title: Vitrification Bisulfite-Seq1

first: Baigao

last: Yang

address: Yuaningyuan 2

institute: Institute of Animal Sciences of CAAS

description: Library name: B1_M4

data_processing:
Raw DNA methylation sequencing reads were filtered using the FastQC tool to remove adapters, low-quality bases, and contaminated sequences. The filtered DNA methylation sequences were then compared with the reference genome (Suscrofa11.1) using the bs_seeker2-align.py tool in BS_seeker2 (v2.1.1). The paired-end sequencing data were compared separately. The bs_seeker2- call_methyl.py tool in bs_seeker2 (v2.1.1) was used to detect methylation sites and amounts, with significance thresholds set at a q-value < 0.05 and a minimum methylation difference of 20% between groups.
Assembly: Suscrofa11.1
Supplementary files format and content: Methylation data for intergroup comparisons are in .xls files. All files are compressed to gz format.

source_name: Blastocyst

extract_protocol:
Single-Cell Whole-Genome DNA Methylation Sequencing Whole-genome bisulfite sequencing (WGBS) steps were used to perform single-cell methylome amplification, as described by [66], with some modifications. Briefly, single cells were sorted into a cell lysis buffer containing 20 mM Tris-EDTA [pH 8.0], 20 mM KCl, and 0.3% Triton X-100, along with 1 mg/mL protease (Qiagen) and 60 fg unmethylated lambda DNA (Fermentas). Lastly, the total volume was adjusted to 4.5 μL with nuclease-free water. The cells were then lysed for 3 hours at 50°C and heat-inactivated for 30 minutes at 75 °C. Bisulfite conversion was performed in a 150 mL reaction (125 μL CT conversion reagent, 20 μL Nuclease-free water, and 5 μL single cell lysate) using the EZ-96 DNA Methylation-Direct™ MagPrep kit (Invitrogen) following the manufacturer’s standard protocol. First, the double-stranded DNA was denatured for 8 minutes at 98 °C; then, the reaction was incubated for 3.5 hours at 64 °C to ensure complete bisulfite conversion. All these steps were performed in a PCR thermocycler. After this step, the converted DNA was purified using Zymo-Spin columns (Zymo) with 10 ng tRNA (Roche) as a carrier; the DNA was finally eluted in 20 mL of elution buffer. The purified DNA was subjected to two rounds of amplification in 24 μL reactions using bisulfite-converted DNA (19.5 μL), 10× Blue Buffer (2.5 μL), and 10 μM oligo1 primer ((Biotin) CTACACGACGCTCTTCCGATCTNNNNNNNNN) (1 μL). It was incubated at 65 °C for 3 minutes, followed by a 4 °C pause. Next, 50 U of Klenow exo-(NEB) were added, and the samples were incubated at 4 °C for 5 minutes, then warmed to 37 °C at a rate of +1 °C per 15 seconds and held at 37 °C for 30 minutes. This random priming and extension were repeated 3 times (10 rounds). The samples were incubated with 20 U of exonuclease I (NEB) for 1 hour at 37 °C before purifying the DNA using 0.8× Ampure XP beads (Beckman Clulter). The beads were eluted in 39 μL of QIAGEN EB according to the manufacturer’s guidelines.  Samples were eluted in 10 μM oligo2 (TGCTGAACCGCTCTTCCGATCTNNNNNNNNN), 10 mM dNTP, and 10× Blue buffer and incubated at 95°C for 45 seconds. They were then immediately transferred to ice before adding 50 U of Klenow exo-(NEB) and incubated at 4°C for 5 minutes, followed by a temperature increase of 1 °C every 15 seconds until reaching 37°C, where they were held for 90 minutes. DNA was purified using 0.9× Ampure XP beads (Beckman Coulter), and the beads were then eluted in 23 μL of QIAGEN EB according to the manufacturer’s guidelines. The 23 μL DNA samples were supplemented with 15 μM Universal PCR Primer (NEB), 15 μM Index Primer (NEB), and 2× Kapa HiFi Mix. Libraries were then amplified using PCR as follows: 95 °C for 2 minutes, followed by 13-14 repeats of (94 °C for 80 seconds, 65 °C for 30 seconds, 72 °C for 30 seconds), and then 72 °C for 3 minutes, with a final hold at 4 °C. Amplified libraries were purified using 0.8×Ampure XP beads (Beckman Clulter) twice, final elute with 30 μL NF-H2O, and were assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyser and the KAPA Library Quantification Kit for Illumina (KAPA Biosystems). The final quality-ensured libraries were used for pair-ended deep sequencing on an Illumina HiSeqX-ten Sequencer, and all clusters that passed the filter were converted into FASTQ files using a standard Illumina pipeline.
Single-Cell Whole-Genome DNA Methylation Sequencing Whole-genome bisulfite sequencing (WGBS) steps were used to perform single-cell methylome amplification, as described by [66], with some modifications. Briefly, single cells were sorted into a cell lysis buffer containing 20 mM Tris-EDTA [pH 8.0], 20 mM KCl, and 0.3% Triton X-100, along with 1 mg/mL protease (Qiagen) and 60 fg unmethylated lambda DNA (Fermentas). Lastly, the total volume was adjusted to 4.5 μL with nuclease-free water. The cells were then lysed for 3 hours at 50°C and heat-inactivated for 30 minutes at 75 °C. Bisulfite conversion was performed in a 150 mL reaction (125 μL CT conversion reagent, 20 μL Nuclease-free water, and 5 μL single cell lysate) using the EZ-96 DNA Methylation-Direct™ MagPrep kit (Invitrogen) following the manufacturer’s standard protocol. First, the double-stranded DNA was denatured for 8 minutes at 98 °C; then, the reaction was incubated for 3.5 hours at 64 °C to ensure complete bisulfite conversion. All these steps were performed in a PCR thermocycler. After this step, the converted DNA was purified using Zymo-Spin columns (Zymo) with 10 ng tRNA (Roche) as a carrier; the DNA was finally eluted in 20 mL of elution buffer. The purified DNA was subjected to two rounds of amplification in 24 μL reactions using bisulfite-converted DNA (19.5 μL), 10× Blue Buffer (2.5 μL), and 10 μM oligo1 primer ((Biotin) CTACACGACGCTCTTCCGATCTNNNNNNNNN) (1 μL). It was incubated at 65 °C for 3 minutes, followed by a 4 °C pause. Next, 50 U of Klenow exo-(NEB) were added, and the samples were incubated at 4 °C for 5 minutes, then warmed to 37 °C at a rate of +1 °C per 15 seconds and held at 37 °C for 30 minutes. This random priming and extension were repeated 3 times (10 rounds). The samples were incubated with 20 U of exonuclease I (NEB) for 1 hour at 37 °C before purifying the DNA using 0.8× Ampure XP beads (Beckman Clulter). The beads were eluted in 39 μL of QIAGEN EB according to the manufacturer’s guidelines.  Samples were eluted in 10 μM oligo2 (TGCTGAACCGCTCTTCCGATCTNNNNNNNNN), 10 mM dNTP, and 10× Blue buffer and incubated at 95°C for 45 seconds. They were then immediately transferred to ice before adding 50 U of Klenow exo-(NEB) and incubated at 4°C for 5 minutes, followed by a temperature increase of 1 °C every 15 seconds until reaching 37°C, where they were held for 90 minutes. DNA was purified using 0.9× Ampure XP beads (Beckman Coulter), and the beads were then eluted in 23 μL of QIAGEN EB according to the manufacturer’s guidelines. The 23 μL DNA samples were supplemented with 15 μM Universal PCR Primer (NEB), 15 μM Index Primer (NEB), and 2× Kapa HiFi Mix. Libraries were then amplified using PCR as follows: 95 °C for 2 minutes, followed by 13-14 repeats of (94 °C for 80 seconds, 65 °C for 30 seconds, 72 °C for 30 seconds), and then 72 °C for 3 minutes, with a final hold at 4 °C. Amplified libraries were purified using 0.8×Ampure XP beads (Beckman Clulter) twice, final elute with 30 μL NF-H2O, and were assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyser and the KAPA Library Quantification Kit for Illumina (KAPA Biosystems). The final quality-ensured libraries were used for pair-ended deep sequencing on an Illumina HiSeqX-ten Sequencer, and all clusters that passed the filter were converted into FASTQ files using a standard Illumina pipeline.

value: Blastocyst

value: Vitrification


title: VitrificationⅡ RNAseq1

status: Public on Aug 25 2025

type: SRA

city: Beijing

country: China

description: Library name: H1_R10

library_source: transcriptomic

data_processing:
Data Quality, Filtering, and Analysis Raw RNA-seq reads were filtered using the FastQC tool to remove adapter sequences, low-quality bases, and contaminated sequences. The filtered sequences were aligned to the reference genome (Suscrofa11.1) using Tophat (version 2.0.13). Cufflinks (version 2.2.1) was used to normalize and verify the gene expression level between two samples. DESeq2 was used to analyze the differences in gene count matrices of duplicate samples within a group. Genes were considered significantly differentially expressed if they had an adjusted p-value < 0.05 and an absolute log2 fold change (|log2FC|) ≥ 1.2. All fold change values reported in this study refer to log2FC.
Assembly: Suscrofa11.1
Supplementary files format and content: Transcriptome data are in txt format.

molecule: total RNA

organism: Sus scrofa

extract_protocol:
Smart-Seq2 scRNA-Seq was performed using the protocol described by [65], with slight modifications. Briefly, single cells were sorted into cell lysis buffer containing 0.1 μL RNase inhibitor (Clontech), 1.9 μL Triton X-100 solution (1 %), 1 μL dNTP mix (10 mM), and 1 μL oligo-dT primer (5 μM). Reverse transcription was performed containing 0.5 μL SuperScript II reverse transcriptase (200 U/μL, Invitrogen), 0.25 μL RNase inhibitor (40 U/μL, Clontech), 2 μL Superscript II First-Strand Buffer (5×, Invitrogen), 0.5 μL DTT (0.1M, Invitrogen), 2 μL Betain (5 M, Sigma), 0.06 μL MgCl2 (1M, Sigma), 0.1 μL TSO (100 μM). Reverse transcription was carried out at 25 °C for 5 minutes, followed by 42 °C for 60 minutes, then 50 °C for 30 minutes, and finally 72 °C for 10 minutes. PCR preamplification was performed using KAPA HiFi HotStart Ready MIX (KAPA Biosystems) with 22 cycles of PCR and the IS PCR primer reduced to 50 nM (4 cycles at 98 °C for 20 s, 65 °C for 30 s, and 72 °C for 5 min, followed by 18 cycles at 98 °C for 20 s, 67 °C for 15 s, and 72 °C for 5 min, with a final cycle at 72 °C for 5 min.). Subsequently, Amplified samples were purified twice with 0.8X Ampure XP beads (Beckman, A63882). We constructed a library based on the enriched cDNA fragments, which were attached to the C1 beads, using KAPA Hyper Prep Kits (KK8504). We used the NEB U-shape adaptor for ligation. Libraries were sequenced to generate 150-bp paired-end reads on an Illumina Novaseq 6000 platform.
Smart-Seq2 scRNA-Seq was performed using the protocol described by [65], with slight modifications. Briefly, single cells were sorted into cell lysis buffer containing 0.1 μL RNase inhibitor (Clontech), 1.9 μL Triton X-100 solution (1 %), 1 μL dNTP mix (10 mM), and 1 μL oligo-dT primer (5 μM). Reverse transcription was performed containing 0.5 μL SuperScript II reverse transcriptase (200 U/μL, Invitrogen), 0.25 μL RNase inhibitor (40 U/μL, Clontech), 2 μL Superscript II First-Strand Buffer (5×, Invitrogen), 0.5 μL DTT (0.1M, Invitrogen), 2 μL Betain (5 M, Sigma), 0.06 μL MgCl2 (1M, Sigma), 0.1 μL TSO (100 μM). Reverse transcription was carried out at 25 °C for 5 minutes, followed by 42 °C for 60 minutes, then 50 °C for 30 minutes, and finally 72 °C for 10 minutes. PCR preamplification was performed using KAPA HiFi HotStart Ready MIX (KAPA Biosystems) with 22 cycles of PCR and the IS PCR primer reduced to 50 nM (4 cycles at 98 °C for 20 s, 65 °C for 30 s, and 72 °C for 5 min, followed by 18 cycles at 98 °C for 20 s, 67 °C for 15 s, and 72 °C for 5 min, with a final cycle at 72 °C for 5 min.). Subsequently, Amplified samples were purified twice with 0.8X Ampure XP beads (Beckman, A63882). We constructed a library based on the enriched cDNA fragments, which were attached to the C1 beads, using KAPA Hyper Prep Kits (KK8504). We used the NEB U-shape adaptor for ligation. Libraries were sequenced to generate 150-bp paired-end reads on an Illumina Novaseq 6000 platform.

