title: X2PSM_CT_rep2

description:
Library name: H3K27me3_X2PSM_CT_rep2
H3K27me3 CUT&Tag in CBX2_PSM_HT cells

data_processing:
CUT&Tag and CUT&RUN sequencing reads were trimmed using Cutadapt: Illumina adapter sequences were removed, and reads were trimmed to 140 bp. Reads less than 35 bp were discarded. Trimmed reads were aligned to either the mm10 version of Mus musculus genome using bowtie2. Samtools and bedtools were used for processing aligned reads from sam to bed files. Duplicate reads were discarded for further analysis if the reads had the same start and end coordinates.
Assembly: mm10
Supplementary files format and content: Bigwig files contain coverage at 100 bp windows genome-wide  calculated as the number of reads that mapped at that window, normalized by the factor N: N = 2800000000/(Total number of mapped reads), 2800000000 was a number chosen arbitrarily in the range of total mapped base pairs in M. musculus genome.
Library strategy: CUT&Tag

source_name: mESC CBX2-PSM-HaloTag

extract_protocol:
The CUT&RUN of CBX2 in CBX2fl/fl-HaloTag was performed using a CUTANA™ ChIC/CUT&RUN Kit (EpiCypher). Cells were harvested, split to a single-cell suspension, counted, and 0.5 x 10^6 cells were used in each reaction, and reactions were run in duplicate. Cells were washed with PBS, then Wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 x EDTA-free protease Inhibitor), and bound to activated ConA beads for 10 minutes. Supernatant was removed from beads, 50 μL Antibody Buffer ((20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 x EDTA-free protease Inhibitor, 0.1% Digitonin, 2 mM EDTA) with 1:50 Anti-HaloTag® (polyclonal) (Promega) or 1:200 Anti-GFP (monoclonal) (Invitrogen) was added, and cells were gently vortexed to thoroughly resuspend beads before overnight incubation at 4°C on a nutator. The following day, the Antibody buffer was removed with the tubes on a magnetic stand and cells were washed twice with pAG-MNase Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 x EDTA-free protease Inhibitor, 0.1% Digitonin). After the washes, 50 μL pAG-MNase Buffer + 2.5 μL pAG-MNase was added to each reaction, tubes were then vortexed to mix and incubated at RT for 10 minutes. Supernatant was removed and each reaction was washed twice with 200 μL pAG-MNase Buffer. Afterwards 2 mM CaCl2 in pAG-MNase Buffer was added to activate pAG-MNase for chromatin digestion, beads were vortexed to resuspend, and tubes were then incubated at 4°C on a nutator for 2 hours. Stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/mL RNase A, 50 μg/mL Glycogen) + E. coli spike-in was added following digestion and tubes were gently vortexed to mixed then placed in a preheated thermocycler set to 37°C. Reactions were then purified and eluted from included columns, then quantified using a Qubit.  Genome-wide H3K27me3 domain changes were profiled using the CUT&Tag protocol adapted from EpiCypher. Cells were harvested via 0.25% trypsin-EDTA solution and counted using 0.4% trypan blue stain and Countess automated cell counter. A single-cell suspension was prepared by washing cells with cold 1x PBS and resuspending 1.0 x 106 cells in 1 mL cold nuclear extraction buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.1% Triton x-100, 20% glycerol, & 0.5 mM spermidine), then incubated on ice for 10 minutes to isolate nuclei. Biomag Plus Concanavalin A beads were activated with two washes of cold bead activation buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, & 1 mM MnCl22). After activation, beads were added to aliquots of 0.1 x 106 isolated nuclei and incubated at room temperature for 10 minutes. Nuclei:bead samples were resuspended in 50 µL cold Antibody150 buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 2 mM EDTA, & protease inhibitors) followed by the addition of 0.5 µg of anti-H3K27me3 (#9733S, Cell Signaling Technology). To facilitate primary antibody binding, samples were incubated on nutator at room temperature for 1 hour. Samples were resuspended in 50 µL Digitonin150 buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, & protease inhibitors) followed by the addition of 0.5 µg CUTANA anti-rabbit secondary antibody (#13-1047, EpiCypher). Samples were then incubated on nutator at room temperature for 1 hour to facilitate binding, followed by two washes with 200 µL cold Digitonin300 buffer (20 mM HEPES-KOH pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, & protease inhibitors). The tagmentation reaction was performed by resuspending samples in 50 µL cold Tagmentation buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 10 mM MgCl2, & protease inhibitors) and incubating at 37°C in thermocycler for 1 hour. Samples were washed with 50 µL TAPS buffer (10 mM TAPS pH 8.5 & 0.2 mM EDTA) then resuspended in 5 µL SDS Release buffer (10 mM TAPS pH 8.5 & 0.1% SDS) to quench the tagmentation reaction and release adaptor-tagged DNA fragments into solution.
For CUT&RUN, following end repair and adaptor ligation, 1X SPRIselect beads were used to wash prepped DNA and PCR was ran for 15 cycles of denaturation and annealing/extension. The PCR settings were: Initial Denaturation at 98°C for 30 Seconds, Denaturation at 98°C for 10 seconds, Annealing/extension at 65°C for 75 seconds, Final Extension at 65°C for 5 minutes. Following PCR, 1X SPRIselect beads were used to wash amplified library-prepped DNA and each eluted product was ran on a Tapestation (Agilent) for fragment analysis before multiplexing and PE150 sequencing. For CUT&Tag, After incubating samples at 58°C in thermocycler for 1 hour, 15 µL SDS Quench buffer (0.67% Triton x-100), 2 µL i5 universal primer (EpiCypher), 2 µL i7 barcoded primer (EpiCypher), 0.005 ng Escherichia coli spike-in DNA (made in-house), and 25 µL NEBNExt High Fidelity 2x PCR Master Mix were added to each sample for library construction with the following PCR protocol: 5 minutes at 58°C, 5 minutes at 72°C, 45 seconds at 98°C, 14 cycles of 15 seconds at 98°C and 10 seconds at 60°C, with a final extension for 1 minute at 72°C. Libraries were checked for quality using the Qubit dsDNA HS Assay kit and TapeStation High Sensitivity DNA assay kit and then sequencing was performed using Novaseq 6000 (Novogene) to generate 150 bp paired-end reads.

value: mESC CBX2-PSM-HaloTag


title: SR098

status: Public on Feb 05 2026

type: SRA

city: Gainesville

first: Leslie

middle: Anne

last: Smith

state: Fl

address: 1889 Museum Rd

department: Computer Information Science and Engineering

country: USA

institute: University of Florida

description: Library name: SR098

library_source: transcriptomic

data_processing:
After sequencing, the RNA-seq aligner STAR was used to align reads using GRCh38 reference genome. fastqc was used to perform quality control on bam files. Multiqc was used to create report of qc results. Transcripts for each gene are counted using featureCounts from the subread package. Subsequent processing of the expression matrix mimicked refine.bio's RNA-seq processing pipeline for consistent processing across datasets: First duplicate HUGO symbol gene names were summarized by taking the mean, then expression values were quantile normalized using the homo sapien reference quantiles provided by refine.bio (https://api.refine.bio/v1/qn_targets/).
Assembly: GRCh38 reference genome
Supplementary files format and content: Processed samples are included in the ExpressionAllSamples.tsv gene expression matrix tsv file and MetadataAllSamplesAfterAddedSurvival.xlsx along with all other samples used in study. New samples can be identified in MetadataAllSamplesAfterAddedSurvival.xlsx file under dataset Guirgisetal

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
The preparation and subsequent sequencing (using the Illumina NextSeq 550 instrument) followed exactly the protocol described in the Illumina Stranded mRNA Prep Ligation Reference Guide. Quickly summarized, this involved 8 steps - (1) purifying and fragmenting the messenger RNA by capturing mRNAs with polyA tails using oligo(dT) magnetic beads and then fragmenting and priming the RNA , (2) synthesizing the first strand cDNA (complimentary DNA) by reverse transcribing the hexamer-primed RNA-fragments, (3) synthesizing the second strand cDNA to generate blunt-ended and doubled-stranded cDNA fragments, (4) adenylating 3-inch ends by adding an adenine nucleotide and a thymine nucleotide to the ends of the blunt fragments to prevent them from ligating to each other and for providing overhang for ligating the adaptors, (5) ligating anchors to the ends of the cDNA fragments in preparation for dual indexing, (6) cleaning up fragments with magnetic beads
(Numbered steps continued from extraction protocol): (7) amplifying the library using PCR to selectively amplify fragments and add indexes and primer sequences for cluster generation, and (8) cleaning up the library using magnetic beads to purify the dual-indexed libraries. The final libraries were checked using the Agilent 2100 Bioanalyzer and DNA 1000 kit and were then diluted to the starting concentration for the NextSeq550 model. Each of our samples required four lanes on the flow cells that went into the sequencing machine and each lane was run twice.

tag: tissue

value: Whole blood

tag: outcome

value: RAP

tag: age

tag: gender

value: Female

tag: race

value: Caucasian

tag: shock

value: Yes

tag: sofa

tag: respsofa

tag: inhospdeath

value: No

tag: phenotype

value: Hypo

tag: ards


title: KimJ_RNA038 | 014 | CD45

city: Seoul

first: Seoyoon

last: Ham

address: Yonsei-ro 50-1, Seodaemun-gu

country: South Korea

institute: Yonsei University College of Medicine

description: Library name: DSP-1001660011091-D-B06

data_processing:
Raw fastq files were converted to DCC files by the Nanostring geomxngspipeline software.
The DCC files were uploaded to the DSP software and the read counts file was exported for further analysis.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files generated by the Nanostring geomxngspipeline software.
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
FFPE tissue sections (5 µm) were prepared on BOND Plus slides, followed by deparaffinization, rehydration, and antigen retrieval using Tris-EDTA and proteinase K treatment. The tissues were hybridized overnight with GeoMx WTA RNA probes (18,677 genes) and stained with morphology markers (panCK, CD45, CD31, and SYTO 13). ROIs were selected and categorized into four regions: epithelium epidermis (above dermis), epithelium dermis (sinus tracts), dermis superficial inflammation (immune cells near epidermis), and dermis deep inflammation (immune cells near epithelium dermis). Using the DSP instrument, ROIs were segmented into AOIs, and indexed oligonucleotides were UV-released and collected.
Spatial transcriptome libraries were prepared using NanoString's GeoMx Human Whole Transcriptome Atlas kit and Digital Spatial Profiler instrument, followed by library construction with Seq Code primers and AMPure XP bead purification. Sequencing was performed on Illumina NovaSeq 6000 (2 × 151 bp paired-end).

