title: +MyoD_3

value: Embryonic fibroblasts

value: Primary MEFs

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R)

value: day 10


title: TIAN-SNI-NAc-3

status: Public on Jul 24 2023

type: SRA

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

country: USA

institute: Mount Sinai School of Medicine

description:
TIAN-SNI-NAc-3_S3
counts_matrix.txt
fpkm_matrix.txt

library_source: transcriptomic

data_processing:
Reads were processed with the NGS-Data-Charmer pipeline. In brief, adaptors and low-quality bases were removed with Trim Galore.
Trimmed reads were aligned to the human genome with HISAT2 and alignments were de-duplicated with samtools rmdup.
Gene expression was calculated using featureCounts with parameters "-p -O --fraction -t gene" to the GENCODE annotation (vM25).
Assembly: mm10
Supplementary files format and content: counts_matrix.txt is a tab-delimited text file containing the non-normalized gene expression matrix. fpkm_matrix.txt is a tab-delimited text file containing the normalized FPKM (Fragments Per Kilobase per Million) gene expression matrix.

molecule: polyA RNA

organism: Mus musculus

source_name: brain

extract_protocol:
TRIzol Phase Separation
Stranded mRNA Prep Kit (Illumina)

treatment_protocol: Tibial SNI or Sham Surgery (4 weeks) followed by 3 weeks of Saline, 30 mg/kg Tianeptine, or 15 mg/kg Desipramine (intraperitoneal, twice daily)

tag: tissue

value: brain

tag: tissue region

value: nucleus accumbens

tag: surgery

value: sni

tag: strain

tag: treatment

value: TIAN


title: MEFs_3

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
bcl2Fastq v2.20 software used for demultiplexing + basecalling.
Reads trimmed with fastp 0.20.0, options: --out1 trimmed_R1.fastq.gz --thread 8 --trim_front1 0 --trim_tail1 0 --average_qual 0 --adapter_fasta adapters.fa --max_len1 0 --max_len2 0 --disable_trim_poly_g --trim_poly_x --poly_x_min_len 10 --length_required 18 --compression 4
Pseudocounts generated with kallisto v0.46.1, options: -t 8 --bias --bootstrap-samples 10 --seed 42 --single --fragment-length 180 --sd 50
Differential expression analysis: DESeq2
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited raw counts

molecule: total RNA

source_name: Embryonic fibroblasts

extract_protocol:
Total RNA was isolated using the RNAeasy  Mini Kit (Qiagen, #74104) as per the manufacturer’s protocol.
Samples with RIN above 8 were only used for further library preparation steps and library preparation was conducted according to the TruSeq Stranded mRNA protocol (Illumina, Inc., California, USA). Briefly, poly-A enrichment was carried out for total RNA (100-1000 ng), followed by reverse-transcription of poly-A enriched RNA into cDNA. The cDNA was then ligated with TrueSeq adapters including unique dual indices (UDI) after fragmentation, end-repair and adenylation steps. Using PCR, cDNA containing TruSeq adapters on both ends was selectively amplified which was further applied to a Fragment Analyzer to determine the quality and quantity of libraries. The average fragment size was approximately 360 bp.

tag: cell line

tag: cell type

tag: genotype

value: Untreated (iMPC medium)

tag: time


title: 23555A iPSC, WT control, replicate 3

city: Cambridge

first: Richard

last: She

state: Massachusetts

address: 455 Main St Rm 639, Whitehead Institute

institute: Whitehead Institute

data_processing:
Adapters were removed using cutadapt with option -b AGATCGGAAGAGCACACGTCTGAACTCCAGTCA)
Reads were then pseudo-aligned to species-specific transcriptomes using kallisto with options --single -l 200 -s 20
Transcriptomes were extracted from species-specific gtf annotations using the gffread utility using the -w output option
Human transcripts were obtained from the Gencode comprehensive gene annotation v36 (GTF), using genome assembly hg38.
Chimpanzee annotations were obtained from a recent study that produced a hierarchical alignment of primate genome assemblies and annotated the assemblies using the Comparative Annotation Toolkit
Assembly: hg38
Supplementary files format and content: tab-delimited text files are VST-transformed counts for each sample
Supplementary files format and content: using the function vst with option blind=TRUE and ran the DESeq linear model fitting using the function DESeq with betaPrior=TRUE

organism: Homo sapiens

source_name: Pluripotent stem cells

growth_protocol: Pluripotent stem cells were maintained in StemFlex media and Accutase passaged with ROCK inhibitor

extract_protocol:
High quality RNA was extracted by adding RNAse-free Trizol to each pellet and processing with the Zymo Research Direct-zol RNA miniprep kit
RNA-seq library prep was performed using the Illumina TruSeq Stranded Total RNA kit .