tag: tissue

tag: treatment

value: Vitrification II


title: Vitrification Bisulfite-Seq2

description: Library name: B2_M5

library_source: genomic

molecule: genomic DNA


title: VitrificationⅡ Bisulfite-Seq3

description: Library name: H3_M12


title: Control_Bisulfite-Seq3

description: Library name: A3_M3

value: Control


title: VitrificationⅡ Bisulfite-Seq2

description: Library name: H2_M11


title: VitrificationⅠ Bisulfite-Seq2

description: Library name: C2_M8

value: Vitrification I


title: Control_Bisulfite-Seq2

description: Library name: A2_M2


title: Control_Bisulfite-Seq1

description: Library name: A1_M1


title: VitrificationⅠ Bisulfite-Seq3

description: Library name: C3_M9


title: VitrificationⅡ Bisulfite-Seq1

description: Library name: H1_M10


title: VitrificationⅡ RNAseq3

description: Library name: H3_R12


title: VitrificationⅠ Bisulfite-Seq1

description: Library name: C1_M7


title: Vitrification Bisulfite-Seq3

description: Library name: B3_M6


title: VitrificationⅡ RNAseq2

description: Library name: H2_R11


title: Vitrification RNAseq3

description: Library name: B3_R6


title: VitrificationⅠ RNAseq1

description: Library name: C1_R7


title: Vitrification RNAseq2

description: Library name: B2_R5


title: Vitrification RNAseq1

description: Library name: B1_R4


title: Control_RNAseq3

description: Library name: A3_R3


title: BM Obl d10 Sms-KI rep4

type: RNA

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 h at 45 °C on mouse Clariom S Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0.1.36) using  default analysis settings (version 2) and Gene + Exon - SST-RMA as summarization and normalization method.

label: proprietary DNA Labeling Reagent, covalently linked to biotin

organism: Mus musculus

source_name: primary bone marrow osteoblasts, WT

label_protocol: Proprietary labeled 2nd-cycle ss-cDNA was prepared from 100 ng total RNA using the mouse Clariom S kit according to the GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays user guide (version 23 January 2017) from ThermoFisher Scientific

growth_protocol: Primary bone marrow cells were plated at a density of 1300000 cells/cm² in 12-well format cell culture dishes. Cells were cultured for 10 days in alpha-MEM with 10% FCS at 37 °C, 5 % CO2, 95 % rH supplemented with 50 μg/ml ascorbic acid and 10 mM β-glycerophosphate to induce osteogenic differentiation .

extract_protocol: RNA was extraced using the Nucleospin RNA kit (Macherey-Nagel) according to the manufacturer's instructions.

treatment_protocol: not applicable

tag: genotype

tag: batch


title: BM Obl d10 Sms-KI rep1


title: BM Obl d10 WT rep1


title: BM Obl d10 WT rep4


title: BM Obl d10 WT rep2


title: BM Obl d10 Sms-KI rep2


title: BM Obl d10 Sms-KI rep3


title: HiC_AtWX777_rep2

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

country: USA

institute: Indiana University at Bloomington

description: Library name: HiC_AtWX777_rep2

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Agrobacterium tumefaciens Hi-C, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence: GCA_000092025.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For  WGS, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence: GCA_000092025.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the A. tumefaciens C58 genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of A. tumefaciens C58 was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Agrobacterium tumefaciens C58 (NCBI Reference Sequence: GCA_000092025.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of WGS results.

organism: Agrobacterium tumefaciens

source_name: Agrobacterium tumefaciens

growth_protocol: Wild type and mutant cells of Agrobacterium tumefaciens grown in ATGN at 30°C till OD ~0.6 was reached

extract_protocol:
Wild type and mutant cells of Agrobacterium tumefaciens grown in ATGN were crosslinked using 3% formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Nextseq2000 sequencing platforms. Illumina Truseq indexes were used.

tag: cell line

value: Agrobacterium tumefaciens

tag: cell type

value: Bacterial

value: C58Fcir-B:this is the CURED version of C58Fcir-A. This has a J23107 constitutive promoter-driven Cre launched into the Atu2523 gene.

value: Cells grew in ATGN medium at 30°C


title: VitrificationⅠ RNAseq3

description: Library name: C3_R9


title: WGS_AtWX773_rep1

description: Library name: WGS_AtWX773_rep1

value: wild-type


title: WGS_AtWX773_rep2

description: Library name: WGS_AtWX773_rep2


title: WGS_AtWX775_rep1

description: Library name: WGS_AtWX775_rep1

value: C58Fcir-A:this is the UNCURED fused CI-CI2 circular chromosome version with a residual Cre plasmid


title: WGS_AtWX769_rep2

description: Library name: WGS_AtWX769_rep2


title: WGS_AtWX775_rep2

description: Library name: WGS_AtWX775_rep2


title: Control_RNAseq2

description: Library name: A2_R2


title: WGS_AtWX771_rep1

description: Library name: WGS_AtWX771_rep1

value: C58cir:this is the C2 circularized mutant version of the wildtype with dual chromosome (circular-C1/circular-C2) configuration


title: VitrificationⅠ RNAseq2

description: Library name: C2_R8


title: BM Obl d10 WT rep3


title: WGS_AtWX771_rep2

description: Library name: WGS_AtWX771_rep2


title: WGS_AtWX777_rep1

description: Library name: WGS_AtWX777_rep1


title: WGS_AtWX769_rep1

description: Library name: WGS_AtWX769_rep1


title: hela cell lines, rockroi

city: Zürich

first: Giulia

middle: Arianna

last: Moro

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

description:
Library name: hela modified
BD Rhapsody

library_source: transcriptomic single cell

data_processing:
The mapping, barcode filtering and counting was performed using a custom Snakemake pipeline (https://github.com/imallona/rock_roi_method/) based on STARSolo and featureCounts. Count matrices were analysed in R.
Index the reference genome with STAR.
Subset reads matching the WTA cell barcodes and map those to the transcriptome (genome plus GTF) using STARsolo. Detected cell barcodes (cells) are filtered in at two levels: first, by matching to the user-provided cell barcode whitelist; and second, by applying the EmptyDrops algorithm to discard empty droplets. We report two outputs from this step: the filtered-in cells according to the aforementioned filters; and the unbiased, whole-transcriptome WTA count table
Subset reads matching both the TSO CB structure and the filtered in cell barcodes and map those to the transcriptome. Our reasoning is that the expected TSO transcriptional complexity is undefined and not usable to tell apart cells from empty droplets, so we borrow the filtered-in cells from the EmptyDrops results from the WTA analysis.
Assembly: Human for alignment with STARsolo: GRCh38.p13.genome.fa and gencode.v38.basic.annotation.gtf
Supplementary files format and content: STARsolo output files wta: tab-delimited tsv and sparse matrix mtx files; filtered by EmptyDrops barcodes (matrix.mtx, barcodes.tsv, features.tsv)
Supplementary files format and content: STARsolo output files tso: tab-delimited tsv and sparse matrix mtx files; raw counts (matrix.mtx, barcodes.tsv, features.tsv)

organism: Homo sapiens

source_name: HeLa cells, Kyoto line

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle Medium 1X (41965-039) with 10% FBS (GIBCO, 10270-106; no PIS) in a 10 cm dish and maintained in an incubator at 37 °C and 5% CO2. Cells were split at 80% confluence. To dissociate the cells, the medium was removed and 2 mL of Trypsin-EDTA were added to the dish. The Trypsin-EDTA was immediately removed and the dish was placed in the incubator at 37 °C and 5% CO2 for 1 minute. 10 mL of medium was then added to the dish and the cell mixture was plated depending on the wanted confluency.

extract_protocol:
Cells were dissociated using Trypsin-EDTA, filtered through a cell strainer and resuspended in BD Rhapsody Sample Buffer
Libraries were generated on a BD Rhapsody Express machine. Libraries for unmodified samples (unmod) were generated following manufacturers recommendations for the WTA assay. The protocol for v1 BD Rhapsody was used (i.e. a single RPE reaction) and applied to enhanced beads, either with prior RoCKseq modification (rockroi condition) or without modification (unmod). Briefly, the protocol for the modified sample differs from the standard WTA protocol due to the following points: 1) addtion of N1 primer to the RPE PCR (for unmod_roi, rock and rockroi conditions); 2) addition of ROIseq primers to the pool of randomeres during RPE extension (for unmod_roi and rockroi conditions); 3) separate indexing reaction for the samples in which the N1 primer is added; 4) custom sequencing primer

value: HeLa cells, Kyoto line


title: Control_RNAseq1

description: Library name: A1_R1


title: HiC_AtWX777_rep1

description: Library name: HiC_AtWX777_rep1


title: hela cell lines, unmodified

description:
Library name: hela unmodified
BD Rhapsody


title: HiC_AtWX775_rep1

description: Library name: HiC_AtWX775_rep1


title: HiC_AtWX775_rep2

description: Library name: HiC_AtWX775_rep2


title: HiC_AtWX771_rep2

description: Library name: HiC_AtWX771_rep2


title: HiC_AtWX771_rep1

description: Library name: HiC_AtWX771_rep1


title: HiC_AtWX769_rep1

description: Library name: HiC_AtWX769_rep1


title: HiC_AtWX773_rep2

description: Library name: HiC_AtWX773_rep2


title: HiC_AtWX773_rep1

description: Library name: HiC_AtWX773_rep1


title: Pt23-Tumor18

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

hyb_protocol: Samples were hybridized using Affymetrix kit materials nad protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was processed using SCAN (SCAN.UPC package from Bioconductor)
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented, and biotinylated using the WT-Ovation FFPE system (NuGEN) according the manufacturer's recommendations with minor modifications.

extract_protocol: After pathologic review, tissue was harvested from formalin-fixed, paraffin-embedded slides by macrodissection under RNase-free conditions. Total RNA was extracted and purified using the RNease FFPE kit (Qiagen)

tag: gender

value: male

tag: gleason score of the biopsy

tag: nccn risk group

value: high

tag: t stage

tag: psa

tag: tumorpurityscore

tag: race

value: African American

tag: gleason score of the patient

tag: age at biopsy


title: Pt37-Tumor3


title: WGS_AtWX777_rep2

description: Library name: WGS_AtWX777_rep2


title: HiC_AtWX769_rep2

description: Library name: HiC_AtWX769_rep2


title: Lamina neurons replicate 2

city: Eugene

first: Chris

last: Doe

state: Oregon

address: 1440 Franklin Blvd

institute: University of Oregon

description: Library name: Sample 2

data_processing:
Genes by cell matrix was created using 10x Genomics Cellranger v7.1.0 . After quality control using scanpy, data was normalization, feature selection, and dimensionality reduction was done using the self-assembling-manifold package. Cells were clustered using the Leiden algorithm, and clusters corresponding to L1-L5 were identified based on marker gene expression.
Assembly: BDGP6.46
Supplementary files format and content: h5ad encoded AnnData containting lamina neurons' gene expression, dimensionality reductions, and type annotations.

