual-index chemistry.

value: Lung AT2 cells


title: 207854510094_R02C01

value: Heart

value: F

value: 5. Tissue-specific methylation


title: pair1, intra, 50% CICI, rep1

description: Library name: pair1_50_rep1


title: pair1, intra, 20% CICI, rep1

description: Library name: pair1_20_rep1


title: pair1, intra, 10% CICI, rep1

description: Library name: pair1_10_rep1


title: Basal cells from normal donor 5


title: Alveolar Epithelial Type 2 cells from normal donor 1, ATAC-seq


title: Alveolar Epithelial Type 2 cells from normal donor 2, ATAC-seq


title: Alveolar Epithelial Type 2 cells from IPF donor 3, ATAC-seq

value: IPF


title: Alveolar Epithelial Type 2 cells from IPF donor 1, RNA-seq

description:
IPF.AT2.rep1
AT2_IPF_v_NORMAL_bulkRNAseq_tableofcounts_FINAL-1.csv


title: Alveolar Epithelial Type 2 cells from normal donor 1, RNA-seq

description:
NORMAL_AT2_rep1
AT2_IPF_v_NORMAL_bulkRNAseq_tableofcounts_FINAL-1.csv


title: Alveolar Epithelial Type 2 cells from IPF donor 2, ATAC-seq


title: Alveolar Epithelial Type 2 cells from normal donor 2, RNA-seq

description:
Normal.AT2rep2
AT2_IPF_v_NORMAL_bulkRNAseq_tableofcounts_FINAL-1.csv


title: Input_Con_1

status: Public on Nov 14 2024

city: Fuzhou

first: Jiaxin

last: Wen

address: No.1 Xuefu North Road, Fuzhou, Fujian, China

institute: Fujian Medical University

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: mm10
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and m6A methylation status changes for each gene.

source_name: placenta

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: placenta

value: trophoblast

value: Wild type

value: Control

tag: rip antibody

value: none (input)


title: 269044-Blastoids cultured in postimplantation (4 days)

status: Public on Sep 24 2024

city: Vienna

first: HEIDAR

last: HEIDARI KHOEI

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

data_processing:
scRNA-seq reads were processed with cellranger v7.2.0 with default settings and using the prebuild 10X GRCh38 reference refdata-gex-GRCh38-2020-A
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files
Supplementary files format and content: tab-separated text files including celltype per CellID

source_name: naive hPSCs

extract_protocol:
The structures (human blastoids, rapalink-1 treated blastoids and potimplantation cultures dissociated into single cells. Live cells were enriched using EasySep™ Dead Cell Removal (Annexin V) Kit removal kit (Stem cell technologies). Cells counting was performed using nucleocounter NC-250 (ChemoMetec).
Desired number of cells were used for generation of Gel Beads in Emulsions (GEMs) using 10X Genomics chromium X at VBCF-NGS, Vienna. For 96 HR samples, 1000 cells were targeted using Chromium Next GEM Single Cell 3ʹ LT Kit v3.1 (PN-1000325) on chip L (PN-1000321) and for post implantation samples 10000 cells were targeted using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (PN-1000128) on chip G (PN-1000127) according to manufacture’s protocols (CG000399 and CG000315, respectively (10X Genomics, Pleasanton, CA)). cDNA were amplified for 11 cycles. Libraries were purified using Ampure XP bead purification protocol and were analyzed using fragment analyzer and qPCR for distributtion and quantity. Libraries were pooled together and sequenced on NovaSeq instrument series flowcell (Illumina, San Diego, CA) using paired end readmode for a total of 300 cycles.

value: naive hPSCs

value: Postimplantation culture

value: no


title: 267607-96 h Blastoids

value: Blastoid


title: ssHi-C RE-deleted, DSB 2 hr

status: Public on Jul 29 2024

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

country: France

institute: ENS Lyon

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function with mapping quality set to 30 or 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
For ssHi-C, sparse matrices generated by hicstuff pipeline function were processed with the sshicstuff pipeline function to isolate fragments of interest
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz)
Supplementary files format and content: Hi-C and unfiltered ssHi-C contact data in cooler format, either per fragment (for ssHiC samples) or binned at 1kb (for HiC samples)
Supplementary files format and content: Unfiltered ssHi-C contact data in graal (sparse) format, per fragment
Supplementary files format and content: Tabulated ssHi-C contact data filtered with ssHiCstuff, binned at 1kb
Library strategy: ssHi-C

source_name: RE-deleted, DSB 2 hr

growth_protocol: Cells were grown to exponential phase in YP-lactate media and synchronized in G1 with alpha-factor for 3 hours. Cells were washed 3 times in pre-warmed YP-lactate and released in S-phase in YP-lactate supplemented with 2% galactose. For Scc1-AID depletion experiment, 2 mM IAA were added at the time of release. For Pol3/Rfc1-AID depletion, 50 ug/mL doxycycline and  2 mM IAA were added 1 hour post-release.

