title: old naked mole-rat anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 4

description:
10x Genomics
nmr_spleen.T.cells_24y_4

extract_protocol:
Spleens were removed by dissection, transferred to a sterile petri dish containing PBS with 5% FBS, and minced using surgical blades. Spleen fragments were then ground through 100 μm and 40 μm cell strainers, pelleted, and resuspended in the ACK lysis buffer as described in the thymus tissue collection section. Cell density and viability were determined using Countness II Cell Counter. Subsequently, splenocytes were resuspended at 1 million cells per ml of 0.04% BSA/PBS. In order to sort out the splenocyte T-cell subsets for constructing 10× GEM single-cell libraries, splenocytes were resuspended at 1 million cells per ml of FACS buffer (PBS with 1% FBS and 5mM EDTA).splenocytes were pre-incubated with the isotype control antibodies (100 ug/ml mIgG1 & 50 ug/ml rat IgG1) per 1 million cells/100ul FACS buffer for 10 minutes. Following that, cells were washed and resuspended at 2 million cells per 1 ml FACS buffer, and incubated with an anti-NMR CD3e (Abbvie-clone-5, Alexa 647, 1:100) and an anti-mouse CD11b (which cross reacts with the NMR CD11b,) (M1/70, R-PE, 5 ug/ml) on ice for 40 minutes. Cells were then washed and resuspended in the FACS buffer containing Sytox Blue Live/Dead dye for cell sorting using FACS BD Aria. Viable, single cells were gated, and the CD11b-/CD3e+ cells were collected for the generation of 10× GEM single-T-cell libraries.
Single cells were captured in droplet emulsion using the Chromium Controller (10× Genomics, Pleasanton, CA), and GEM single-cell libraries were constructed according to the 10× Genomics protocol using the Chromium Single-Cell 30 Gel Bead and Library 3’ V3 kit (10× Genomics, Pleasanton, CA). In brief, cell suspensions were diluted in PBS with 0.04% BSA to a final concentration of 1×106 cells/mL (1,000 cells per μL). Cells were loaded in each channel with a target output of 10,000 cells per sample. All reactions were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA) with a 96 Deep Well Reaction Module. Twelve cycles were used for cDNA amplification and sample index PCR. Amplified cDNA and final libraries were evaluated using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a high sensitivity chip.
paired-end ilimina next-seq

value: spleen

value: mostly spleen T cells

value: 24 years


title: E198K induced pluirpotent stem cell sample 1

status: Public on Nov 30 2023

type: SRA

city: Sacramento

first: Julian

last: Halmai

state: CA

address: 2921 Stockton Blvd

department: Department of Neurology

country: USA

institute: UC Davis

library_source: transcriptomic

data_processing:
star align 2.7a
edgeR
Assembly: hg38
Supplementary files format and content: .csv with raw reads per gene

molecule: total RNA

organism: Homo sapiens

source_name: induced pluripotent stem cell

growth_protocol: iPSCs were converted to a feeder-free culture system using StemFlex medium on matrigel, passaged and frozen using dispase. Undifferentiated human iPSCs were cultured in Corning Matrigel hESC Qualified Matrix with StemFlex medium kit. Cells were routinely cultured at 37C in a standard 5% CO2 incubator with every other day medium change.  hiPSCs were plated into Aggrewell 800 plates in embryoid body (EB) medium containing Knockout DMEM/F12, 15% Gibco™ KnockOut™ Serum Replacement, 100X MEM non-essential amino acids, 100X Glutamax Supplement, 0.55mM 2-Mercaptoethanol and Y-27632 RHO/ROCK pathway inhibitor. On day 2, EBs were plated in suspension in low-attachment plates in EB medium supplemented with Noggin  and SB43152 over 4 days with media change on day 4. On day 5, EBs were plated onto Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix and subsequently transitioned to neural stem cell medium containing Neurobasal Medium , GlutaMAX Supplement (100X), MEM Non-Essential Amino Acids Solution (100X), Penicillin-Streptomycin Solution, N2 Supplement and 10ug/mL Recombinant Human FGF basic/FGF2/bFGF,  over days 6 – 12. Rosettes were enzymatically lifted using Accutase and plated on poly-L-ornithine solution (PLO) and laminin from Engelbreth-Holm-Swarm murine sarcoma basement membrane coated plates supplemented with neural stem cell medium.  For assessments in midbrain iPSC-derived neurons, Isogenic and E198K NSCs were plated at a density of 50,000 cells/cm2 on poly-L-ornithine (PLO) and laminin coated plates in NSC media. 24-hours post-seeding media was changed to STEMdiff Midbrain Neuron Differentiation Kit supplemented with Human Recombinant Sonic hedgehog (Shh) C2411 to differentiate NSCs into midbrain NSCs. Once midbrain NSCs reached 80% confluency, cells were plated at 15,000 cells/cm2 on poly-L-ornithine (PLO) and laminin coated plates to allow for midbrain NSCs to mature into midbrain neurons in STEMdiff Midbrain Neuron Maturation Kit over 9 days.  iPSCs were converted to a feeder-free culture system using StemFlex medium on matrigel, passaged and frozen using dispase. Undifferentiated human iPSCs were cultured in Corning Matrigel hESC Qualified Matrix with StemFlex medium kit. Cells were routinely cultured at 37C in a standard 5% CO2 incubator with every other day medium change.  hiPSCs were plated into Aggrewell 800 plates in embryoid body (EB) medium containing Knockout DMEM/F12, 15% Gibco™ KnockOut™ Serum Replacement, 100X MEM non-essential amino acids, 100X Glutamax Supplement, 0.55mM 2-Mercaptoethanol and Y-27632 RHO/ROCK pathway inhibitor. On day 2, EBs were plated in suspension in low-attachment plates in EB medium supplemented with Noggin  and SB43152 over 4 days with media change on day 4. On day 5, EBs were plated onto Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix and subsequently transitioned to neural stem cell medium containing Neurobasal Medium , GlutaMAX Supplement (100X), MEM Non-Essential Amino Acids Solution (100X), Penicillin-Streptomycin Solution, N2 Supplement and 10ug/mL Recombinant Human FGF basic/FGF2/bFGF,  over days 6 – 12. Rosettes were enzymatically lifted using Accutase and plated on poly-L-ornithine solution (PLO) and laminin from Engelbreth-Holm-Swarm murine sarcoma basement membrane coated plates supplemented with neural stem cell medium.  For assessments in midbrain iPSC-derived neurons, Isogenic and E198K NSCs were plated at a density of 50,000 cells/cm2 on poly-L-ornithine (PLO) and laminin coated plates in NSC media. 24-hours post-seeding media was changed to STEMdiff Midbrain Neuron Differentiation Kit supplemented with Human Recombinant Sonic hedgehog (Shh) C2411 to differentiate NSCs into midbrain NSCs. Once midbrain NSCs reached 80% confluency, cells were plated at 15,000 cells/cm2 on poly-L-ornithine (PLO) and laminin coated plates to allow for midbrain NSCs to mature into midbrain neurons in STEMdiff Midbrain Neuron Maturation Kit over 9 days.

extract_protocol:
Cells were lysed using TriZol Reagent and RNA extractions were performed on with the Direct-zol RNA Miniprep kit (Zymo Research). 500ng total RNA was used to construct libraries according to Novogene sample submission guidelines.
Library construction was performed by Novogene.

treatment_protocol: An iPSC isogenic line was created with a sgRNA targeting the patient-specific E198K variant in PPP2R5D using CRISPR-mediated homology-directed repair, courtesy of Synthego.  Sanger sequencing of the E198K and isogenic iPSC lines was conducted to verify the patient variant and correction of the mutation.

tag: cell line

value: induced pluripotent stem cell

tag: cell type

tag: genotype


title: isogenic induced pluirpotent stem cell sample 3

value: WT

tag: treatment

value: sgRNA targeting the patient-specific E198K variant in PPP2R5D


title: Drought4_29d_rep3

city: Tsukuba

first: FUMIYUKI

last: SOMA

state: Ibaraki

address: 2-1-2 Kan-non-dai

department: Institute of Crop Science

country: Japan

institute: National Agriculture and Food Research Organization

data_processing:
Reads were mapped to the IRGSP-1.0 genome assembly and MSU7 gene models using the STAR aligner (Dobin et al., 2013)
Read counts were quantified using the featureCounts (Liao et al., 2014) with option” -S 2 -p -B -C -T”.
Supplementary files format and content: Tab-delimited text files include row counts for each Sample

organism: Oryza sativa

growth_protocol: Rice plants were grown in a growth chamber under a 14 h light/10 h dark photoperiod, with 50% R.H. at daytime and 60% R.H. at nighttime. The temperature in the growth chamber varied from 25°C to 30℃ at daytime,

extract_protocol:
Total RNA was extracted using TRIzol RNA Isolation Reagents (Thermo Fisher) according to manufacturer’s instructions.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional mRNA-seq kit (New England Biolabs)

treatment_protocol: The water level in each pot was maintained at 6 cm above the bottom of the pot under WW conditions. Drought stress was initiated at each indicated days after sowing by withdrawing water supply.

tag: tissue

value: Nipponbare


title: adult female naked mole-rat cervical thymus short-read 10x scRNA-seq, replicate 2

city: South San Francisco

first: Nimrod

middle: Daniel

last: Rubinstein

address: 1170 Veterans blvd

institute: Calico

description:
10x Genomics
nmr.female.cervical.thymus_2

data_processing:
Cell Ranger mkfastq for demultiplexing
Cell Ranger count for generating gene-barcode-matrix
HetGla2.0 + GCF_000247695.1 and Heterocephalus_glaber_female 1.0 combined annotations
barcodes.tsv.gz is the gunzipped list of sequenced barcodes. genes.tsv.gz is the gunzipped list of sequenced genes. matrix.mtx.gz is the gunzipped compressed sparse gene-barcode-matrix

organism: Heterocephalus glaber

source_name: cervical thymus

extract_protocol:
Thoracic tissue was dissected using sterile surgical techniques and subsequently transferred to a petri dish containing PBS. Fat tissue surrounding the thymic parenchyma was carefully removed with microscissors and tissue forceps under a surgical microscope. Excess liquid/PBS was carefully removed with Kimwipes before weight measurement. For histological analysis, the tissues were fixed in 10% formalin and following standard tissue processing procedures. For the purpose of creating single-cell suspensions, thymic tissues were ground through 100 μm and 40 μm cell strainers (Falcon 352360 and 352340, Corning, NY) with a syringe plunger. Cells were subsequently pelleted (300g, 3 minutes, 4 ̊C), resuspended in 5 mL of ACK lysis buffer (Lonza BP10-548E, Basel, Switzerland) for 5 minutes at room temperature, and washed and resuspended with PBS with 0.04% BSA. Cell density and viability were determined using the Countness II Cell Counter (Thermofisher AMQAF1000). The cells were pelleted and resuspended at 1 million cells per ml of 0.04% BSA/PBS prior generating the 10× GEM single-cell libraries.
Single cells were captured in droplet emulsion using the Chromium Controller (10× Genomics, Pleasanton, CA), and GEM single-cell libraries were constructed according to the 10× Genomics protocol using the Chromium Single-Cell 30 Gel Bead and Library 3’ V3 kit (10× Genomics, Pleasanton, CA). In brief, cell suspensions were diluted in PBS with 0.04% BSA to a final concentration of 1×106 cells/mL (1,000 cells per μL). Cells were loaded in each channel with a target output of 10,000 cells per sample. All reactions were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA) with a 96 Deep Well Reaction Module. Twelve cycles were used for cDNA amplification and sample index PCR. Amplified cDNA and final libraries were evaluated using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a high sensitivity chip.
paired-end ilimina next-seq