value: Pluripotent stem cells

value: induced pluripotent stem cells

value: WT

value: Growth in StemFlex media


title: RT103_1-cfMCC-SEQ

city: Washington

first: Anton

last: Wellstein

state: DC

address: 3970 Reservoir Road, N.W.,

department: Oncology

institute: Georgetown University

library_source: genomic

data_processing:
Library strategy: MCC-seq (MethylC-capture sequencing)
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20 --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 10 --three_prime_clip_R2 10 --retain_unpaired -r1 20 -r2 20” (https://github.com/FelixKrueger/TrimGalore).
Trimmed paired-end FASTQ reads were mapped to the human genome  (GRCh37/hg19 build) using Bismark (V 0.22.3) with parameters “--non-directional” (Kreuger et al. 2011), then converted to BAM files using SAMtools (V 1.12) (Li et al., 2009). BAM files were sorted and indexed using Samtools (V1.12).
Reads were stripped from non-CpG nucleotides and converted to BETA and PAT files using wgbstools (V 0.1.0) (Loyfer and Kaplan, 2022).
Assembly: hg19
Supplementary files format and content: BETA, PAT, and index files were generated using wgbstools bam2pat (https://github.com/nloyfer/wgbs_tools) with default parameters

molecule: genomic DNA

source_name: Serum

extract_protocol:
Circulating cell-free DNA was extracted from 4 mL human serum, using the QIAamp Circulating Nucleic Acid kit (Qiagen, Cat. No. 55114) according to the manufacturer’s instructions. Cell-free DNA was quantified via Qubit fluorometer using the dsDNA Assay Qubit fluorometer Kits (ThermoFisher Scientific, Cat. No. Q32853 and Q10212 respectively). As a quality control, fragment size distribution of isolated cfDNA was verified based on analysis using a 2100 Bioanalyzer TapeStation using either a High Sensitivity DNA Assay or DNA 1000 Assay (Agilent Technologies, Santa Cruz, CA, USA) dependent on concentration determined via either Qubit dsDNA BR or HS Assay. Additional purification using Beckman Coulter beads was implemented to remove high-molecular weight DNA reflective of cell-lysis and leukocyte contamination (Agencourt AMPure cat#A63880) (Maggi et al. 2018).
Cell-free DNA from serum was subject to bisulfite conversion using the Zymo EZ DNA Methylation Gold kit  (#D5005 Zymo Research, Irvine, CA). Whole Genome Bisulfite Sequencing libraries were generated using the Zymo Research Pico Methyl-Seq Library Prep Kit (#D5455 Zymo Research, Irvine, CA). WGBS libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA) and then pooled to meet the required 1ug DNA input necessary for targeted enrichment. Hybridization capture was carried out according to the SeqCap Epi Enrichment System protocol (Roche NimbleGen, Inc.; Pleasanton, CA) using xGen Universal Blocker-TS Mix (Integrated DNA Technologies, USA) as the blocking reagent and SeqCap Epi CpGiant probe pools (human) or SeqCap Epi Developer probe pools (mouse samples). MethylC-Capture Sequencing (MCC-seq) libraries were assessed using Qubit Fluorometer (ThermoFisher) and Agilent Bioanalyzer DNA 1000 assays (Agilent Technologies, Inc., USA). MCC-seq libraries with inclusion of 15-20% spike-in PhiX Control v3 library (Illumina; San Diego, CA) were clustered on a Illumina Novaseq 6000 S4 flow cell followed by 150-bp paired-end sequencing.

treatment_protocol: Breast cancer patients undergoing adjuvant radiation-therapy were enrolled and provided signed informed consent in this IRB approved study at Medstar Georgetown University Hospital (IRB protocol # 2013-0049). Serial serum samples were collected from 15 patients at Baseline (before radiation treatment), End-of-Treatment (EOT; 30 minutes after the last radiation treatment), and Recovery (one month after cessation of radiation treatment). For serum isolation, peripheral blood (~8-12 ml) was collected in red-top venous puncture tubes and allowed to clot at room temperature for 30 minutes before centrifugation at 1500 x g for 20 min at 4ºC to separate the serum fraction. The serum was aliquoted in 0.5 mL fractions to avoid multiple freeze-thaw cycles and stored at −80ºC until use.

value: Serum

value: Baseline


title: RT104_2-cfMCC-SEQ

value: Radiation


title: TIAN-SNI-NAc-2

description:
TIAN-SNI-NAc-2_S2
counts_matrix.txt
fpkm_matrix.txt


title: RT102_3-cfMCC-SEQ

value: Recovery


title: 23555A iPSC, WT control, replicate 1


title: 23555A iPSC, WT control, replicate 2


title: +MyoD+F/R/C+SP_2

value: Embryonic fibroblasts

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R); in presence of F/R/C+SP


title: TIAN-SNI-NAc-1

description:
TIAN-SNI-NAc-1_S1
counts_matrix.txt
fpkm_matrix.txt


title: RT102_2-cfMCC-SEQ


title: TIAN-Sham-NAc-4

description:
TIAN-Sham-NAc-4_S16
counts_matrix.txt
fpkm_matrix.txt

value: sham


title: +MyoD+F/R/C+CP_2

value: Primary MEFs

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R); in presence of F/R/C+CP

value: day 10


title: RT102_1-cfMCC-SEQ


title: 21792A iPSC, WT control, replicate 2


title: 21792A iPSC, WT control, replicate 3


title: +MyoD+F/R/C_2

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R); in presence of F/R/C


title: TIAN-Sham-NAc-3

description:
TIAN-Sham-NAc-3_S15
counts_matrix.txt
fpkm_matrix.txt

value: brain

value: nucleus accumbens

value: TIAN


title: 21792A iPSC, WT control, replicate 1

value: Pluripotent stem cells

value: induced pluripotent stem cells


title: +MyoD_2

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R)