extract_protocol:
Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm.
Hi-C and ssHi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells, with addition of the annealing oligonucleotide mix at 7 nM each in the lysis buffer prior to incubation at 62°C for 10 minutes.
DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions. For ssHi-C, two rounds of targeted capture using the IDT xGen Hybridization buffer and enhancer using biotinylated oligonucleotides at 0.6 uM each. The library was digested with MfeI and SspI in NEB cutsmart buffer prior to sequencing.

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

value: S. cerevisiae culture


title: 267608-Blastoids treated with Rapalink-1 for 3 days

value: Rapalink-1 treated blastoid


title: Alveolar Epithelial Type 2 cells from normal donor 3, RNA-seq

description:
NORMAL_AT2_rep3
AT2_IPF_v_NORMAL_bulkRNAseq_tableofcounts_FINAL-1.csv

value: Normal


title: Pool of 3 B16/F10-BrM brains

status: Public on Aug 30 2024

city: Madrid

first: Manuel

last: Valiente

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

data_processing:
STARSolo
Assembly: GRCm38
Supplementary files format and content: Data matrices form STARSolo output

source_name: Brain microenvironment enriched in astrocytes

extract_protocol:
Mouse brains were processed with the Adult Brain Dissociation Kit (Miltenyi, ref. 130-107-677) using gentleMACS C Tubes (Miltenyi, ref. 130-093-237) and the gentleMACS™ Octo Dissociator (Miltenyi, ref.  130-096-427). For myelin removal, a 30% percoll gradient was used. To isolate the highest possible amount of astrocytes, Anti-ACSA-2 (Miltenyi, ref. 130-097-678) microbeads were used and for dead cell removal, Debris Removal solution (Miltenyi, ref. 130-109-398) was added prior to analysis.
~10,000 cells per condition were loaded onto a 10x Chromium Single Cell Controller chip B (10x Genomics) as described by the manufacturer (Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3, PN-1000075). Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, cDNA amplification and library construction were all performed as recommended in the manufacturer's protocol.

value: Brain

value: 10 weeks old


title: IP_Con_1


title: Alveolar Epithelial Type 2 cells from IPF donor 2, RNA-seq

description:
IPF.AT2.rep2
AT2_IPF_v_NORMAL_bulkRNAseq_tableofcounts_FINAL-1.csv

value: Lung AT2 cells


title: Alveolar Epithelial Type 2 cells from IPF donor 1, ATAC-seq


title: Input_Con_2


title: Hi-C WT, no donor, DSB 2 hr

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function with mapping quality set to 30 or 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
For ssHi-C, sparse matrices generated by hicstuff pipeline function were processed with the sshicstuff pipeline function to isolate fragments of interest
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz)
Supplementary files format and content: Hi-C and unfiltered ssHi-C contact data in cooler format, either per fragment (for ssHiC samples) or binned at 1kb (for HiC samples)
Supplementary files format and content: Unfiltered ssHi-C contact data in graal (sparse) format, per fragment
Supplementary files format and content: Tabulated ssHi-C contact data filtered with ssHiCstuff, binned at 1kb

source_name: WT, no donor, DSB 2 hr


title: Hi-C Scc1-depleted DSB 2 hr

source_name: Scc1-depleted DSB 2 hr


title: 269045-Rapalink-1 treated blastoids cultured in postimplantation (4 days)