value: Skin

tag: disease


title: Micro-C, CBX2_WT_rep3

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
Library name: X2_WT_rep3
Micro-C

library_source: genomic

data_processing:
Micro-C data processing and analysis: Micro-C datasets were processed using the ENCODE Hi-C data processing pipeline, aligning to the mm10 reference genome (UCSC notation) without specifying a restriction enzyme map. Each condition was processed independently. Finally, hic files were produced using the Juicer software suite. 68 The resultant interaction maps were normalized using the Knight-Ruiz (KR) matrix balancing algorithm, and all downstream analyses were performed on a 5 kb resolution. Pile-up analysis and contact intensity distribution: Micro-C data with a 5-kb resolution were used as input for the analyses. These analyses were performed using the coolpup.py package (version 0.9.5) running on Python version 3.10.12. 53 This package was employed under default settings to generate interaction profiles that quantitatively assess the average interaction strength between designated pairs of genomic intervals within each identified cluster. Interaction profiles were visualized using the plot_coolpup.py module. Subsequently, the distribution of interaction profile values was analyzed to detect significant differences between the two experimental conditions. Outliers in interaction values were removed, retaining data within the 20th and 80th percentiles. A two-sided Mann-Whitney U test was applied to the distribution data, where a p-value of less than 0.0001 was annotated with three asterisks (***), denoting statistical significance.
Assembly: mm10
Supplementary files format and content: .cool file with 5000bp Bin

molecule: genomic DNA

organism: Mus musculus

source_name: mESC CBX2fl/fl-HaloTag

growth_protocol: Female mouse embryonic stem cells (PGK12.1 provided by Dr. Neil Brockdoff from University of Oxford, UK) were cultured at 37°C and 5% CO2 on 0.2% gelatin, in mESC medium which consists of Dulbecco’s Modified Eagle Medium (DMEM) media supplemented with 15% Fetal Bovine Serum (VWR), 0.1 mM β-mercaptoethanol (Gibco), 2.0 mM L-Glutamine (Gibco), 100 Units/mL Penicillin-Streptomycin (Gibco), 1× MEM Non-Essential Amino Acids (Gibco), 10 µg/mL Ciprofloxacin (Sigma), and 10^3 units/mL leukemia inhibitor factor (LIF).

extract_protocol:
Micro-C experiments were performed using a Dovetail® Micro-C Kit (Cantata Bio). 1.0 × 10⁶ cells were frozen at -80°C for at least 30 minutes and then thawed at room temperature for 5 minutes. The thawed pellet was resuspended in 200 µL of the freshly prepared DSG solution and nutated for 10 minutes at room temperature. Following nutation, 5.4 µL of 37% formaldehyde was added to a final concentration of 1%, and the mixture was nutated for an additional 10 minutes. After washing with 1× Wash buffer, the cells were resuspended in 50 µL of a MNase digest master mix (50 µL 1× Nuclease Digest Buffer + 0.5 µL MNase Enzyme Mix). The tube was then incubated in an agitating thermal mixer at 37°C at 1250 RPM for 18 minutes for in situ MNase digestion. After digestion, the reaction was stopped by adding 5 μL of 0.5 M EGTA, and QC was performed to confirm a 50-90% mono-nucleosome digestion profile. 3 μL of 20% SDS was added to the digested samples. The mixture was then incubated at 22°C for 5 minutes in the thermal mixer at 1250 RPM. Up to 1500 ng of lysate per sample was mixed with Chromatin Capture Beads. Once mixed, samples were incubated at room temperature for 10 minutes. The beads were collected on the magnetic rack and then washed 3 times with 1× Wash buffer. 53 μL of an End Polishing Master Mix (50 μL End Polishing Buffer + 3 μL End Polishing Enzyme Mix) was added to the washed sample. After the end polishing, 50 µl Bridge Ligation Mix was added to the beads, followed by 1 µl Bridge Ligase. Once thoroughly mixed, the reactions were incubated at 22°C for 30 minutes in an agitating thermal mixer set at 1,250 rpm. Following the bridge ligation, 50 μL Intra-Aggregate Ligation Mix was added to each sample. The samples were mixed and incubated at 22°C for 4 hours in an agitating thermal mixer at 1,250 rpm. After intra-aggregate ligation, samples were resuspended with 51.5 µL of Crosslink Reversal Solution (55 µL Crosslink Reversal Buffer + 1.7 µL Proteinase K) and incubated at 55°C for 10 minutes, then the temperature was increased to 65°C for overnight. DNAs were purified using SPRIselect beads and eluted with 95 μL TE Buffer pH 8.0. The eluted DNAs were quantified using a Qubit fluorometer and dsDNA HS kit.
For Micro-C 150 ng of purified DNA was used to prepare a library for each replicate using the NEBNext Ultra II kit. 25 μL of Streptavidin beads was washed and mixed with 95 μL of purified and adaptor-ligated DNA. The beads were then washed with LWB, NWB, and 1× Wash buffer. 45 µL Index PCR Master Mix (25 µL Hot Start PCR Ready Mix + 20 µL water per sample) was added to the beads, followed by 5 µL of a unique UDI Primer Pair. The PCR reactions were performed with the following settings: Enzyme activation at 98°C for 3 minutes, followed by 12 cycles of denaturation at 98°C for 20 seconds, annealing at 65°C for 30 seconds, extension at 72°C for 30 seconds, and a final extension at 72°C for 1 minute. After amplification, 47 μL of the supernatant was collected, and 53 µL of TE Buffer (pH 8.0) was added to the solution, followed by 50 μL of SPRIselect beads. 145 µl of the supernatant was collected and mixed with 30 μL of SPRIselect beads. After washing, the beads were air-dried, and the DNA fragments were eluted with 30 μL TE Buffer (pH 8.0). The final elution was quantified with a Qubit fluorometer and a dsDNA HS kit, and the fragments were analyzed on a Tapestation to confirm a size distribution of 350-1,000 bp. NSG was performed to obtain a total of 300 million to 800 million reads between the replicates for each condition

treatment_protocol: To conditionally deplete CBX2, CBX2 fl/fl-HT mESCs were treated with 1.0 µM 4-Hydroxytamoxifen (4-OHT, Sigma) for 48 hours

tag: cell line

value: mESC CBX2fl/fl-HaloTag

tag: cell type

value: mESC


title: SR092

description: Library name: SR092

value: Male


title: KimJ_RNA038 | 012 | panck

description: Library name: DSP-1001660011091-D-B03


title: Micro-C, CBX2_KO_rep1

description:
Library name: X2_KO_rep1
Micro-C

tag: treatment

value: 48 hours of 1.0 µM 4-Hydroxytamoxifen


title: SR080

description: Library name: SR080

value: ED

value: African American


title: SR078

description: Library name: SR078

value: Normo


title: SR079

description: Library name: SR079

value: CCI


title: PGK_WT_CT_rep1

description:
Library name: H3K27me3_PGK_WT_CT_rep1
H3K27me3 CUT&Tag in PGK12.1 Parental WT cells

source_name: mESC PGK12.1

value: mESC PGK12.1


title: KimJ_RNA038 | 011 | CD45

description: Library name: DSP-1001660011091-D-B02


title: SR073

description: Library name: SR073

value: Whole blood

value: yes


title: CBX2_CR_PSM_rep2

description:
Library name: CBX2PSM_HT_CR_rep2
HaloTag CUT&RUN

data_processing:
CUT&Tag and CUT&RUN sequencing reads were trimmed using Cutadapt: Illumina adapter sequences were removed, and reads were trimmed to 140 bp. Reads less than 35 bp were discarded. Trimmed reads were aligned to either the mm10 version of Mus musculus genome using bowtie2. Samtools and bedtools were used for processing aligned reads from sam to bed files. Duplicate reads were discarded for further analysis if the reads had the same start and end coordinates.
Assembly: mm10
Supplementary files format and content: Bigwig files contain coverage at 100 bp windows genome-wide  calculated as the number of reads that mapped at that window, normalized by the factor N: N = 2800000000/(Total number of mapped reads), 2800000000 was a number chosen arbitrarily in the range of total mapped base pairs in M. musculus genome.
Library strategy: CUT&RUN

source_name: mESC CBX2_PSM_HT

value: mESC CBX2_PSM_HT


title: KimJ_RNA038 | 011 | panck

description: Library name: DSP-1001660011091-D-B01


title: X2PSM_CT_rep1

description:
Library name: H3K27me3_X2PSM_CT_rep1
H3K27me3 CUT&Tag in CBX2_PSM_HT cells

value: mESC CBX2-PSM-HaloTag


title: KimJ_RNA038 | 010 | CD45

description: Library name: DSP-1001660011091-D-A12


title: SR067

description: Library name: SR067

value: RAP

value: Female

value: Yes


title: SR069

description: Library name: SR069

value: No


title: SR060

description: Library name: SR060


title: KimJ_RNA038 | 010 | panck

description: Library name: DSP-1001660011091-D-A11

value: Skin


title: SR059

description: Library name: SR059

value: Hypo


title: PGK_HT_CR_rep2

description:
Library name: PGK_HT_CR_rep2
HaloTag CUT&RUN


title: SR061

description: Library name: SR061


title: CBX2_CR_PSM_rep1

description:
Library name: CBX2PSM_HT_CR_rep1
HaloTag CUT&RUN


title: KimJ_RNA038 | 009 | panck

description: Library name: DSP-1001660011091-D-A10


title: SR076

description: Library name: SR076

value: CON

value: Male

value: Caucasian


title: KimJ_RNA038 | 016 | CD45

description: Library name: DSP-1001660011091-D-B08


title: SR052

description: Library name: SR052

value: African American


title: PGK_HT_CR_rep1

description:
Library name: PGK_HT_CR_rep1
HaloTag CUT&RUN


title: KimJ_RNA038 | 008 | panck

description: Library name: DSP-1001660011091-D-A09


title: RS069

description: Library name: RS069


title: CBX2_KO_rep2

description:
Library name: X2_pHT_KO_rep2
HaloTag CUT&RUN

value: mESC CBX2fl/fl-HaloTag

value: 48 hours of 1.0 µM 4-Hydroxytamoxifen


title: RS068

description: Library name: RS068


title: SR043

description: Library name: SR043


title: KimJ_RNA038 | 007 | panck

description: Library name: DSP-1001660011091-D-A08


title: RS066

description: Library name: RS066


title: CBX2_KO_rep1

description:
Library name: X2_pHT_KO_rep1
HaloTag CUT&RUN


title: RS065

description: Library name: RS065

value: Normo


title: KimJ_RNA038 | 005 | panck

description: Library name: DSP-1001660011091-D-A06


title: KimJ_RNA038 | 006 | panck

description: Library name: DSP-1001660011091-D-A07


title: adipose-derived stem cells,White differentiation with 50 μM sodium alginate co-stimulation,Day6,s1003

city: Nabjing

first: Yufan

last: Gan

address: Longmian Avenue

country: China

institute: Nanjing Medical University

description: Library name: s1003

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence using CLC genomic benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC  genomic benchwork(parameters-mismath cost:3 length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Inguinal white adipose tissue

growth_protocol: Adipose-derived stem cells from subcutaneous fat were maintained in DMEM/F-12 supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using AG RNAex Pro Reagent (Accurate Biotechnology(Hunan)Co.Ltd).1.3μg of total RNA was used for the construction of sequencing libraries.
RNA libraries of RNA-seq were prepared using SMARTER mRNA-Seq Library Prep KIt following manufacturer's protocols.