value: cervical thymus

value: all cells

tag: age

value: 2 years

tag: Sex

value: female

tag: colony/strain


title: isogenic induced pluirpotent stem cell sample 2


title: adult male mouse thymus short-read 10x scRNA-seq, replicate 1

description:
10x Genomics
mouse.male.thymus_1

data_processing:
Cell Ranger mkfastq for demultiplexing
Cell Ranger count for generating gene-barcode-matrix
mm10 + Gencode vM25 primary assembly annotation
barcodes.tsv.gz is the gunzipped list of sequenced barcodes. genes.tsv.gz is the gunzipped list of sequenced genes. matrix.mtx.gz is the gunzipped compressed sparse gene-barcode-matrix

organism: Mus musculus

source_name: thymus

value: thymus

value: 2 months

value: male


title: adult female naked mole-rat bone-marrow cells short-read 10x scRNA-seq, replicate 1 library 1

description:
10x Genomics
nmr.BM.F_1_1

source_name: bone marrow

extract_protocol:
Femurs and tibias of the euthanized animals were dissected using sterile surgical techniques and transferred to a petri dish containing the basal medium (Minimal Essential Medium supplemented with 10% FBS and 1X antibiotics antimycotic solution (Gibco)). The dorsal and distal ends of femurs and tibias were cut with scissors to reveal the bone marrow cavity, and the bone marrow cells were flushed out with the basal medium using needles/syringes. Cells were then passed through 100 μm and 40 μm cell strainers, washed, pelleted, and resuspended in 5 mL of ACK lysis buffer (Lonza BP10-548E, Basel, Switzerland) for 5 minutes at room temperature. After determining their density and viability, cells were resuspended at 1 million cells per ml of 0.04% BSA/PBS prior to generating the 10× GEM single-cell libraries.
Single cells were captured in droplet emulsion using the Chromium Controller (10× Genomics, Pleasanton, CA), and GEM single-cell libraries were constructed according to the 10× Genomics protocol using the Chromium Single-Cell 30 Gel Bead and Library 3’ V3 kit (10× Genomics, Pleasanton, CA). In brief, cell suspensions were diluted in PBS with 0.04% BSA to a final concentration of 1×106 cells/mL (1,000 cells per μL). Cells were loaded in each channel with a target output of 10,000 cells per sample. All reactions were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA) with a 96 Deep Well Reaction Module. Twelve cycles were used for cDNA amplification and sample index PCR. Amplified cDNA and final libraries were evaluated using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a high sensitivity chip.
paired-end ilimina next-seq

value: bone marrow


title: old naked mole-rat anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 2

description:
10x Genomics
nmr_spleen.T.cells_24y_2

source_name: spleen


title: Drought4_29d_rep2


title: E198K induced pluirpotent stem cell sample 3


title: old naked mole-rat anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 1

description:
10x Genomics
nmr_spleen.T.cells_24y_1


title: Drought4_29d_rep1


title: isogenic induced pluirpotent stem cell sample 1


title: adult male mouse bone-marrow cells short-read 10x scRNA-seq, replicate 2 library 1

description:
10x Genomics
mouse.BM.M_2_1


title: adult male mouse thymus short-read 10x scRNA-seq, replicate 2

description:
10x Genomics
mouse.male.thymus_2


title: adult female naked mole-rat bone-marrow cells short-read 10x scRNA-seq, replicate 1 library 2

description:
10x Genomics
nmr.BM.F_1_2


title: old naked mole-rat anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 3

description:
10x Genomics
nmr_spleen.T.cells_24y_3


title: adult naked mole-rat anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 3

description:
10x Genomics
nmr_spleen.T.cells_2y_4

value: MS 61


title: lps3

city: Shanghai

first: Jiayi

last: Mao

address: Zhi Zao Ju road

country: China

institute: shanghai ninth people's hospital

data_processing:
Libraries were sequenced using the llumina Novaseq 6000 sequencing platform and 150 bp double-ended reads were generated. raw reads in fastq format were processed by fastp software, and low quality reads were removed to obtain clean reads for subsequent data analysis. Reference genome alignments were performed using HISAT2 software and gene expression quantity (FPKM) calculations were performed, and reads counts (counts) for each gene were obtained by HTSeq-count. PCA analysis of genes (counts) as well as mapping was performed using R (v 3.2.0) to assess sample biological replicates.
DESeq2 software was used to analyze differentially expressed genes, which were consistent with q value < 0.05 and foldchange > 2 or foldchange < Genes with a threshold of 0.5 were defined as differentially expressed genes (DEGs). Hierarchical clustering analysis of DEGs was performed using R (v 3.2.0) to show the expression patterns of genes in different groups and samples. The R package ggradar was used to create a radar map of the top 30 genes to show the expression changes of up-regulated or down-regulated genes.
Subsequently, GO, KEGG Pathway, Reactome and WikiPathways enrichment analysis of differentially expressed genes were performed based on hypergeometric distribution algorithm to screen significant enriched functional entries. R (v 3.2.0) was used to draw bar chart, chord chart or enrichment analysis circle chart for significant enrichment functional items
Gene set enrichment analysis was performed using GSEA software. The predefined gene sets were used to rank the genes according to their degree of differential expression in the two types of samples, and then to test whether the prespecified gene sets were enriched at the top or bottom of the ranking table
After the sequences were reassembly assembled by StringTie2, the known annotated genes were compared with the reference genome using Cuffcompare software for gene structure expansion and novel transcript identification
Differentially expressed miRNAs were identified with the threshold of p value < 0.05. While the p value was calculated with DEG algorithm [5] in the R package for experiment with biological replicates, and with Audic Claverie statistic [6] for experiment without biological replicates.
Supplementary files format and content: FORMAT: .txt; CONTENT: Statistical table of the number of reads on the gene alignment of each sample
Supplementary files format and content: FORMAT: .txt; CONTENT: Summary table of gene expression in each sample

source_name: cells stimulated by PMA and then culculated with lps

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA purity and quantification were identified using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Transcriptome libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep kit according to the manufacturer's instructions. Transcriptome sequencing and analysis were performed by Shanghai Ouyi Biotechnology Co., LTD (Shanghai, China).

value: Suspended cells, adherent cells after PMA stimulation

value: PMA and LPS


title: Drought3_29d_rep2


title: adult naked mole-rat anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 1

description:
10x Genomics
nmr_spleen.T.cells_2y_2

value: spleen

value: mostly spleen T cells

value: MS 60


title: lps2

value: WT


title: adult naked mole-rat anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 2

description:
10x Genomics
nmr_spleen.T.cells_2y_3

value: MS 74


title: lps1


title: adult male mouse bone-marrow cells short-read 10x scRNA-seq, replicate 2 library 2

description:
10x Genomics
mouse.BM.M_2_2


title: adult male mouse bone-marrow cells short-read 10x scRNA-seq, replicate 1 library 2

description:
10x Genomics
mouse.BM.M_1_2


title: adult male mouse bone-marrow cells short-read 10x scRNA-seq, replicate 1 library 1

description:
10x Genomics
mouse.BM.M_1_1


title: fecal microbiota_sample R40

city: Boston

first: Samuel

last: Beck

state: MA

address: 609 Albany st.

department: Dermatology

institute: Boston University School of Medicine

library_source: genomic

data_processing:
Unique amplicon sequences variants were inferred from raw reads using the DADA2 pipeline
Potential sequencing errors and chimeric sequences were also removed with the Dada2 pipeline
Taxonomy assignment was performed using Uclust from Qiime v.1.9.1 with the Zymo Research Database, a 16S database
Composition visualization, alpha-diversity, and beta-diversity analyses were performed with Qiime v.1.9.1
Assembly: Zymo Research Database
Supplementary files format and content: tab determined text file includes species composition for each sample

molecule: genomic DNA

organism: feces metagenome

source_name: feces

growth_protocol: DONOR MICE: Young and old C57BL6J mice maintained on chow. RECIPIENT MICE: Young A/J mice are were maintained on chow diet

extract_protocol:
fecal DNA was extracted using the ZymoBIOMICS®-96 MagBead DNA Kit (Zymo)
libraries prepared using the 16SNGS Library Prep Kit and proprietary primers targeting V3-V4 of the 16S rRNA gene (Zymo)
Cleaned and quantified libraries were sequenced on an IlluminaMiSeq instrument with a v3 reagent kit (600 cycles) and 10% PhiX spike-in (Illumina)

treatment_protocol: Fecal material collected from donors over a 2-3 week period. Recipient mice received antibiotics to deplete resident microbes then received 3 fecal microbiota transplants from young or old donor mice (D1 matched to R1, D2 with R2 etc). Recipients were then subjected to 6 weekly injections of azoxymethane (5-10 mg/kg). Mice were maintained for 19 weeks after final azoxymethane injection during which time they received monthly FMT boosters from the respective donor.

value: feces

value: Female

tag: fmt donor/recipient

value: Recipient

tag: matched recipient/donor

tag: strain

value: A/J wildtype

value: FMT from old donor


title: Well-watered2_29d_rep2

value: Nipponbare


title: adult female mouse bone-marrow cells short-read 10x scRNA-seq, replicate 2 library 2

description:
10x Genomics
mouse.BM.F_2_2

value: all cells

value: 2 months

value: female


title: adult female mouse bone-marrow cells short-read 10x scRNA-seq, replicate 2 library 1

description:
10x Genomics
mouse.BM.F_2_1

value: bone marrow


title: ABS3

source_name: cells stimulated by PMA and then culculated with lps and ABs

value: Suspended cells, adherent cells after PMA stimulation

value: PMA and LPS and ABS


title: ABS2


title: fecal microbiota_sample R39


title: adult female mouse bone-marrow cells short-read 10x scRNA-seq, replicate 1 library 2

description:
10x Genomics
mouse.BM.F_1_2


title: Drought3_29d_rep3


title: Drought3_29d_rep1


title: Well-watered2_29d_rep1


title: ABS1


title: Well-watered2_29d_rep3


title: adult female mouse bone-marrow cells short-read 10x scRNA-seq, replicate 1 library 1

description:
10x Genomics
mouse.BM.F_1_1


title: ctrl3

source_name: cells stimulated by PMA and then culculated with pbs

value: PMA and PBS


title: Drought2_29d_rep3


title: fecal microbiota_sample R38


title: fecal microbiota_sample R37


title: old mouse anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 4

description:
10x Genomics
mouse_spleen.T.cells_24m_4

extract_protocol:
Spleens were removed by dissection, transferred to a sterile petri dish containing PBS with 5% FBS, and minced using surgical blades. Spleen fragments were then ground through 100 μm and 40 μm cell strainers, pelleted, and resuspended in the ACK lysis buffer as described in the thymus tissue collection section. Cell density and viability were determined using Countness II Cell Counter. Subsequently, splenocytes were resuspended at 1 million cells per ml of 0.04% BSA/PBS. In order to sort out the splenocyte T-cell subsets for constructing 10× GEM single-cell libraries, splenocytes were resuspended at 1 million cells per ml of FACS buffer (PBS with 1% FBS and 5mM EDTA).splenocytes were pre-incubated with 1ug mouse Fc blocker (BD 553141) per 1 million cells/100ul FACS buffer for 5 minutes, and incubated with an anti-mouse CD3e (clone 17A2, eFlour450, 2 ug/ml) and an anti-mouse CD11b (M1/70, Alexa 488, 2 ug/ml) on ice for 40 minutes.after incubation, cells were washed and resuspended in the FACS buffer containing Sytox Blue Live/Dead dye for cell sorting using FACS BD Aria. Viable, single cells were gated, and the CD11b-/CD3e+ cells were collected for the generation of 10× GEM single-T-cell libraries
Single cells were captured in droplet emulsion using the Chromium Controller (10× Genomics, Pleasanton, CA), and GEM single-cell libraries were constructed according to the 10× Genomics protocol using the Chromium Single-Cell 30 Gel Bead and Library 3’ V3 kit (10× Genomics, Pleasanton, CA). In brief, cell suspensions were diluted in PBS with 0.04% BSA to a final concentration of 1×106 cells/mL (1,000 cells per μL). Cells were loaded in each channel with a target output of 10,000 cells per sample. All reactions were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA) with a 96 Deep Well Reaction Module. Twelve cycles were used for cDNA amplification and sample index PCR. Amplified cDNA and final libraries were evaluated using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a high sensitivity chip.
paired-end ilimina next-seq