organism: Drosophila melanogaster

source_name: eye

extract_protocol:
Papain (100 U/ml in Complete Schneider’s Medium [CSM]) was freshly prepared and activated at 37 °C for 30 min, while Liberase TM aliquots were thawed at RT. Adult brains were dissected in cold CSM, and the optic lobes were pooled in Rinaldini’s Solution (RS) on ice. For each dissociation, 300 μl of activated papain was combined with 4.1 μl Liberase (0.18 WU/ml) to prepare the dissociation solution. After a brief wash with RS and its removal, the dissociation solution was added to the lobes. Samples were incubated at 25 °C, 1000 rpm for 15 min, with gentle mixing at 5 min and 10 min. Lobes were washed twice with RS, followed by two washes with CSM, and then stored in fresh CSM. Cell suspensions were filtered through a 20 μm strainer into low-adhesion tubes on ice, rinsed with 500 μl CSM, and centrifuged at 300 × g for 5 min at RT. Pellets were resuspended in PBSB (PBS + 0.04% BSA) and submitted directly for 10x Genomics scRNA-seq.
10x Genomics scRNA-seqencing pipeline

value: eye

value: lamina neurons

value: Oregon-R

tag: Sex

value: female


title: Pt23-Tumor2


title: Lamina neurons replicate 1

description: Library name: Sample 1


title: P89_rep3

first: Xin

last: Zhang

state: Beijing

address: No.5 Yiheyuan Road

department: School of Life Sciences, BIOPIC

institute: Peking University

data_processing:
The data was filtered using FASTP.
Then the reads were aligned to hg19 genome using hisat2.
htseq-count were applied to the aligned data to count the gene count.
Genome_build: hg19
Supplementary_files_format_and_content: The gene count matrix of single clones in the plate and from the CDX were integrated to an expression matrix file separately. Each column represents a sample id and each row represents a gene name.

source_name: HeLa cell line single clone cell line-derived xenograft

extract_protocol:
Cells in the plate and from the nude mouse were collected and the total RNA were extracted using QIANGEN RNase Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: original HeLa cell line


title: Hypertrophic Scar Replicate 2 [HS-rep2(Sup)]

city: Nanchang

first: dewu

last: liu

state: Jiangxi

address: 17 Yongwaizheng Street

institute: The First Affiliated Hospital of Nanchang University

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL Blocking Agent and 1 μL of Fragmentation Buffer, heated at 60°C for 30 min and combined with 25 μL Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization
IP (Cy5-labelled) intensities were normalized as relative intensities by the RNA spike-in calibration controls.

source_name: human,hypertrophic scar tissue

label_protocol: The “IP” RNAs and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit.

extract_protocol: Total RNA extracted from tissues using Trizol following manufacturer's instructions. total RNA and m6A spike-in control mixture were added to IP buffer containing 2 μg anti-m6A rabbit polyclonal antibody (Synaptic Systems). The reaction was incubated with head-over-tail rotation at 4°C for 2 hours. Dynabeads™ M-280 Sheep Anti-Rabbit IgG suspension per sample was blocked with 0.5% BSA at 4°C for 2 hours, washed three times with IP buffer, and resuspended in the total RNA-antibody mixture prepared above. The RNA binding to the m6A-antibody beads was carried out with head-over-tail rotation at 4°C for 2 hours. The beads were then washed. Transferred supernatant as “Sup”. The enriched RNA as IP was eluted with Elution buffer. The RNA was extracted by acid phenol-chloroform and ethanol precipitated.

tag: tissue

value: Hypertrophic scar

tag: scar age

value: 8 months

tag: sample type

value: Sup RNA


title: P89_rep2

value: HeLa cell line single clone cell line-derived xenograft


title: P89_rep1


title: Pt5-Tumor4

value: Caucasian


title: Normal Skin Replicate 1 [NS-rep1(IP)]

source_name: human,normal skin tissue

value: Full-thickness skin

value: IP RNA


title: P56_rep3


title: Normal Skin Replicate 2 [NS-rep2(Sup)]


title: Pt37-Tumor1


title: Pt5-Tumor1


title: Hypertrophic Scar Replicate 1 [HS-rep1(Sup)]

value: 5 months


title: Pt7-Tumor15


title: Pt55-Tumor2


title: Hypertrophic Scar Replicate 2 [HS-rep2(IP)]


title: Pt11-Tumor2

value: very high


title: Pt57-Tumor16

value: male

value: favorable intermediate


title: Normal Skin Replicate 2 [NS-rep2(IP)]


title: Hypertrophic Scar Replicate 1 [HS-rep1(IP)]


title: Normal Skin Replicate 1 [NS-rep1(Sup)]


title: Pt5-Tumor16

value: high


title: Pt10-Tumor3


title: Pt27-Tumor7


title: Pt55-Tumor3


title: Pt11-Tumor1


title: Pt11-Tumor3Tumor4


title: Pt5-Tumor2


title: Pt27-Tumor1


title: Pt10-Tumor1


title: Pt48-Tumor4

value: prostatic ductal


title: P17_rep2


title: P17_rep3


title: P17_rep1


title: G58_rep3


title: P56_rep2


title: Pt48-Tumor1


title: P56_rep1


title: G58_rep1


title: G53_rep3


title: G53_rep1


title: G53_rep2


title: G36_rep2


title: G36_rep3


title: G36_rep1


title: G58_rep2


title: D95_rep2


title: D75_rep3


title: Pt16-Tumor5

value: African American


title: Pt16-Tumor1


title: Pt22-Tumor15Tumor16


title: Pt19-Tumor15


title: Pt21-Tumor7Tumor8


title: Pt50-Tumor1

value: Asian


title: Pt21-Tumor5


title: D75_rep2


title: Pt39-Tumor17Tumor18

value: unfavorable intermediate


title: Pt39-Tumor1Tumor2


title: D95_rep3


title: D75_rep1


title: D23_rep3


title: D95_rep1


title: Pt19-Tumor13


title: Pt21-Tumor3


title: D23_rep1


title: A87_rep3


title: Pt39-Tumor15


title: A87_rep2


title: Pt22-Tumor2Tumor13

value: AfricanAmerican


title: Pt16-Tumor3


title: Pt50-Tumor3


title: Pt3-Tumor13


title: Pt29-Tumor20


title: Pt32-Tumor14


title: Pt29-Tumor17


title: Pt40-Tumor14


title: A87_rep1


title: Pt29-Tumor15Tumor16


title: A38_rep3


title: D23_rep2


title: A38_rep2


title: A21_rep3


title: A38_rep1


title: Pt29-Tumor14


title: Pt3-Tumor15


title: A21_rep1


title: neo_tn_1

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

data_processing:
Mapper.pl in miRDeep2 was used for preprocessing and adapter removal (-d -e -h -k TGGAATTCTCGGGTGCCAAGG -l 18 -m -v). Quantifier.pl in miRDeep2 was used to map sequencing reads to miRNAs (-t mmu -d -e 0 -W). Sequences of precursors and mature miRNAs in mouse were downloaded from miRbase v22.
Assembly: mm10
Supplementary files format and content: Text file includes raw counts for each sample

source_name: spleen

extract_protocol:
To purify subsets of CD44hiCD122hi and CD44loCD122lo CD8+ T cells from neonatal and adult gBT-I mice, CD8+ T cells were enriched using anti-CD8α microbeads (Miltenyi Biotec) and were subsequently labeled with antibodies against CD4, CD8, CD44, and CD122 and sorted to >95% purity on a fluorescence-activated cell sorting (FACS) Aria III (BD Biosciences).
Libraries were prepared with Illumina TruSeq Small RNA Prep Kit using 50-100ng total RNA as input, size selected for insert sizes ~18-35bp.
small RNA-seq

value: spleen

value: CD8+ T cells


title: A21_rep2


title: scG6_rep2

source_name: HeLa cell line single clone

value: HeLa cell line single clone


title: neo_vm_2


title: scG6_rep1


title: Pt18-Tumor3


title: Pt41-Tumor6


title: Pt41-Tumor3


title: Pt34-Tumor5Tumor17


title: Pt14-Tumor5


title: scD4_rep1


title: scD2_rep2


title: adult_tn_2


title: Pt34-Tumor14


title: scB7_rep1


title: scD2_rep1


title: scB7_rep2


title: Pt18-Tumor4


title: adult_vm_2


title: adult_tn_1


title: Pt15-Tumor15Tumor16


title: scA9_rep1


title: adult_vm_1


title: scA2_rep1


title: Run2, IL21- Tfh, H. poly, rep2

city: Parkville

first: Joanna

last: Groom

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

description:
Library name: Run2_S52
column names in raw_counts and lcpm csv(s) corresponds to sample number:52
52

data_processing:
The RNA was sequenced via the Illumina NextSeq 500 System on a HiSeq paired-end run. The Rsubread aligner (Yang et al, Nucleic Acids Research, 2019) was used to align sequencing reads to the GRCm39 Mus musculus reference genome release version 103, and Rsubread::featureCounts() was used to quantify transcripts counts.
Counts from the two runs were summed. Low expressing genes with less than 5 counts per sample in more than 90% of the samples were removed using edgeR::filterByExpr(). Samples with low library (<1M), with low RNA quality and samples from the spleen were filtered out.
The filtered data is normalised using the " Trimmed Mean of M values” (TMM) method.
The normalised/scaled log2-transformed counts per million (logCPM) of the data is provided as inputs.
Assembly: GRCm39 Mus musculus reference genome v103
Supplementary files format and content: 41 of 52 samples retained after QC and filtering where 11 samples were removed (including 8 samples from the spleen). Filtered raw counts and TMM normalised log2-transformed counts per million (logCPM) of the the QC filtered data is provided.

source_name: lymph node

extract_protocol:
RNA was isolated from the sorted cells via an RNeasy Plus Micro Kit (QIAGEN),
Library was prepared using a SMART-seq PLUS Kit (Takarabio).

treatment_protocol: T cells from mice infected with LCMV, influenza A, Trichuris muris, Heligmosomoides polygyrus or Citrobacter rodentium.

value: lymph node

value: IL-21- T follicular helper (Tfh)

tag: treatment

value: H. poly


title: neo_vm_1


title: scD4_rep2


title: WT chm13 cells

city: Kansas City

first: Tamara

last: Potapova

state: Missouri

institute: Stowers Institute for Medical Research

description: Library name: CHM13_p35

data_processing:
Chm13 untreated reads were trimmed for adapters and low quality using trim galore with auto-detect adapters and a quality score cutoff of 20. GSK-3484862 treated reads were not trimmed.
Alignment to chm13 (v2.0) using the bisulfite sequencing aligner Bismark (v0.24.0). End to end alignment was used for untreated but local alignment was used for GSK-3484862 treated.
Alignments were deduplicated and extracted into bed coverage format to give a C and T count at each reference position. Complementary CpGs on the two strands were merged into a single site. Positions were later filtered by requiring coverage of 5 or more reads.
To assess rDNA alone, reads were aligned to the reference sequence KY962518.1 instead of chm13. The bismark local alignment option was used but reads were not deduplicated. This is due to the high copy number of the rDNA gene which creates many real duplicate alignments that are useful for methylation quantificaiton. Methylation extraction was performed to give bed coverage files with CpGs merged from both strands. Positions were filtered by requiring coverage of 10 or more reads.
Assembly: chm13 v2.0
Supplementary files format and content: Bed coverage files for whole genome and KY962518.1 alignments
Supplementary files format and content: The columns are unlabelled but have the format of: chromosome, start position, end position, methylation percentage, count methylated, count unmethylated.
Library strategy: EM-seq

source_name: hydatidiform mole

extract_protocol:
Genomic DNA from untreated and 5uM GSK-3484862 treated cells was isolated using QIAamp DNA Micro Kit (Qiagen).
The library was made according to the manufacturer’s directions for the NEBNext Enzymatic Methyl-seq kit (New England Biolabs, Cat. No. E7120S) using the S220 Focused-ultrasonicator (Covaris) to shear to 300bp and 4 cycles of library PCR amplification.