treatment_protocol: adipogenic differentiation was induced by treatment of 4-day post confluent cells(designated day 0) with 1μg/ml insulin(Merck),1μM Dexamethasone(Merck),0.5mM  3-Isobutyl-1-methylxanthine(Merck),and 1μM Rosiglitazone(MCE) in the presence of DMEM/F-12 supplemented with 10% fetal bovine serum(FBS) and antibiotics.  At the same time, 0 μM, 50 μM, and 100 μM sodium alginate were added separately for co-stimulation(n=3)until day 2. Change the medium and maintain adipocyte differentiation with a medium containing only Insulin and rotglitazone.  Meanwhile, add 0 μM, 50 μM and 100 μM sodium alginate for co-stimulation respectively (n=3).  Collect the cell RNA on the 7th day

value: Inguinal white adipose tissue

value: primary cells

value: Mature white adipocyte

tag: genotype

value: wild type C57

value: The cells were whitened for 6 days and co-stimulated by adding 100μM sodium alginate

tag: batch

value: paired-end


title: RS063

description: Library name: RS063

tag: tissue

value: Whole blood

value: RAP

value: Yes


title: RS062

description: Library name: RS062

tag: outcome

value: Female

value: No


title: adipose-derived stem cells,White differentiation with 50 μM sodium alginate co-stimulation,Day6,s1002

description: Library name: s1002


title: RS067

description: Library name: RS067

value: CCI

tag: age

value: Hypo

value: yes


title: KimJ_RNA038 | 004 | panck

description: Library name: DSP-1001660011091-D-A05

value: Skin


title: RS060

description: Library name: RS060

tag: gender

value: Male

value: African American


title: KimJ_RNA038 | 002 | panck

description: Library name: DSP-1001660011091-D-A03


title: RS058

description: Library name: RS058

tag: race

value: Caucasian


title: RS064

description: Library name: RS064

tag: shock

value: Normo


title: KimJ_RNA038 | 003 | panck

description: Library name: DSP-1001660011091-D-A04


title: RS056

description: Library name: RS056

tag: sofa


title: KimJ_RNA038 | 001 | panck

description: Library name: DSP-1001660011091-D-A02


title: RS053

description: Library name: RS053

value: ED

tag: respsofa


title: adipose-derived stem cells,White differentiation with 50 μM sodium alginate co-stimulation,Day6,s501

description: Library name: s501

value: Inguinal white adipose tissue

value: primary cells

value: Mature white adipocyte

value: wild type C57

value: The cells were whitened for 6 days and co-stimulated by adding 50μM sodium alginate


title: RS059

description: Library name: RS059

value: Whole blood

value: RAP

tag: inhospdeath


title: adipose-derived stem cells,White differentiation with 50 μM sodium alginate co-stimulation,Day6,s502

description: Library name: s502

value: paired-end


title: adipose-derived stem cells,White differentiation with 50 μM sodium alginate co-stimulation,Day6,s503

description: Library name: s503


title: SW620_0701086641

city: Doha

first: Cristina

last: Maccalli

address: Doha

country: Qatar

institute: Sidra Medicine

description:
Library name: 701086641
Illumina Truseq

data_processing:
Processing of total RNA-Seq data was done using the Bcbio RNAseq pipeline (Bcbio v1.2.3).
a quality check of raw data was done using FastQC version 0.11.9.
Alignment was done using STAR (version 2.6.1)
Differential expression analyses were performed using the limma R package (v3.6.0) from the Bioconductor R project.
Assembly: hg38 genome
Supplementary files format and content: tsv format with cpm log2 data
Supplementary files format and content: tsv format with LogFC data and stat of differential expressed genes in CIC vs FBS samples.

growth_protocol: CICs were cultured as colon-spheres in Advanced DMEM/F12 medium  containing 20 ng/ml of EGF , 50 ng/ml FGF-2. Differenciated cells were cultured in the presence of RPMI 1640 supplemented with 10% FBS

extract_protocol:
RNA extraction and purification from CICs and FBS cell lines were performed using the AllPrep DNA/RNA Mini Kit  The amount and the quality of nucleic acids have been assessed by the Nanodrop 8000 and Qubit PicoGreen assay and RNA RIN threshold has been determined by the 2100 BioAnalyzer.
Total RNA was used for library preparation using the Illumina Truseq Stranded Total RNA HMR kit which assists in depleting ribosomal RNA (rRNA) using biotinylated oligos combined with streptavidin-coated magnetic beads.

value: FBS

value: A


title: adipose-derived stem cells,White differentiation with 0 μM sodium alginate co-stimulation,Day6,s03

description: Library name: s03

value: The cells were whitened for 6 days without co-stimulation with sodium alginate


title: RS051

description: Library name: RS051

value: Female

value: Yes

value: No

tag: phenotype

value: Hypo


title: RS055

description: Library name: RS055

value: Male

value: Caucasian

value: Normo

tag: ards


title: RS057

description: Library name: RS057

value: African American


title: RS052

description: Library name: RS052


title: RS054

description: Library name: RS054


title: adipose-derived stem cells,White differentiation with 50 μM sodium alginate co-stimulation,Day6,s1001

description: Library name: s1001

value: Inguinal white adipose tissue

value: primary cells

value: Mature white adipocyte

value: The cells were whitened for 6 days and co-stimulated by adding 100μM sodium alginate


title: adipose-derived stem cells,White differentiation with 0 μM sodium alginate co-stimulation,Day6,s02

description: Library name: s02

value: wild type C57


title: RS049

description: Library name: RS049

value: Whole blood

value: RAP


title: SW480_0701086621

description:
Library name: 701086621
Illumina Truseq

value: FBS

value: A


title: 1869Col_0701086631

description:
Library name: 701086631
Illumina Truseq


title: RS047

description: Library name: RS047


title: adipose-derived stem cells,White differentiation with 0 μM sodium alginate co-stimulation,Day6,s01

description: Library name: s01

value: The cells were whitened for 6 days without co-stimulation with sodium alginate

value: paired-end


title: s-041-IR-hT-Zeb2os

city: Amsterdam

first: Monika

middle: M.

last: Gladka

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam University Medical Centers

description: Library name: Sample 13

data_processing:
Data analysis was performed by uploading Fastq files on UseGalaxy.eu. Fastq files were trimmed using the algorithm “Trim Galore” and mapped on the GRCm38/mm10 mouse genome. Deseq2 analysis was performed across groups to identify significantly up- or down-regulated genes and to generate normalized counts used for Z-score assessment across groups.
Assembly: GRCm38/mm10
Supplementary files format and content: DeSeq2 output containing DEGs across conditions. For each gene pvalue and adjp are provided

source_name: heart

extract_protocol:
Total RNA was isolated from  mouse hearts (apex) using ReliaPrep™ RNA Miniprep Systems (Promega, #Z6012) according to the manufacturer’s protocol.
750ng of total RNA was used for RNA Library Prep performed using KAPA Hyperprep with RiboErase (Roche) according to the manufacturer’s instructions.

value: heart

value: wild-type

value: 10-12 week old

tag: strain


title: RS045

description: Library name: RS045

value: Female

value: Caucasian

value: Yes

value: No

value: Hypo


title: 111011col_0701086611

description:
Library name: 701086611
Illumina Truseq

tag: cell line


title: 1872col_0701086601

description:
Library name: 701086601
Illumina Truseq

tag: cell type


title: RS050

description: Library name: RS050

value: Normo


title: RS043

description: Library name: RS043

value: Male

value: African American

value: yes


title: RS042

description: Library name: RS042

value: Whole blood

value: RAP


title: RS048

description: Library name: RS048


title: RS041

description: Library name: RS041


title: 1247col_0701086591

description:
Library name: 701086591
Illumina Truseq

value: FBS

value: A


title: RS040

description: Library name: RS040


title: 1076col_0701086581

description:
Library name: 701086581
Illumina Truseq


title: s-037-IR-hT-Zeb2os

description: Library name: Sample 10


title: s-038-IR-hT-Zeb2os

description: Library name: Sample 11


title: RS038

description: Library name: RS038

value: Asian


title: CSC59_0701086571

description:
Library name: 701086571
Illumina Truseq

value: CIC


title: RS039

description: Library name: RS039


title: RS036

description: Library name: RS036


title: s-034-IR-hT-empty

description: Library name: Sample 9

value: heart

value: wild-type


title: s-033-IR-hT-empty

description: Library name: Sample 8

value: 10-12 week old


title: CSC57_0701086561

description:
Library name: 701086561
Illumina Truseq


title: RS030

description: Library name: RS030

value: Female

value: Caucasian


title: RS029

description: Library name: RS029

value: No


title: RS031

description: Library name: RS031

value: CON


title: RS028

description: Library name: RS028

value: Yes

value: Hypo


title: s-039-IR-hT-Zeb2os

description: Library name: Sample 12

value: Male


title: s-031-IR-hT-empty

description: Library name: Sample 7


title: RS027

description: Library name: RS027

value: ED

value: African American


title: CSC20_0701086541

description:
Library name: 701086541
Illumina Truseq


title: RS025

description: Library name: RS025

value: Whole blood

value: CCI


title: RS035

description: Library name: RS035

value: RAP

value: Normo


title: CSC21_0701086551

description:
Library name: 701086551
Illumina Truseq

value: CIC

value: A


title: CSC14_0701086531

description:
Library name: 701086531
Illumina Truseq


title: RS023

description: Library name: RS023

value: yes


title: s-027-SHAM-hT-Zeb2os

description: Library name: Sample 5

value: heart

value: wild-type

value: 10-12 week old


title: RS024

description: Library name: RS024

value: No


title: CSC13_0701086521

description:
Library name: 701086521
Illumina Truseq


title: s-028-SHAM-hT-Zeb2os

description: Library name: Sample 6


title: RS022

description: Library name: RS022

value: Female


title: RS015

description: Library name: RS015

value: Caucasian

value: Yes


title: CSC9_0701086501

description:
Library name: 701086501
Illumina Truseq


title: RS014

description: Library name: RS014

value: Hypo


title: RS018

description: Library name: RS018


title: CSC11_0701086511

description:
Library name: 701086511
Illumina Truseq


title: s-025-SHAM-hT-empty

description: Library name: Sample 3

value: Male


title: RS019

description: Library name: RS019


title: RS013

description: Library name: RS013


title: s-026-SHAM-hT-Zeb2os

description: Library name: Sample 4


title: s-024-SHAM-hT-empty

description: Library name: Sample 2


title: RS010

description: Library name: RS010


title: RS009

description: Library name: RS009


title: s-023-SHAM-hT-empty

description: Library name: Sample 1


title: CSC8_0701086491

description:
Library name: 701086491
Illumina Truseq


title: CSC7_0701086481

description:
Library name: 701086481
Illumina Truseq


title: RS008

description: Library name: RS008


title: RO injection AAV9_hTNNT2_Zeb2os_31

description: Library name: Sample 19

data_processing:
Data analysis was performed by uploading Fastq files on UseGalaxy.eu. Fastq files were trimmed using the algorithm “Trim Galore” and mapped on the GRCm38/mm10 mouse genome. Deseq2 analysis was performed across groups to identify significantly up- or down-regulated genes and to generate normalized counts used for Z-score assessment across groups.
Assembly: GRCm38/mm10
Supplementary files format and content: DeSeq2 output containing DEGs across conditions. For each gene pvale and adjp are provided