value: spleen

value: mostly spleen T cells

value: 24 months

value: male


title: fecal microbiota_sample R35

value: feces


title: ctrl1

value: WT


title: ctrl2


title: Drought2_29d_rep1


title: Drought2_29d_rep2


title: old mouse anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 2

description:
10x Genomics
mouse_spleen.T.cells_24m_2


title: fecal microbiota_sample R34

value: Female

value: Recipient


title: fecal microbiota_sample R33

value: A/J wildtype

value: FMT from old donor


title: Drought1_29d_rep3

value: Nipponbare


title: old mouse anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 1

description:
10x Genomics
mouse_spleen.T.cells_24m_1


title: SNU16 cells,H2O2,24h,rep2

city: Jining

first: Mingliang

last: Liu

state: Shandong

address: Affiliated Hospital of Jining Medical College, Jining 272007, China

institute: Affiliated Hospital of Jining Medical University

data_processing:
Clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data(raw reads).
Index of the reference genome(Homo_sapiens.GRCh38.109) was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
(Stringtie- 1.3.3b) was used to count the read numbers mapped to each gene. And then FPKM was calculated, which expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two samples was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Significantly differential expression genes were screened based on the following criteria: Corrected P-value < 0.05.
Assembly: Homo_sapiens.GRCh38.109
Supplementary files format and content: tab-delimited text file include FPKM values for each sample.

growth_protocol: SNU16 cells were maintained in 1640 supplemented with 10％ fetal bovine serum （FBS）and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen) .
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit  for Illumina (NEB E7420) following manufacturer's protocols.

treatment_protocol: SNU16 cells were treated with 7,69uM 5-FU or 80uM H2O2 for 24 h,respectively.

value: gastric cancer cells

tag: time


title: Drought1_29d_rep2


title: fecal microbiota_sample R32


title: fecal microbiota_sample R31


title: adult mouse anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 4

description:
10x Genomics
mouse_spleen.T.cells_2m_4

value: 2 months


title: Drought1_29d_rep1


title: SNU16 cells,H2O2,24h,rep1


title: SNU16 cells,5-FU,24h,rep3


title: Well-watered1_29d_rep3


title: adult mouse anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 3

description:
10x Genomics
mouse_spleen.T.cells_2m_3


title: fecal microbiota_sample R30

value: Male


title: old mouse anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 3

description:
10x Genomics
mouse_spleen.T.cells_24m_3


title: Well-watered1_29d_rep2


title: SNU16 cells,5-FU,24h,rep1


title: SNU16 cells,H2O2,24h,rep3


title: fecal microbiota_sample R28


title: fecal microbiota_sample R29


title: Well-watered1_29d_rep1


title: SNU16 cells,5-FU,24h,rep2


title: adult mouse anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 2

description:
10x Genomics
mouse_spleen.T.cells_2m_2


title: mEmerald positive (infected) AMs, replicate 1 [bcgSC.mEmPos.AD66]

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

data_processing:
Stranded paired-end reads of length 76 were preprocessed: The first three nucleotides of R2  were removed as described in the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian User Manual (v2: 063017) and read ends consisting of 50 or more of the same nucleotide were removed.
The remaining read pairs were aligned to the mouse genome (mm10) + Mtb H37Rv genome using the gsnap aligner (v. 2018-07-04) allowing for novel splicing. (gsnap options: -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 )
Concordantly mapping read pairs (average 15-million / sample) that aligned uniquely were assigned to exons using the subRead program and gene definitions from Ensembl Mus_Musculus GRCm38.78 coding and non-coding genes.
Assembly: mm10 + Mtb H37Rv
Supplementary files format and content: rawCounts.tsv contains the raw counts for each sample generated by subRead, tab-separated

source_name: Lung

extract_protocol:
RNA isolation was performed using TRIzol (Invitrogen), two sequential chloroform extractions, Glycoblue carrier (Thermo Fisher), isopropanol precipitation, and washes with 75% ethanol.
cDNA libraries were constructed and amplified using the SMARTer Stranded Total RNA-Seq Kit (v2) - Pico Input Mammalian (Clontech) per the manufacturers instructions. Libraries were amplified and then sequenced on an Illumina NextSeq (2 x 75, paired-end).

treatment_protocol: BCG-Pasteur was cultured in Middlebrook 7H9 broth at 37°C to an OD of 0.1–0.3. Bacteria was diluted in PBS and 1e6 CFU in 200 ml was injected sub-cutaneously.

value: Lung

value: Alveolar macrophages

value: scBCG


title: adult mouse anti-CD3 sorted splenocyte short-read 10x scRNA-seq, replicate 1

description:
10x Genomics
mouse_spleen.T.cells_2m_1

value: spleen


title: fecal microbiota_sample R27


title: SNU16 cells,control,24h,rep3

value: un-treated


title: mEmerald negative (bystander) AMs, replicate 1 [bcgSC.mEmNeg.AD66]

description: mEmerald negative (uninfected) AMs, replicate 1


title: Drought2_26d_rep2


title: Drought2_26d_rep3


title: SNU16 cells,control,24h,rep1


title: Naïve AM, replicate 1 [bcgSC.naive.AD66]

description: Naïve AM, replicate 1


title: fecal microbiota_sample R25


title: fecal microbiota_sample R24


title: WT-5

city: Uppsala

first: Andor

last: Pivarcsi

address: Husargatan 3

department: Department of Medical Biochemistry and Microbiology (IMBIM)

country: Sweden

institute: Uppsala University

description: Biological replicate 5

data_processing:
Quality control
Trimming
Alignment to human genome
FeatureCounts
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text files include quantified reads from FeatureCounts

growth_protocol: UT-SCC-7 cells were cultured in DMEM with 10% FBS, 1% HEPES, 1% NEA and 1% P+S

extract_protocol:
RNA was extracted using miRNeasy Mini Kit  (QIAGEN). rRNA-depletion library
Sequencing libraries were prepared from 1000ng total RNA using the TruSeq stranded total RNA library preparation kit with RiboZero Gold treatment (cat# 20020599, Illumina Inc.)

treatment_protocol: Two single guide RNAs targeting the upstream and downstream sequence of PVT1 exon2 together with Cas9 protein were used for establishing PVT1 E2KO UT-SCC-7 cell line, wildtype UT-SCC-7 cells are used as control.

value: human cSCC cells

value: wildtype


title: mEmerald negative (bystander) AMs, replicate 1 [bcgSC.mEmNeg.AD65]


title: mEmerald positive (infected) AMs, replicate 1 [bcgSC.mEmPos.AD65]


title: Drought1_26d_rep2


title: WT-4

description: Biological replicate 4


title: Naïve AM, replicate 1 [bcgSC.naive.AD65]

description: Naïve AM, replicate 1


title: WT-3

description: Biological replicate 3


title: fecal microbiota_sample R23

value: feces


title: Drought1_26d_rep1


title: Well-watered1_26d_rep3


title: SNU16 cells,control,24h,rep2

value: WT


title: fecal microbiota_sample R21


title: WT-2

description: Biological replicate 2


title: fecal microbiota_sample R26


title: HUDEP2, ATAC, Y2A, rep2

city: Rochester

first: Laurie

last: Steiner

state: New York

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Sequencing reads were aligned to hg38 genome using Bowtie2. PCR duplicates were removed using Picard.
The RPKM normalization method was adopted to generate read count genome browser tracks from bamCoverage.
Assembly: hg38
Supplementary files format and content: bigWig files

growth_protocol: HUDEP-2 cells were cultured via published methods in Vinjamur et al. 2018.

extract_protocol:
Library construction and strategy according to Schulz et al 2019, Cell Reports
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit with standard protocols, cleaned up using Ampure XP beads and pooled together for paired-end sequencing.

value: Human erythroid progenitor cell line

value: HEXIM1 Y2A Overexpression


title: HUDEP2, ATAC, Y2A, rep3


title: WT-1

description: Biological replicate 1


title: HUDEP2, ATAC, Y2A, rep1


title: Well-watered1_26d_rep2


title: fecal microbiota_sample R19

value: Female

value: Recipient

value: A/J wildtype

value: FMT from young donor


title: HUDEP2, ATAC, OE, rep3

value: HEXIM1 Overexpression


title: Drought2_26d_rep1

value: Nipponbare


title: Drought2_23d_rep3


title: PVT1 exon2 KO-5

description: Biological replicate 5

value: PVT1 exon2 knockout


title: Drought1_26d_rep3


title: Well-watered1_26d_rep1


title: fecal microbiota_sample R18


title: PVT1 exon2 KO-4

description: Biological replicate 4


title: fecal microbiota_sample R17


title: fecal microbiota_sample R20


title: fecal microbiota_sample R15


title: HUDEP2, ATAC, OE, rep2


title: PVT1 exon2 KO-3

description: Biological replicate 3


title: fecal microbiota_sample R16


title: HUDEP2, ATAC, OE, rep1


title: HUDEP2, ATAC, EV, rep3


title: Drought1_23d_rep3


title: Y-PRP-exos, rep2

city: Chengdu

first: Xia

last: Kang

address: Rongdu Avenue, #270

institute: General Hospital of Western Theater Command

description:
Reads_count_miRNA-young.xlsx
002ZH30_2_Reads

data_processing:
Cutadapt (version 2.7) was used to remove short reads with low quality
perl5 (26) was used to recognize UMIs and remove UMIs shorter than 12 reads
bowtie (verson 1.2.2) was used to compare the miRBase database
quantification of miRNAs
Supplementary files format and content: Excel file includes raw counts for each Sample

source_name: platelet rich plasma

extract_protocol: Library was performed using the QIAseq miRNA Library Kit according to the manufracturer's protocol.