value: hydatidiform mole

tag: cell line

value: extraembryonic tissues

tag: genotype

value: genomic DNA

value: paired-end

tag: batch


title: Pt13-Tumor2

tag: gender

value: male

tag: gleason score of the biopsy

value: Caucasian


title: Pt31-Tumor1Tumor2

tag: nccn risk group

value: favorable intermediate

tag: t stage


title: Pt13-Tumor1

value: high

tag: psa

tag: tumorpurityscore


title: Pt17-Tumor6

tag: race

value: Asian

tag: gleason score of the patient


title: Pt31-Tumor3Tumor4

tag: age at biopsy


title: Run2, IL21- Tfh, Citrobacter, rep3

description:
Library name: Run2_S50
column names in raw_counts and lcpm csv(s) corresponds to sample number:50
50

tag: cell type

tag: strain

value: Citrobacter


title: Sublibrary 8

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

description:
Library name: Sample 8
Parse Biosciences

data_processing:
Raw data generated using the Parse Biosciences Single Cell Whole Transcriptome Kit v1.3.1 (Parse Biosciences, Seattle, WA) were processed following the Parse Biosciences pipeline, optimized for split-pool combinatorial barcoding data. Libraries were sequenced on an Illumina platform, producing paired-end reads with 150 bp for both Read 1 and Read 2, where Read 1 contained the combinatorial barcodes and Read 2 captured the cDNA sequence. The sequencing data were demultiplexed to generate FASTQ files for downstream processing. Raw FASTQ files were processed using the Parse Biosciences pipeline, which first identified and extracted cell-specific barcodes from Read 1 to assign reads to individual cells. Reads were then aligned to the human reference genome (GRCh38) using a splice-aware aligner to map gene expression accurately. Unique molecular identifiers (UMIs) were extracted, and PCR duplicates were removed by collapsing identical UMIs associated with the same gene. This process generated a digital gene expression (DGE) matrix representing the counts of unique transcripts per gene per cell.
Assembly: GRCh38
Supplementary files format and content: digital gene expression (DGE), comma seprated files, h5ad

molecule: polyA RNA

source_name: liver

growth_protocol: Terminally differentiated human hepatic cells (NoSpin HepaRG™) provided directly from the distributer (Lonza, Morrisville, NC) were seeded at 3X10^3 cells/cm2 in 24-well plates coated with rat tail collagen (Sigma-Aldrich, Saint Louis, MO) at a density of approximately 5 µg/cm2. After dispersion and seeding, cells were allowed to settle in the plate at room temperature for ~2 hrs in a biosafety cabinet before being transferred to an incubator set at 37°C, 5% CO2. Cells were incubated for 7 days in HepaRG Base Medium with Supplement (MH100; Lonza) plus Thawing and Plating additive (MHTAP; Lonza) before treatments, changing the media every 48-72 hrs. During cellular treatment, 0.1% DMSO was used as a vehicle control, corresponding to the final vehicle percentage for all solubilized chemicals. Treatments were carried out for 24 hrs before termination.

extract_protocol:
Following treatment, cells were dissociated into a single cell suspension, cell counts and viability were determined with a fluorometric Nexcelom Cellometer automated cell counter (Nexcelom Biosciences, Lawrence, MA) using Acridine Orange (AO)/Propidium Iodide (PI) stain (Perkin Elmer, Inc., Waltham, MA), following manufacturer’s instructions, and then the cells were fixed and processed for single-cell library construction. Cells were initially incubated for 11 min at 37°C in 0.25% Trypsin-EDTA (Thermo Fisher Scientific) with 40 mM DTT, 0.1 mg/ml actinomycin D, 1 mg/ml anisomycin, and 6 mM RNaseOUT recombinant ribonuclease inhibitor (Thermo Fisher Scientific, Waltham, MA) in 250 µl volume, followed by an additional 15 min 37°C incubation after adding 250 µl 0.5% Collagenase Type 1 (Worthington, Lakewood, NJ) in EBSS (Earle's Balanced Salt Solution) and DTT (Dithiothreitol) 40mM  DTT (Dithiothreitol) and 6mM RNaseOUT. Using a wide-bore pipette tip, cells were then dissociated by gentle pipetting for 10 min, 2 ml of 37°C HepaRG Base Medium was added to stop enzymatic activity, and cells were pelleted at 200 xg for 3 min at 4°C. After media removal, cells were resuspended in 1 ml cell suspension media (1X PBS, 0.5% Opti-Prep Density Gradient Medium (Sigma-Aldrich), 0.1% Bovine Serum Albumin Fraction V (Thermo Fisher Scientific, Waltham, MA), 6 mM RNaseOUT) pre-chilled to 4°C. The cells were pelleted twice more at 200 xg for 3 min at 4°C, washing each time with fresh Cell Suspension Media. After the final wash, cells were filtered through a 40 µm nylon cell strainer, transferred, and stored in a Lo-Bind tube. Cells were fixed using the Parse Cell Fixation kit (v1.3.0) before library preparation, following manufacturer’s instructions. After dissociation, less than 4 million cells were used for the fixation protocol to avoid increased doublet rates (averaged ~9X10^5 cells per sample at 93% viability). Cells were spun at 200 xg for 10 m at 4°C, and pellets were resuspended in kit Cell Buffer + 0.5% BSA. Cells were filtered through a 40 µm strainer and incubated in 4°C kit fixation solution after a 3X mix by pipetting and incubated on ice for 10 m. 4°C kit Permeabilization solution was then added, mixed 3X by pipetting, and incubated 3m on ice. Kit neutralization buffer was then added, the tube was inverted once to mix, and fixed cells were pelleted at 200xg for 10 m at 4°C. Pellets were then suspended to obtain a minimum concentration of 600 cell/µl, cells were then passed through a 40 µm strainer, and finally, DMSO was added slowly over 3 steps, with a 3X flick mix and 1 m incubation with each aliquot. Cells were then counted and then slow frozen to -80°C storage until prepped for sequencing.
Library preparation was performed with the Parse Biosciences Single Cell Whole Transcriptome kit (v1.3.1), following manufacturer’s instructions. Briefly, approximately 2X10^3 cells were loaded per well, after thawing the fixed samples in a 37°C heat block. Samples were then barcoded in four “split, then pool” rounds. In round 1, cells were reverse transcribed, and barcodes were added in situ using primers. Samples were then pooled and redistributed, and another round (2) of barcodes was added by ligation. Again, samples were pooled and redistributed, and a third round of barcodes was added using an in situ round of ligation. After each pooling, cells were spun in a swing-bucket centrifuge for 10m at 200 xg at 4°C, where indicated. Finally, a sublibrary barcoding was distributed using eight aliquots of the round 3 pool, adding 8 Illumina indices after lysing the aliquots. No more than 1.3X10^4 cells were added to each sublibrary based on counts performed before the final barcoding. Afterward, barcoded cDNA was bead purified, template switched, amplified, and SPRI bead clean-up was performed. Sublibraries were then quality checked on a Bioanalyzer and quantified. Subsequently, 100 ng of each sublibrary amplified cDNA was enzyme fragmented, end-repaired, and A-tails were added. Fragmented sublibraries were then double-sided SPRI bead selected, indexing adapters were ligated, SPRI bed cleaned, and then amplified using Illumina indices. After a post-amplification double-sided SPRI bead clean-up, sequencing libraries where quality checked on Bioanalyzer and quantified High Sensitivity DNA chip (Agilent). Sequencing was performed on the 8 sublibraries (all sublibraries contain all samples) using the paired-end protocol on an Illumina NovaSeq 6000 with an S4 flow cell (labeled as Samples1-8 in raw fastq files).

treatment_protocol: A set of 8 chemicals (including DMSO control) was tested to investigate distinct mechanisms of cellular stress responses. Chemical concentrations were selected to ensure that they did not induce significant cell dealth in HepaRG cells by keeping them below the AC50 for cytotoxicity.   Brefeldin A, recognized for its role in inducing the unfolded protein response (UPR) by disrupting ER-to-Golgi protein transport, was used at concentrations ranging from 0.001, 0.01, and  0.100 µM. Etoposide, a well-known DNA damage response (DDR) activator and a topoisomerase II inhibitor, was included at doses of 0.25, 2.5, and 25 µM to assess DDR activation and cytotoxicity. For investigating oxidative stress response (OSR), tert-butylhydroquinone was chosen for its ability to activate the NRF2 pathway, a key player in cellular defense against oxidative stress, and was tested at concentrations of 3, 30, and 300 µM. Rotenone, known to induce mitochondrial stress by inhibiting the mitochondrial electron transport chain, was tested at concentrations of 0.2, 0.4, and 0.8 µM. Cycloheximide, a protein synthesis inhibitor impacting many cellular processes, was tested at concentrations of 0.200, 2.000, and 20.000 µM. Tunicamycin, another UPR inducer known for inhibiting N-linked glycosylation, was tested at concentrations of 0.001, 0.010, and 0.100 µM. Lastly, troglitazone, a PPARγ agonist influencing lipid metabolism and mitochondrial function and can modulate PPARα pathway activity, was tested at concentrations of 0.001, 0.010, and 0.100 µM. 0.1% dimethyl sulfoxide (DMSO) was used as the vehicle control for all treatments. These test chemicals, spanning a range of concentrations, were selected to provide a comprehensive view of transcriptional concentration responses across different cellular stress pathways without reaching a concentration level of each producing significant cell loss.

tag: tissue

value: liver

value: HepaRG

value: hepatocyte


title: Run2, IL21- Tfh, T. muris, rep2

description:
Library name: Run2_S47
column names in raw_counts and lcpm csv(s) corresponds to sample number:47
47

value: T. muris


title: scA2_rep2

value: HeLa cell line single clone


title: Sublibrary 7

description:
Library name: Sample 7
Parse Biosciences


title: Run2, IL21- Tfh, T. muris, rep1

description:
Library name: Run2_S46
column names in raw_counts and lcpm csv(s) corresponds to sample number:46
46

value: lymph node

value: IL-21- T follicular helper (Tfh)


title: Sublibrary 6

description:
Library name: Sample 6
Parse Biosciences


title: Run2, IL21- Tfh, LCMV spl, rep2

description:
Library name: Run2_S45
sample not in processed data after filtering
45

value: spleen

value: LCMV spl


title: Run2, IL21- Tfh, H. poly, rep1

description:
Library name: Run2_S51
column names in raw_counts and lcpm csv(s) corresponds to sample number:51
51

value: H. poly


title: scA9_rep2


title: Run2, IL21- Tfh, LCMV, rep2

description:
Library name: Run2_S43
column names in raw_counts and lcpm csv(s) corresponds to sample number:43
43

value: LCMV


title: Run2, IL21- Tfh, LCMV spl, rep1

description:
Library name: Run2_S44
sample not in processed data after filtering
44


title: Sublibrary 5

description:
Library name: Sample 5
Parse Biosciences


title: HK-2 cells, IR model, PRDM16_LV, cell2

city: Wuhan

first: Yuting

last: Zhu

state: Hubei

address: 1277 Jiefang Avenue

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
The image data obtained by the high-throughput sequence was converted into sequence data (reads) by CASAVA base recognition, and the file was in fastq format. Reads containing adapters or low-quality reads were removed. All subsequent analyses were based on high-quality analysis of clean data.
FeatureCounts (v2.0.1) was used to calculate the number of reads mapped to each gene. The FPKM for each gene was calculated based on gene length and the number of reads mapped to that gene. DESeq2 software (1.16.1) was used to perform differential expression analysis between two comparison groups.
GO and KEGG enrichment analysis of differentially expressed genes were performed using clusterProfiler in R software (4.2.0), and GO terms or KEGG pathways with corrected P values less than 0.05 were considered as statistically significant.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts and FPKM for each gene and each sample

extract_protocol:
Total RNA was extracted with RNAiso Plus reagent (Takara), more than 800ng total RNA was used for library construction.
Illumina’s NEBNext®UltraTM RNA Library Prep Kit was used in library construction.