value: M

value: FVB/NRj


title: RS020

description: Library name: RS020

value: Whole blood


title: RS005

description: Library name: RS005

value: ED


title: RS006

description: Library name: RS006

value: RAP

value: African American


title: CSC2_0701086461

description:
Library name: 701086461
Illumina Truseq

value: CIC

value: A


title: RO injection AAV9_hTNNT2_Zeb2os_32

description: Library name: Sample 20

value: heart


title: RS003

description: Library name: RS003


title: RO injection AAV9_hTNNT2_Zeb2os_30

description: Library name: Sample 18

value: wild-type

value: F


title: LP2042

description: Library name: LP2042

value: No


title: CSC16_0701086451

description:
Library name: 701086451
Illumina Truseq


title: CSC5_0701086471

description:
Library name: 701086471
Illumina Truseq


title: LP2043

description: Library name: LP2043


title: RO injection AAV9_hTNNT2_Zeb2os_29

description: Library name: Sample 17


title: RO injection AAV9_hTNNT2_Zeb2os_28

description: Library name: Sample 16


title: LP2039

description: Library name: LP2039

value: Normo


title: LP2036

description: Library name: LP2036

value: Caucasian

value: yes


title: LP2037

description: Library name: LP2037

value: Female

value: Yes


title: RS002

description: Library name: RS002


title: CSC33_0701086441

description:
Library name: 701086441
Illumina Truseq


title: RO injection AAV9_hTNNT2_control_21

description: Library name: Sample 15


title: LP2035

description: Library name: LP2035

value: Male


title: RO injection AAV9_hTNNT2_control_20

description: Library name: Sample 14

value: FVB/NRj


title: LP2030

description: Library name: LP2030

value: Whole blood

value: Other

value: Hypo


title: LP2032

description: Library name: LP2032

value: RAP


title: CSC3_0701086431

description:
Library name: 701086431
Illumina Truseq

value: CIC


title: 14583CSC_0701086411

description:
Library name: 701086411
Illumina Truseq

value: A


title: RO injection AAV9_hTNNT2_control_9

description: Library name: Sample 13

value: heart


title: 1247CSC_0701086401

description:
Library name: 701086401
Illumina Truseq


title: RO injection AAV9_hTNNT2_control_8

description: Library name: Sample 12

value: wild-type


title: LP2034

description: Library name: LP2034


title: LP2027

description: Library name: LP2027

value: African American


title: 111011CSC_0701086421

description:
Library name: 701086421
Illumina Truseq


title: LP2023

description: Library name: LP2023

value: No


title: 1076CSC_0701086391

description:
Library name: 701086391
Illumina Truseq


title: LP2020

description: Library name: LP2020

value: CCI


title: LP2019

description: Library name: LP2019


title: RO injection AAV9_CMV_Zeb2os_26

description: Library name: Sample 10

value: F


title: LP2018

description: Library name: LP2018

value: Caucasian

value: yes


title: LP2029

description: Library name: LP2029

value: Female


title: SAMPLE_70  Placenta

city: Laval

first: Cathy

last: Vaillancourt

state: QC

address: 531 boulevard des Prairies

department: Centre Armand Frappier Santé Biotechnologie

country: Canada

institute: INRS

description: Library name: sample70

data_processing:
Adapter trimming and quality filtering were performed using fastp v0.23.2 (Chen et al. 2018).
Read quality check was performed on raw and trimmed data using FastQC v0.11.9 (Andrews 2010) and summarized with MultiQC v1.12 (Ewels et al. 2016).
Transcript quantification was performed using Kallisto v0.48.0 (Bray et al. 2016) against the Homo sapiens transcriptome (GRCh38, Ensembl release 110; protein_coding transcripts).
Principal component analysis (PCA) was conducted using FactoMineR v2.9 R package (Lê, Josse, and Husson 2008).
PCA and volcano plots were generated using ggplot2 v3.4.4 (Wickham 2011).
Differential expression analysis was performed with DESeq2 v1.40.2 package (Love, Huber, and Anders 2014). Gene were considered differential expressed genes with an adjusted p-value (q value) < 0.05 and absolute fold change > 1.5.
Pathway enrichment analyses were performed using gprofiler2 (Kolberg et al. 2020), querying GO, Biological Processes, KEGG, Reactome, and WikiPathways databases, with FDR correction and a significance threshold of 0.05.
All R analysis were conducted in R v4.3.1 (Team 2014).
Assembly: GRCh38 Ensembl release 110 (Homo_sapiens. Ensembl110_110.protein_coding)
Supplementary files format and content: Processed data files include: (1) Gene-level raw count matrices generated by Kallisto, containing counts for all annotated protein-coding genes across all samples.(2) Normalized expression values (DESeq2 normalized counts) for downstream visualization and analysis. All processed files are provided in tab-delimited text format.

source_name: Placenta

extract_protocol:
Placental villous biopsies were collected immediately after delivery and either snap-frozen and stored at -80°C or placed in RNALater solution for 24 h at 4°C prior to storage at -80°C until processing. Frozen biopsies were ground on dry ice, and approximately 20 mg of powdered tissue was homogenized in lysis buffer using QIAshredder columns (QIAGEN, Canada). Frozen RNALater-preserved placenta biopsies were cut on dry ice and thawed directly into lysis buffer in prefilled tubes containing garnet shards and a 6 mm zirconium bead (Benchmark Scientific, USA). Mechanical lysis was performed using a BeadBug homogenizer (Benchmark Scientific, USA), followed by complete homogenization through the QIAshredder columns (QIAGEN, Canada). Total RNA was extracted using the RNeasy Mini kit (QIAGEN, Canada) according to the manufacturer’s instructions. RNA purity (OD260/280 ratio ≥ 1.8) and concentration (ng/μL) were determined using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Canada).
rRNA-depleted libraries (HMR rRNA depletion) were prepared from 125 ng of total RNA at Génome Québec and sequenced on an Illumina NovaSeq platform (Illumina, USA).

treatment_protocol: No experimental treatment was applied. Placental samples were obtained from pregnancies with or without a documented history of maternal SARS-CoV-2 infection during pregnancy, as determined by clinical diagnostic testing. The exposure variable corresponds to maternal infection status (COVID+ vs COVID-) and reflects a naturally occurring condition rather than an experimental intervention.

value: Placenta

tag: sars-cov-2 test_during_pregnancy

value: COVID -

tag: fetal sex

value: Male


title: RO injection AAV9_hTNNT2_control_7

description: Library name: Sample 11

tag: genotype

value: FVB/NRj


title: SAMPLE_68  Placenta

description: Library name: sample68

tag: tissue


title: LP2014

description: Library name: LP2014

value: Whole blood

tag: outcome

value: Yes

value: Hypo


title: LP2013

description: Library name: LP2013

value: RAP

tag: age


title: LP2015

description: Library name: LP2015

tag: gender


title: SAMPLE_69  Placenta

description: Library name: sample69


title: SAMPLE_67  Placenta

description: Library name: sample67


title: RO injection AAV9_CMV_Zeb2os_24

description: Library name: Sample 8

value: heart


title: LP2016

description: Library name: LP2016

tag: race

value: Normo


title: SAMPLE_66  Placenta

description: Library name: sample66


title: LP2012

description: Library name: LP2012

value: African American

tag: shock


title: LP2011

description: Library name: LP2011

value: Other

tag: sofa

value: No


title: LP2010

description: Library name: LP2010

tag: respsofa


title: RO injection AAV9_CMV_Zeb2os_23

description: Library name: Sample 7

value: wild-type

value: F


title: RO injection AAV9_CMV_Zeb2os_22

description: Library name: Sample 6

value: M


title: RO injection AAV9_CMV_Zeb2os_25

description: Library name: Sample 9


title: LP2028

description: Library name: LP2028

tag: inhospdeath


title: RO injection AAV9_CMV_control_18

description: Library name: Sample 5


title: LP2008

description: Library name: LP2008

value: ED

value: Caucasian

tag: phenotype


title: LP2009

description: Library name: LP2009

value: CCI

tag: ards


title: LP2007

description: Library name: LP2007

value: Male


title: LP2006

description: Library name: LP2006

value: Female

value: yes


title: SAMPLE_65  Placenta

description: Library name: sample65

value: Placenta

value: COVID -


title: RO injection AAV9_CMV_control_17

description: Library name: Sample 4

tag: strain

value: FVB/NRj


title: SAMPLE_64  Placenta

description: Library name: sample64


title: SAMPLE_63  Placenta

description: Library name: sample63

value: COVID +


title: LP2005

description: Library name: LP2005

value: Whole blood

value: RAP

value: Yes

value: Normo


title: RO injection AAV9_CMV_control_16

description: Library name: Sample 3

value: heart

value: wild-type


title: SAMPLE_62  Placenta

description: Library name: sample62


title: LP2003

description: Library name: LP2003

value: African American

value: Hypo


title: RO injection AAV9_CMV_control_15

description: Library name: Sample 2

value: M


title: LP2004

description: Library name: LP2004

value: No


title: SAMPLE_61  Placenta

description: Library name: sample61


title: LP009

description: Library name: LP009

value: ED


title: LP008

description: Library name: LP008

value: Male

value: Caucasian


title: RO injection AAV9_CMV_control_14

description: Library name: Sample 1

value: F


title: LP005

description: Library name: LP005

value: CCI

value: Female

value: yes


title: LP001

description: Library name: LP001

value: Whole blood


title: SAMPLE_60  Placenta

description: Library name: sample60

value: Placenta

value: COVID +


title: R300_KO3

city: hangzhou

first: jue

last: xie

state: zhejiang

address: Qingchun road

department: Department of Blood Transfusion

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

description: Library name: Sample 12

data_processing:
Reads were quality controlled with FastQC (Version 0.12.1)
fastp (version0.23.4) was used to trim low quality sequences
HISAT (Version 2. 2.2.1) was used to map reads to the mouse reference genome
featureCounts (Version 2.0.3) was used to perform gene expression quantification
Differential expression analysis was conducted with the DESeq2 package (version 1.42.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: peritoneal macrophage

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was evaluated (Agilent 2100 Bioanalyzer, Agilent Technologies, Palo Alto, CA, USA) and verified by RNase-free agarose gel electrophoresis. Next, mRNA was enriched (Oligo(dT) beads), fragmented, and reverse-transcribed (NEBNext Ultra RNA Library Prep Kit for Illumina, NEB #7530, New England Biolabs, Ipswich, MA, USA). The cDNA was end-repaired, A-tailed, adapter-ligated, purified (AMPure XP Beads, 1.0X), and PCR-amplified.

treatment_protocol: Eight-week-old male mice were euthanized at predetermined time points, and peritoneal macrophages were harvested for subsequent analyses.