title: RT101_3-cfMCC-SEQ

value: Serum


title: MEFs_2

value: Untreated (iMPC medium)


title: TIAN-Sham-NAc-2

description:
TIAN-Sham-NAc-2_S14
counts_matrix.txt
fpkm_matrix.txt


title: RT101_2-cfMCC-SEQ

value: Radiation


title: 20961B iPSC, WT control, replicate 3

value: WT

value: Growth in StemFlex media


title: TIAN-Sham-NAc-1

description:
TIAN-Sham-NAc-1_S13
counts_matrix.txt
fpkm_matrix.txt


title: 20961B iPSC, WT control, replicate 2


title: +MyoD+F/R/C+SP_1

value: Embryonic fibroblasts

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R); in presence of F/R/C+SP


title: RT101_1-cfMCC-SEQ

value: Baseline


title: TIAN-Sham-NAc-6

description:
TIAN-Sham-6_S4
counts_matrix.txt
fpkm_matrix.txt

value: sham


title: +MyoD+F/R/C+CP_1

value: Primary MEFs

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R); in presence of F/R/C+CP

value: day 10


title: 20961B iPSC, WT control, replicate 1


title: +MyoD+F/R/C_1

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R); in presence of F/R/C


title: TIAN-Sham-NAc-5

description:
TIAN-Sham-5_S3
counts_matrix.txt
fpkm_matrix.txt

value: brain

value: nucleus accumbens

value: TIAN


title: WTC11 iPSC, WT control, replicate 3

value: Pluripotent stem cells

value: induced pluripotent stem cells


title: +MyoD_1

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R)


title: Saline-SNI-NAc-4

description:
Saline-SNI-NAc-4_S12
counts_matrix.txt
fpkm_matrix.txt

value: sni

value: saline


title: Saline-SNI-NAc-3

description:
Saline-SNI-NAc-3_S11
counts_matrix.txt
fpkm_matrix.txt


title: WTC11 iPSC, WT control, replicate 2

value: WT

value: Growth in StemFlex media


title: MEFs_1

value: Embryonic fibroblasts

value: Untreated (iMPC medium)


title: WTC11 iPSC, WT control, replicate 1


title: mouse_Gr1Neutrophil-MCC-SEQ

data_processing:
Library strategy: MCC-seq (MethylC-capture sequencing)
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20 --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 10 --three_prime_clip_R2 10 --retain_unpaired -r1 20 -r2 20” (https://github.com/FelixKrueger/TrimGalore).
Trimmed paired-end FASTQ reads were mapped to the mouse genome (NCBI37/mm9 build) using Bismark (V 0.22.3) with parameters “--non-directional” (Kreuger et al. 2011), then converted to BAM files using SAMtools (V 1.12) (Li et al., 2009). BAM files were sorted and indexed using Samtools (V1.12).
Reads were stripped from non-CpG nucleotides and converted to BETA and PAT files using wgbstools (V 0.1.0) (Loyfer and Kaplan, 2022).
Assembly: mm9
Supplementary files format and content: BETA, PAT, and index files were generated using wgbstools bam2pat (https://github.com/nloyfer/wgbs_tools) with default parameters.
Supplementary files format and content: blocks file (bed) was generated using wgbstools segment, and then compressed and indexed using tabix (samtools)
Supplementary files format and content: rlen file (bin) contains read length across blocks based on coverage in serum background samples

source_name: Blood; spleen

extract_protocol:
Genomic DNA from tissues was extracted with DNeasy Blood and Tissue Kit (Qiagen; Germantown, MD) following the manufacturer’s instructions and quantified via Qubit fluorometer dsDNA BR Assay Kit (ThermoFisher Scientific, Cat. No. Q32853). Extracted DNA was stored at  -20°C for bisulfite conversion and MCC-seq library preparation.
Genomic DNA was fragmented via sonification using a Covaris M220 instrument to the recommended target 150-200 base pairs and subject to bisulfite conversion using the Zymo EZ DNA Methylation Gold kit  (#D5005 Zymo Research, Irvine, CA). Whole Genome Bisulfite Sequencing libraries were generated using the Zymo Research Pico Methyl-Seq Library Prep Kit (#D5455 Zymo Research, Irvine, CA). WGBS libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA) and then pooled to meet the required 1ug DNA input necessary for targeted enrichment. Hybridization capture was carried out according to the SeqCap Epi Enrichment System protocol (Roche NimbleGen, Inc.; Pleasanton, CA) using xGen Universal Blocker-TS Mix (Integrated DNA Technologies, USA) as the blocking reagent and SeqCap Epi CpGiant probe pools (human) or SeqCap Epi Developer probe pools (mouse samples). MethylC-Capture Sequencing (MCC-seq) libraries were assessed using Qubit Fluorometer (ThermoFisher) and Agilent Bioanalyzer DNA 1000 assays (Agilent Technologies, Inc., USA). MCC-seq libraries with inclusion of 15-20% spike-in PhiX Control v3 library (Illumina; San Diego, CA) were clustered on a Illumina Novaseq 6000 S4 flow cell followed by 150-bp paired-end sequencing.