treatment_protocol: PRDM16 overexpressing and control HK-2 cell lines were constructed by lentivirus transfection. HK-2 cells were exposed to a single dose of 8 Gy X-ray irradiation and harvested at the 7th day post-irradiation.

value: human proximal tubular cells

value: irradiation and PRDM16 lentivirus


title: HK-2 cells, IR model, PRDM16_LV, cell3


title: Run2, IL21- Tfh, Citrobacter, rep1

description:
Library name: Run2_S48
column names in raw_counts and lcpm csv(s) corresponds to sample number:48
48


title: Pt6-Tumor2

value: male

value: Caucasian


title: Sublibrary 4

description:
Library name: Sample 4
Parse Biosciences


title: Run2, IL21- Tfh, Influenza A, rep2

description:
Library name: Run2_S41
column names in raw_counts and lcpm csv(s) corresponds to sample number:41
41

value: Influenza A


title: Run2, IL21- Tfh, LCMV, rep1

description:
Library name: Run2_S42
column names in raw_counts and lcpm csv(s) corresponds to sample number:42
42


title: HK-2 cells, IR model, PRDM16_LV, cell1


title: Pt17-Tumor1

value: high

value: Asian


title: Pt6-Tumor1


title: Run2, IL21- Tfh, Influenza A, rep1

description:
Library name: Run2_S40
column names in raw_counts and lcpm csv(s) corresponds to sample number:40
40


title: Run2, IL21- Tfh, Citrobacter, rep2

description:
Library name: Run2_S49
column names in raw_counts and lcpm csv(s) corresponds to sample number:49
49

value: Citrobacter


title: Run2, IL21+ Tfh, H. poly, rep2

description:
Library name: Run2_S39
column names in raw_counts and lcpm csv(s) corresponds to sample number:39
39

value: IL-21+ T follicular helper (Tfh)


title: Sublibrary 2

description:
Library name: Sample 2
Parse Biosciences

value: liver

value: HepaRG

value: hepatocyte


title: HK-2 cells, IR model, NC_LV, cell3

value: irradiation and NC lentivirus


title: Run2, IL21+ Tfh, Citrobacter, rep3

description:
Library name: Run2_S37
column names in raw_counts and lcpm csv(s) corresponds to sample number:37
37

value: lymph node


title: Run2, IL21+ Tfh, H. poly, rep1

description:
Library name: Run2_S38
column names in raw_counts and lcpm csv(s) corresponds to sample number:38
38


title: HK-2 cells, IR model, NC_LV, cell2


title: Run2, IL21+ Tfh, Citrobacter, rep2

description:
Library name: Run2_S36
column names in raw_counts and lcpm csv(s) corresponds to sample number:36
36


title: Sublibrary 1

description:
Library name: Sample 1
Parse Biosciences


title: Run2, IL21+ Tfh, Citrobacter, rep1

description:
Library name: Run2_S35
column names in raw_counts and lcpm csv(s) corresponds to sample number:35
35


title: HK-2 cells, IR model, NC_LV, cell1


title: Run2, IL21+ Tfh, T. muris, rep2

description:
Library name: Run2_S34
column names in raw_counts and lcpm csv(s) corresponds to sample number:34
34

value: T. muris


title: Run2, IL21+ Tfh, LCMV sp, repl2

description:
Library name: Run2_S32
sample not in processed data after filtering
32

value: spleen

value: LCMV sp


title: Model3_MOD_Mus musculus_lacrimal gland

city: Hangzhou

first: Jiajun

last: Xie

state: Zhejiang

address: No. 88 Jiefang Rd

institute: Zhejiang University, Eye Center of Second Affiliated Hospital, School of Medicine, China

description: Library name: sample6

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/) to map reads to the reference genome of mus musculus Ensembl_v101. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: mus_musculus Ensembl_v101
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: lacrimal gland

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: lacrimal gland

value: lacrimal gland cells

value: NOD/Ltj


title: ES24_5-GEX

city: Baltimore

first: Isha

last: Gurumurthy

address: 1650 Orleans Street, CRB1, 4M

department: Oncology

institute: Johns Hopkins University

description:
Library name: ES24_5-GEX
10x Genomics

data_processing:
Cell Ranger v9.0.0 was used to demultiplex the FASTQ reads, align them to the GRCh38 human transcriptome, and extract their cell and unique molecular identifier (UMI) barcodes. The output of this pipeline is a digital gene expression (DGE) matrix for each sample, which records the number of UMIs for each gene that are associated with each cell barcode.
Assembly: Hg38
Supplementary files format and content: Tab-separated values, matrix files and comma separated values

source_name: peripheral blood mononuclear cells

extract_protocol:
Cell suspensions were loaded onto a 10x Genomics Chromium X (Pleasanton,CA) using the 5’ V2 Gel bead kit. Cell capture, GEM generation, cDNA amplification and library preparation were performed according to manufacturer protocol.
5’ gene expression and T cell repertoire libraries were prepared using 10X genomics Chromium X as per the manufacter 's protocol. The libraries were assessed for concentration and fragment size using the DNA High Sensitivity Assay on a GX Touch (Revity, Waltham, MA). The libraries were pooled, assessed by qPCR using the KAPA Library Quantification Kit (Complete, Universal) (Kapa Biosystems, Woburn, MA) and sequenced on an Illumina NovaSeq 6000 using 150bp PE reads (Illumina, San Diego, CA).

value: peripheral blood mononuclear cells

value: primary cells

value: CD4+ T cells


title: Run2, IL21+ Tfh, LCMV spl, rep1

description:
Library name: Run2_S31
sample not in processed data after filtering
31

value: LCMV spl


title: Model2_MOD_Mus musculus_lacrimal gland

description: Library name: sample5


title: ES24_4-TCR

description:
Library name: ES24_4-TCR
10x Genomics

data_processing:
Cell Ranger v9.0.0 was used to demultiplex the FASTQ reads, align them to the GRCh38 human transcriptome, and extract their cell and unique molecular identifier (UMI) barcodes. The output of this pipeline is a digital gene expression (DGE) matrix for each sample, which records the number of UMIs for each gene that are associated with each cell barcode.
Assembly: Hg38
Supplementary files format and content: Tab-separated values, matrix files and comma separated values
Library strategy: TCR-Seq


title: Run2, IL21+ Tfh, LCMV, rep2

description:
Library name: Run2_S30
column names in raw_counts and lcpm csv(s) corresponds to sample number:30
30

value: LCMV


title: ES24_4-GEX

description:
Library name: ES24_4-GEX
10x Genomics


title: Control3_ICR_Mus musculus_lacrimal gland

description: Library name: sample3

value: control ICR


title: Model1_MOD_Mus musculus_lacrimal gland

description: Library name: sample4


title: Run2, Tfr, H. poly, rep2

description:
Library name: Run2_S26
column names in raw_counts and lcpm csv(s) corresponds to sample number:26
26

value: T follicular regulatory (Tfr)

value: H. poly


title: Run2, IL21+ Tfh, Influenza A, rep1

description:
Library name: Run2_S27
column names in raw_counts and lcpm csv(s) corresponds to sample number:27
27

value: IL-21+ T follicular helper (Tfh)

value: Influenza A


title: Sublibrary 3

description:
Library name: Sample 3
Parse Biosciences

value: liver

value: HepaRG

value: hepatocyte


title: Run2, IL21+ Tfh, LCMV, rep1

description:
Library name: Run2_S29
column names in raw_counts and lcpm csv(s) corresponds to sample number:29
29

value: lymph node


title: Run2, IL21+ Tfh, Influenza A, rep2

description:
Library name: Run2_S28
column names in raw_counts and lcpm csv(s) corresponds to sample number:28
28


title: Run2, Tfr, H. poly, rep1

description:
Library name: Run2_S25
column names in raw_counts and lcpm csv(s) corresponds to sample number:25
25


title: ES24_3-TCR

description:
Library name: ES24_3-TCR
10x Genomics


title: Run2, Tfr, Citrobacter, rep3

description:
Library name: Run2_S24
column names in raw_counts and lcpm csv(s) corresponds to sample number:24
24

value: Citrobacter


title: Run2, Tfr, Citrobacter, rep2

description:
Library name: Run2_S23
column names in raw_counts and lcpm csv(s) corresponds to sample number:23
23


title: Control2_ICR_Mus musculus_lacrimal gland

description: Library name: sample2

value: lacrimal gland

value: lacrimal gland cells


title: Control1_ICR_Mus musculus_lacrimal gland

description: Library name: sample1


title: ES24_5-TCR

description:
Library name: ES24_5-TCR
10x Genomics

value: peripheral blood mononuclear cells


title: Run2, Tfr, Citrobacter, rep1

description:
Library name: Run2_S22
column names in raw_counts and lcpm csv(s) corresponds to sample number:22
22


title: Run2, IL21+ Tfh, T. muris, rep1

description:
Library name: Run2_S33
column names in raw_counts and lcpm csv(s) corresponds to sample number:33
33

value: T. muris


title: ES24_2-TCR

description:
Library name: ES24_2-TCR
10x Genomics

value: primary cells

value: CD4+ T cells


title: Run2, Tfr, T. muris, rep2

description:
Library name: Run2_S21
column names in raw_counts and lcpm csv(s) corresponds to sample number:21
21


title: Run2, Tfr, T. muris, rep1

description:
Library name: Run2_S20
column names in raw_counts and lcpm csv(s) corresponds to sample number:20
20


title: ES24_2-GEX

description:
Library name: ES24_2-GEX
10x Genomics


title: Run2, Tfr, LCMV spl, rep2

description:
Library name: Run2_S19
sample not in processed data after filtering
19

value: spleen

value: LCMV spl


title: Endothelial cells, SRBI-knockdown, rep3

city: New York

first: Genome Technology Center

last: (GTC)

address: 550 First Avenue

institute: NYU Langone Health

description:
Library name: 12
SRBI-KO-counts.normalized-Goldberg-08-19-2025.xlsx

data_processing:
RNA sequencing data was generated from four paired-end 50 Illumina NovaSeq 6000 runs. Per-read per-sample FASTQ files were generated using the bcl2fastq2 Conversion software (v2.20) to convert per-cycle BCL base call files outputted by the sequencing instrument into the FASTQ format. The alignment program, STAR (v2.7.3a), was used for mapping reads of every sample to the mouse reference genome mm10. The feature Counts (Subread package v1.6.3) software was used to generate matrices of read counts for annotated genomic features. The miRge v3.0 software was utilized to generate count matrices for the miRNA-seq data.
Assembly: mouse reference genome mm10 (UCSC; GRCm38)
Supplementary files format and content: xlsx Excel files contain normalized counts for each bulk RNA-seq sample
Supplementary files format and content: csv file includes raw counts for each miRNA-seq sample

source_name: Endothelial cells

extract_protocol:
Total RNA was extracted from PL and PLA murine cell lines using the RNeasy Plus Universal Mini Kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries for bulk RNA-seq were prepared using the Illumina Truseq Stranded mRNA library prep kit following manufacturer's protocols. miRNA libraries for miRNA-seq were prepared using the NEBnext Multiplex Small RNA Library Prep for Illumina Kit following manufacturer's protocols.