title: Input_Con_3


title: IP_Con_3


title: Hi-C WT, DSB 2 hr replicate 2

source_name: WT, DSB 2 hr


title: Hi-C WT, DSB 4 hr replicate 3

source_name: WT, DSB 4 hr


title: IP_Con_2


title: Pool of 3 naive brains

value: Brain microenvironment enriched in astrocytes


title: Hi-C WT, DSB 4 hr + Noco

source_name: WT, DSB 4 hr + Noco


title: scBCR, adult male, subject P11, bone marrow, year 1 day-0, replicate 1

status: Public on Jun 13 2024

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

data_processing:
Bulk BCR: Demultiplexed pair-end reads were preprocessed using pRESTO v.0.5.7. Initial germline V(D)J gene annotation was  performed using IgBLAST v1.9.0. IgBLAST output was processed using  Change-O v0.4.0.
scBCR: Demultiplexed pair-end FASTQ reads were preprocessed using the “cellranger vdj” command from 10 × Genomics’ Cell Ranger v.3.1.0 for alignment against the GRCh38 human reference v.3.1.0 (refdata-cellranger-vdj-GRCh38-alts-ensembl-3.1.0). Initial germline V(D)J gene annotation was performed as described for bulk sequencing BCR reads
Processed BCR sequences from bulk sequencing and single-cell sequencing (Extended Data Table 4), were combined with monoclonal antibody sequences for further analysis.
Combined BCR sequences were called for genotyping using the function findNovelAlleles() and inferGenotype() from TIgGER v.0.2.11 ([MH5] ). Individual genotypes, including novel V gene alleles missing from IMGT/ GENE-DB, were computationally inferred and used to finalize V(D)J annotations.
Assembly: GRCh38
Supplementary files format and content: tar.gz: compressed archive of 10X Genomics Cell Ranger output files.
Supplementary files format and content: tsv: AIRR-seq rearrangement format

source_name: bone marrow

extract_protocol:
PBMCs were isolated from blood. Fine-needle aspiration was performed on axillary lymph nodes. RNA was purified from whole PBMCs and sorted PBs from participants using the RNeasy Micro Kit (Qiagen).
Bulk BCR: Reverse transcription, unique molecular identifier (UMI) barcoding, cDNA amplification, and Illumina linker addition to B cell heavy chain transcripts were performed using the human NEBNext Immune Sequencing Kit (NEB) according to the manufacturer’s instructions.  scBCR libraries were prepared as recommended by the 10× Genomics Chromium Single Cell V(D)J Reagent Kit (v1 Chemistry) user guide, with appropriate modifications to the PCR cycles based on the calculated cDNA concentration

tag: isolate

value: bone marrow

value: plasma cells


title: Hi-C WT, DSB 4 hr replicate 2

tag: tissue


title: Hi-C Scc1-depleted DSB 4 hr

source_name: Scc1-depleted DSB 4 hr


title: scBCR, adult male, subject P11, bone marrow, year 1 day-35, replicate 1


title: scBCR, adult male, subject P11, bone marrow, year 1 day-180, replicate 1


title: scBCR, adult male, subject P05, bone marrow, year 2 day-28, replicate 1


title: Hi-C metaphase-arrested (cdc20) replicate 2

source_name: metaphase-arrested (cdc20)


title: scBCR, adult male, subject P11, bone marrow, year 1 day-90, replicate 2


title: scBCR, adult male, subject P05, bone marrow, year 2 day-0, replicate 2


title: scBCR, adult male, subject P05, bone marrow, year 2 day-90, replicate 1


title: scBCR, adult male, subject P11, bone marrow, year 1 day-35, replicate 2


title: scBCR, adult male, subject P05, bone marrow, year 2 day-0, replicate 1


title: Hi-C WT, no donor, DSB 4 hr

source_name: WT, no donor, DSB 4 hr


title: scBCR, adult male, subject P11, bone marrow, year 1 day-90, replicate 1


title: scBCR, adult male, subject P11, bone marrow, year 1 day-180, replicate 2


title: Hi-C metaphase-arrested (cdc20) replicate 1


title: scBCR, adult male, subject P05, bone marrow, year 1 day-28, replicate 2


title: scBCR, adult male, subject P05, bone marrow, year 1 day-180, replicate 2


title: scBCR, adult male, subject P04, bone marrow, year 1 day-180, replicate 2


title: scBCR, adult male, subject P05, bone marrow, year 1 day-90, replicate 2


title: scBCR, adult male, subject P05, bone marrow, year 1 day-28, replicate 1


title: scBCR, adult male, subject P11, bone marrow, year 1 day-0, replicate 2


title: scBCR, adult male, subject P04, bone marrow, year 1 day-28, replicate 2


title: scBCR, adult male, subject P04, bone marrow, year 1 day-180, replicate 1


title: scBCR, adult male, subject P05, bone marrow, year 1 day-0, replicate 1


title: scBCR, adult male, subject P05, bone marrow, year 1 day-180, replicate 1


title: scBCR, adult male, subject P05, bone marrow, year 1 day-0, replicate 2


title: scBCR, adult male, subject P04, bone marrow, year 2 day-0, replicate 2


title: scBCR, adult male, subject P04, bone marrow, year 1 day-28, replicate 1


title: scBCR, adult male, subject P05, bone marrow, year 1 day-90, replicate 1


title: scBCR, adult male, subject P04, bone marrow, year 1 day-0, replicate 2


title: P11 adult male, bone marrow, year 1 day-90, replicate 1

description:
adult male, bone marrow, year 1 day-90, replicate 1
P11_BMPC_d90_1_Y1