value: peritoneal macrophage

tag: treatment

value: R300-opsonized platelet


title: SAMPLE_59  Placenta

description: Library name: sample59


title: R300_KO2

description: Library name: Sample 11

tag: cell type


title: K088

description: Library name: K088

value: RAP

value: Yes


title: K081

description: Library name: K081

value: African American

value: Normo


title: SAMPLE_58  Placenta

description: Library name: sample58

tag: sars-cov-2 test_during_pregnancy


title: K085

description: Library name: K085

value: No


title: K087

description: Library name: K087

value: Hypo


title: LP2002

description: Library name: LP2002


title: LP2024

description: Library name: LP2024

value: ED


title: Blank_KO3

description: Library name: Sample 9

value: Con


title: K077

description: Library name: K077

value: Male

value: Caucasian


title: K080

description: Library name: K080

value: Female


title: SAMPLE_56  Placenta

description: Library name: sample56

value: COVID -

tag: fetal sex


title: Blank_KO2

description: Library name: Sample 8

tag: genotype


title: K079

description: Library name: K079

tag: tissue

value: Whole blood


title: SAMPLE_55  Placenta

description: Library name: sample55

value: Placenta


title: K074

description: Library name: K074

tag: outcome

value: yes


title: K072

description: Library name: K072

tag: age


title: Blank_KO1

description: Library name: Sample 7

value: peritoneal macrophage


title: R300_KO1

description: Library name: Sample 10

value: R300-opsonized platelet


title: K071

description: Library name: K071

value: RAP

tag: gender


title: R300_WT3

description: Library name: Sample 6


title: SAMPLE_54  Placenta

description: Library name: sample54

value: COVID +


title: K069

description: Library name: K069

tag: race

value: African American


title: SAMPLE_52  Placenta

description: Library name: sample52


title: K067

description: Library name: K067

tag: shock

value: Normo


title: K068

description: Library name: K068

value: No

tag: sofa


title: SAMPLE_51  Placenta

description: Library name: sample51


title: K061

description: Library name: K061

value: CCI

value: Other

value: Yes

tag: respsofa

value: Hypo


title: K059

description: Library name: K059

value: Male

value: Caucasian

tag: inhospdeath


title: R300_WT1

description: Library name: Sample 4


title: K058

description: Library name: K058

tag: phenotype


title: SAMPLE_53  Placenta

description: Library name: sample53


title: K070

description: Library name: K070

value: Female

tag: ards


title: Blank_WT3

description: Library name: Sample 3

value: Con


title: SAMPLE_49  Placenta

description: Library name: sample49

value: Placenta


title: R300_WT2

description: Library name: Sample 5


title: K054

description: Library name: K054

value: Whole blood


title: Blank_WT2

description: Library name: Sample 2

value: peritoneal macrophage


title: K056

description: Library name: K056


title: Blank_WT1

description: Library name: Sample 1


title: K053

description: Library name: K053

value: ED


title: SAMPLE_47  Placenta

description: Library name: sample47

value: COVID -


title: SAMPLE_50  Placenta

description: Library name: sample50


title: K057

description: Library name: K057


title: K050

description: Library name: K050

value: RAP

value: yes


title: Lung CD45minus, HTO

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

description: Library name: HTO-CD45moins_NGS21-S232_BHYM7CDSXY

library_source: transcriptomic single cell

data_processing:
Single-cell RNA-seq data were processed using Cell Ranger (v3.0.2) for demultiplexing, alignment to the mouse reference genome (GRCm38/mm10), filtering, unique molecular identifier (UMI) counting, and generation of gene- barcode matrices (cellranger count).
CITE-seq-Count (Version 1.4.4) was used to count the hashtags within each cell and produce the read counts table.
Downstream analysis was carried out in R (v4.0.3) using the Seurat package (v4.0.0). For each sample, filtered matrices containing cell barcodes and gene features were used to construct Seurat objects.
Assembly: GRCm38
Supplementary files format and content: barcode sequences corresponding to column indices
Supplementary files format and content: tsv files containing for each feature the feature ID, the name and the type of features
Supplementary files format and content: mtx files describing hte count of genes for all cells

molecule: polyA RNA

source_name: Lung

extract_protocol:
Lungs were collected from IM-DTR mice at 0, 12, 24, and 48 hours following interstitial macrophage depletion induced by intraperitoneal injection of 50 ng diphtheria toxin (DT), with three to four mice analyzed per time point. Single-cell suspensions were obtained after enzymatic digestion and non-hematopoietic CD45- niche cells were isolated by MACS using CD45 MicroBeads (MiltenyiBiotec, 130-052-301). Lung endothelial cells, epithelial cells and fibroblasts werethen FACS sorted as separately as CD45+CD31+EpCAM-, CD45-CD31-EpCAM+ and   CD45-CD31-EpCAM- cells, respectively.
Sorted  lung endothelial cells, epithelial cells and fibroblasts were pooled at an equicellular ratio of 1:1:1. Cells were then barcoded per timepoint post-DT injection with TotalSeq™-A anti-mouse Hashtag antibodies (BioLegend).
Hashtag barcoded cells were washed, pooled, spun down and resuspended in PBS with 0.04% UltraPure™ BSA (Thermo Fisher Scientific, AM2616) at a final concentration of 500 cells/μl. Cell suspensions were loaded into the Chromium Controller (10x Genomics) at a target recovery of 3 x 10³ cells per timepoint post-DT injection. Cells were encapsulated, partitioned, and their polyA RNAs captured and barcoded using Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 (10x Genomics). The cDNAs were amplified and libraries compatible with Illumina sequencers were generated using Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 (10x Genomics). For Hash Tag Oligonucleotide (HTO) library, 1 μl HTO additive primer v2 (0.2 μM stock) were added to the mix at the cDNA amplification step. The libraries were sequenced on an Illumina NovaSeq sequencer on an SP100 cell flow (read 1, 28 cy; read 2, 76 cy; index i7, 10 cy; index i5, 10 cy) with a sequencing depth of 20,000 reads per cell.

value: Lung

value: Stromal cells, Endothelial cells, Epithelial cells

tag: strain

value: Intraperitoneal injection of 50 ng diphtheria toxin (DT), 0, 12, 24 and 48 hours before sacrifice.


title: K051

description: Library name: K051

value: CCI

value: No

value: Normo


title: K052

description: Library name: K052

value: Male

value: Yes

value: Hypo


title: K049

description: Library name: K049

value: Female

value: Caucasian


title: SAMPLE_48  Placenta

description: Library name: sample48

value: Placenta


title: SAMPLE_45  Placenta

description: Library name: sample45


title: Young, OE, Rep4

city: Ulm

first: Julian

last: Niemann

address: Meyerhofstrasse

department: Institute of Molecular Medicine

country: Germany

institute: University Ulm

description: Library name: Sample_16

data_processing:
For data processing see: https://pubmed.ncbi.nlm.nih.gov/29891535/ (Leins et al. 2018), https://pubmed.ncbi.nlm.nih.gov/30235201/ (Florian et al. 2018)
Assembly: GRCm38
Supplementary files format and content: Txt File containing all Samples and Genes in a Count Matrix

source_name: Bone Marrow

growth_protocol: LT-HSCs were extracted via FACS from murine young (12weeks) and aged (>80weeks) C57BL6 mice and cells cultured in IMDM +10%FBS, 1% P/S and cytokines (SCF, TPO, G-CSF) at 37°C in 3% O2

extract_protocol:
RNA was extracted from freshly sorted GFP positive HSCs using the SMART Seq. v4 Ultra Low Input RNA Kit (Takara Bio) following manufacturers protocols
Library was constructed using Nextera XT library Kit (Illumina) following manufacturers protocols

treatment_protocol: Young and Aged HSCs were transduced for 16h with lentiviral particles for Control or Ube2g1-OE at MOI 30. Next day, cells were washed and cultured in fresh media for antoher 24 hours prior to resorting for GFP.

value: Bone Marrow

value: Hematopoietic Stem Cell


title: K046

description: Library name: K046

value: Whole blood


title: Lung CD45minus, Gex

description: Library name: CD45moins_NGS21-S230

tag: treatment


title: SAMPLE_44  Placenta

description: Library name: sample44

value: COVID +


title: K040

description: Library name: K040

value: RAP

value: African American


title: Young, Control, Rep4

description: Library name: Sample_15

tag: cell type

value: Control


title: SAMPLE_46  Placenta

description: Library name: sample46

tag: sars-cov-2 test_during_pregnancy

value: COVID -


title: Old, OE, Rep4

description: Library name: Sample_14


title: K039

description: Library name: K039

value: ED


title: K038

description: Library name: K038

value: CCI

value: No

value: yes


title: K041

description: Library name: K041

value: Normo


title: K037

description: Library name: K037

value: Male


title: K042

description: Library name: K042


title: SAMPLE_43  Placenta

description: Library name: sample43

tag: fetal sex

value: Female


title: SAMPLE_42  Placenta

description: Library name: sample42


title: K045

description: Library name: K045

value: Yes

value: Hypo


title: LP003

description: Library name: LP003

value: Caucasian


title: K035

description: Library name: K035

value: Other


title: K033

description: Library name: K033

value: Whole blood


title: K032

description: Library name: K032


title: SAMPLE_41  Placenta

description: Library name: sample41

value: Placenta

value: COVID +


title: Old, OE, Rep3

description: Library name: Sample_12

value: Bone Marrow

value: Hematopoietic Stem Cell

tag: genotype


title: SAMPLE_40  Placenta

description: Library name: sample40

tag: tissue


title: Old, Control, Rep3

description: Library name: Sample_11

value: Control


title: K029

description: Library name: K029

tag: outcome

value: RAP


title: Old, Control, Rep4

description: Library name: Sample_13


title: K028

description: Library name: K028

tag: age

value: African American


title: SAMPLE_39  Placenta

description: Library name: sample39


title: Young, OE, Rep3

description: Library name: Sample_10


title: SAMPLE_38  Placenta

description: Library name: sample38


title: K030

description: Library name: K030

tag: gender

value: No


title: Young, Control, Rep3

description: Library name: Sample_9


title: K025

description: Library name: K025

tag: race


title: K026

description: Library name: K026

tag: shock


title: SAMPLE_37  Placenta

description: Library name: sample37


title: SAMPLE_36  Placenta

description: Library name: sample36


title: K034

description: Library name: K034

tag: sofa


title: Old, OE, Rep2

description: Library name: Sample_8


title: K024

description: Library name: K024

value: ED

tag: respsofa

value: yes


title: K023

description: Library name: K023

value: Male

tag: inhospdeath

value: Normo


title: K022

description: Library name: K022

tag: phenotype


title: Young, OE, Rep2

description: Library name: Sample_6


title: Old, Control, Rep2

description: Library name: Sample_7


title: SAMPLE_34  Placenta

description: Library name: sample34


title: SAMPLE_35  Placenta

description: Library name: sample35

value: COVID -


title: K027

description: Library name: K027

value: Female

value: Hypo

tag: ards


title: K020

description: Library name: K020

value: Caucasian


title: K019

description: Library name: K019

value: Whole blood

value: Yes


title: K021

description: Library name: K021


title: K015

description: Library name: K015


title: Old, OE, Rep1

description: Library name: Sample_4

tag: strain


title: SAMPLE_33  Placenta

description: Library name: sample33

value: Placenta

value: COVID +


title: Old, Control, Rep1

description: Library name: Sample_3

value: Bone Marrow

value: Hematopoietic Stem Cell


title: K018

description: Library name: K018

value: RAP


title: K014

description: Library name: K014

value: African American


title: SAMPLE_32  Placenta

description: Library name: sample32


title: K011

description: Library name: K011

value: No


title: Young, OE, Rep1

description: Library name: Sample_2


title: SAMPLE_31  Placenta

description: Library name: sample31


title: Young, Control, Rep1

description: Library name: Sample_1

value: Control


title: K009

description: Library name: K009

value: yes


title: Young, Control, Rep2

description: Library name: Sample_5


title: SAMPLE_30  Placenta

description: Library name: sample30

value: Male


title: K017

description: Library name: K017

value: Normo


title: SAMPLE_28  Placenta

description: Library name: sample28


title: K012

description: Library name: K012


title: C3

first: Ryan

last: Sheridan

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description:
Library name: C3
scRNA-seq for ankle tissue from CHIKV-infected mice, enriched for CHIKV RNA sequences

data_processing:
Reads were aligned and count matrices were generated using the 10x Genomics Cell Ranger software
Downstream analysis including CHIKV RNA quantification, gene expression normalization, sample integration, and cell clustering was performed using the Seurat R package.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5, raw count matrix from Cell Ranger in HDF5 format
Supplementary files format and content: count_matrix.h5, processed count matrix in HDF5 format, separate matrices are provided for all cells, macrophages, and T cells.
Supplementary files format and content: metadata.tsv.gz, cell metadata for count_matrix.h5 matrices

source_name: ankle

extract_protocol:
28 days post infection joint-associated tissue was collected from the ipsilateral ankle and a single cell suspension was generated by mechanical and enzymatic digestion.
Cells were assayed using the 10x Genomics Next GEM single-cell 3’ expression kit according to manufacturer’s instructions. scRNA-seq libraries were enriched for molecules aligning to the CHIKV genome using previously published methods. The unenriched and CHIKV-enriched libraries were sequenced separately on an Illumina NovaSeq 6000.