value: platelet rich plasma

tag: developmental stage

value: young


title: PVT1 exon2 KO-2

description: Biological replicate 2


title: fecal microbiota_sample R13


title: fecal microbiota_sample R14


title: Y-PRP-exos, rep1

description:
Reads_count_miRNA-young.xlsx
002ZH30_1_Reads


title: HUDEP2, ATAC, EV, rep2


title: Drought1_23d_rep2


title: Drought1_23d_rep1


title: PVT1 exon2 KO-1

description: Biological replicate 1


title: fecal microbiota_sample R12


title: O-PRP-exos, repB

description:
Reads_count_miRNA-Old.xlsx
B_Reads

value: old


title: fecal microbiota_sample R11


title: Well-watered1_23d_rep3


title: Drought2_23d_rep2


title: HUDEP2, HEXIM1, Y2A, rep3

tag: chip antibody

value: HEXIM1 (D5Y5K) Rabbit mAb #12604 from Cell Signaling


title: HUDEP2, HEXIM1, Y2A, rep2


title: HUDEP2, ATAC, EV, rep1


title: O-PRP-exos, repA

description:
Reads_count_miRNA-Old.xlsx
A_Reads


title: Drought2_23d_rep1


title: Well-watered1_23d_rep2


title: fecal microbiota_sample R8

value: Male


title: fecal microbiota_sample R9


title: Well-watered1_23d_rep1


title: Ctrl_iPSC_CM_3

first: Farshad

last: Farshidfar

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

description:
TT001 study
TT001-62
Zhou_2023_PairedEnd_TranscriptMatrix.TPM.txt
Zhou_2023_PairedEnd_TranscriptMatrix.counts.txt
Zhou_2023_PairedEnd_TranscriptMatrix.length.txt

data_processing:
Read alignment by Salmon (ver. 1.8.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl human reference genome release 108
Exclusion of mitochondrial genes and renormalization to TPM.
Assembly: hg38 v.13
Supplementary files format and content: TXT

source_name: iPSC-CM

growth_protocol: Isolation of primary adult human and pig cardiac fibroblasts. Adult human or pig left ventricles were minced into small pieces and digested in cardiac fibroblast digestion medium (10μg/mL Liberase TH, 10 μg/mL Liberase TM, 1 unit/mL DNase I, 0.01% Polaxomer) for 1 h in 37ºC. After digestion, the cells were filtered through a 70 μM strainer into a 50 mL falcon tube. Cells were pelleted by spinning down for 5 min at 1200Å~g and placed in fibroblast growth medium. The medium was replaced every two days. Four days later, AHCFs or APCFs were frozen or re-plated for viral transduction.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to vender’s protocol. RNAs were retrotranscribed to cDNA using iScript Supermix™ (Bio-Rad). qPCR was performed using TaqMan. Gene Expression Master Mix (Thermo Scientific) mRNA levels were normalized by comparison to GAPDH mRNA.
100ng total RNA was extracted via polyA-tail specific protocol according to Illumina protocol. Sequencing libraries were generated using the TruSeq stranded RNA sample prep kit (Illumina). The libraries were sequenced as 75 bp single-end reads using an Illumina NovaSeq SP platform with an average of 35M reads per sample. Indexed libraries that met appropriate cut-offs for both quantity and quality were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution was determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.6 ng/ul were used for sequencing.

treatment_protocol: AHCFs or APCFs were seeded into culture dishes or plates at a density of 5Å~103/cm2 in fibroblast growth medium (day -1). One day after plating cells (day 0), fibroblast growth medium was removed, and virus medium was added. One day after viral transduction (day 1), virus medium was replaced by iCM medium composed of 4 parts Dulbecco’s Modified Eagle’s Medium (DMEM) and 1-part Gibco. Media 199, 10% FBS, 1% nonessential amino acids, 1% penicillin/streptomycin, for every two days until day 4. On day 4, medium was changed to 75% iCM media and 25% RPMI + B27. On day 7, medium was changed to 50% iCM and 50% RPMI + B27. On day 11, medium was changed to 25% iCM and 75% RPMI + B27. On day 14, medium was changed to RPMI + B27+FFV (10ng/mL rhFGF, 15ng/ml rhFGF-10, and 5ng/mL rhVEGF) every day until day 21.

value: iPSC-CM

value: No treatment


title: Ctrl_iPSC_CM_2

description:
TT001 study
TT001-61
Zhou_2023_PairedEnd_TranscriptMatrix.TPM.txt
Zhou_2023_PairedEnd_TranscriptMatrix.counts.txt
Zhou_2023_PairedEnd_TranscriptMatrix.length.txt

value: WT


title: HUDEP2, HEXIM1, Y2A, rep1

value: Human erythroid progenitor cell line


title: HUDEP2, HEXIM1, OE, rep2


title: fecal microbiota_sample R7

value: feces


title: HUDEP2, HEXIM1, OE, rep3


title: Drought2_20d_rep3


title: HUDEP2, HEXIM1, OE, rep1


title: Drought2_20d_rep2


title: Ctrl_mixture

description:
TT001 study
TT001-56
Zhou_2023_PairedEnd_TranscriptMatrix.TPM.txt
Zhou_2023_PairedEnd_TranscriptMatrix.counts.txt
Zhou_2023_PairedEnd_TranscriptMatrix.length.txt

source_name: Cardiac Fibroblast + iPSC-CM (9/1 ratio)


title: Drought2_20d_rep1


title: Drought1_20d_rep3


title: fecal microbiota_sample R5


title: DKO, ZFX05, FLAG, rep1

city: Los Angeles

first: Peggy

middle: J

last: Farnham

state: California

address: 1450 Biggy St

department: Biochemistry and Molecular Biology

institute: USC Keck School of Medicine

data_processing:
Sequencing results were aligned to hg38 using bwa
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: peak files with quantitative data and bigWig files

source_name: HEK293T ZFX/ZNF711 KO (DKO)

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Chromatin was prepared using the protocol previously published (PMID: 29429977). Briefly, cells were crosslinked by 1%formedelhyde for 10 mins and lysised into nuclei. Nuclei were sonicated using BioRuptor to break into chromatin fragments.
Libraries were prepared using KAPA Hyper Prep Kit (Kapa #KK8505) according to provided protocol

treatment_protocol: Cells that were transfected were transfected using Lipofectamine 3000 (30µl P3000, 43.4µl Lipofectamine 3000). 15 µg of plasmid was added to each 10cm plate.

value: HEK293T ZFX/ZNF711 KO (DKO)

value: Human embryonic kidney


title: fecal microbiota_sample R4

value: Recipient

value: A/J wildtype


title: Ctrl_iPSC_CM_1

description:
TT001 study
TT001-60
Zhou_2023_PairedEnd_TranscriptMatrix.TPM.txt
Zhou_2023_PairedEnd_TranscriptMatrix.counts.txt
Zhou_2023_PairedEnd_TranscriptMatrix.length.txt


title: HUDEP2, HEXIM1, EV, rep2


title: DKO, ZFX04, FLAG, rep1


title: HUDEP2, HEXIM1, EV, rep1


title: DKO, ZFX02, FLAG, rep2


title: HUDEP2, GATA1, Y2A, rep3

data_processing:
Sequencing reads were aligned to hg38 genome using Bowtie2. PCR duplicates were removed using Picard.
The RPKM normalization method was adopted to generate read count genome browser tracks from bamCoverage.
Assembly: hg38
Supplementary files format and content: bigWig files
Library strategy: CUT&RUN

value: HEXIM1 Y2A Overexpression

value: Anti-GATA1 antibody (ab11852) from abcam


title: Drought1_20d_rep1

value: Nipponbare


title: Drought1_20d_rep2


title: Well-watered1_20d_rep3


title: HUDEP2, HEXIM1, EV, rep3


title: fecal microbiota_sample R1

value: FMT from young donor


title: fecal microbiota_sample R2


title: HUDEP2, GATA1, Y2A, rep2


title: fecal microbiota_Sample D40

value: female

value: Donor

value: C57BL6/J wildtype


title: HUDEP2, GATA1, Y2A, rep1


title: DKO, ZFX01, FLAG, rep1


title: DKO, ZFX01, FLAG, rep2


title: fecal microbiota_Sample D39


title: HUDEP2, Ser5Pol2, Y2A, rep3

value: Phospho-Rpb1 CTD (Ser5) (D9N5I) Rabbit mAb  #13523 from Cell Signaling


title: Well-watered1_20d_rep1


title: DKO, ZFXWT, FLAG, rep2


title: fecal microbiota_Sample D38


title: HUDEP2, Ser5Pol2, Y2A, rep2


title: Drought2_17d_rep3


title: fecal microbiota_sample R3

value: Male


title: DKO, ZFXWT, FLAG, rep1


title: HUDEP2, Ser5Pol2, Y2A, rep1


title: USC_RNA499, DKO, ZFX-05, rep3

data_processing:
RNA-seq results were trimmed then aligned to hg38 using STAR
Raw gene counts were created using Quantify to annotation model (Partek E/M) from Partek Flow modules (version 10.0.21.1103 at project initiation).
Assembly: hg38 - GENCODE Genes - release 36

extract_protocol:
RNA was harvested using Trizole Phase Separation
RNA libraries for RNA-seq were prepared using NEBNext Ultra™ II RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: ZFX/ZNF711 Knockout


title: Drought2_17d_rep2


title: fecal microbiota_Sample D37


title: DKO, ZFX02, FLAG, rep1


title: Drought2_17d_rep1


title: fecal microbiota_Sample D35


title: fecal microbiota_Sample D34


title: HUDEP2, TotalPol2, Y2A, rep3

value: Rpb1 CTD (4H8) Mouse mAb #2629 from Cell Signaling


title: Drought1_17d_rep3


title: Well-watered1_20d_rep2


title: USC_RNA498, DKO, ZFX-05, rep2


title: Drought1_17d_rep2


title: HUDEP2, TotalPol2, Y2A, rep2

value: Human erythroid progenitor cell line


title: fecal microbiota_Sample D32

value: feces


title: fecal microbiota_Sample D33


title: HUDEP2, TotalPol2, Y2A, rep1


title: USC_RNA496, DKO, ZFX-04, rep3

value: HEK293T ZFX/ZNF711 KO (DKO)


title: Drought1_17d_rep1


title: HUDEP2, GATA1, OE, rep3

value: HEXIM1 Overexpression


title: Well-watered1_17d_rep3


title: USC_RNA495, DKO, ZFX-04, rep2

value: Human embryonic kidney


title: fecal microbiota_Sample D31


title: HUDEP2, GATA1, OE, rep2


title: USC_RNA494, DKO, ZFX-04, rep1


title: Well-watered1_17d_rep2


title: fecal microbiota_Sample D30

value: male


title: fecal microbiota_Sample D29


title: HUDEP2, GATA1, OE, rep1


title: HUDEP2, GATA1, EV, rep3

value: WT


title: USC_RNA497, DKO, ZFX-05, rep1


title: USC_RNA493, DKO, ZFX-02, rep3


title: USC_RNA492, DKO, ZFX-02, rep2


title: HUDEP2, GATA1, EV, rep2

value: Anti-GATA1 antibody (ab11852) from abcam


title: USC_RNA491, DKO, ZFX-02, rep1


title: fecal microbiota_Sample D28


title: Drought2_14d_rep2

value: Nipponbare


title: USC_RNA490, DKO, ZFX-01, rep3


title: HUDEP2, GATA1, EV, rep1


title: Drought2_14d_rep3


title: Drought2_14d_rep1


title: fecal microbiota_Sample D27


title: HUDEP2, Ser5Pol2, OE, rep3


title: fecal microbiota_Sample D26


title: Drought1_14d_rep3


title: USC_RNA489, DKO, ZFX-01, rep2


title: fecal microbiota_Sample D25


title: HUDEP2, Ser5Pol2, OE, rep2


title: USC_RNA488, DKO, ZFX-01, rep1


title: Drought1_14d_rep2


title: fecal microbiota_Sample D24


title: USC_RNA487, DKO, ZFX-WT, rep3

value: ZFX-WT


title: HUDEP2, Ser5Pol2, OE, rep1


title: HUDEP2, Ser5Pol2, EV, rep3


title: USC_RNA486, DKO, ZFX-WT, rep2


title: Drought1_14d_rep1


title: Well-watered1_14d_rep3


title: fecal microbiota_Sample D23


title: fecal microbiota_Sample D21


title: fecal microbiota_Sample D20

value: female


title: Well-watered1_14d_rep2


title: USC_RNA485, DKO, ZFX-WT, rep1


title: HUDEP2, Ser5Pol2, EV, rep2


title: Well-watered1_14d_rep1


title: USC_RNA484, DKO, pCMV6, rep3

value: Control (pCMV6-Entry)