data_processing: Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function.  Demultiplexed pair-end FASTQ reads were first preprocessed on a by-sample basis using the ‘cellranger count’ command from 10× Genomics’ Cell Ranger v.3.1.0 for alignment against the GRCh38 human reference v.3.0.0 (refdata-cellranger-GRCh38- 3.0.0). The feature biotypes were retrieved using biomaRt v.2.42.0 ([MH8] ) from Ensembl release 93 ([MH9] ).  Additional quality control was performed as follows. (1) To remove presumably lysed cells, cells with mitochondrial content greater than 15% of all transcripts were removed. (2) To remove likely doublets, cells with more than 7,000 features were removed. (3) Genes that were expressed in less than 5 cells in any sample and cells with detectable expression of fewer than 400 genes were removed.  Gene expression analysis of CellRanger output was performed using Seurat v.4.0.3.1.1  Assembly: GRCh38  Supplementary files format and content: tar.gz: compressed archive of 10X Genomics Cell Ranger output files.  Supplementary files format and content: Rds: Seurat analyses saved as R objects

extract_protocol: PBMCs were isolated using Vacutainer CPT tubes (BD); the remaining red blood cells were lysed with ammonium chloride lysis buffer (Lonza). Cells were immediately used or cryopreserved in 10% dimethylsulfoxide (DMSO) in FBS. A qualified physician’s assistant performed ultrasound guided fine needle aspirate (FNA) of axillary lymph nodes under the supervision of a radiologist. Lymph node dimensions and cortical thickness were measured prior to each FNA. Six passes were made using 25-gauge needles, which were flushed with 3 ml of RPMI 1640 supplemented with 10% FBS and 100 U/ml penicillin/streptomycin, followed by three 1 ml rinses. Red blood cells were lysed with ammonium chloride lysis buffer. Cells were washed twice with PBS supplemented with 2% FBS and 2 mM EDTA and immediately used or cryopreserved in 10% DMSO in FBS.  Libraries were prepared using 10x Genomics' Chromium Next GEM single cell 5' gene expression workflow.


title: P11 adult male, bone marrow, year 1 day-180, replicate 2

description:
adult male, bone marrow, year 1 day-180, replicate 2
P11_BMPC_d180_2_Y1


title: P05 adult male, bone marrow, year 2 day-90, replicate 1

description:
adult male, bone marrow, year 2 day-90, replicate 1
P05_BMPC_d90_1_Y2


title: P11 adult male, bone marrow, year 1 day-0, replicate 2

description:
adult male, bone marrow, year 1 day-0, replicate 2
P11_BMPC_d0_2_Y1


title: P11 adult male, bone marrow, year 1 day-90, replicate 2

description:
adult male, bone marrow, year 1 day-90, replicate 2
P11_BMPC_d90_2_Y1


title: scBCR, adult male, subject P04, bone marrow, year 1 day-0, replicate 1


title: scBCR, adult male, subject P04, bone marrow, year 2 day-0, replicate 1


title: P11 adult male, bone marrow, year 1 day-0, replicate 1

description:
adult male, bone marrow, year 1 day-0, replicate 1
P11_BMPC_d0_1_Y1


title: P11 adult male, bone marrow, year 1 day-35, replicate 1

description:
adult male, bone marrow, year 1 day-35, replicate 1
P11_BMPC_d35_1_Y1


title: P05 adult male, bone marrow, year 1 day-90, replicate 2

description:
adult male, bone marrow, year 1 day-90, replicate 2
P05_BMPC_d90_2_Y1


title: P05 adult male, bone marrow, year 1 day-90, replicate 1

description:
adult male, bone marrow, year 1 day-90, replicate 1
P05_BMPC_d90_1_Y1


title: P05 adult male, bone marrow, year 2 day-0, replicate 1

description:
adult male, bone marrow, year 2 day-0, replicate 1
P05_BMPC_d0_1_Y2


title: P05 adult male, bone marrow, year 2 day-0, replicate 2

description:
adult male, bone marrow, year 2 day-0, replicate 2
P05_BMPC_d0_2_Y2


title: P05 adult male, bone marrow, year 1 day-0, replicate 2

description:
adult male, bone marrow, year 1 day-0, replicate 2
P05_BMPC_d0_2_Y1


title: P04 adult male, bone marrow, year 1 day-28, replicate 2

description:
adult male, bone marrow, year 1 day-28, replicate 2
P04_BMPC_d28_2_Y1


title: P11 adult male, bone marrow, year 1 day-35, replicate 2

description:
adult male, bone marrow, year 1 day-35, replicate 2
P11_BMPC_d35_2_Y1