treatment_protocol: WT C57BL/6J mice were inoculated with the chikungunya virus strain AF15561 or were mock infected

value: ankle

tag: treatment

value: CHIKV infected mice

tag: library type

value: mRNA


title: SAMPLE_27  Placenta

description: Library name: sample27

tag: sars-cov-2 test_during_pregnancy


title: C2

description:
Library name: C2
scRNA-seq for ankle tissue from CHIKV-infected mice, enriched for CHIKV RNA sequences


title: K008

description: Library name: K008

value: Hypo


title: SAMPLE_26  Placenta

description: Library name: sample26

tag: fetal sex


title: K004

description: Library name: K004

value: Whole blood


title: K006

description: Library name: K006

value: ED

value: Caucasian

value: Yes


title: K002

description: Library name: K002


title: K003

description: Library name: K003


title: C1

description:
Library name: C1
scRNA-seq for ankle tissue from CHIKV-infected mice, enriched for CHIKV RNA sequences


title: K001

description: Library name: K001


title: K013

description: Library name: K013

value: CCI


title: K010

description: Library name: K010


title: K005

description: Library name: K005


title: U1

description:
Library name: U1
scRNA-seq for ankle tissue from mock-infected mice, enriched for CHIKV RNA sequences

value: mock infected mice


title: U2

description:
Library name: U2
scRNA-seq for ankle tissue from mock-infected mice, enriched for CHIKV RNA sequences


title: A3

description:
Library name: A3
scRNA-seq for ankle tissue from CHIKV-infected mice


title: SAMPLE_24  Placenta

description: Library name: sample24

value: Placenta

value: COVID -


title: SAMPLE_20  Placenta

description: Library name: sample20

value: COVID +


title: SAMPLE_23  Placenta

description: Library name: sample23

value: Female


title: LN229, vector, rep 1

city: Chengdu

first: yanjia

last: Hu

state: Sichuan

address: No.37, Guoxue Lane, Wuhou District, Chengdu City

department: Cancer Center

institute: Sichuan University West China Hospital

description: Library name: LN229, vector, rep 1

data_processing:
Total RNA sample detection
mRNA enrichment
cDNA synthesis
Terminal repair
segment slection and PCR amplification
Assembly: hg38
Supplementary files format and content: HISAT2. The table title includes gene sample and sample names.

source_name: brain

extract_protocol:
Trizol and Chloroform
NEB common library construction

value: brain

tag: cell line

tag: cell type

value: cancer cell


title: LN229, LACTB overexpression, rep 3

description: Library name: LN229, LACTB overexpression, rep 3

tag: tissue


title: LN229, LACTB overexpression, rep 2

description: Library name: LN229, LACTB overexpression, rep 2


title: A2

description:
Library name: A2
scRNA-seq for ankle tissue from CHIKV-infected mice


title: SAMPLE_25  Placenta

description: Library name: sample25

value: Male


title: SAMPLE_18  Placenta

description: Library name: sample18


title: M_L_C

city: NYC

first: Nayeli

last: Gutierrez

state: NYC

address: Hess CSM Building, 1470 Madison Ave, 6, 108

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Transcript abundances were estimated using Salmon 1.2.1 (Patro et al., 2017) against a transcriptome index built on Ensembl GRCh38 release 99. Abundances were aggregated and collapsed to the gene level using tximeta 1.6.2 (Love et al., 2020) in an R 4.0.0 environment.
Normalization and differential gene expression analysis was performed using DESeq2 1.28.1 (Love et al., 2014).
To quantify alternative splicing, RNA-Seq reads were aligned to the human genome (GRCh38 release 99) using STAR 2.7.3a (Dobin et al., 2013), and alternative splicing events were identified using rMATS version 4.0.1 (Shen et al., 2014). Statistically significant splicing events were defined using an inclusion level difference of 10% and false discovery rate (FDR) of 0.05.
Assembly: NA
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include --- raw counts for each sample

growth_protocol: LSD1/CoREST Expression: BL21 RP plus were transformed with two vectors, pET15b containing His-TEV-trLSD1 and pCDF DUET1 containing His-TEV-SUMO-trCoREST1. The transformed cells were incubated on an agar plate (25mg/ml Ampicillin, 100 mg/ml Streptomycin and 50 mg/ml Chloramphenicol) overnight at 37°C. One colony was picked from the plate, inoculated in a starter LB media overnight at 37 °C with all three antibiotics. Starter culture was then inoculated into LB media (dilution 1:50) and growth at 37°C until the OD600 ~ 0.6. The cultures were then chilled a 4°C for 20 minutes approximately and then added with 0.4 mM of IPTG and induced at 18°C overnight. Cells were harvested and dissolved in Hepes 50 mM, pH 8, 300 mM NaCl and 0.5 mM TCEP containing a mixture of protease inhibitors.

extract_protocol:
RNA samples were extracted using the RNeasy mini kit (Qiagen) as permanufacturer’s instructions.
A modified TruSeq protocol was used to preparepoly(A)-selected, unstranded Illumina libraries. Briefly, 0.5X AMPure XPbeads were added to the sample library to select for fragments less than 400base pairs followed by 1x beads to select for fragments more than 100 basepairs. Fragments were then amplified using PCR (15 cycles) and separated bygel electrophoresis with 2% agarose gel. The 300 base pair DNA fragments were isolated and sequenced on Illumina HiSeq 2000 (~100 million 101 bp reads per sample).

treatment_protocol: PRMT1, PRMT5/MEP50, and PRMT7 inhibition assays were performed by Reaction Biology Corporation (Malvern, PA, USA) using the HotSpot HMT Assay. Briefly, human recombinant PRMT1 (cat. n. HMT-11-119), PRMT5/MEP50 Complex (cat. n. HMT-22-148), PRMT7 (cat. n. HMT-21-382) were used at a concentration of 5 nM, 1 nM, and 60 nM, respectively. The appropriate substrate (5 μM Histone H4 for PRMT1, 5 μM Histone H2A for PRMT5/MEP50, and 5 μM GST-GAR for PRMT7) was added to the reaction buffer (50 mM Tris-HCl (pH 8.5), 5 mM MgCl2, 50 mM NaCl, 0.01% Brij35, 1 mM DTT, 1% DMSO). The MT enzyme was delivered into the substrate solution and the mixture was mixed gently. Afterwards, the tested compounds dissolved in DMSO were delivered into the enzyme/substrate reaction mixture by using Acoustic Technology (Echo 550, LabCyte Inc. Sunnyvale, CA) in nanoliter range, and 1 μM 3H-SAM was also added into the reaction mixture to initiate the reaction.

value: Acute myeloid leukemia cells

tag: genotype

value: PRMT5 +/+

value: MS023 + LSD1


title: LN229, vector, rep-2

description: Library name: LN229, vector, rep-2


title: MC4455_C


title: SAMPLE_22  Placenta

description: Library name: sample22


title: LN229, LACTB overexpression, rep 1

description: Library name: LN229, LACTB overexpression, rep 1


title: M3

description:
Library name: M3
scRNA-seq for ankle tissue from mock-infected mice

value: ankle

value: mRNA


title: U3

description:
Library name: U3
scRNA-seq for ankle tissue from mock-infected mice, enriched for CHIKV RNA sequences


title: PRT220_C


title: LN229, vector, rep 3

description: Library name: LN229, vector, rep 3


title: SAMPLE_21  Placenta

description: Library name: sample21


title: PRT220_A


title: M_L_A


title: A1

description:
Library name: A1
scRNA-seq for ankle tissue from CHIKV-infected mice

value: CHIKV infected mice


title: MC4491_A


title: MC4491_C


title: SAMPLE_19  Placenta

description: Library name: sample19


title: M2

description:
Library name: M2
scRNA-seq for ankle tissue from mock-infected mice


title: MC4491_B


title: HH>Tor.WT, infected, rep 3

city: Tampere

first: Laura

last: Vesala

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
The reads obtained from the HiSeq 3000 instrument were base called using the instrument manufacturer’s Bcl2fastq2 version 1.8.4 base calling software.
The read alignment was performed in two stages: first, the reads were aligned against the drosophile reference genome using Star version 2.5.0 [1]. Then the reads were associated with known genes and the number of reads associated with each gene was counted using subreads package (v. 1.5.0)
The gene-wise read counts were normalised using the CPM normalisation method
Assembly: dm6
Supplementary files format and content: excel file containing normalized read counts of the samples

organism: Drosophila melanogaster

source_name: hemocyte

growth_protocol: Drosophila larvae were grown from egg to 3rd instar larvae at 29°C

extract_protocol:
RNA was extracted using  Norgen single Cell RNA purification kit (Norgen Biotek Corp, Ontario, Canada) including a DNase treatment (RNase free Dnase I kit, Norgen).
The samples were prepared for the sequencing using Illumina TruSeq Stranded mRNA Sample Preparation Kit

treatment_protocol: Hemolymph was released by dissecting larvae open in drops of ice-cold 1xPBS. Samples were kept on ice, centrifuged 7 min at 2500g at +4°C to spin the hemocytes down. After centrifuging, excess plasma was pipetted off and hemocytes frozen at -80°C

value: hemocyte

value: 48 hours after Leptopilina boulardi strain G486 infection


title: SAMPLE_17  Placenta

description: Library name: sample17


title: HH>Tor.WT, infected, rep 2


title: SAMPLE_16  Placenta

description: Library name: sample16


title: DMSO_C

value: DMSO


title: MC4455_B


title: M1

description:
Library name: M1
scRNA-seq for ankle tissue from mock-infected mice

value: mock infected mice


title: HH>Tor.WT, infected, rep 1


title: SAMPLE_15  Placenta

description: Library name: sample15

value: Placenta


title: HH x w1118, infected, rep 3


title: SAMPLE_9  Placenta

description: Library name: sample9

value: COVID -


title: SAMPLE_14  Placenta

description: Library name: sample14

value: COVID +


title: SAMPLE_11  Placenta

description: Library name: sample11

value: Female


title: P_L_C

value: PRT220 + LSD1


title: MC4455_A


title: P_L_B


title: iWAT_SVF_12CD, scRNA seq

city: Beijing

first: Meng

last: Xie

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description:
Library name: iWAT_SVF_12CD
10x Genomics

data_processing:
Raw fastq sequencing data were processed using Cell Ranger 7.0.0 with the "--include-introns" option enabled to include reads mapping to the introns annotated in Ensembl, and the mm10 mouse reference genome was utilized to quantify gene expression levels.
Assembly: mm10
Supplementary files format and content: *barcodes.tsv.gz: gzipped tab-separated values (TSV) file containing unique cell barcodes. *features.tsv.gz: gzipped tab-separated values (TSV) file containing feature (gene) information, including gene names and identifiers. *matrix.mtx.gz: gzipped Matrix Market (MTX) file containing the sparse expression matrix with gene counts per cell, indexed by cell barcodes and features.