title: HUDEP2, Ser5Pol2, EV, rep1


title: HUDEP2, TotalPol2, OE, rep3


title: fecal microbiota_Sample D18

value: Donor

value: C57BL6/J wildtype


title: fecal microbiota_Sample D19


title: HUDEP2, TotalPol2, OE, rep2


title: USC_RNA482, DKO, pCMV6, rep1


title: Roc 4

type: RNA

city: Lille

first: Alexandre

last: Berthier

address: U1011, Bâtiment J&K, Bd du Pr Leclerc

country: France

institute: Inserm

hyb_protocol: Following fragmentation, 2,3 microgrammes of ssDNA were hybridized for 16 hr at 45C on Clariom S Human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing:
data were processed using our in-house Galaxy instance with “GIANT” (Galaxy-based interactive tools for Analysis of Transcriptomic data).  It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis using apt-probeset-summarize tool (v.2.10.2). Normalization done on gene level with NetAffx Annotation Release 36.
Clariom_S_Human.r1.pgf
Clariom_S_Human.r1.na36.hg38.transcript.csv
Log2 RMA

label: biotin

source_name: Roc 4

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: DMEM/F12 [D6434] + L-glutamine + P/S + 12,5% SVF

extract_protocol: Total RNA was extracted using Nucleospin RNA kit from Macherey Nagel according to the manufacturer's instructions.

treatment_protocol: 2h synchronization (100nM dexamethasone) then 1µM homoharringtonine or 100nM Rocaglamide A during 4h. Vehicule = 0,1% DMSO

value: Roc


title: HUDEP2, TotalPol2, OE, rep1


title: fecal microbiota_Sample D17


title: Roc 1

source_name: Roc 1


title: Roc 3

source_name: Roc 3


title: fecal microbiota_Sample D16


title: BxPC3_WB436B_0.1μM_3_bio rep 3

first: Huang

last: Chen

address: Road of Dongchuan  500

institute: East China Normal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie V0.12.2.
Assembly: mm8
Supplementary files format and content: gene_sample_FPKM_with_symbol.txt: Tab-delimited text file includes FPKM values for each sample.

growth_protocol: BxPC3 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1 ug-1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

treatment_protocol:
BxPC3 cells transfected with siRNA against STAT3.
BxPC3 treated with 0.1 μM WB436B.

value: Pancreatic ductal adenocarcinoma


title: HH 4

source_name: HH 4

value: HH


title: HUDEP2, TotalPol2, EV, rep3

value: Human erythroid progenitor cell line

value: Rpb1 CTD (4H8) Mouse mAb #2629 from Cell Signaling


title: BxPC3_WB436B_0.1μM_2_bio rep 2


title: BxPC3_WB436B_0.1μM_1_bio rep 1


title: fecal microbiota_Sample D14

value: feces


title: USC_RNA483, DKO, pCMV6, rep2

value: HEK293T ZFX/ZNF711 KO (DKO)

value: ZFX/ZNF711 Knockout


title: fecal microbiota_Sample D13


title: HH 3

source_name: HH 3


title: HH 2

source_name: HH 2


title: fecal microbiota_Sample D11


title: AC16  treated 12h with 5µM of Digoxin-rep2

hyb_protocol: Following fragmentation, 3.5microgrammes of ssDNA were hybridized for 16 hr at 45C on HuGene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing:
data were processed using our in-house Galaxy instance with “GIANT” (Galaxy-based interactive tools for Analysis of Transcriptomic data).  It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis using apt-probeset-summarize tool (v.2.10.0). Normalization done on gene level with NetAffx Annotation Release 36.
HuGene2.0ST.mps
HuGene-2_0-st-v1.na36.hg19.probeset.csv
Log2 RMA

treatment_protocol: 2h synchronization (100nM dexamethasone) then 5microM Digoxin during 0-6-12-18 or 24h. Vehicule = chloroform/ethanol


title: BxPC3_siSTAT3_2_biol rep 2

value: STAT3 knockdown


title: HH1


title: fecal microbiota_Sample D9

value: male


title: AC16  treated 12h with 5µM of Digoxin-rep1


title: Dmso 3

source_name: Dmso 3

value: Dmso


title: AC16 at T12_control-rep3

source_name: AC16 at T12_control-rep3


title: fecal microbiota_Sample D8


title: BxPC3_Vehicle_3_biol rep 3

value: Vehicle


title: Well-watered1_17d_rep1

data_processing:
Reads were mapped to the IRGSP-1.0 genome assembly and MSU7 gene models using the STAR aligner (Dobin et al., 2013)
Read counts were quantified using the featureCounts (Liao et al., 2014) with option” -S 2 -p -B -C -T”.
Supplementary files format and content: Tab-delimited text files include row counts for each Sample

value: Nipponbare


title: Dmso 2

source_name: Dmso 2


title: BxPC3_Vehicle_2_biol rep 2


title: Dmso 1

source_name: Dmso 1


title: fecal microbiota_Sample D7

source_name: feces


title: HUDEP2, TotalPol2, EV, rep2

value: WT


title: AC16 at T12_control-rep1

source_name: AC16 at T12_control-rep1


title: fecal microbiota_Sample D6


title: HUDEP2, TotalPol2, EV, rep1


title: BxPC3_siSTAT3_3_biol rep 3


title: fecal microbiota_sample R6

value: Male

value: Recipient

value: A/J wildtype

value: FMT from young donor


title: AC16 at T12_control-rep2

source_name: AC16 at T12_control-rep2


title: fecal microbiota_Sample D5

value: Donor

value: C57BL6/J wildtype


title: AC16  treated 6h with 5µM of Digoxin-rep3


title: Ho-34TB

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt.
Quantified reads were aligned to the mouse genome (GRCh38) by STAR (v2.6.1a) and then gene-level read counts were generated based on the annotations of Gencode (v28).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes gene-level read counts.

source_name: HBV positive HCC

extract_protocol:
Total RNA was extracted from tissue using an NucleoSpin RNA kit (MACHEREY-NAGEL, Düren, Germany).
Libraries were constructed using SureSelect Strand-Specific RNA kit according to the manufacturers

value: Hepatocellular carcinoma

tag: gender

value: M

value: wt


title: fecal microbiota_Sample D4

value: feces


title: BxPC3_siSTAT3_1_biol rep 1

value: Pancreatic ductal adenocarcinoma


title: AC16  treated 6h with 5µM of Digoxin-rep1


title: Ho-63T


title: Ho-36T


title: fecal microbiota_Sample D2


title: Ho-28T


title: fecal microbiota_Sample D1


title: C. difficile strain R20291_pMTL84151-03890 transconjugant  Replicate 2

city: Tainan

first: JunJia

last: Gong

address: University Rd, No. 1

department: Institute of Basic Medical Sciences

institute: National Cheng Kung University

description: Biological replicate 2 of 3. Clostridioides difficile strain R20291_pMTL84151-03890 transconjugant.

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Scanned images are analyzed by Feature extraction10.7.3.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Clostridioides difficile R20291

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: C. difficile transconjugants were cultured on BHIS agar plates containing 300 ug/mL of D-cycloserine and 15 ug/mL of thiamphenicol

extract_protocol: The total RNA of C. difficile strains was extracted using RNeasy minikit (QIAGEN) according to the manufacturer’s instructions

value: bacterial cells

value: conjugated with pMTL84151-03890


title: C. difficile strain R20291_pMTL84151-03890 transconjugant  Replicate 3

description: Biological replicate 3 of 3. Clostridioides difficile strain R20291_pMTL84151-03890 transconjugant.


title: C. difficile strain R20291_pMTL84151-03890 transconjugant  Replicate 1

description: Biological replicate 1 of 3. Clostridioides difficile strain R20291_pMTL84151-03890 transconjugant.


title: P-S7 FOV4 replicate 2

city: Lubbock

first: Mauricio

last: Ulloa

state: Texas

address: 3810 4th Street

department: PA, CSRL

institute: USDA-ARS

description: FOV4 susceptible genotype

data_processing:
We first performed quality assessment of the resulting reads from the Illumina platform using FastQC (version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and processed sequencing libraries using Trimmomatic (version 0.39;) to remove adapter read sequences.
We then quantified gene expression using the pseudo-alignment RNA-seq quantification program kallisto version 0.46.1.
We then integrated transcript-level abundances from kallisto tocount-based statistical analysis in edgeR (version 3.13) to produce the table of read counts per locus.
Assembly: TheG. barbadense P-S6 genome release was used as a reference genome to align the reads(https://doi.org/10.1186/s12864-022-09102-6)
Supplementary files format and content: The table of counts is a tab-separated plaint text file (.txt) which contains the counts per million reads corresponding to each locus per library (rows), and each RNA-seq library sample (columns) is named according to genotype, condition and biological replicate (for example SJ2_ctl1 would be Acala SJ2-control conditions-replicate 1; rkn means root-knot nematode infested).

organism: Gossypium barbadense

source_name: Root tissue (18 days-old plants)

growth_protocol: Cotton plants were grown in a Greenhouse in pots with soil. Air temperatures in the greenhouse were maintained between 280 C and 350 C during the day and 240 C at night.

extract_protocol:
The root samples from each genotype were grounded in liquid nitrogen, and total RNA was isolated three biological replicates following the manufacturer’s instructions using Spectrum TM Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA). The yield and purity of RNA were analyzed with a ND-1000 Spectrophotometer (Nano Drop Technology, Wilmington, DE, USA). Only RNA samples with 1.8 - 2.2 ratio of absorbance 260/280 nm were used for analysis.
For each genotype, 2 mg of RNA from each of the three biological-replicates used for cDNA library preparation. The cDNA libraries were prepared following the TruSeq RNA Sample Preparation v2 low sample (LS) protocol guide (Illumina Inc., San Diego, CA USA)

treatment_protocol: Two treatments control (ctl) and FOV4 infected  (FOV4) plants.  To produce inoculum, the isolate was grown in 9-cm-diameter Petri dishes containing 20 ml potato dextrose agar (PDA) with 3 mM streptomycin per liter at room temperature for 1 week. Then a few patches of 2-3-mm-squre of fresh grown culture were cut and put into 500 ml flasks containing potato dextrose liquid medium with 3 mM streptomycin at 28 oC with rotation for 3-4 days.  The conidial suspension was then filtered through eight layers of cheesecloth to remove hyphae, quantified with the aid of a hemacytometer, and diluted with water to obtain 1 x 106 conidia per ml. Cultivars or genotypes were germinated in seedling trays for one week and then seedlings were uprooted. Roots were rinsed with tap water and immediately dipped for 3 min into an aqueous suspension of FOV4 inoculum containing 1 x 106 conidia per ml. The non-inoculated control plants were processed the same way except they were dipped into water without FOV4. Seedlings were then transplanted into steam-sterilized U.C. Mix #2 (Baker, 1957) soil in new pots with five plants in each pot and placed in a warm greenhouse maintained between 24-28 degrees Celcius. At 11 days after inoculation (dai), the plant and soil ball were removed from the pots, and the soil removed gently from roots by washing under continuous water flow. The washed roots were placed immediately in 50ml screw-top plastic vials, liquid nitrogen was added, and the vials placed in a -80 C freezer with the tops off to allow vaporization of the liquid N.