title: P04 adult male, bone marrow, year 1 day-180, replicate 1

description:
adult male, bone marrow, year 1 day-180, replicate 1
P04_BMPC_d180_1_Y1


title: P04 adult male, bone marrow, year 1 day-180, replicate 2

description:
adult male, bone marrow, year 1 day-180, replicate 2
P04_BMPC_d180_2_Y1


title: P05 adult male, bone marrow, year 2 day-28, replicate 1

description:
adult male, bone marrow, year 2 day-28, replicate 1
P05_BMPC_d28_1_Y2


title: P05 adult male, bone marrow, year 1 day-0, replicate 1

description:
adult male, bone marrow, year 1 day-0, replicate 1
P05_BMPC_d0_1_Y1


title: P04 adult male, bone marrow, year 2 day-0, replicate 2

description:
adult male, bone marrow, year 2 day-0, replicate 2
P04_BMPC_d0_2_Y2


title: P05 adult male, bone marrow, year 1 day-28, replicate 2

description:
adult male, bone marrow, year 1 day-28, replicate 2
P05_BMPC_d28_2_Y1


title: P05 adult male, bone marrow, year 1 day-180, replicate 2

description:
adult male, bone marrow, year 1 day-180, replicate 2
P05_BMPC_d180_2_Y1


title: P05 adult male, bone marrow, year 1 day-28, replicate 1

description:
adult male, bone marrow, year 1 day-28, replicate 1
P05_BMPC_d28_1_Y1


title: P04 adult male, bone marrow, year 2 day-0, replicate 1

description:
adult male, bone marrow, year 2 day-0, replicate 1
P04_BMPC_d0_1_Y2


title: P05 adult male, bone marrow, year 1 day-180, replicate 1

description:
adult male, bone marrow, year 1 day-180, replicate 1
P05_BMPC_d180_1_Y1


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 2 day-35, replicate 1

source_name: PBMC

value: PBMC

value: male


title: P11 adult male, bone marrow, year 1 day-180, replicate 1

description:
adult male, bone marrow, year 1 day-180, replicate 1
P11_BMPC_d180_1_Y1


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 1 day-120, replicate 1


title: P04 adult male, bone marrow, year 1 day-0, replicate 2

description:
adult male, bone marrow, year 1 day-0, replicate 2
P04_BMPC_d0_2_Y1


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 1 day-0, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-6, replicate 1


title: scBCR, adult male, subject P11, PBMC ASC, year 2 day-6, replicate 1


title: P04 adult male, bone marrow, year 1 day-28, replicate 1

description:
adult male, bone marrow, year 1 day-28, replicate 1
P04_BMPC_d28_1_Y1


title: scBCR, adult male, subject P05, PBMC, year 1 day-90, replicate 2


title: scBCR, adult male, subject P11, PBMC ASC, year 1 day-6, replicate 1


title: scBCR, adult male, subject P05, PBMC, year 1 day-28, replicate 1


title: scBCR, adult male, subject P05, PBMC, year 1 day-12, replicate 2


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 2 day-0, replicate 1


title: scBCR, adult male, subject P05, PBMC, year 1 day-0, replicate 1


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 1 day-35, replicate 1


title: scBCR, adult male, subject P05, PBMC, year 1 day-12, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-90, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-60, replicate 1


title: scBCR, adult male, subject P05, PBMC, year 1 day-60, replicate 1


title: scBCR, adult male, subject P05, PBMC, year 1 day-90, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-13, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-60, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-28, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-180, replicate 1


title: P04 adult male, bone marrow, year 1 day-0, replicate 1

description:
adult male, bone marrow, year 1 day-0, replicate 1
P04_BMPC_d0_1_Y1


title: scBCR, adult male, subject P05, PBMC, year 1 day-180, replicate 2


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-120, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-0, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-5, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-0, replicate 1


title: scBCR, adult male, subject P05, PBMC, year 1 day-5, replicate 2


title: scBCR, adult male, subject P05, PBMC, year 1 day-5, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-28, replicate 1


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 2 day-90, replicate 1


title: scBCR, adult male, subject P05, PBMC, year 1 day-0, replicate 2


title: scBCR, adult male, subject P05, PBMC, year 1 day-120, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-90, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-12, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-120, replicate 1

source_name: Lymph Node

value: Lymph Node


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-120, replicate 3


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-60, replicate 3


title: scBCR, adult male, subject P05, PBMC, year 1 day-28, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-180, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-180, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-90, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-60, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-60, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-90, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-120, replicate 4


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-120, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-28, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-12, replicate 3


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-28, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-28, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-7, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-5, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-60, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-7, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-28, replicate 3


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-0, replicate 3


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-28, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-0, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-28, replicate 3