treatment_protocol: Peripheral blood and spleens were isolated from healthy C57Bl6 mice (age 3mo). Spleens were dissociated to single cells and FACS sorted using cell-type specific antibodies. Buffy coat (n=4), CD19+ B cell (n=1), CD4 T cell (n=1), CD8 T cell (n=1) and Gr1+ Neutrophil (n=1) methylomes were generated using the following antibodies: FITC anti-mouse CD45 (cat#103107), Alexa Fluor 647 anti-mouse CD3 (cat#100209), Brilliant Violet 711 anti-mouse CD4 (cat#100549), Brilliant Violet 421 anti-mouse CD8a (cat#100737), PE anti-mouse CD19 (cat#152407), PE/Cy7 anti-mouse Ly-6G/Ly-6C (Gr-1) (cat#108415) (all BioLegend 1:20).

value: Blood; spleen

value: Neutrophil


title: mouse_CD8Tcell-MCC-SEQ


title: Treponema denticola infected 16 weeks Female Mice 10

type: RNA

city: GAINESVILLE

first: LAKSHMYYA

last: KESAVALU

state: FLORIDA

address: 1600 SW ARCHER ROAD Rm D10-23

department: PERIODONTOLOGY/DENTISTRY

institute: UNIVERSITY OF FLORIDA

hyb_protocol: We used high-throughput nCounter® miRNA Expression Panels (Nanostring Technologies, Seattle, WA, USA) to effectively identify the DE of miRNA in both sexes. Nanos- Int. J. Mol. Sci. 2022, 23, 5107 14 of 18 tring nCounter® analysis can identify 577 miRNAs in any sample, and by using molecular barcodes, it can detect even a low number of miRNAs without the need for reverse transcription or amplification. miRNA expression profiling was performed using the Nanostring nCounter® Mouse miRNA Assay kit v1.5 (Nanostring Technologies). This assay is a highly sensitive multiplexed method that detects miRNAs using molecular barcodes called nCounter reporter probes without the need for reverse transcription. Sample preparation involved annealing, ligation, and purification. These steps were carried out based on the experimental procedure described in the nCounter® miRNA assay panel kit. Briefly, the annealing master mix was prepared by combining 13 µL of annealing buffer, 26 µL of nCounter miRNA Tag reagent, and 6.5 of diluted (1:500) miRNA assay controls. Next, 3.5 µL of the annealing master mix was aliquoted into each tube of the strip tube and 100 ng of the total RNA from six left mandibles from each group (maximum 3-µL volume) with 260/280 and 260/230 ratios of greater than 2 was added to the respective tubes. The strip tube was placed in the Thermal Cycler with the following conditions: 94 ◦C for 1 min, 65 ◦C for 1 min, 45 ◦C for 1 min, and 48 ◦C for hold. After annealing, 2.5 µL of the ligation master mix (19.5 µL of polyethylene glycol (PEG) and 13 µL of ligation buffer) was added to all the tubes in the strip tube. The strip tube was incubated at 48 ◦C for 5 min, followed by the addition of 1 µL of ligase into each tube without removing the strip tubes from the Thermal Cycler. Ligation was performed with the following conditions: 48 ◦C for 3 min, 47 ◦C for 3 min, 46 ◦C for 3 min, 45 ◦C for 3 min, 65 ◦C for 10 min, and 4 ◦C for hold. To remove the unligated tags, a purification step was performed after adding 1 µL of ligation cleanup enzyme to all the tubes and incubating the tubes at 37 ◦C for 1 h, 70 ◦C for 10 min, and 4 ◦C for hold. Forty microliters of RNase-free water were added to each tube in the strip tube and the sample was ready for hybridization with the nCounter reporter and capture probes. After denaturation at 85 ◦C for 5 min, a 5-µL aliquot from the miRNA sample preparation tube was taken along with the 10 µL of miRNA reporter code, 10 µL of hybridization buffer, and 5 µL miRNA capture probe. The strip tubes were incubated at 65 ◦C for 18 h in the Thermal cycler, and the samples were immediately processed for post-hybridization with the nCounter analysis system at the Molecular Pathology Core at the University of Florida. The nCounter® Mouse miRNA Assay kit v1.5 provided six positive hybridization controls and eight negative control probes to monitor hybridization efficiency. All components and reagents needed for sample preparation at the reparation station were taken from the nCounter master kit (Nanostring Technologies). Twelve samples per cartridge were processed in a single run, which took 3 h. This was followed by digital analysis, which involved the transfer of the cartridge to the multichannel epifluorescence digital analyzer. A cartridge definition file with a maximum fields of view (FOV) count of 555 per flow cell was taken for digital analysis. The number of images taken per scan corresponded to the number of immobilized reporter probes on the cartridge. A separate Reporter Code Count (RCC) file for each sample containing the count for each probe was downloaded and used for data analysis.