value: Endothelial cells

value: SRBI-knockdown


title: Run2, Tfr, LCMV spl, rep1

description:
Library name: Run2_S18
sample not in processed data after filtering
18

value: T follicular regulatory (Tfr)


title: ES24_1-TCR

description:
Library name: ES24_1-TCR
10x Genomics


title: Run2, Tfr, LCMV, rep2

description:
Library name: Run2_S17
column names in raw_counts and lcpm csv(s) corresponds to sample number:17
17

value: LCMV


title: Endothelial cells, SRBI-knockdown, rep1

description:
Library name: 10
SRBI-KO-counts.normalized-Goldberg-08-19-2025.xlsx


title: Endothelial cells, SRBI-knockdown, rep2

description:
Library name: 11
SRBI-KO-counts.normalized-Goldberg-08-19-2025.xlsx


title: ES24_1-GEX

description:
Library name: ES24_1-GEX
10x Genomics


title: Endothelial cells, control, rep2

description:
Library name: Control_2
EC-chylo-control-counts.normalized-Goldberg-08-19-2025.xlsx


title: Endothelial cells, control, rep3

description:
Library name: Control_3
EC-chylo-control-counts.normalized-Goldberg-08-19-2025.xlsx


title: Run2, Tfr, LCMV, rep1

description:
Library name: Run2_S16
sample not in processed data after filtering
16


title: Run2, Teff, H. poly, rep1

description:
Library name: Run2_S12
column names in raw_counts and lcpm csv(s) corresponds to sample number:12
12

value: T effector (Teff)

value: H. poly


title: P079 T-cells, Infected Macrophages, GEX

city: Cleveland

first: Robert

last: Schauner

state: Ohio

address: 10900 Euclid Ave

department: Division of Infectious Diseases and HIV Medicine

institute: Case Western Reserve University

description: Library name: P079-Infected-GEX

data_processing:
Demultiplexed FASTQ files were mapped to the human genome and TCR sequences, simultaneously, using Cell Ranger Multi V7.1 (10X Genomics) on the 10X Cloud server and the GRCh38.p14 reference genome.
Assembly: GRCh38.p14
Supplementary files format and content: Tab-separated values, comma-separated values, and Market Matrix

source_name: blood

extract_protocol:
Activated CD4+ were resuspended in 0.04% BSA in PBS
Sequencing of mRNA from single T cells was performed using the 10x Genomics Chromium Next GEM Single Cell 5’ V2 platform (10X Genomics, Pleasanton, CA, USA). Activated CD4+ were resuspended in 0.04% BSA in PBS and loaded onto the 10X Chromium Controller. RNA was reverse-transcribed, and cDNA was isolated and PCR-amplified according to the 10X Genomics NextGEM 5’ V2 scRNAseq User Guide (Rev D). Quality control and quantification of cDNA and final libraries was performed on either the Agilent fragment analyzer or Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). V(D)J amplification and library preparation, and gene expression library construction were performed using 10X Genomics kits according to the User Guide.

value: blood

tag: ltbi status

value: LTBI

value: Mtb-infected macrophages


title: P079 T-cells, Infected Macrophages, TCR

description: Library name: P079-Infected-TCR

library_source: other

molecule: other

tag: treatment


title: Run2, Tfr, Influenza A, rep1

description:
Library name: Run2_S14
column names in raw_counts and lcpm csv(s) corresponds to sample number:14
14

value: lymph node

value: Influenza A


title: ES24_3-GEX

description:
Library name: ES24_3-GEX
10x Genomics

value: peripheral blood mononuclear cells

tag: cell line


title: Run2, Teff, Citrobacter, rep3

description:
Library name: Run2_S11
column names in raw_counts and lcpm csv(s) corresponds to sample number:11
11

value: Citrobacter


title: Endothelial cells, control, rep1

description:
Library name: Control_1
EC-chylo-control-counts.normalized-Goldberg-08-19-2025.xlsx


title: Run2, Teff, H. poly, rep2

description:
Library name: Run2_S13
column names in raw_counts and lcpm csv(s) corresponds to sample number:13
13


title: Run2, Teff, Citrobacter, rep2

description:
Library name: Run2_S10
column names in raw_counts and lcpm csv(s) corresponds to sample number:10
10


title: Leukopack 5 T-cells, Infected Macrophages, TCR

description: Library name: Lkpk5-Infected-TCR

value: non-LTBI


title: Run2, Teff, Citrobacter, rep1

description:
Library name: Run2_S9
column names in raw_counts and lcpm csv(s) corresponds to sample number:9
9


title: Endothelial cells, chylomicron-treated, rep3

description:
Library name: CHYLO3-EC
Column name in normalized counts EC-chylo-control-counts.normalized-Goldberg-08-19-2025.xlsx: CHYLO3
EC-chylo-control-counts.normalized-Goldberg-08-19-2025.xlsx

value: chylomicron-treated


title: Run2, Teff, T. muris, rep2

description:
Library name: Run2_S8
column names in raw_counts and lcpm csv(s) corresponds to sample number:8
8

value: T. muris


title: Run2, Tfr, Influenza A, rep2

description:
Library name: Run2_S15
column names in raw_counts and lcpm csv(s) corresponds to sample number:15
15


title: Run2, Teff, T. muris, rep1

description:
Library name: Run2_S7
sample not in processed data after filtering
7


title: Endothelial cells, chylomicron-treated, rep2

description:
Library name: CHYLO2-EC
Column name in normalized counts EC-chylo-control-counts.normalized-Goldberg-08-19-2025.xlsx: CHYLO2
EC-chylo-control-counts.normalized-Goldberg-08-19-2025.xlsx


title: Leukopack 5 T-cells, Infected Macrophages, GEX

description: Library name: Lkpk5-Infected-GEX


title: Run2, Teff, LCMV spl, rep2

description:
Library name: Run2_S6
sample not in processed data after filtering
6

value: spleen

value: LCMV spl


title: Run2, Teff, LCMV, rep2

description:
Library name: Run2_S4
sample not in processed data after filtering
4


title: Leukopack 4 T-cells, Infected Macrophages, GEX

description: Library name: Lkpk4-Infected-GEX


title: Endothelial cells, chylomicron-treated, rep1

description:
Library name: CHYLO1-EC
Column name in normalized counts EC-chylo-control-counts.normalized-Goldberg-08-19-2025.xlsx: CHYLO1
EC-chylo-control-counts.normalized-Goldberg-08-19-2025.xlsx

value: Endothelial cells


title: Peritoneal macrophages, SRBI-knockdown, rep3

description:
Library name: SRBI3
PMACs-counts.normalized-Goldberg-08-19-2025.xlsx

source_name: peritoneal macrophages

value: peritoneal macrophages

tag: genotype

value: SRBI-knockdown


title: Leukopack 3 T-cells, Infected Macrophages, TCR

description: Library name: Lkpk3-Infected-TCR


title: Run2, Teff, Influenza A, rep2

description:
Library name: Run2_S2
column names in raw_counts and lcpm csv(s) corresponds to sample number:2
2

value: T effector (Teff)


title: Peritoneal macrophages, SRBI-knockdown, rep2

description:
Library name: SRBI2
PMACs-counts.normalized-Goldberg-08-19-2025.xlsx


title: Run1, IL21- Tfh, H. poly, rep1

description:
Library name: Run1 S51
column names in raw_counts and lcpm csv(s) corresponds to sample number:51
51

value: IL-21- T follicular helper (Tfh)

value: H. poly


title: Run1, IL21- Tfh, H. poly, rep2

description:
Library name: Run1 S52
column names in raw_counts and lcpm csv(s) corresponds to sample number:52
52


title: Peritoneal macrophages, SRBI-knockdown, rep1

description:
Library name: SRBI1
PMACs-counts.normalized-Goldberg-08-19-2025.xlsx


title: Run1, IL21- Tfh, Citrobacter, rep3

description:
Library name: Run1 S50
column names in raw_counts and lcpm csv(s) corresponds to sample number:50
50


title: Leukopack 3 T-cells, Infected Macrophages, GEX

description: Library name: Lkpk3-Infected-GEX

value: blood


title: Run1, IL21- Tfh, Citrobacter, rep2

description:
Library name: Run1 S49
column names in raw_counts and lcpm csv(s) corresponds to sample number:49
49


title: Leukopack 2 T-cells, Infected Macrophages, TCR

description: Library name: Lkpk2-Infected-TCR

value: Mtb-infected macrophages


title: Run1, IL21- Tfh, Citrobacter, rep1

description:
Library name: Run1 S48
column names in raw_counts and lcpm csv(s) corresponds to sample number:48
48

value: lymph node


title: Run1, IL21- Tfh, T. muris, rep2

description:
Library name: Run1 S47
column names in raw_counts and lcpm csv(s) corresponds to sample number:47
47


title: Peritoneal macrophages, control, rep2

description:
Library name: control2
PMACs-counts.normalized-Goldberg-08-19-2025.xlsx


title: Run1, IL21- Tfh, T. muris, rep1

description:
Library name: Run1 S46
column names in raw_counts and lcpm csv(s) corresponds to sample number:46
46


title: Peritoneal macrophages, control, rep3

description:
Library name: control3
PMACs-counts.normalized-Goldberg-08-19-2025.xlsx


title: Run1, IL21- Tfh, LCMV spl, rep2

description:
Library name: Run1 S45
sample not in processed data after filtering
45


title: Run1, IL21- Tfh, LCMV spl, rep1

description:
Library name: Run1 S44
sample not in processed data after filtering
44


title: Leukopack 2 T-cells, Infected Macrophages, GEX

description: Library name: Lkpk2-Infected-GEX


title: CL018 T-cells, Infected Macrophages, TCR

description: Library name: CL018-Infected-TCR

value: LTBI


title: Peritoneal macrophages, control, rep1

description:
Library name: control1
PMACs-counts.normalized-Goldberg-08-19-2025.xlsx


title: Run2, Teff, LCMV spl, rep1

description:
Library name: Run2_S5
sample not in processed data after filtering
5


title: Leukopack 4 T-cells, Infected Macrophages, TCR

description: Library name: Lkpk4-Infected-TCR


title: CL018 T-cells, Infected Macrophages, GEX

description: Library name: CL018-Infected-GEX


title: Peritoneal macrophages, chylomicron-treated, rep3

description:
Library name: Chylo3
PMACs-counts.normalized-Goldberg-08-19-2025.xlsx


title: Run1, IL21- Tfh, LCMV, rep2

description:
Library name: Run1 S43
column names in raw_counts and lcpm csv(s) corresponds to sample number:43
43

value: LCMV


title: CL013 T-cells, Infected Macrophages and Mtb lysate, TCR

description: Library name: CL013-Lysate-TCR

value: Mtb-infected macrophages and Mtb-lysate


title: Run2, Teff, LCMV, rep1

description:
Library name: Run2_S3
column names in raw_counts and lcpm csv(s) corresponds to sample number:3
3


title: Run2, Teff, Influenza A, rep1

description:
Library name: Run2_S1
column names in raw_counts and lcpm csv(s) corresponds to sample number:1
1

value: Influenza A


title: Run1, IL21- Tfh, Influenza A, rep2

description:
Library name: Run1 S41
column names in raw_counts and lcpm csv(s) corresponds to sample number:41
41