value: FOV4 infected (FOV4)


title: Ho-34TA

value: mut


title: BxPC3_Vehicle_1_biol rep 1

value: Vehicle


title: C. difficile strain R20291_pMTL84151 transconjugant  Replicate 2

description: Biological replicate 2 of 3. Clostridioides difficile strain R20291_pMTL84151 transconjugant, control.

value: conjugated with pMTL84151 vector plasmid


title: C. difficile strain R20291_pMTL84151 transconjugant  Replicate 3

description: Biological replicate 3 of 3. Clostridioides difficile strain R20291_pMTL84151 transconjugant, control.


title: AC16  treated 6h with 5µM of Digoxin-rep2


title: P-S7 FOV4 replicate 1

description: FOV4 susceptible genotype


title: AC16 at T6_control-rep1

source_name: AC16 at T6_control-rep1


title: Dicer-E1859A single cleavage replicate 2

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
First, we used cutadapt (-a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 10) to remove the adapters from the raw reads.
Next, we joined the pair-end reads using fastq-join, and then filtered out the low-quality reads using fastq_quality_filter (-q 20 -p 90).
We removed any duplicated reads containing the same 4 nt or 6 nt randomized barcodes in both ends using fastx_collapser. We then processed the control RNA (OS), double cleavage (DC), and single cleavage (SC) samples separately.
For the OS libraries, we used cutadapt (cutadapt -u 4 -u -6) to remove the 4-nt randomized barcodes in the 5'-end and 6-nt randomized barcodes in the 3'-end of the OS reads. We split the resulting read into two segments (FL-OS and 32N) using cutadapt (cutadapt -g GCTTGC…GCAAGC -m 32 -M 32 --discard-untrimmed). We discarded any shRNA/32N pairs that contained the 32N barcode shared by two or more shRNAs. We aligned the resulting FL-OS sequences with the reference sequences containing 23,296 possible variants of 6 shRNA subgroups using BWA. We selected only the perfectly aligned FL-OS sequences for further analysis. The raw counts of each FL-OS were the sum of read counts of the FL-OS in the unique FL-OS/32N-dictionary.
For DC and SC, we used cutadapt to remove randomized barcodes in both ends (cutadapt -u 4 -u -4: 4 nt in both ends for DC reads; cutadapt -u 4 -u -6: 4 nt in 5'-end and 6 nt in 3'-end for SC reads). We then split the processed reads into two fragments, including a cleaved shRNA product (CP) and a 32N barcode, using cutadapt (cutadapt -g GCTTGC…GCAAGC -m 32 -M 32 --discard-untrimmed). For each pair of CP and 32N, we used the 32N barcode sequence to assign the CP to the OS sequence in a pair with the barcode in the dictionary. We determined the cleavage sites by mapping the CP and OS using the local alignment mode of pairwise2 from Biopython. We labeled the modes of DICER cleavage as SC-5p (single cleavage on 5'-strand), SC-3p (single cleavage on 3'-strand), or DC (double cleavage) based on the reported mapping coordinates (x, y), where x and y are the 5p and 3p cleavage sites counting from the first nt of shRNA variants.
Assembly: home-made reference shRNA sequences
Supplementary files format and content: Bed files of control samples contain the raw read count of each shRNA in the control library.
Supplementary files format and content: Bed files of the single cleavage and double cleavage samples contains the assigned cleavage sites, cleavage accuracy, positional cleavage efficiency, global cleavage efficiency.

organism: synthetic RNA

extract_protocol:
We first ligated the control RNA and single cleavage products to the 4N-RA3 adapter using T4 RNA Ligase 2, truncated KQ enzyme (NEB, M0373L). The resulting 4N-RA3-ligated RNA were then gel-purified. Next, we mixed the purified RNAs in a reverse transcription (RT) mixture containing cirRTP primer and Superscript IV Reverse Transcriptase (Invitrogen) and incubated the mixture for 60 min at 50°C. To degrade the RNAs, we added 0.1 M NaOH to the RT mixture and incubated it at 98°C for 10 min. We then purified the resulting cDNAs and circularized them using CircLigase ssDNA ligase (Epicentre). After separating the circularized cDNAs from linear cDNAs in an 18% urea-PAGE gel and gel-purifying them, we amplified the purified circularized DNAs by PCR using RP1 and RPI1 and one of the RPIx primers, respectively. We used the RP1 and RPIx primer systems from the Truseq Illumina primers. For the double cleavage (DC) fragments, we ligated them to the 4N-RA3 adapter and separated the resulting 4N-RA3-ligated DC from unligated DC and free 4N-RA3 in a 12% Urea-PAGE gel, which we then gel-purified. We ligated the purified 4N-RA3-ligated DC with the 4N-RA5 primer using T4 RNA ligase 1, and reverse-transcribed the double-ligated DC using Superscript IV Reverse Transcriptase and RTP primer. Finally, we amplified the resulting cDNA by PCR using RP1 and RPIx.
adapter ligation, circularization

tag: group

value: Dicer-E1859A single cleavage


title: fecal microbiota_Sample D3

data_processing:
Unique amplicon sequences variants were inferred from raw reads using the DADA2 pipeline
Potential sequencing errors and chimeric sequences were also removed with the Dada2 pipeline
Taxonomy assignment was performed using Uclust from Qiime v.1.9.1 with the Zymo Research Database, a 16S database
Composition visualization, alpha-diversity, and beta-diversity analyses were performed with Qiime v.1.9.1
Assembly: Zymo Research Database
Supplementary files format and content: tab determined text file includes species composition for each sample

value: male


title: Ho-12T


title: P-S7 control replicate 2

description: FOV4 susceptible genotype

value: Control (ctl)


title: AC16 at T0_control-rep2

source_name: AC16 at T0_control-rep2


title: Ho-66T


title: Dicer-E1859A double cleavage replicate 2

value: Dicer-E1859A double cleavage


title: AC16 at T0_control-rep1

source_name: AC16 at T0_control-rep1


title: P-S7 control replicate 1

description: FOV4 susceptible genotype


title: T1T


title: AC16 at T6_control-rep3

source_name: AC16 at T6_control-rep3


title: P-S6 FOV4 replicate 2

description: FOV4 resistant genotype


title: AC16 at T0_control-rep3

source_name: AC16 at T0_control-rep3


title: C. difficile strain R20291_pMTL84151 transconjugant  Replicate 1

description: Biological replicate 1 of 3. Clostridioides difficile strain R20291_pMTL84151 transconjugant, control.


title: AC16 at T6_control-rep2

source_name: AC16 at T6_control-rep2


title: Ho-55T

value: F


title: Dicer-E1859A double cleavage replicate 1


title: HO-81BT


title: P-S6 FOV4 replicate 1

description: FOV4 resistant genotype


title: Dicer-E1859A single cleavage replicate 1


title: HO-42T


title: P-S6 control replicate 2

description: FOV4 resistant genotype


title: HO-16T


title: Dicer-R1855A single cleavage replicate 1

value: Dicer-R1855A single cleavage


title: Dicer-R1855A single cleavage replicate 2


title: HO-40T

value: Hepatocellular carcinoma


title: Dicer-R1855A double cleavage replicate 1

value: Dicer-R1855A double cleavage


title: Dicer-R1855A double cleavage replicate 2


title: 31. cl.21 - 2D [RF201106_31]

city: GRONINGEN

first: Raphael

last: Fagundes Rosa

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Gene expression was normalized using the trimmed mean of M-values normalization method (TMM) and then 2log-transformation was applied. Finally, gene expression means were centered to zero and standard deviations scaled to one.
Assembly: GRCh38
Supplementary files format and content: txt file includes raw counts per sample

source_name: Colon

growth_protocol: Caco-2 cells were maintained on Glutamax™ Dulbecco’s Modified Eagle Medium (DMEM, ThermoFisher Scientific Inc), supplemented with 10% fetal calf serum (FCS, Invitrogen), 1% non-essential amino acids (NEAA, Gibco) and 1% PSF antibiotic cocktail (penicillin (10 U/ml), streptomycin sulfate (100 μg/ml) and fungi zone; Lonza, Bazel, Switzerland).

extract_protocol:
Isolation of RNA from Caco-2 cells after HoxBan (co)culturing was performed using the RNeasy Plus Mini Kit (Qiagen; reference number: 74134) according to the manufacturer’s protocol.
Sample preparation was performed using the QuantSeq 3’mRNA-Seq Library Prep Kit sample preparation kit (Lexogen; reference number 015.95).

value: Colon

value: intestinal epithelial


title: P3-79 replicate 2

description: FOV4 susceptible genotype

value: Pima 3-79


title: 29. WT - monoculture [RF201106_29]

value: WT

value: monoculture


title: 28. WT - co-culture [RF201106_28]

value: co-culture


title: Control sample replicate 2

value: Control sample


title: P3-79 replicate 1

description: FOV4 susceptible genotype

value: FOV4 infected (FOV4)


title: 27. WT - 2D [RF201106_27]


title: HO-29T

value: M

value: mut

value: wt


title: 32. e.v. - 2D [RF201106_32]


title: F3T


title: Control sample replicate 1


title: S2002T


title: P3-79 control replicate 1

description: FOV4 susceptible genotype

value: Control (ctl)


title: Mabs-S WT

city: Montigny-le-Bretonneux

first: Frédéric

last: Crémazy

address: 2 avenue de la source de la Bièvre

institute: UVSQ/INSERM

data_processing:
Sequence reads were trimmed using fastp (v0.23.2) followed by mapping to the M. abscessus ATCC 19977 genome (NCBI accession number NC_010397.1) using Bowtie2.
PCR duplicates were marked by Picard and further removed with samtools and only reads with MAPQ > 30 were kept for analysis.
bigWig files were obtained using the plotCoverage command from deepTools (v3.5.1).
Peak calling was performed using MACS (v.1.3.3) with a FDR = 0,0029 and normalized against input libraires.
Assembly: NC_010397.1/GCF_000069185.1
Supplementary files format and content: bigWig

organism: Mycobacteroides abscessus

source_name: Mycobacterium

growth_protocol: 50 ml of culture grown until OD600=0.6 in 7H9 medium supplemented with 1% Glucose.

extract_protocol:
Cells were fixed with 1% formaldehyde, followed by quenching with glycine. They were then washed in phosphate-buffered saline (PBS) and lysed using VK05 beads and a Precellys grinder (3 X 6,700 rpm - 20 seconds with 60-second intervals).
The NEBNext® UltraTM II DNA Library Prep Kit for Illumina was used for library preparation following manufacturer's protocol.