data_processing: Initial data analysis was performed using nSolver 4.0. Initially, RCC files were imported into nSolver and imaging quality control (QC), binding density QC, positive control linearity QC, and positive control limit of detection QC were carried out as recommended in the system QC parameters. The lanes were flagged when the percent FOV registration was less than 75% for imaging QC. Binding density was outside the range from 0.1 to 2.25 for binding density QC, and the positive control R2 value was less than 0.95. All 24 samples passed the QC, and no flag lanes were observed. Raw data were generated after passing the QC. To reduce the background signal/noise, the background threshold count value was set to 52 and calculated by taking an average of eight negative control probe counts from all 24 samples. Codeset content normalization parameters were chosen, and the normalization was performed based on the top 100 miRNA genes expressed. The normalized factor was calculated based on the geometric mean values of the miRNA genes expressed in each sample. Fold changes in the genes were calculated based on the ratio of the difference in the means of the log-transformed normalized data to the square root of the sum of the variances of the samples in the two groups. The limma R library was used to calculate fold changes. Clustering of miRNA for the final heatmap of DE miRNA was done using the Partitioning Around Medoids method with the fpc R library.

organism: Treponema denticola

source_name: Infected 16 weeks

growth_protocol: The oral spirochete T. denticola ATCC 35405 strain was grown in GM-1 broth. Bacteria was cultured and harvested in a Coy anaerobic chamber at 37 ◦C for 2 to 3 days. The log-phase culture of T. denticola was harvested by centrifugation at 8000 rpm for 10 min, and the pellet was washed with 5 mL of phosphate-buffered saline (PBS) followed by suspension in 1 mL of reduced transport fluid (RTF).

extract_protocol: Total RNA isolated from the mandible tissue using mirVana miRNA isolation kit (Ambion, Austin, TX, USA). mandibles from each mouse were entirely homogenized using the handheld rotor-stator homogenizer with sterile individual TissueRuptor disposable probes (Qiagen; Germantown, MD, USA) for each sample. After homogenization, each sample was lysed in a denaturing lysis solution that stabilized RNAs and inactivated RNases. The samples were subjected to an acid-phenol:chloroform extraction that removed all the cellular components such as protein, DNA, and other cellular products. The aqueous phase was removed, transferred to the fresh nuclease-free microcentrifuge tube, and 1.25 volume of 100% ethanol was added. This mixture was transferred to the filter cartridge placed into the collection tube and centrifuged for 15 s at 10,000× g. The filter cartridge was washed with 700 µL of wash solution-1 followed by washing with wash solution-2/3. After washing, the total RNA was eluted from the filter cartridge with 100 µL of nuclease-free water. RNA yield and purity were determined using a Take3 micro-volume plate in Epoch Microplate Spectrophotometer (BioTek), and quantification was performed in technical duplicates for each sample.

treatment_protocol: 100 million bacterial cells suspended in reduced transport fluid is mixed with equal volume of 6% carboxymethylcellulose (CMC) and administed orally. 0.1 ml cell suspension/mice.

value: Left Mandibles

tag: condition

value: Treponema denticola infected 16 weeks

tag: Sex

value: Female


title: H1 ESC, WT control, replicate 3

value: Embryonic stem cells


title: Treponema denticola infected 16 weeks Female Mice 9

description: miRNA expression profiling was performed using the Nanostring nCounter® Mouse miRNA Assay kit v1.5 (Nanostring Technologies).


title: H1 ESC, WT control, replicate 2


title: Treponema denticola infected 16 weeks Female Mice 7


title: Treponema denticola infected 16 weeks Female Mice 8


title: Saline-SNI-NAc-5

description:
Saline-SNI-5_S5
counts_matrix.txt
fpkm_matrix.txt

value: brain

value: nucleus accumbens


title: Treponema denticola infected 16 weeks Female Mice 6


title: H1 ESC, WT control, replicate 1

value: Pluripotent stem cells


title: Saline-Sham-NAc-4

description:
Saline-Sham-NAc-4_S24
counts_matrix.txt
fpkm_matrix.txt

value: sham


title: Saline-Sham-NAc-3

description:
Saline-Sham-NAc-3_S23
counts_matrix.txt
fpkm_matrix.txt


title: Treponema denticola infected 16 weeks Male Mice 3

value: Male


title: Treponema denticola infected 16 weeks Male Mice 5


title: memory Th2  T cells, resting unstimulated, rep2

city: Barcelona

first: Gregoire

last: Stik

state: select a state

address: 88 Dr Aiguader

country: Spain

institute: CRG

data_processing:
For mapping, a fragment-based strategy as implemented in TADbit was used, which is similar to previously published protocols (Stadhouders et al., 2018). Briefly, each side of the sequenced read was mapped in full length to the reference genome (hg38, Dec 2017 GRCh38)
After this step, if a read was not uniquely mapped, we assumed the read was chimeric due to ligation of several DNA fragments.
We next searched for ligation sites, discarding those reads in which no ligation site was found. Remaining reads were split as often as ligation sites were found. Individual split read fragments were then mapped independently. These steps were repeated for each read in the input FASTQ files. Multiple fragments from a single uniquely mapped read will result in as many contacts as possible pairs can be made between the fragments.
We used the TADbit filtering module to remove non-informative contacts and to create contact matrices.
The matrices obtained were normalized for sequencing depth and genomic biases using OneD.
Assembly: hg38
Supplementary files format and content: bed files of normalized hic matrix at 50kb resolution

source_name: Peripheral blood

extract_protocol:
T cells were FACS sorted from human peripheral blood samples of three healthy donors. Naive T cells were defined as CD4+CD127+CD25-CD45RA+; memory Th2 cells as CD4+CD127+CD25-CD45RA-CCR6-CXCR3/5-CCR4+
Cells were collected and crosslinked with 1% formaldehyde. Nuclei were digested with MboI followed by fill-in with bio-dATP, in-situ ligation and DNA extraction. DNA was sonicated and libraries were constructed using the the NEBNext DNA Library Prep Kit (New England Biolabs). Libraries were amplified for 8-12 cycles using Illumina TruSeq primers. Amplified libraries were purified and size-selected (>250bp) using Ampure XP beads.