title: Peritoneal macrophages, chylomicron-treated, rep2

description:
Library name: Chylo2
PMACs-counts.normalized-Goldberg-08-19-2025.xlsx

value: chylomicron-treated


title: Run1, IL21- Tfh, Influenza A, rep1

description:
Library name: Run1 S40
column names in raw_counts and lcpm csv(s) corresponds to sample number:40
40


title: Run1, IL21+ Tfh, H. poly, rep2

description:
Library name: Run1 S39
column names in raw_counts and lcpm csv(s) corresponds to sample number:39
39

value: IL-21+ T follicular helper (Tfh)


title: Peritoneal macrophages, chylomicron-treated, rep1

description:
Library name: Chylo1
PMACs-counts.normalized-Goldberg-08-19-2025.xlsx


title: CL013 T-cells, Infected Macrophages and Mtb lysate, GEX

description: Library name: CL013-Lysate-GEX


title: CL013 T-cells, Infected Macrophages, TCR

description: Library name: CL013-Infected-TCR


title: Endothelial cell media circulating miRNA, SRBI-knockdown, rep3

description:
Library name: SRBI-3
miR.Counts-Goldberg-08-19-2025.csv


title: Run1, IL21+ Tfh, Citrobacter, rep3

description:
Library name: Run1 S37
column names in raw_counts and lcpm csv(s) corresponds to sample number:37
37

value: Citrobacter


title: Run1, IL21+ Tfh, Citrobacter, rep2

description:
Library name: Run1 S36
column names in raw_counts and lcpm csv(s) corresponds to sample number:36
36


title: Run1, IL21+ Tfh, H. poly, rep1

description:
Library name: Run1 S38
column names in raw_counts and lcpm csv(s) corresponds to sample number:38
38


title: Run1, IL21+ Tfh, Citrobacter, rep1

description:
Library name: Run1 S35
column names in raw_counts and lcpm csv(s) corresponds to sample number:35
35


title: CL012 T-cells, Infected Macrophages and Mtb lysate, TCR

description: Library name: CL012-Lysate-TCR


title: Endothelial cell media circulating miRNA, SRBI-knockdown, rep2

description:
Library name: SRBI-2
miR.Counts-Goldberg-08-19-2025.csv


title: Endothelial cell media circulating miRNA, SRBI-knockdown, rep1

description:
Library name: SRBI-1
miR.Counts-Goldberg-08-19-2025.csv


title: Run1, IL21+ Tfh, LCMV spl, rep2

description:
Library name: Run1 S32
sample not in processed data after filtering
32

value: spleen

value: LCMV spl


title: Run1, IL21+ Tfh, T. muris, rep1

description:
Library name: Run1 S33
column names in raw_counts and lcpm csv(s) corresponds to sample number:33
33

value: T. muris


title: CL013 T-cells, Infected Macrophages, GEX

description: Library name: CL013-Infected-GEX


title: Endothelial cell media circulating miRNA, control, rep3

description:
Library name: control-3
miR.Counts-Goldberg-08-19-2025.csv

value: Endothelial cells


title: Run1, IL21+ Tfh, T. muris, rep2

description:
Library name: Run1 S34
column names in raw_counts and lcpm csv(s) corresponds to sample number:34
34


title: Run1, IL21+ Tfh, LCMV, rep2

description:
Library name: Run1 S30
column names in raw_counts and lcpm csv(s) corresponds to sample number:30
30


title: Run1, IL21- Tfh, LCMV, rep1

description:
Library name: Run1 S42
column names in raw_counts and lcpm csv(s) corresponds to sample number:42
42


title: CL012 T-cells, Infected Macrophages and Mtb lysate, GEX

description: Library name: CL012-Lysate-GEX


title: Run1, IL21+ Tfh, LCMV, rep1

description:
Library name: Run1 S29
column names in raw_counts and lcpm csv(s) corresponds to sample number:29
29


title: CL012 T-cells, Infected Macrophages, TCR

description: Library name: CL012-Infected-TCR


title: CL012 T-cells, Infected Macrophages, GEX

description: Library name: CL012-Infected-GEX


title: Run1, IL21+ Tfh, Influenza A, rep2

description:
Library name: Run1 S28
column names in raw_counts and lcpm csv(s) corresponds to sample number:28
28


title: Endothelial cell media circulating miRNA, control, rep2

description:
Library name: control-2
miR.Counts-Goldberg-08-19-2025.csv


title: Endothelial cell media circulating miRNA, control, rep1

description:
Library name: control-1
miR.Counts-Goldberg-08-19-2025.csv


title: Run1, IL21+ Tfh, Influenza A, rep1

description:
Library name: Run1 S27
column names in raw_counts and lcpm csv(s) corresponds to sample number:27
27


title: Run1, Tfr, H. poly, rep2

description:
Library name: Run1 S26
column names in raw_counts and lcpm csv(s) corresponds to sample number:26
26

value: T follicular regulatory (Tfr)


title: Run1, Tfr, H. poly, rep1

description:
Library name: Run1 S25
column names in raw_counts and lcpm csv(s) corresponds to sample number:25
25


title: CL011 T-cells, Infected Macrophages and Mtb lysate, TCR

description: Library name: CL011-Lysate-TCR


title: Endothelial cell media circulating miRNA, chylomicron-treated, rep2

description:
Library name: Chylo-24-2
miR.Counts-Goldberg-08-19-2025.csv


title: CL011 T-cells, Infected Macrophages, TCR

description: Library name: CL011-Infected-TCR


title: CL011 T-cells, Infected Macrophages and Mtb lysate, GEX

description: Library name: CL011-Lysate-GEX


title: Run1, Tfr, Citrobacter, rep1

description:
Library name: Run1 S22
column names in raw_counts and lcpm csv(s) corresponds to sample number:22
22


title: Run1, Tfr, Citrobacter, rep2

description:
Library name: Run1 S23
column names in raw_counts and lcpm csv(s) corresponds to sample number:23
23


title: Run1, Tfr, T. muris, rep2

description:
Library name: Run1 S21
column names in raw_counts and lcpm csv(s) corresponds to sample number:21
21


title: Run1, IL21+ Tfh, LCMV spl, rep1

description:
Library name: Run1 S31
sample not in processed data after filtering
31


title: Run1, Tfr, T. muris, rep1

description:
Library name: Run1 S20
column names in raw_counts and lcpm csv(s) corresponds to sample number:20
20


title: Run1, Tfr, LCMV spl, rep1

description:
Library name: Run1 S18
sample not in processed data after filtering
18


title: Run1, Tfr, LCMV spl, rep2

description:
Library name: Run1 S19
sample not in processed data after filtering
19


title: Endothelial cell media circulating miRNA, chylomicron-treated, rep1

description:
Library name: Chylo-24-1
miR.Counts-Goldberg-08-19-2025.csv


title: CL010 T-cells, Infected Macrophages, TCR

description: Library name: CL010-Control-TCR

value: non-LTBI


title: Run1, Tfr, LCMV, rep2

description:
Library name: Run1 S17
column names in raw_counts and lcpm csv(s) corresponds to sample number:17
17


title: CL011 T-cells, Infected Macrophages, GEX

description: Library name: CL011-Infected-GEX


title: Run1, Tfr, Influenza A, rep2

description:
Library name: Run1 S15
column names in raw_counts and lcpm csv(s) corresponds to sample number:15
15


title: CL010 T-cells, Infected Macrophages, GEX

description: Library name: CL010-Control-GEX


title: Run1, Tfr, Influenza A, rep1

description:
Library name: Run1 S14
column names in raw_counts and lcpm csv(s) corresponds to sample number:14
14


title: HMPV, nasal turbinates replicate 1, scRNAseq

city: Pittsburgh

first: John

last: Williams

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh School of Medicine

description:
Library name: WT NT 202-1
10X Genomics

data_processing:
Sequencing outputs were processed with Cellranger.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Nasal turbinates

extract_protocol:
Cells were collected from mice euthanized day 1 post-infection. Following collection, nasal turbinates were flushed twice with 1-mL R10 (RPMI 1640 media supplemented with 10% FBS, 2 mM glutamine, 50 μg/ml gentamicin, 2.5 μg/ml amphotericin B, and 50 μM β-mercaptoethanol). Nasal turbinates were minced and digested with 2 mg/mL collagenase, 20 μg/mL DNase (Roche), and 2 U/mL dispase (Corning) for 60 minutes in a shaker at 37C. Nasal turbinate preparations were passed through a 70-μM cell strainer and incubated with ACK lysis buffer (Sigma-Aldrich) to remove red blood cells. Cells were washed 5 times with 10mL of PBS+10% FBS and centrifuged at 500xg for 5’, followed by a final wash and centrifugation at 200xg for 10’. Dead cells were removed by magnetic separation using Annexin V kit (STEMCELL Technologies).
The 10X Genomics 3’ CellPlex Kit was used and cells were tagged by lipid-conjugated Barcode oligonucleotides according to manufacturer’s instructions. Cells were passed through a 40-μM filter and cell viability was determined using Cellometer 2000 (all showing >90% viability) prior to loading on 10X Chromium instrument. Following established techniques using Chromium Single Cell 3’ Library V2 kit (10X), libraries were constructed and RNA-seq was performed on each sample targeting 20,000 reads per cell.

value: Nasal turbinates

tag: age

value: 6-7 weeks old

tag: Sex

value: Female

value: C2-202 HMPV (5E5 PFU) intratracheally


title: Run1, Tfr, LCMV, rep1

description:
Library name: Run1 S16
sample not in processed data after filtering
16

value: lymph node


title: Run1, Teff, H. poly, rep2

description:
Library name: Run1 S13
column names in raw_counts and lcpm csv(s) corresponds to sample number:13
13

value: T effector (Teff)

value: H. poly


title: HMPV, nasal turbinates replicate 2, scRNAseq

description:
Library name: WT NT 202-2
10X Genomics


title: CL007 T-cells, Infected Macrophages and Mtb lysate, TCR

description: Library name: CL007-Lysate-TCR

value: blood

value: LTBI

value: Mtb-infected macrophages and Mtb-lysate


title: Mock, nasal turbinates replicate 1, scRNAseq

description:
Library name: WT NT Mock-1
10X Genomics

value: Mock lysate intratracheally


title: Mock, nasal turbinates replicate 2, scRNAseq

description:
Library name: WT NT Mock-2
10X Genomics


title: Endothelial cell media circulating miRNA, chylomicron-treated, rep3

description:
Library name: Chylo-24-3
miR.Counts-Goldberg-08-19-2025.csv

value: chylomicron-treated


title: Run1, Tfr, Citrobacter, rep3

description:
Library name: Run1 S24
column names in raw_counts and lcpm csv(s) corresponds to sample number:24
24

value: Citrobacter


title: Run1, Teff, H. poly, rep1

description:
Library name: Run1 S12
column names in raw_counts and lcpm csv(s) corresponds to sample number:12
12


title: CL007 T-cells, Infected Macrophages and Mtb lysate, GEX

description: Library name: CL007-Lysate-GEX


title: Run1, Teff, Citrobacter, rep3

description:
Library name: Run1 S11
column names in raw_counts and lcpm csv(s) corresponds to sample number:11
11


title: Run1, Teff, Citrobacter, rep1

description:
Library name: Run1 S9
column names in raw_counts and lcpm csv(s) corresponds to sample number:9
9


title: Mouse skin, radiated, Week 4, Rep 4

city: Bronx

first: Kosaku

last: Shinoda

state: New York

address: 1301 Morris Park Ave

department: Medicine

institute: Albert Einstein College of   Medicine/Montefiore Medical Center

description:
Library name: Sample 34
W4-4

data_processing:
Fastq files were trimmed for  adaptor and low quality sequence using Trim Galore v0.6.7
Transcript-level counts were estimated by Kallisto v0.46.2
Outputs from Kallisto were imported into R using the Bioconductor package tximport (v1.28.0), and the expression levels of each gene were estimated.
Assembly: mm10
Supplementary files format and content: comma-separated text file including gene-level raw counts for each sample

source_name: Skin

extract_protocol:
Samples were extracted for total RNA using the RNeasy mini-kit (Qiagen) protocol.
Samples were sent to Azenta (GENEWIZ) for RNA sequencing, and bioinformatic analysis was performed using Kallisto and DESeq2 software.