source_name: Adipose tissue

extract_protocol:
iWAT and eWAT were dissected, washed twice with HBSS, then minced and digested in 1 mg/ml collagenase type I (Sigma-Aldrich, C0130) dissolved in digestion buffer (0.1 M HEPES-Na, 120 mM NaCl, 50 mM KCl, 5 mM D-glucose, 1 mM CaCl₂, 1.5% BSA) for 45 min at 37°C with continuous shaking (150 rpm). Digestion was quenched by adding an equal volume of growth medium (Advanced DMEM/F-12 [Gibco, 12634028] supplemented with 10% FBS, 1% GlutaMAX [Thermo, 35050061], 1% MEM NEAA [Thermo, 11140050], and 1% penicillin-streptomycin [Gibco, 15140122]). The suspension was sequentially filtered through 100-μm and 40-μm cell strainers (Fisher Scientific), with centrifugation (450 g for 10 min) between steps. Erythrocyte lysis was performed by resuspending the pellet in red blood cell lysis buffer (5 min, 37°C), followed by neutralization with growth medium and final filtration with the 40-μm strainer.
Isolated cells were stained with 7-AAD at a concentration of 5 μg/mL and subjected to FACS sorting. Number of cells were quantified with a Countstar Rigel S5 Automated Cell Counter. Approximately 20,000 cells were applied to the Chromium microfluidic chips with 3’ v3 chemistry and barcoded with a 10x Chromium Controller using the Single-Cell 3′ Reagent Kit v3.1 (10x Genomics). The following program was used for GEM-Reverse Transcription: 53℃ for 45 min, 85℃ for 5 min, and held at 4℃. The resulting emulsions were lysed for cDNA isolation and purification with the Cleanup Mix containing DynaBeads and SPRIselect reagent (Thermo Scientific) and amplified with PCR. cDNA quality was assessed with an Agilent 2100 Bioanalyzer. cDNA amplicon size was optimized by enzymatic fragmentation and size selection. P5, P7, i7, and i5 sample indexes and TruSeq Read 2 (read 2 primer sequence) were added by end repair, A-tailing, adaptor ligation, and PCR, respectively. Final libraries containing the P5 and P7 primers were sequenced by an Illumina NovaSeq 6000 sequencer with 150 bp paired-end reads, aiming for a coverage of approximately 50,000 raw reads per cell.

value: Adipose tissue

value: 12-week Chow Diet


title: MS023_A

value: Acute myeloid leukemia cells


title: DMSO_B

value: PRMT5 +/+


title: eWAT_SVF_18HFD, scRNA seq

description:
Library name: eWAT_SVF_18HFD
10x Genomics

value: 18-week High Fat Diet


title: SAMPLE_12  Placenta

description: Library name: sample12


title: HH>Tor.WT, uninfected, rep 1

value: uninfected, "healthy" larvae


title: SAMPLE_10  Placenta

description: Library name: sample10


title: HH x w1118, infected, rep 2


title: HH>Tor.WT, uninfected, rep 2


title: iWAT_SVF_Switch, scRNA seq

description:
Library name: iWAT_SVF_Switch
10x Genomics


title: iWAT_SVF_12HFD, scRNA seq

description:
Library name: iWAT_SVF_12HFD
10x Genomics

value: 12-week High Fat Diet


title: HH>Tor.WT, uninfected, rep 3


title: eWAT_SVF_Switch, scRNA seq

description:
Library name: eWAT_SVF_Switch
10x Genomics


title: iWAT_SVF_18CD_2, scRNA seq

description:
Library name: iWAT_SVF_18CD_2
10x Genomics

value: 18-week Chow Diet


title: eWAT_SVF_18CD_2, scRNA seq

description:
Library name: eWAT_SVF_18CD_2
10x Genomics


title: P_L_A


title: HH x w1118, uninfected, rep 3

value: hemocyte

value: uninfected wild type larvae


title: HH x w1118, infected, rep 1

value: 48 hours after Leptopilina boulardi strain G486 infection


title: SAMPLE_8  Placenta

description: Library name: sample8

value: Male


title: eWAT_SVF_18CD, scRNA seq

description:
Library name: eWAT_SVF_18CD
10x Genomics


title: SAMPLE_7  Placenta

description: Library name: sample7

value: Placenta


title: PRT220_B


title: SAMPLE_6  Placenta

description: Library name: sample6

value: COVID -


title: HH x w1118, uninfected, rep 2


title: HH x w1118, uninfected, rep 1


title: MS023_C


title: M_L_B

value: MS023 + LSD1


title: Phox2b H2B-CFP high intensity 2

city: Nashville

first: E Michelle

last: Southard-Smith

state: TN

address: 2215 Garland Ave,

department: Medicine, Genetic Medicine

institute: Vanderbilt University Medical Center

description:
Library name: count-4828-MS-18
16.5 embryonic day Phox2b H2B-CFP+ high intensity nuclei

library_source: genomic single cell

data_processing:
CellRanger ATAC pipeline version 1.2.0 was used to align FASTQ files to the mm10 genome.
Signac (v1.5.0)/Seurat (v4.0.4) default processing was used to generate Seurat objects for each run, which were subsequently integrated by batch using Harmony (v0.1).
Bright sample 2 was left out of this processing due to low quality (10 times fewer fragments per cell then the rest of the samples).
Post-UMAP and clustering generation, MACS2 (v2.2.7.1) was used for peak calling.
Assembly: mm10-1.2.0
Supplementary files format and content: Harmony integrated Seurat/Signac object in .RDS format

source_name: Fetal Gut (stomach to anus)

extract_protocol:
Cold-active protease (Native Bacillus Licheniformis) with added DNaseI were used to dissociate pooled E16.5 Phox2b H2B-CFP guts (stomach to anus, 6 guts for 4828-MS-15+4828-MS-16 and 12 pooled guts for 4828-MS-17+4828-MS-18) at 5°C in a waterbath and thermo-mixer. Dissociated cells were pelleted and washed in L-15 media with added BSA, HEPES, penicillin, streptomycin, amphotericin, and DNaseI. Cell suspensions were filled through 40µm nylon mesh. Fluorescence-activated cell sorting was used to simuntaneously sort CFP high intensity and CFP low intensity cells from nonfluorescent cells. Nuclei were isolated using the 10x Genomics protocol number CG000209_Rev D. Prior to encapsulation, nuclei were counted via Countess Automated Cell Counter or hemocytometer to determine concentration of nuclei. These nuclei were encapsulated using the 10x Genomics platform for snATAC-seq on bright nuclei and dim nuclei separately.
Nuclei were encapsulated using the 10x Genomics platform for snATAC-seq on bright nuclei and dim nuclei separately. Two replicates were generated with the first bright and dim replicates generated from 6 pooled fetal guts and the second generated from 12 pooled fetal guts.

value: Fetal Gut (stomach to anus)

value: Phox2b H2B-CFP+ (enteric nervous system progenitors)

value: Phox2b H2B-CFP

tag: batch


title: eWAT_SVF_12HFD, scRNA seq

description:
Library name: eWAT_SVF_12HFD
10x Genomics

value: Adipose tissue


title: R40, PBMC before treatment, scTCR-seq

city: Hidaka-City, Saitama

first: Satoshi

last: Yamasaki

department: Department of Respiratory Medicine

country: Japan

institute: Saitama Medical University

description:
Library name: R40_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files
Library strategy: TCR-Seq

molecule: other

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Manufactured protocol of Chromium system (10x genomics)
Library construction was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) protocol (CG000331), 10x Genomics).

value: Peripheral Blood Mononuclear Cells

value: CD3+ T cell

tag: disease

value: Renal cancer


title: SAMPLE_4 Placenta

description: Library name: sample4

value: Female


title: SAMPLE_3 Placenta

description: Library name: sample3


title: LSD1_C

value: Acute myeloid leukemia cells

value: PRMT5 +/+


title: R40, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: R40_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files
Library strategy: CITE-seq

molecule: protein

tag: adt

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD127/TotalSeq-C0390 ; AntibodyAnti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: MS023_B


title: SAMPLE_5 Placenta

description: Library name: sample5

value: COVID +


title: LSD1_B


title: Phox2b H2B-CFP high intensity 1

description:
Library name: count-4828-MS-16
16.5 embryonic day Phox2b H2B-CFP+ high intensity nuclei


title: SAMPLE_1 Placenta

description: Library name: sample1


title: LSD1_A


title: eWAT_SVF_12CD, scRNA seq

description:
Library name: eWAT_SVF_12CD
10x Genomics

value: 12-week Chow Diet


title: Phox2b H2B-CFP low intensity 1

description:
Library name: count-4828-MS-15
16.5 embryonic day Phox2b H2B-CFP+ low intensity nuclei


title: R38, PBMC before treatment, scTCR-seq

description:
Library name: R38_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: Phox2b H2B-CFP low intensity 2

description:
Library name: count-4828-MS-17
16.5 embryonic day Phox2b H2B-CFP+ low intensity nuclei


title: DMSO_A

value: DMSO


title: TCR from uninfected clones from donor OM5334

city: New York

first: Alberto

last: Herrera

state: New York

department: Medicine

institute: Weill Cornell Medicine

description:
Library name: BJ_clones_8_3_TCR
VDJ library: read1 file contains cell barcode and UMI; read2 file contains VDJ fragment

data_processing:
FASTQ files from the 10x gene expression, surface protein, and TCR α/β libraries were processed using Cell Ranger v7.0.1 or v9.0.1 (10x Genomics), using either the count or the multi pipeline (when TCR libraries were available) with default parameters.
RNA transcripts from ECCITE-seq were mapped to a modified version of Cell Ranger’s GRCh38-2020-A reference package (GRCh38 / GENCODE v32 annotations), with the addition of the HIV-1 HXB2 reference sequence. TCR α/β libraries were mapped to Cell Ranger’s cellranger-vdj-GRCh38-alts-ensembl-7.1.0 reference package.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: *.h5 (feature barcode matrices in HDF5 format)
Supplementary files format and content: CellRanger output files: *.filtered_contig_annotations.csv (high-level annotations of each high-confidence contigs from cell-associated barcodes)
Supplementary files format and content: CellRanger output files: *.feature_reference.csv

source_name: peripheral blood

growth_protocol: Memory CD4+ T-cells (mCD4) were isolated from the PBMCs  of people with HIV (PWH) by negative selection using EasySep™ Human Memory CD4+ T Cell Enrichment Kit (STEMCELL Technologies), plated (10 cells/well, 96-well plates), and stimulated with irradiated allogeneic HIV-negative PBMCs (1x106/mL) in R10-100 with ARVs (RPMI 1640 supplemented with 10% FBS and 1% penicillin/streptomycin, 1% HEPES buffer, 1% L-Glutamine supplemented with 100 Units/mL of IL-2, 1 µM Nevirapine, 1 µM Emtricitabine, 1 µM Tenofovir, 10 µM Enfuvirtide, and 10 µg/mL 10-1074 bNAb) with CD3 and CD28 antibodies for 21 days. Feeder PBMCs were depleted of CD8+ T-cells and NK cells using EasySep™ Human CD8 Positive Selection Kit II and EasySep™ Human CD56 Positive Selection Kit II (STEMCELL Technologies) before being co-cultured with mCD4 T-cells from PWH. At the end of stimulation cycle, p24 ELISA was performed on all plates. Cells from p24 ELISA-positive wells were plated in serial 3-fold dilution (96-well plates), stimulated at the same condition as aforementioned, and subjected to p24 ELISA after 21 days. After the second round of plating and ELISA, cells from p24 ELISA-positive wells were expanded under the same stimulation condition. Clonal purity of isolated infected populations was determined using IPDA and further serial dilution subs were performed as needed.