value: Mycobacterium

tag: morphotype

value: Smooth

value: anti-FLAG


title: 26. e.v. - 2D [RF201106_26]

tag: cell line


title: 25. e.v. - monoculture [RF201106_25]

tag: cell type


title: 30. cl.21 - co-culture [RF201106_30]

tag: genotype


title: P-S6 control replicate 1

description: FOV4 resistant genotype

tag: treatment


title: 24. cl.21 - monoculture [RF201106_24]

tag: tissue


title: HO-78T

value: Hepatocellular carcinoma


title: Mabs-S Lsr2-FLAG_rep 2


title: 23. e.v. - 2D [RF201106_23]


title: HO-60T


title: HO-56T


title: MLT_scRNAseq

city: Qingdao

first: Jun-Jie

last: Wang

address: Changcheng 700

department: Qingdao Agricultural University

institute: College of Life Sciences

library_source: transcriptomic single cell

data_processing:
The upstream analysis was performed with the CellRanger software launched by 10 × Genomics.
The R package Seurat (v4.2.0) was applied fThe R package Seurat (v4.2.0) was applied for data processing, dimensionality reduction and cell clustering analysis.
DoubletFinder package (v2.0.3) is used to remove the cell of potential do the DoubletFinder package (v2.0.3) is used to remove the cell of potential doublet with the default parameters.
Monocle2 package was mainly used to construct the pseudotime trajectory of the oocyte data set.
The FindAllMarkers function of Seurat is used to perform the gene differential expression analysis.
Assembly: mm9
Supplementary files format and content: The tab-delimited text file includes gene reads for each sample.
Supplementary files format and content: The tab-delimited text file includes annotation result of gene for each sample.

source_name: Ovary

extract_protocol:
Total RNA was extracted and reversed into cDNA according to the procedure of commercial test kit from 10× Genomics.
The 10× Genomics single cell 3ʹ gene library was constructed according to the standard procedure.

treatment_protocol: From E16.5 to postnatal day 3 (PD3), the pregnant mice were treated with DEHP via oral gavage once a day at 9:00 am; at the same time, MLT was the administrated after the treatment of DEHP around 17:00 pm, which produced the ovarian samples of pups from DEHP plus MLT group. And the samples of MLT group were obtained from mice with same volume of DMSO replaced with DEHP, and the treatment of MLT as stated above.

value: Ovary

value: Ovarian cells


title: DEHP_MLT_RNAseq

value: DEHP


title: Mabs-S Lsr2-FLAG_input


title: 22. e.v. - co-culture [RF201106_22]

value: Colon

value: intestinal epithelial


title: P3-79 control replicate 2

description: FOV4 susceptible genotype

value: Pima 3-79


title: 21. cl.21 - co-culture [RF201106_21]

value: co-culture


title: HO-50T


title: 20. WT - co-culture [RF201106_20]

value: WT


title: Mabs-R WT

value: Rough


title: Mabs-R Lsr2-FLAG_rep 3


title: E14.5 mouse embryonic maxillary prominence_rep2

first: Jian

last: Sun

address: Quxi Road No.500

institute: Shanghai Ninth People's Hospital

data_processing:
The PE150 raw reads of RNA-Seq libraries were filtered by removing adaptor sequences, contamination and low-quality (phred quality < 20) reads. Reads quality was assessed using FastQC.
Sequenced reads were then mapped to the mm10 genome using STAR aligner version 2.7.3a. Reads were counted using htseq-count version 0.12.4 at the union mode.

source_name: maxillary prominence

growth_protocol: C57BL/6 mice were purchased from Shanghai Jihui Laboratory Animal Care Co.Ltd. All mice were maintained in SPF conditions at the Animal Center of the Ninth People’s hospital affiliated to Shanghai Jiaotong University School of medicine. Female and male mice between the ages of 8 to 12 weeks were used.

extract_protocol:
Total RNA was extracted using Trizol from freshly dissected maxillary prominence tissues from 7 littermates. For each developmental stage (E14.5), three independent RNA samples were prepared. RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For each sample, 2 μg total RNA was used as input material for the library preparations. Sequencing libraries were then generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and eluted with EB buffer, followed by terminal repair, A-tailing and adapter ligation. The ligated products were retrieved and PCR amplification was performed to generate sequencing libraries. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurately quantified using a StepOnePlusTM Real-Time PCR System. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina HiSeq X ten platform and 150 bp paired-end reads were generated.

treatment_protocol: On Embryo 14.5, pregnant C57BL/6 female were euthanized via isoflurane and cervical dislocation. Embryos were dissected from uterus and transferred ice-cold PBS in a 6-cm Petri dish using a disposable glass pipette. Intact maxillary prominences were carefully dissected out from embryos using fine forceps under a stereomicroscope and used for library construction as described below.

tag: age

value: embryo 14.5

value: wild type


title: E14.5 mouse embryonic maxillary prominence_rep1-1 and rep 1-2


title: HO-45T

value: M

value: mut

value: wt


title: 19. WT - monoculture [RF201106_19]

value: monoculture


title: Mabs-R Lsr2-FLAG_rep 2

value: Mycobacterium

value: anti-FLAG


title: HO-68T

value: Hepatocellular carcinoma


title: 18. e.v. - co-culture [RF201106_18]


title: P2XT-Scr

first: Xiaoxiao

last: He

state: Shanghai

address: 280 South Chongqing Road, Shanghai 200025

department: Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,Faculty of Basic Medicine

institute: Shanghai Jiao Tong University School of Medicine

description: gene expression

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: leukemia leukemia-initiating cells

extract_protocol:
Wild Type (P2XT-Scr) and P2x7 knockout (P2XT-KD)  AML leukemia leukemia-initiating cells  were lysed by TRIzol reagent for extraction of RNA. RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) according to  the manufacturer's recommendations. After clean-up, RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored by RNA electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wild Type (P2XT-Scr) and P2x7 knockout (P2XT-KD)  AML leukemia leukemia-initiating cells were sorted from bone marrow based on Mac1+ C-kit+.

value: 8 weeks


title: Mabs-S Lsr2-FLAG_rep 3

value: Smooth


title: HO-20T


title: 17. cl.21 - co-culture [RF201106_17]

value: Colon


title: T6T

value: F


title: Mabs-R Lsr2-FLAG_rep 1


title: Mabs-R Lsr2-FLAG_input


title: Mabs-S Lsr2-FLAG_rep 1


title: HO-10T


title: 16. WT - monoculture [RF201106_16]

value: intestinal epithelial


title: E12.5 mouse embryonic maxillary prominence mesenchymal cells_sample3-rep1

description: e12_3_BAMPE_peaks.removeblacklist.narrowPeak

data_processing:
PE150 ATAC-Seq reads were aligned to mm10 reference genome using Bowtie2. Bioinformation analysis. Read coverage in each 50bp genomic bin was calculated using the bamCoverage function in deepTools version 3.3.1 and normalized using the RPGC (reads per genome content) method.
The bigwig files of read coverage were visualized using IGV. Peaks corresponding to the open region in genome were detected using MACS2 callpeak function with the following parameters:” -f BAMPE -g mm --nomodel --shift 100 --extsize 200”.

source_name: maxillary prominence mesenchymal cells

extract_protocol:
Maxillary mesenchyme was separated from maxillary ectoderm using a protocol described previously (Hong Li et al., Journal of Visualized Experiments, 2013). 10 mg/ml Dispase II (Roche, Cat# 4942078001) in Hepes-buffered Saline (HBS) (50 mM Hepes/KOH pH 7.4, 150 mM NaCl) was prepared freshly and diluted 1:10 in PBS right before use. Dissected embryos were treated with 1 mg/ml Dispase II at 37 °C for 30 min. Maxillary prominences were then dissected out and pipetted up and down 5 times using a long glass pasture pipette. Maxillary ectoderm was peeled off from maxillary prominences very slowly using forceps to minimize disruption of tissue structure. The mesenchyme samples were washed with PBS and centrifuged at 4 °C, 800 x g for 5 min.
Around 50,000 freshly prepared maxillary mesenchyme cells were used for each ATAC-Seq library preparation. The cells were lysed in 1 × Lysis Buffer (10mM Tris-HCl(pH7.4),10mM NaCl, 3mM MgCl2, 0.5% NP-40) to get the nuclei, and TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme Biotech, TD501) was used to construct the transposase-treated libraries. Libraries were amplified for 5-9 PCR cycles and size selected using VAHTS DNA Clean Beads (Vazyme Biotech, N411-01-AA). The mass concentration and molar concentration of libraries were assessed by Qubit 3.0 Fluorometer and StepOnePlusTM Real-Time PCR system, respectively, and lengths of inserted fragments were detected with Agilent HS 2100 Bioanalyzer. Qualified libraries were sequencing on an Illumina HiSeq X ten platform under pair-end 150 bp mode.

treatment_protocol: On Embryo 10.5(E10.5), 11.5, or 12.5, pregnant C57BL/6 female were euthanized via isoflurane and cervical dislocation. Embryos were dissected from uterus and transferred ice-cold PBS in a 6-cm Petri dish using a disposable glass pipette. Intact maxillary prominences were carefully dissected out from embryos using fine forceps under a stereomicroscope.

value: embryo 12.5


title: E12.5 mouse embryonic maxillary prominence mesenchymal cells_sample2-rep4

description: e12_2_BAMPE_peaks.removeblacklist.narrowPeak


title: HO-8T


title: P-ES50-2

city: Hangzhou City

first: Ruoshi

state: Zhejiang

address: No. 79 Qingchun Road

institute: Zhejiang University

description:
sample name:
Ra17

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

extract_protocol:
In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). Firststrand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization.

value: myocardium

value: 50   micromol/L PE, 48h, then Electric shock of 1500V/cm, 50times,100  microseconds


title: P-ES50-3

description:
sample name:
Ra18


title: E12.5 mouse embryonic maxillary prominence mesenchymal cells_sample2-rep3

city: Shanghai


title: T5T


title: P-ES50-1

description:
sample name:
Ra16


title: 15. e.v. - monoculture [RF201106_15]


title: 13. WT - monoculture YCFAmuc [RF201106_13]

value: WT

value: monoculture YCFAmuc


title: P2XT-KD

description: gene expression


title: LT1T

value: M


title: 12. WT - 2D [RF201106_12]


title: HO-67T


title: E12.5 mouse embryonic maxillary prominence mesenchymal cells_sample2-rep1

value: wild type


title: E12.5 mouse embryonic maxillary prominence mesenchymal cells_sample3-rep2


title: E12.5 mouse embryonic maxillary prominence mesenchymal cells_sample1-rep2

description: e12_1_BAMPE_peaks.removeblacklist.narrowPeak


title: P-ES10-1

description:
sample name:
Ra13

value: 50   micromol/L PE, 48h, then Electric shock of 1500V/cm, 10times,100  microseconds


title: 11. e.v. - monoculture [RF201106_11]

value: monoculture


title: 14. e.v. - co-culture [RF201106_14]

value: co-culture


title: E12.5 mouse embryonic maxillary prominence mesenchymal cells_sample1-rep1


title: P-ES10-2

description:
sample name:
Ra14


title: HO-32T

value: wt


title: P-3

description:
sample name:
Ra12

value: 50   micromol/L PE, 48h


title: E11.5 mouse embryonic maxillary prominence mesenchymal cells_sample3-rep3

description: e11_3_BAMPE_peaks.removeblacklist.narrowPeak

value: embryo 11.5


title: 8. WT - 2D [RF201106_8]


title: 9. WT - Poop + YCFAmuc [RF201106_9]

value: Poop + YCFAmuc


title: HO-31T

value: Hepatocellular carcinoma

value: mut


title: E11.5 mouse embryonic maxillary prominence mesenchymal cells_sample3-rep2


title: P-ES10-3

description:
sample name:
Ra15


title: HO-15T


title: P-1

description:
sample name:
Ra10


title: HO-30T

value: F


title: E12.5 mouse embryonic maxillary prominence mesenchymal cells_sample2-rep2

value: embryo 12.5


title: ES50-3

description:
sample name:
Ra9

value: myocardium

value: Electric shock of 1500V/cm, 50times,100  microseconds


title: 7. cl.21 - monoculture [RF201106_7]