treatment_protocol: Radiation conducted for the four groups of mice at initial time point. Output was delivered over 420 seconds at a dose rate of 3.6 Gy/min for a total of 25 Gy. After radiation, treated skin was shaved over the left flank with an electric razor. Skin biopsies were taken at each time point from the radiated site, stored in RNAlater, and frozen at -80 degrees Celsius.

value: Skin


title: Run1, Teff, Citrobacter, rep2

description:
Library name: Run1 S10
column names in raw_counts and lcpm csv(s) corresponds to sample number:10
10


title: CL007 T-cells, Infected Macrophages, TCR

description: Library name: CL007-Infected-TCR

value: Mtb-infected macrophages


title: Mouse skin, control, Week 4, Rep 4

description:
Library name: Sample 35
W4-4C


title: Run1, Teff, LCMV spl, rep2

description:
Library name: Run1 S6
sample not in processed data after filtering
6

value: spleen

value: LCMV spl


title: Mouse skin, radiated, Week 4, Rep 3

description:
Library name: Sample 32
W4-3


title: Run1, Teff, T. muris, rep1

description:
Library name: Run1 S7
sample not in processed data after filtering
7

value: T. muris


title: Run1, Teff, LCMV, rep2

description:
Library name: Run1 S4
sample not in processed data after filtering
4

value: LCMV


title: CL003 T-cells, Infected Macrophages and Mtb lysate, TCR

description: Library name: CL003-Lysate-TCR


title: Run1, Teff, LCMV spl, rep1

description:
Library name: Run1 S5
sample not in processed data after filtering
5


title: CL003 T-cells, Infected Macrophages and Mtb lysate, GEX

description: Library name: CL003-Lysate-GEX


title: Mouse skin, control, Week 4, Rep 2

description:
Library name: Sample 31
W4-2C


title: Run1, Teff, LCMV, rep1

description:
Library name: Run1 S3
column names in raw_counts and lcpm csv(s) corresponds to sample number:3
3


title: CL003 T-cells, Infected Macrophages, TCR

description: Library name: CL003-Infected-TCR


title: Mouse skin, radiated, Week 4, Rep 2

description:
Library name: Sample 30
W4-2


title: Run1, Teff, Influenza A, rep1

description:
Library name: Run1 S1
column names in raw_counts and lcpm csv(s) corresponds to sample number:1
1

value: Influenza A


title: Mouse skin, control, Week 4, Rep 1

description:
Library name: Sample 29
W4-1C


title: Run1, Teff, Influenza A, rep2

description:
Library name: Run1 S2
column names in raw_counts and lcpm csv(s) corresponds to sample number:2
2


title: CL002 T-cells, Infected Macrophages, TCR

description: Library name: CL002-Infected-TCR

value: non-LTBI


title: 4C_9.5dpcPI_mb_lot2

city: Yokohama

first: Shinsuke

last: Ito

state: Kanagawa

address: 1-7-22 Suehirocho

department: IMS

country: Japan

institute: RIKEN

description: Library name: Sample 6

data_processing:
Reads were aligned to UCSC mm9 or UCSC mm10 using bowtie2. The SAM files were converted to the BAM format using Samtools. The PCR duplicates were removed by Picardtools. The BAM files were converted to bigwig files by deepTools2 for visualization. The bigwig files were normalized to reads per million mapped sequence reads (RPKM).
Assembly: mm9
Supplementary files format and content: txt
Library strategy: 4C-seq

source_name: 9.5 dpc mouse embryonic midbrain

growth_protocol: Embryos were disected out at day 9 pregnancy. Embryos with 15 to 20 somites were classified as 9.0 dpc and more than 20 somites were classified as 9.5 dpc.

extract_protocol:
Tissues were cross-linking by 1% formaldehyde for 10 min at room temperature. Cross-linked cells were washed once with wash buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM spermidine), added permeabilization buffer I (10 mM Tris-HCl (pH8.0), 10 mM NaCl, 0.2% NP-40) and chilled on ice for 20 minutes. After centrifuge, pellets were suspended with permeabilization buffer II (10 mM Tris-HCl (pH8.0), 50 mM NaCl, 10 mMgCl2, 10 ug/ml BSA, 0.2% SDS) and leave 37 degrees for 10 minutes and then add 28 ul 20 % Triton x-100 and leave 37 degrees for 10 min. After discard supernatant, pellets are washed with DpnII buffer twice and then add restriction enzyme DpnII to cell suspension by DpnII buffer. Incubate at 37 degree for cover night. Digested samples were washed with wash buffer (10 mM Tris-HCl (pH8.0), 50 mM NaCl, 10 mMgCl2, 10 ug/ml BSA) and then ligate in 100 ul size at 16 degree for overnight. 3.3 ul of 500 mM EDTA, 1 ul of 10 % SDS and 1 ul of 20 mg/ml ProinaseK to those ligated samples, and then treated 65 degree for 6 hours and 55 degrees overnight. DNA from those samples were purified with SPRI beads and eluted DNA samples were used as 3D samples.
3D samples were digested and ligated with adaptor by using NEBNext Ultra II FS DNA prep kit (NEB E7805) following manufacturer’s instruction. And ligates were amplified with bait primer I (CCGTTCTCGGCCTGATTATTAGCG) and adaptor primer (CAAGCAGAAGACGGCATACGAGAT). Then, further amplification by PCR with bait primer II (AATGATACGGCGACCACCGAGATCTACAC(index P5)ACACTCTTTCCCTACACGACGCTCTTCCGATCTCATTTCGCCCTTTGATTTATTG) and adaptor primer.

treatment_protocol: Midbrain part of embryos were disected out and store in Bambanker(GC Lymphotec: CS-02-001) at -80 degree.

value: 9.5 dpc mouse embryonic midbrain

value: Bortezomib+

value: WT

tag: chip antibody

value: no


title: 4C_9.5dpcPI_mb_lot1

description: Library name: Sample 5


title: Mouse skin, radiated, Week 4, Rep 1

description:
Library name: Sample 28
W4-1


title: Run1, Teff, T. muris, rep2

description:
Library name: Run1 S8
column names in raw_counts and lcpm csv(s) corresponds to sample number:8
8

value: lymph node

value: T effector (Teff)


title: 4C_9.5dpc_mb_lot2

description: Library name: Sample 4

value: Tamoxifen-


title: CL007 T-cells, Infected Macrophages, GEX

description: Library name: CL007-Infected-GEX

value: blood

value: LTBI


title: CL002 T-cells, Infected Macrophages, GEX

description: Library name: CL002-Infected-GEX


title: Mouse skin, control, Week 4, Rep 3

description:
Library name: Sample 33
W4-3C

value: Skin


title: 4C_9.5dpc_mb_lot1

description: Library name: Sample 3


title: 4C_9.0dpc_mb_lot2

description: Library name: Sample 2

source_name: 9.0 dpc mouse embryonic midbrain

value: 9.0 dpc mouse embryonic midbrain


title: hESC H9 cells, in-vitro, Day35

city: Milan

first: Elena

last: Cattaneo

address: Via Celoria, 26

department: Bioscience

country: Italy

institute: University of Milan

description: Library name: STR_progenitors_DIV35

data_processing:
nf-core scrnaseq pipeline v2.5.1
Assembly: GRCh38
Supplementary files format and content: Features_matrix_grafts.mtx Matrix file includes raw counts of grafted cells
Supplementary files format and content: Features_matrix_vitro.mtx Matrix file includes raw counts of in-vitro cells
Supplementary files format and content: Features_processed_grafts.tsv tab-delimited text file includes gene names of grafted cells
Supplementary files format and content: Features_processed_vitro.tsv tab-delimited text file includes gene names of in-vitro cells
Supplementary files format and content: MetaData_processed_grafts.tsv tab-delimited text file includes processed dataset metadeta of grafted cells
Supplementary files format and content: MetaData_processed_vitro.tsv tab-delimited text file includes processed dataset metadeta of in-vitro cells

source_name: In-vitro cells

extract_protocol:
Nuclei were thawed in ice and transferred in a glass douncer with 1mL of nuclei lysis buffer till complete homogenization.The nuclei suspension was centrifuged at 500 g for 5 min at 4 °C, and resuspended in cold resuspension buffer. The resuspended nuclei were then filtered through a 30 μm nylon mesh into pre-coated 1.5ml eppendorfs. DRAQ7 was added immediately before fluorescence-activated nuclear sorting. Intact nuclei were identified based on DRAQ7 and side scatter (SSC) signals and sorted with the BD FACSAria III Cell Sorter using a 100 μm nozzle into collection tubes coated with D-PBS supplemented with 2% BSA.
10,000 to 12,000 nuclei per sample (in up to 45 μl total volume) were collected for the library preparation. Single nuclei were captured using the Chromium Single Cell 3´ Chips (10X Genomics, cat. no. PN-120233, v3.1) loaded with master mix and barcoded beads. After pooling and amplification, the quality of the resulting libraries was checked by a Bioanalyzer (DNA HS kit, Agilent) and sequencing was performed on an Illumina NovaSeq 6000 in 100 bp paired-end mode.

value: In-vitro cells

value: hESC H9

value: hESC differentiated into MSN enriched culture


title: 4C_9.0dpc_mb_lot1

description: Library name: Sample 1


title: hESC H9 cells, in-vitro, Day15

description: Library name: STR_progenitors_DIV15


title: R2_trp4 hESC H9 cells, graft, Month6

description: Library name: R2_trp4

source_name: Brain graft

value: Brain graft


title: Mouse skin, control, Week 3, Rep 4

description:
Library name: Sample 27
W3-4C


title: Mouse skin, radiated, Week 3, Rep 4

description:
Library name: Sample 26
W3-4


title: CL003 T-cells, Infected Macrophages, GEX

description: Library name: CL003-Infected-GEX

value: Mtb-infected macrophages


title: Mouse skin, control, Week 3, Rep 2

description:
Library name: Sample 23
W3-2C


title: 4C_Skp1a_mut_mb

description: Library name: Sample 8

value: Tamoxifen+

value: Skp1a KO


title: Mouse skin, control, Week 3, Rep 3

description:
Library name: Sample 25
W3-3C


title: 4C_Skp1a_cont_mb

description: Library name: Sample 7

value: 9.5 dpc mouse embryonic midbrain


title: Mouse skin, control, Week 3, Rep 1

description:
Library name: Sample 21
W3-1C


title: Mouse skin, radiated, Week 3, Rep 2

description:
Library name: Sample 22
W3-2


title: R12_trp2 hESC H9 cells, graft, Month6

description: Library name: R12_trp2


title: R12_trp3 hESC H9 cells, graft, Month6

description: Library name: R12_trp3


title: R10_trp1 hESC H9 cells, graft, Month6

description: Library name: R10_trp1


title: Mouse skin, radiated, Week 3, Rep 1

description:
Library name: Sample 20
W3-1


title: Mouse skin, control, Week 2, Rep 4

description:
Library name: Sample 19
W2-4C


title: Mouse skin, control, Week 2, Rep 3

description:
Library name: Sample 17
W2-3C