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-12, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-0, replicate 1


title: scBCR, adult male, subject P04, PBMC, year 2 day-7


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-7, replicate 3


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 2 day-0


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-12, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-60, replicate 1


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 2 day-14


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-120, replicate 1


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 1 day-120


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-5, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-0, replicate 2


title: scBCR, adult male, subject P04, PBMC, year 1 day-5


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-0, replicate 2


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 2 day-90


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-120, replicate 2


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 1 day-12


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-14, replicate 1


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 1 day-0


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-12, replicate 1


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-90, replicate 2


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-5, replicate 1


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-60, replicate 2


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-60, replicate 1


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-0, replicate 2


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-14, replicate 2


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-0, replicate 1


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-0, replicate 2


title: scBCR, adult male, subject P04, lymph node, year 1 day-0, replicate 1


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-5, replicate 2


title: adult male, PBMC ASC year 2 day-6, replicate 1

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function.
Demultiplexed pair-end FASTQ reads were first preprocessed on a by-sample basis using the ‘cellranger count’ command from 10× Genomics’ Cell Ranger v.3.1.0 for alignment against the GRCh38 human reference v.3.0.0 (refdata-cellranger-GRCh38- 3.0.0). The feature biotypes were retrieved using biomaRt v.2.42.0 ([MH8] ) from Ensembl release 93 ([MH9] ).
Additional quality control was performed as follows. (1) To remove presumably lysed cells, cells with mitochondrial content greater than 15% of all transcripts were removed. (2) To remove likely doublets, cells with more than 7,000 features were removed. (3) Genes that were expressed in less than 5 cells in any sample and cells with detectable expression of fewer than 400 genes were removed.
Gene expression analysis of CellRanger output was performed using Seurat v.4.0.3.1.1
Assembly: GRCh38
Supplementary files format and content: tar.gz: compressed archive of 10X Genomics Cell Ranger output files.
Supplementary files format and content: Rds: Seurat analyses saved as R objects

extract_protocol:
PBMCs were isolated using Vacutainer CPT tubes (BD); the remaining red blood cells were lysed with ammonium chloride lysis buffer (Lonza). Cells were immediately used or cryopreserved in 10% dimethylsulfoxide (DMSO) in FBS.   A qualified physician’s assistant performed ultrasound guided fine needle aspirate (FNA) of axillary lymph nodes under the supervision of a radiologist. Lymph node dimensions and cortical thickness were measured prior to each FNA. Six passes were made using 25-gauge needles, which were flushed with 3 ml of RPMI 1640 supplemented with 10% FBS and 100 U/ml penicillin/streptomycin, followed by three 1 ml rinses. Red blood cells were lysed with ammonium chloride lysis buffer. Cells were washed twice with PBS supplemented with 2% FBS and 2 mM EDTA and immediately used or cryopreserved in 10% DMSO in FBS.
Libraries were prepared using 10x Genomics' Chromium Next GEM single cell 5' gene expression workflow.