value: Colon

value: intestinal epithelial


title: E11.5 mouse embryonic maxillary prominence mesenchymal cells_sample3-rep1


title: E11.5 mouse embryonic maxillary prominence mesenchymal cells_sample2

description: e11_2_BAMPE_peaks.removeblacklist.narrowPeak


title: 6. WT - monoculture YCFAinul [RF201106_6]

value: WT

value: monoculture YCFAinul


title: E11.5 mouse embryonic maxillary prominence mesenchymal cells_sample1

description: e11_1_BAMPE_peaks.removeblacklist.narrowPeak

value: wild type


title: HO-13T

value: M


title: HO-33T


title: 10. WT - Poop + YCFAinul [RF201106_10]

value: Poop + YCFAinul


title: ES50-2

description:
sample name:
Ra8


title: HO-9T


title: E10.5 mouse embryonic maxillary prominence mesenchymal cells_sample3-rep4

description: e10_3_BAMPE_peaks.removeblacklist.narrowPeak

value: embryo 10.5


title: ES50-1

description:
sample name:
Ra7


title: P-2

description:
sample name:
Ra11

value: 50   micromol/L PE, 48h


title: 5. WT - 2D [RF201106_5]


title: ES10-3

description:
sample name:
Ra6

value: Electric shock of 1500V/cm, 10times,100  microseconds


title: HO-2T

value: wt


title: 4. cl.21 - monoculture [RF201106_4]

value: monoculture


title: E10.5 mouse embryonic maxillary prominence mesenchymal cells_sample3-rep3


title: ES10-2

description:
sample name:
Ra5


title: s2104T

value: Hepatocellular carcinoma


title: s1671T


title: E10.5 mouse embryonic maxillary prominence mesenchymal cells_sample3-rep2


title: 2. cl.21 - 2D [RF201106_2]


title: E10.5 mouse embryonic maxillary prominence mesenchymal cells_sample3-rep1


title: 3. WT - co-culture [RF201106_3]

value: co-culture


title: ES10-1

description:
sample name:
Ra4


title: E10.5 mouse embryonic maxillary prominence mesenchymal cells_sample2-rep4

description: e10_2_BAMPE_peaks.removeblacklist.narrowPeak


title: s845T


title: s949T

value: mut


title: NC-3

description:
sample name:
Ra3

value: myocardium

value: No treatment


title: E10.5 mouse embryonic maxillary prominence mesenchymal cells_sample2-rep3


title: 1. cl.21 - 2D [RF201106_1]

value: Colon


title: MyA_hCF_S10

city: South San Francisco

description:
TT007 study
MyA_S10
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt

data_processing:
Read alignment by Salmon (ver. 1.8.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl human reference genome release 108
Exclusion of mitochondrial genes and renormalization to TPM.
Assembly: hg38 v.13
Supplementary files format and content: TXT

source_name: Cardiac Fibroblast

value: Cardiac Fibroblast

value: MyA cassette


title: NC-2

description:
sample name:
Ra2


title: GFP_hCF_S9

description:
TT007 study
GFP_S9
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt

value: WT

value: GFP cassette


title: NC-1

description:
sample name:
Ra1


title: E10.5 mouse embryonic maxillary prominence mesenchymal cells_sample2-rep2

value: wild type


title: T3T

value: M


title: HO-81T


title: E10.5 mouse embryonic maxillary prominence mesenchymal cells_sample2-rep1

value: embryo 10.5


title: s797T


title: MyD3_hCF_S4

description:
TT007 study
MyD3_S4
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt

value: MyD3 cassette


title: Mabs-S WT Rep 3 RNA-seq

data_processing:
Sequence reads were trimmed using fastp (v0.23.2).
Trimmed sequences were mapped on M. abscessus ATCC19977 reference genome using STAR (v2.7.6a).
Read count extraction was performed using FeatureCounts (V2.0.0).
Differential Expression Gene analysis was done using the SARtools package (v1.7.1) including DEseq2.
Assembly: NC_010397.1/GCF_000069185.1
Supplementary files format and content: Counts_DEG_analysis.xlsx: Excel file containing read counts, normalized read counts and DEG analysis results.

growth_protocol: Wild-type and lsr2 mutant strains were cultivated until they reached the exponential growth phase in 7H9 medium supplemented with 1% Glucose, until reaching an optical density (OD600) of approximately 0.6 or ~ 2.4 × 10^8 cells/mL.

extract_protocol:
For each strain, a total of 4.8 × 10^9 cells were collected, and the total RNA was extracted from three biological replicates using the Total RNA Miniprep kit (NEB).
After rRNA depletion, sequencing libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer’s instructions.

value: Mycobacterium

value: Smooth


title: HO-6T

value: wt


title: E10.5 mouse embryonic maxillary prominence mesenchymal cells_sample1-rep2

description: e10_1_BAMPE_peaks.removeblacklist.narrowPeak


title: GFP_hCF_S8

description:
TT007 study
GFP_S8
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to vender’s protocol. RNAs were retrotranscribed to cDNA using iScript Supermix™ (Bio-Rad). qPCR was performed using TaqMan. Gene Expression Master Mix (Thermo Scientific) mRNA levels were normalized by comparison to GAPDH mRNA.
100ng total RNA was extracted via polyA-tail specific protocol according to Illumina protocol. Sequencing libraries were generated using the TruSeq stranded RNA sample prep kit (Illumina). The libraries were sequenced as 75 bp single-end reads using an Illumina NovaSeq SP platform with an average of 35M reads per sample. Indexed libraries that met appropriate cut-offs for both quantity and quality were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution was determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.6 ng/ul were used for sequencing.


title: E10.5 mouse embryonic maxillary prominence mesenchymal cells_sample1-rep1


title: MyD3_hCF_S2

description:
TT007 study
MyD3_S2
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt


title: HO-5T

value: Hepatocellular carcinoma


title: MyD3_hCF_S3

description:
TT007 study
MyD3_S3
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt


title: Mabs-S WT Rep 1 RNA-seq


title: GFP_hCF_S13

description:
TT007 study
GFP_S13
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt


title: Mabs-S Delta_Lsr2 Rep 3 RNA-seq

value: Lsr2 KO


title: E12.5 mouse embryonic maxillary prominence_rep3

extract_protocol:
Total RNA was extracted using Trizol from freshly dissected maxillary prominence tissues from 7 littermates. For each developmental stage (E10.5, E11.5 and E12.5), three independent RNA samples were prepared. RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For each sample, 2 μg total RNA was used as input material for the library preparations. Sequencing libraries were then generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and eluted with EB buffer, followed by terminal repair, A-tailing and adapter ligation. The ligated products were retrieved and PCR amplification was performed to generate sequencing libraries. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurately quantified using a StepOnePlusTM Real-Time PCR System. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina HiSeq X ten platform and 150 bp paired-end reads were generated.

treatment_protocol: On Embryo 10.5(E10.5), 11.5, or 12.5, pregnant C57BL/6 female were euthanized via isoflurane and cervical dislocation. Embryos were dissected from uterus and transferred ice-cold PBS in a 6-cm Petri dish using a disposable glass pipette. Intact maxillary prominences were carefully dissected out from embryos using fine forceps under a stereomicroscope and used for library construction as described below.

value: embryo 12.5


title: old naked mole-rat anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 4

first: Nimrod

last: Rubinstein

address: 1170 Veterans blvd

institute: Calico

description:
mostly TCR RNA
10x Genomics
nmr_spleen.TCRs_24y_4

data_processing:
PacBio SMRT LINK V11 software to generate circular consensus sequences (CCS), requiring a predicted accuracy ≥ Q20.
HetGla2.0 + GCF_000247695.1 and Heterocephalus_glaber_female 1.0 combined annotations
demultiplex.<sample_name>.bam is a file containing the CCS demultipled reads

source_name: spleen

extract_protocol:
Spleens were removed by dissection, transferred to a sterile petri dish containing PBS with 5% FBS, and minced using surgical blades. Spleen fragments were then ground through 100 μm and 40 μm cell strainers, pelleted, and resuspended in the ACK lysis buffer as described in the thymus tissue collection section. Cell density and viability were determined using Countness II Cell Counter. Subsequently, splenocytes were resuspended at 1 million cells per ml of 0.04% BSA/PBS. In order to sort out the splenocyte T-cell subsets for constructing 10× GEM single-cell libraries, splenocytes were resuspended at 1 million cells per ml of FACS buffer (PBS with 1% FBS and 5mM EDTA).splenocytes were pre-incubated with the isotype control antibodies (100 ug/ml mIgG1 & 50 ug/ml rat IgG1) per 1 million cells/100ul FACS buffer for 10 minutes. Following that, cells were washed and resuspended at 2 million cells per 1 ml FACS buffer, and incubated with an anti-NMR CD3e (Abbvie-clone-5, Alexa 647, 1:100) and an anti-mouse CD11b (which cross reacts with the NMR CD11b,) (M1/70, R-PE, 5 ug/ml) on ice for 40 minutes. Cells were then washed and resuspended in the FACS buffer containing Sytox Blue Live/Dead dye for cell sorting using FACS BD Aria. Viable, single cells were gated, and the CD11b-/CD3e+ cells were collected for the generation of 10× GEM single-T-cell libraries.
Biotinylated lockdown probes targeting all constant regions of the four TCR loci were added tp the 10× Chromium Next Gen Single-Cell 3’ V3 3′-barcoded scRNA-seq cDNA libraries using the xGen Hybridization and Wash kit with customized Discovery Pools from Integrated DNA Technologies, Inc (IDT, Coralville, Iowa).500 ng of amplified cDNA was mixed with the blocking probes and xGen human Cot DNA, and the mixtures were dried down in a SpeedVac system (ThermoFisher). The hybridization and washing steps were performed according to the protocol from IDT. The hybridization and post-capture amplification steps were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA). Fourteen cycles were used for post-capture PCR amplification, and the amplified cDNA was evaluated using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a high sensitivity chip.
Amplified cDNA at >200ng per sample was used to generate Pacific Biosciences (PB) SMRTcell libraries. Full-length PB sequencing was performed on the PB Sequel II platform at Histogenetics (Ossining, NY)

value: spleen

value: mostly spleen T cells

value: 24 years

tag: Sex

value: male


title: Mabs-S Delta_Lsr2 Rep 1 RNA-seq


title: MyA_hCF_S12

description:
TT007 study
MyA_S12
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt

value: Cardiac Fibroblast

value: MyA cassette


title: MyA_hCF_S11

description:
TT007 study
MyA_S11
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt

value: WT


title: E14.5 mouse embryonic maxillary prominence_rep3

value: embryo 14.5

value: wild type


title: Mabs-S Delta_Lsr2 Rep 2 RNA-seq


title: old naked mole-rat anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 3

description:
mostly TCR RNA
10x Genomics
nmr_spleen.TCRs_24y_3

tag: colony/strain


title: E12.5 mouse embryonic maxillary prominence_rep1


title: Mabs-R WT Rep 3 RNA-seq

value: Rough


title: MyA_hCF_3

description:
TT005 study
MyA-3_S17
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt

value: MyA-oriented cassette


title: Mabs-R WT Rep 2 RNA-seq

value: Mycobacterium


title: E11.5 mouse embryonic maxillary prominence_rep3

value: embryo 11.5


title: MyA_hCF_2

description:
TT005 study
MyA-2_S16
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt


title: E11.5 mouse embryonic maxillary prominence_rep2


title: Mabs-R WT Rep 1 RNA-seq


title: E11.5 mouse embryonic maxillary prominence_rep1