extract_protocol:
Following 2 weeks of rest from stimulation with  CD3 and CD28 antibodies and feeders in R10-100 with ARVs, cells were stained with DNA oligo-barcoded antibodies and loaded onto the 10x Chromium single-cell workflow (10X Genomics) as previously described61 with a few modifications. Approximately 0.05-0.3 x 106 cells per sample were resuspended in R10 media and incubated with the TotalSeq™-C Human Universal Cocktail (Biolegend) for 30 minutes at 4°C. In some cases, TotalSeq™-C hashing antibodies #1, #3 and #4 (Biolegend) were spiked into individual samples, which allowed for multiplexing of ARCs and uninfected clone combinations into the same 10X lane. After staining, cells were washed 3 times in R10 media, followed by centrifugation (400 × g for 5 minutes at 4°C) and supernatant aspiration. After the final wash, cells were resuspended in PBS and filtered through 70-µm cell strainers
All experiments were performed using the 10x genomics V(D)J solution which incorporates scRNA-seq with additional profiling of protein surface markers . Antibody oligo counts are listed in the ADT and HTO tables. Stained cells from each sample were pooled and loaded into the 10X Chromium Single Cell Immune Profiling workflow according to the manufacturer’s instructions (CG000330, revision G)

value: peripheral blood

value: CD4+ T cells


title: 3A replicate 3

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

description: Library name: 3A-3

data_processing:
RNA sequencing (RNA-seq) libraries were prepared by Azenta Life Sciences and sequenced on an Illumina NextSeq 500 platform, generating paired-end reads. Raw FASTQ files were trimmed using Trim Galore to remove adaptor sequences and low-quality bases. Alignment to the Homo sapiens reference genome (GRCh38/hg38) was performed using the align() function from the Rsubread package (v2.12.3; Liao Y, Smyth GK, Shi W (2019)), generating sorted BAM files. The mapping efficiency was assessed using the propmapped() function. Gene-level quantification was conducted using the featureCounts() function in Rsubread, with annotation from the inbuilt hg38 gene model. Only uniquely mapped, properly paired reads were counted.
Downstream analysis was performed in R using the edgeR and limma packages (edgeR;Robinson MD, McCarthy DJ, Smyth GK (2010), limma; Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015)). Raw counts were converted into a DGEList object and annotated using the org.Hs.eg.db database from Bioconductor. Lowly expressed genes were filtered out using a threshold of ≥0.5 counts-per-million (CPM) in at least six libraries. Normalization for library size and composition bias was performed using the trimmed mean of M-values (TMM) method.
Differential expression analysis was carried out using the limma-voom pipeline. The voom() function was used to model the mean-variance relationship and generate precision weights, which were then used in linear modeling via the lmFit() function. Contrast matrices were defined for each comparison, and empirical Bayes moderation of variance estimates was applied using the eBayes() function. Adjusted p-values were calculated using the Benjamini–Hochberg procedure to control the false discovery rate. Genes with an adjusted p-value < 0.05 were considered significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: normalized raw counts for all samples

source_name: Skin

growth_protocol: Cells grown to ˜50-80% confluence in full media on collagen-coated 10cm dishes.

extract_protocol:
Cells were trypsinized in 2mL TrypLE, quenched 4mL full medium, spin down in 15 mL conical tubes. Cell pellets were then resuspended in 1mL PBS and transferred to centrifuge tubes. Cells were pelleted again. "Dry" cell pellets were shipped on dry ice to Azenta Life Sciences for RNA isolation and sequencing.
Library preparation by Azenta Life Sciences; https://www.genewiz.com/public/services/next-generation-sequencing/rna-seq

treatment_protocol: No treatment.

value: Skin

value: Immortalized mouse keratinocytes


title: R38, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: R38_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: ADT from uninfected clones from donor OM5334

description:
Library name: BJ_clones_8_3_ADT
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

data_processing:
FASTQ files from the 10x gene expression, surface protein, and TCR α/β libraries were processed using Cell Ranger v7.0.1 or v9.0.1 (10x Genomics), using either the count or the multi pipeline (when TCR libraries were available) with default parameters.
RNA transcripts from ECCITE-seq were mapped to a modified version of Cell Ranger’s GRCh38-2020-A reference package (GRCh38 / GENCODE v32 annotations), with the addition of the HIV-1 HXB2 reference sequence. TCR α/β libraries were mapped to Cell Ranger’s cellranger-vdj-GRCh38-alts-ensembl-7.1.0 reference package.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: *.h5 (feature barcode matrices in HDF5 format)
Supplementary files format and content: CellRanger output files: *.filtered_contig_annotations.csv (high-level annotations of each high-confidence contigs from cell-associated barcodes)
Supplementary files format and content: CellRanger output files: *.feature_reference.csv
Library strategy: CITE-seq

value: TotalSeq-C Human Universal Cocktail, V1.0 (BioLegend Cat. No. 399905)


title: iWAT_SVF_18HFD, scRNA seq

description:
Library name: iWAT_SVF_18HFD
10x Genomics

value: 18-week High Fat Diet


title: iWAT_SVF_18CD, scRNA seq

description:
Library name: iWAT_SVF_18CD
10x Genomics

value: Adipose tissue

value: 18-week Chow Diet


title: 3A replicate 2

description: Library name: 3A-2


title: R38, PBMC before treatment, scRNA-seq

description:
Library name: R38_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files

value: Peripheral Blood Mononuclear Cells

value: CD3+ T cell


title: mRNA from uninfected clones from donor OM5334

description:
Library name: BJ_clones_8_3_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: LrpprcP27A9

city: Memphis

first: Yong-Dong

last: Wang

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description:
Library name: LrpprcP27A9
LrpprcP27A replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm39/mm39 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include TPM values for all 6 samples

source_name: skeletal muscles

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase.
RNA sequencing libraries for each sample were prepared with 1 mg total RNA by using the TruSeq RNA Sample Prep v2 Kit (Illumina) per the manufacturer’s instructions, and sequencing was completed on the Illumina NovaSeq 6000.

value: skeletal muscles

value: electroporated with the dihydroxylation-resistant LrpprcP27A variant


title: 3A replicate 1

description: Library name: 3A-1


title: R21, PBMC before treatment, scTCR-seq

description:
Library name: R21_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

value: Renal cancer


title: LrpprcP27A8

description:
Library name: LrpprcP27A8
LrpprcP27A replicate 2


title: ADT and HTO from ARC GS from donor GS

description:
Library name: BJ_clones_8_2_ADT_HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads, HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Oligo reads

tag: hto

value: TotalSeq-C Hashtag 3 TTCCGCCTCTCTTTG (Uninfected clones), TotalSeq-C Hashtag 1 GTCAACTCTTTAGCG (ARC GS)


title: R21, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: R21_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD127/TotalSeq-C0390 ; AntibodyAnti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: LrpprcP27A4

description:
Library name: LrpprcP27A4
LrpprcP27A replicate 1


title: Control replicate 2

description: Library name: 546-2


title: LrpprcWT9

description:
Library name: LrpprcWT9
Lrpprc WT replicate 3

value: electroporated with wild-type LrpprcWT


title: I644, PBMC before treatment, scTCR-seq

description:
Library name: I644_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

extract_protocol:
Manufactured protocol of Chromium system (10x genomics)
Library construction was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v1.1 or v2 (Dual Index) protocol (CG000208 or CG000331), 10x Genomics).

value: Lung cancer


title: TCR from dARC COG5 3 weeks and uninfected clone from donor OM5334

description:
Library name: BJ_clones_8_1_TCR
VDJ library: read1 file contains cell barcode and UMI; read2 file contains VDJ fragment

value: peripheral blood


title: I644, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I644_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: Control replicate 1

description: Library name: 546-1


title: TCR from ARC GS from donor GS

description:
Library name: BJ_clones_8_2_TCR
VDJ library: read1 file contains cell barcode and UMI; read2 file contains VDJ fragment

value: CD4+ T cells


title: LrpprcWT8

description:
Library name: LrpprcWT8
Lrpprc WT replicate 2


title: LrpprcWT4

description:
Library name: LrpprcWT4
Lrpprc WT replicate 1


title: R21, PBMC before treatment, scRNA-seq

description:
Library name: R21_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: ADT and HTO from dARC COG5 3 weeks and uninfected clone from donor OM5334

description:
Library name: BJ_clones_8_1_ADT_HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads, HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Oligo reads

value: TotalSeq-C Hashtag 3 TTCCGCCTCTCTTTG (Uninfected clone 3 weeks), TotalSeq-C Hashtag 1 GTCAACTCTTTAGCG (dARC COG5 3 weeks)


title: mRNA from ARC GS from donor GS

description:
Library name: BJ_clones_8_2_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: I644, PBMC before treatment, scRNA-seq

description:
Library name: I644_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v1.1 kit. Captures 5' end of polyA+ transcripts.


title: Control replicate 3

description: Library name: 546-3

value: Skin

value: Immortalized mouse keratinocytes


title: KPPC_vehicle

city: ST LOUIS

first: KIAN

middle: HUAT

last: LIM

state: MO

address: 660 S. Euclid Avenue  Campus Box 8069, St. Louis

department: internal Medicine

institute: WashU

description:
Library name: Sample 1
10x genomics

data_processing:
Demultiplexing, barcodes processing, gene counting and aggreegation were made using Cell Ranger software v2.1.1
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreatic cancer

extract_protocol:
Pancreatic tumors were harvested immediately after euthanasia cardiac punctured. Isolated fresh tumor tissues were washed with cold PBS, minced and dissociated to single-cell suspensions using enzymatic digestion buffer containing HBSS supplemented with 10% FBS, 2 mg/mL collagenase A (Roche), and 50 μg/mL DNase-I (Roche), for 45 minutes at 37°C with continuous rotation. Digested single-cell suspensions were filtered through 40-μm nylon strainers (Fisher Scientific) and cells were counted with using TC20 automated cell counter (Biorad). Single-cell suspensions were used for scRNAseq.
scRNAseq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6 week old KPPC mice treated with vehicle or Takinib (50mg/kg) for 14 days

value: Pancreatic cancer

value: pancreas

value: tumor


title: I628, PBMC before treatment, scTCR-seq

description:
Library name: I628_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

value: Peripheral Blood Mononuclear Cells


title: MAP3K7fwt_KPPC_2

description:
Library name: Sample 4
10x genomics

treatment_protocol: scRNAseq analysis of 8 week-old KPPC WT, MAP3K7f/f   KPPC and MAP3K7f/wt KPPC mice

value: KPPC mice