title: adult male, PBMC enriched for IgD B cell, year 1 day-35, replicate 1


title: adult male, PBMC enriched for IgD B cell, year 2 day-90, replicate 1


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-90, replicate 1


title: adult male, PBMC enriched for IgD B cell, year 2 day-35, replicate 1


title: adult male, PBMC, year 1, day-90, replicate 2


title: adult male, PBMC enriched for IgD B cell, year 1 day-0, replicate 1


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-12, replicate 2


title: adult male, PBMC enriched for IgD B cell, year 2 day-0, replicate 1


title: adult male, PBMC, year 1, day-90, replicate 1


title: adult male, PBMC enriched for IgD B cell, year 1 day-120, replicate 1


title: adult male, PBMC, year 1, day-60, replicate 1


title: adult male, PBMC ASC year 1 day-6, replicate 1


title: adult male, PBMC, year 1, day-5, replicate 2


title: adult male, PBMC, year 1, day-28, replicate 2


title: adult male, PBMC, year 1, day-5, replicate 1


title: adult male, PBMC, year 1, day-120, replicate 1


title: adult male, PBMC, year 1, day-28, replicate 1


title: adult male, PBMC, year 1, day-0, replicate 2


title: adult male, PBMC, year 1, day-12, replicate 1


title: adult male, PBMC, enriched for IgD B cells, year 2, day-90, replicate 1


title: adult male, PBMC, year 1, day-12, replicate 2


title: adult male, PBMC, year 1, day-0, replicate 1


title: adult male, PBMC, enriched for IgD B cells, year 1, day-60, replicate 1


title: adult male, PBMC, enriched for IgD B cells, year 2, day-60, replicate 1


title: adult male, PBMC, enriched for IgD B cells, year 2, day-6, replicate 1


title: adult male, PBMC, enriched for IgD B cells, year 1, day-180, replicate 1


title: adult male, PBMC, enriched for IgD B cells, year 1, day-5, replicate 1


title: adult male, PBMC, enriched for IgD B cells, year 2, day-28, replicate 1


title: adult male, PBMC, year 1, day-180, replicate 2


title: adult male, PBMC, enriched for IgD B cells, year 2, day-0, replicate 1


title: adult male, PBMC, enriched for IgD B cells, year 1, day-12, replicate 1


title: adult male, Lymph node, year 1, day-90, replicate 1


title: adult male, PBMC, enriched for IgD B cells, year 1, day-28, replicate 1


title: adult male, PBMC, enriched for IgD B cells, year 2, day-13, replicate 1


title: adult male, PBMC, enriched for IgD B cells, year 1, day-0, replicate 1


title: adult male, Lymph node, year 2, day-7, replicate 2


title: adult male, Lymph node, year 2, day-60, replicate 2


title: adult male, PBMC, enriched for IgD B cells, year 1, day-120, replicate 1


title: adult male, Lymph node, year 1, day-90, replicate 2


title: adult male, PBMC, enriched for IgD B cells, year 1, day-90, replicate 1


title: adult male, Lymph node, year 2, day-60, replicate 1


title: adult male, Lymph node, year 1, day-60, replicate 1


title: adult male, Lymph node, year 2, day-60, replicate 3


title: adult male, Lymph node, year 1, day-60, replicate 2


title: adult male, Lymph node, year 2, day-28, replicate 2


title: adult male, Lymph node, year 1, day-5, replicate 2


title: adult male, Lymph node, year 2, day-7, replicate 3


title: adult male, Lymph node, year 2, day-28, replicate 3


title: adult male, Lymph node, year 1, day-5, replicate 1


title: adult male, Lymph node, year 1, day-28, replicate 3


title: adult male, Lymph node, year 1, day-28, replicate 1


title: adult male, Lymph node, year 1, day-28, replicate 2


title: adult male, Lymph node, year 1, day-180, replicate 1


title: adult male, Lymph node, year 2, day-7, replicate 1


title: adult male, Lymph node, year 2, day-28, replicate 1


title: adult male, Lymph node, year 2, day-120, replicate 3


title: adult male, Lymph node, year 2, day-120, replicate 4


title: adult male, Lymph node, year 2, day-0, replicate 3


title: adult male, Lymph node, year 2, day-0, replicate 2


title: adult male, Lymph node, year 2, day-120, replicate 2


title: adult male, Lymph node, year 1, day-0, replicate 2


title: adult male, Lymph node, year 2, day-0, replicate 1


title: adult male, Lymph node, year 1, day-12, replicate 2


title: adult male, Lymph node, year 1, day-12, replicate 3


title: adult male, PBMC ASC, year 2 day-7


title: adult male, Lymph node, year 1, day-12, replicate 1


title: adult male, PBMC enriched for IgD B cell, year 2 day-90


title: adult male, Lymph node, year 1, day-0, replicate 1


title: adult male, PBMC ASC, year 1 day-5


title: adult male, Lymph node, year 2, day-120, replicate 1


title: adult male, PBMC enriched for IgD B cell, year 2 day-14


title: adult male, PBMC enriched for IgD B cell, year 1 day-120


title: adult male, PBMC enriched for IgD B cell, year 2 day-0


title: adult male, Lymph node, year 2 day-90, replicate 2


title: adult male, PBMC enriched for IgD B cell, year 1 day-12