treatment_protocol: Primary human T cells were cultured overnight in in RPMI 1640 medium supplemented with glutamine, penicillin-streptomycin and 10% FCS. Cells were stimulated with anti-human CD3/CD28 Dynabeads (Thermo Fisher Scientific) at a 1:1 cell-to-bead ratio and human IL-2 (50 U ml−1).

tag: individual

value: healthy donor 2

value: Peripheral blood

value: primary T cells

tag: cell subtype

value: memory Th2  T cells


title: Treponema denticola infected 16 weeks Male Mice 4


title: memory Th2  T cells, resting unstimulated, rep3

value: healthy donor 3


title: mouse_BuffyCoat_D-MCC-SEQ

source_name: Blood

value: Blood

value: lymphocyte


title: mouse_BuffyCoat_C-MCC-SEQ


title: Saline-Sham-NAc-2

description:
Saline-Sham-NAc-2_S22
counts_matrix.txt
fpkm_matrix.txt

value: saline


title: Saline-SNI-NAc-2

description:
Saline-SNI-NAc-2_S10
counts_matrix.txt
fpkm_matrix.txt

value: sni


title: Treponema denticola infected 16 weeks Male Mice 2

value: Left Mandibles

value: Treponema denticola infected 16 weeks


title: mouse_BuffyCoat_B-MCC-SEQ


title: Saline-SNI-NAc-1

description:
Saline-SNI-NAc-1_S9
counts_matrix.txt
fpkm_matrix.txt


title: memory Th2  T cells, stimulated, rep3

value: anti-CD3/CD28 antibodies


title: memory Th2  T cells, resting unstimulated, rep1

value: healthy donor 1


title: Treponema denticola infected 16 weeks Male Mice 1


title: Saline-Sham-NAc-5

description:
Saline-Sham-5_S6
counts_matrix.txt
fpkm_matrix.txt

value: brain

value: nucleus accumbens


title: mouse_CD4Tcell-MCC-SEQ

value: Blood; spleen


title: Saline-Sham-NAc-1

description:
Saline-Sham-NAc-1_S21
counts_matrix.txt
fpkm_matrix.txt

value: sham


title: mouse_BuffyCoat_A-MCC-SEQ


title: SHAM 16 weeks female Mice 10

source_name: Control Mice 16 weeks

value: Sham group 16 weeks

value: Female


title: mouse_CD19Bcell-MCC-SEQ


title: 8GyC-cfMCC-SEQ

data_processing:
Library strategy: MCC-seq (MethylC-capture sequencing)
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20 --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 10 --three_prime_clip_R2 10 --retain_unpaired -r1 20 -r2 20” (https://github.com/FelixKrueger/TrimGalore).
Trimmed paired-end FASTQ reads were mapped to the mouse genome (NCBI37/mm9 build) using Bismark (V 0.22.3) with parameters “--non-directional” (Kreuger et al. 2011), then converted to BAM files using SAMtools (V 1.12) (Li et al., 2009). BAM files were sorted and indexed using Samtools (V1.12).
Reads were stripped from non-CpG nucleotides and converted to BETA and PAT files using wgbstools (V 0.1.0) (Loyfer and Kaplan, 2022).
Assembly: mm9
Supplementary files format and content: BETA, PAT, and index files were generated using wgbstools bam2pat (https://github.com/nloyfer/wgbs_tools) with default parameters

extract_protocol:
Circulating cell-free DNA was extracted from 0.5mL mouse serum, using the QIAamp Circulating Nucleic Acid kit (Qiagen, Cat. No. 55114) according to the manufacturer’s instructions. Cell-free DNA was quantified via Qubit fluorometer using the dsDNA Assay Qubit fluorometer Kits (ThermoFisher Scientific, Cat. No. Q32853 and Q10212 respectively). As a quality control, fragment size distribution of isolated cfDNA was verified based on analysis using a 2100 Bioanalyzer TapeStation using either a High Sensitivity DNA Assay or DNA 1000 Assay (Agilent Technologies, Santa Cruz, CA, USA) dependent on concentration determined via either Qubit dsDNA BR or HS Assay. Additional purification using Beckman Coulter beads was implemented to remove high-molecular weight DNA reflective of cell-lysis and leukocyte contamination (Agencourt AMPure cat#A63880) (Maggi et al. 2018).
Cell-free DNA from serum was subject to bisulfite conversion using the Zymo EZ DNA Methylation Gold kit  (#D5005 Zymo Research, Irvine, CA). Whole Genome Bisulfite Sequencing libraries were generated using the Zymo Research Pico Methyl-Seq Library Prep Kit (#D5455 Zymo Research, Irvine, CA). WGBS libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA) and then pooled to meet the required 1ug DNA input necessary for targeted enrichment. Hybridization capture was carried out according to the SeqCap Epi Enrichment System protocol (Roche NimbleGen, Inc.; Pleasanton, CA) using xGen Universal Blocker-TS Mix (Integrated DNA Technologies, USA) as the blocking reagent and SeqCap Epi CpGiant probe pools (human) or SeqCap Epi Developer probe pools (mouse samples). MethylC-Capture Sequencing (MCC-seq) libraries were assessed using Qubit Fluorometer (ThermoFisher) and Agilent Bioanalyzer DNA 1000 assays (Agilent Technologies, Inc., USA). MCC-seq libraries with inclusion of 15-20% spike-in PhiX Control v3 library (Illumina; San Diego, CA) were clustered on a Illumina Novaseq 6000 S4 flow cell followed by 150-bp paired-end sequencing.

treatment_protocol: C57Bl6 mice (n=18) were irradiated to the upper thorax at varying dose (sham control, 3Gy, 8Gy) for 3 consecutive treatments. Serum was collected 24 hours after the last radiation dose. For serum isolation, blood was collected via cardiac puncture (~1mL) and allowed to clot at room temperature for 30 minutes before centrifugation at 1500 x g for 20 min at 4◦C to separate the serum fraction.

value: Serum

value: 8Gy radiation


title: memory Th2  T cells, stimulated, rep1

value: Peripheral blood

value: primary T cells

value: memory Th2  T cells


title: SHAM 16 weeks female Mice 9


title: SHAM 16 weeks female Mice 8


title: 8GyB-cfMCC-SEQ


title: DMI-SNI-NAc-3

description:
DMI-SNI-NAc-3_S7
counts_matrix.txt
fpkm_matrix.txt

value: DMI


title: naïve CD4+ T cells, resting unstimulated, rep3

value: healthy donor 3

value: naïve CD4+ T cells


title: SHAM 16 weeks female Mice 7

value: Left Mandibles


title: DMI-SNI-NAc-2

description:
DMI-SNI-NAc-2_S6
counts_matrix.txt
fpkm_matrix.txt

value: sni


title: DMI-SNI-NAc-1

description:
DMI-SNI-NAc-1_S5
counts_matrix.txt
fpkm_matrix.txt


title: 3GyC-cfMCC-SEQ

value: 3Gy radiation


title: naïve CD4+ T cells, resting unstimulated, rep1

value: healthy donor 1


title: naïve CD4+ T cells, resting unstimulated, rep2

value: healthy donor 2


title: SHAM 16 weeks female Mice 6


title: DMI-Sham-NAc-4

description:
DMI-Sham-NAc-4_S20
counts_matrix.txt
fpkm_matrix.txt

value: brain

value: nucleus accumbens


title: memory Th2  T cells, stimulated, rep2

value: anti-CD3/CD28 antibodies


title: DMI-SNI-NAc-4

description:
DMI-SNI-NAc-4_S8
counts_matrix.txt
fpkm_matrix.txt


title: naïve CD4+ T cells, stimulated, rep3


title: shamC-cfMCC-SEQ

value: sham


title: naïve CD4+ T cells, stimulated, rep2


title: 3GyB-cfMCC-SEQ

value: Serum


title: shamB-cfMCC-SEQ


title: DMI-Sham-NAc-2

description:
DMI-Sham-NAc-2_S18
counts_matrix.txt
fpkm_matrix.txt


title: SHAM 16 weeks male Mice 4

value: Sham group 16 weeks

value: Male


title: DMI-Sham-NAc-3

description:
DMI-Sham-NAc-3_S19
counts_matrix.txt
fpkm_matrix.txt


title: naïve CD4+ T cells, stimulated, rep1

value: Peripheral blood

value: primary T cells


title: DMI-Sham-NAc-1

description:
DMI-Sham-NAc-1_S17
counts_matrix.txt
fpkm_matrix.txt

value: DMI


title: RD-i-shTRPS1#2 +DOX DM rep3

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

description: TRPS1 knockdown 2

data_processing:
Sequence information was extracted in FastQ format using the tool bcl2FastQ v2.20.0.422 (provided by Illumina).
Reads were mapped to the Homo sapiens genome (GRCh38 with the Ensembl genome annotation Release 99) using STAR (version 2.7.2b, parameters: --alignIntronMax 100000 --outSJfilterReads --outSAMmultNmax Unique --outFilterMismatchNoverLmax 0.04) (PMID: 23104886).
For each gene, reads that map uniquely to one genomic position were counted with FeatureCounts (version 1.6.5, multi-mapping or multi-overlapping reads were not counted, stranded mode was set to “–s 2”, Ensembl release 99 gene annotation) (PMID: 24227677).
Genome_build: GRCh38
Supplementary_files_format_and_content: .xlsx file containing raw read counts per gene over all samples and RPKM

source_name: Rhabdomyosarcoma cell line

growth_protocol: RD cells were cultured in growth medium (GM)(DMEM + 10 % FBS + 1x P/S) or differentiation medium (DM)(DMEM + 2 % HS + 1x P/S) at 37°C, 5 % CO2, and athmospheric O2 in a humidified incubator.