title: adult male, Lymph node, year 1, day-180, replicate 2


title: adult male, Lymph node, year 2 day-60, replicate 2


title: adult male, Lymph node, year 2 day-14, replicate 2


title: adult male, Lymph node, year 2 day-60, replicate 1


title: adult male, PBMC enriched for IgD B cell, year 1 day-0


title: adult male, Lymph node, year 1 day-5, replicate 1


title: adult male, Lymph node, year 1 day-120, replicate 1


title: adult male, Lymph node, year 1 day-5, replicate 2


title: adult male, Lymph node, year 2 day-14, replicate 1


title: adult male, Lymph node, year 1 day-120, replicate 2


title: adult male, Lymph node, year 1 day-12, replicate 1


title: adult male, lymph node, year 1 day-0, replicate 1


title: adult male, Lymph node, year 2 day-0, replicate 2


title: adult male, Lymph node, year 1 day-0, replicate 2


title: Bulk BCR, adult male, subject P11, PBMC, year 2 day-6

description:
P11_BCR.tsv
P11_PBMC-ASC_d6_Y2


title: Bulk BCR, adult male, subject P11, PBMC, year 1 day-0

description:
P11_BCR.tsv
P11_PBMC_d0_Y1


title: Bulk BCR, adult male, subject P05, PBMC, year 1 day-0

description:
P05_BCR.tsv
P05_PBMC_d0_Y1


title: Bulk BCR, adult male, subject P05, PBMC, year 2 day-6

description:
P05_BCR.tsv
P05_PBMC-ASC_d6_Y2


title: Bulk BCR, adult male, subject P11, PBMC, year 1 day-6

description:
P11_BCR.tsv
P11_PBMC-ASC_d6_Y1


title: Bulk BCR, adult male, subject P05, PBMC, year 1 day-5

description:
P05_BCR.tsv
P05_PBMC-ASC_d5_Y1


title: adult male, Lymph node, year 2 day-90, replicate 1


title: Bulk BCR, adult male, subject P04, PBMC, year 1 day-0

description:
P04_BCR.tsv
P04_PBMC_d0_Y1


title: adult male, Lymph node, year 2 day-0, replicate 1


title: Small_D

status: Public on May 24 2024

data_processing:
Trimming for adapters was performed using Cutadapt v1.11
UMI correction
Mapping was performed using Bowtie 2.2.2
Assembly: Sscrofa10.2
Supplementary files format and content: raw_counts: comma separated values containing raw reads, and miRNA names with associated sequence for each sample

source_name: Semitendinosus muscle

extract_protocol:
Muscle samples (30 mg) from porcine foetal pairs (IUGR and NW, n=4 litters) were homogenized in RNABee (AMS Biotechnology, Abingdon, UK) in Lysing Matrix D tubes (MP Biomedicals, Illkirch, France), and extracted according to manufacturer's instructions followed by transfer to a RNeasy Mini Spin column and treatment with RNase-free DNase (Qiagen, Manchester, UK). RNA concentration and quality, as defined by RNA Integrity Number equivalent (RINe) were determined by Tapestation 2200 (Agilent Technologies, Edinburgh, UK). All samples used for sequencing had RINe values >8.5.
QIAseq miRNA Library Prep kit (QIAGEN) following manufacturer's instructions

value: Semitendinosus muscle

tag: phenotype

value: Small

tag: litter

value: D


title: Large_D

value: Large


title: Bulk BCR, adult male, subject P04, PBMC, year 1 day-5

description:
P04_BCR.tsv
P04_PBMC-ASC_d5_Y1


title: Bulk BCR, adult male, subject P04, PBMC, year 2 day-7

description:
P04_BCR.tsv
P04_PBMC-ASC_d7_Y2


title: Large_B

value: B


title: Large_C

value: C


title: Small_C


title: Small_B


title: Small_A

value: A


title: Large_A


title: adult male, Lymph node, year 1 day-12, replicate 2


title: 207760740056_R12C03

status: Public on May 15 2024

data_processing:
SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.
Normalized average Beta

source_name: Human cell line DNA

value: 50% EpigenDX

value: Illumina DVT (Titration Control)


title: 207760740083_R04C03

value: Illumina DVT (Coriell)


title: 207760740030_R12C03


title: 207760740056_R06C03


title: 207760740083_R08C03


title: 207760740041_R12C03


title: 207760740083_R02C03


title: 207760740083_R12C03


title: 207854510042_R03C01

value: 1. Cell line reproducibility


title: 207760740083_R06C03


title: 207854510042_R01C01


title: 207760740056_R04C03


title: 207760740030_R08C03


title: 207760740056_R08C03


title: 207760740030_R02C03


title: 207760740083_R15C03


title: 207760740056_R02C03


title: 207760740041_R08C03


title: 207760740041_R06C03


title: 207760740041_R04C03


title: 207760740041_R02C03


title: 207760740083_R13C03


title: 207760740030_R04C03


title: 207760740083_R11C03


title: 207760740056_R13C03


title: 207760740056_R15C03


title: 207760740056_R09C03


title: 207760740041_R15C03


title: 207760740041_R13C03


title: 207760740056_R11C03


title: 207760740083_R09C03


title: 207760740030_R15C03


title: 207760740030_R09C03


title: 207760740083_R05C03


title: 207760740030_R13C03


title: 207760740083_R01C03


title: 207760740056_R07C03


title: 207760740041_R11C03


title: 207760740083_R07C03


title: 207760740030_R06C03


title: 207760740030_R11C03


title: 207760740083_R03C03


title: 207760740041_R09C03


title: 207760740056_R01C03


title: 207760740041_R01C03


title: 207760740041_R05C03