extract_protocol:
Total RNA was extracted using the chloroform-phenol extraction method.
Libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit (kit) using the RNA purified by the NEBNext® Poly(A) mRNA Magnetic Isolation Module following the manufacturer‘s instruction. 180 ng of total RNA were used as input.

treatment_protocol: RD cells were treated with 1 µM doxycyclin for 2 days in GM and 10 days in DM.

value: Rhabdomyoblast

tag: si rna

value: differentiation medium with doxycycline


title: SHAM 16 weeks male Mice 5

description: miRNA expression profiling was performed using the Nanostring nCounter® Mouse miRNA Assay kit v1.5 (Nanostring Technologies).

value: Left Mandibles


title: 8GyA-cfMCC-SEQ

value: 8Gy radiation


title: SHAM 16 weeks male Mice 2


title: HMGB2_Cl13_3 [ATAC-seq]

city: Irvine

first: Roberto

last: Tinoco

state: CA

address: 3444 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: University of California, Irvine

data_processing:
Paired ended reads from sequencing were QC analyzed with fastqQC(v.11.9) and aligned to mouse mm10 reference genome using bowtie2 (v2.4.1).
Mitochondrialreads and reads mapped todark list (ENCODE Stanford version) were excludedfrom the downstream analysis. Duplicated reads were removed using Picard tools (v2.27.1).
A union peak list was created by merging processed reads from all samples and then calling peaks usingMACS2 (v2.7.1) (-q 0.01 --keep-dup all -f BAMPE).
The number of reads in each peak were then counted using featureCounts (Rsubread v2.6.4) to create a counts matrix.
Normalization of counts matrix was performed using DESeq2 (v1.32.0). Differentially expressed peaks were determined using edgeR (v3.34.1) with an FDR cut-off of0.05 and a |log10FC| cut-off of ≥ 0.3. Peaks were annotated using ChIPSeeker (v1.34.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized abundance measurements for each Sample

source_name: Spleen

extract_protocol:
Following the Omni-ATAC protocol, samples were lysed in lysis buffer (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 10% Np-40, 10% Tween, and 1% Digitonin) on ice for 3 minutes68. Immediately following lysis, nuclei were spun at 500g for 10min at 4°C to remove supernatant.
Nuclei were then incubated with Tn5 transposase for 30min at 37°C. Tagmented DNA was purified using AMPure XP beads and PCR was performed to amplify the library under the following conditions: 72°C for 5min; 98°C for 30s; 5 cycles of 98°C for 10s, 63°C for 30s, and 72°C for 1min; hold at 4°C. Libraries were then purified with warm AMPure XP beads and quantified on a Bioanalyzer.
Libraries were multiplexed and sequenced to a depth of 50million 100bp paired reads on a NextSeq 500

value: Spleen

value: HMGB2 KO P14


title: RD-i-shTRPS1#2 +DOX DM rep2

description: TRPS1 knockdown 2


title: HMGB2_Cl13_2 [ATAC-seq]


title: RNA.MK_4

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: CAKIR;pT3Myc;sb13 HDTV

data_processing:
Trimming of adapters and low quality bases was performed using Trim-Galore v0.4.0
Reads were pseudo-aligned to the reference transcriptome using Kallisto v0.43.0 (PMID: 27043002; quant -b 100)
Genome_build: GENCODE vM23
Supplementary_files_format_and_content: tsv (transcripts abundances inferred using Kallisto)

source_name: Primary Hepatocytes

growth_protocol: Mice were maintained in a specific-pathogen-free environment according to the University Hospital of Tuebingen guidelines and fed with a standard diet.

extract_protocol:
Three days after HDTV, livers were processed according to the Liver Dissociation Kit (Miltenyi Biotec). Immune cells were magnetically depleted using the MACS system and CD45 MicroBeads (Miltenyi Biotec). RFP+ cells were facs sorted using a BD FACSAria™ III Cell Sorter and immediately stored as cell pellet at -80. RNA was isolated using the Rneasy Mini Kit (Qiagen)
SMART Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara)

treatment_protocol: Vectors for HDTV injection were prepared using the QIAGEN EndoFree Maxi Kit (QIAGEN). For transposon-mediated gene transfer, animals received a 25 µg:5 µg ratio of transposon to transposase-encoding plasmid. For HDTV, DNA was suspended in 0.9% saline solution at a final volume of 10% of the animal’s body weight and injected via the tail vein within 5–10 s. A transposon overexpressing KrasG12D and RFP was codelivered with a pT3-EMPTY plasmid to generate K samples. A transposon overexpressing KrasG12D and RFP was codelivered with a pT3-Myc(murine) plasmid to generate MK samples.

value: Liver


title: SHAM 16 weeks male Mice 1


title: RD-i-shTRPS1#2 +DOX DM rep1

description: TRPS1 knockdown 2


title: RNA.MK_3

description: CAKIR;pT3Myc;sb13 HDTV


title: 3GyA-cfMCC-SEQ

value: 3Gy radiation


title: HMGB2_Cl13_1 [ATAC-seq]


title: RD-i-shTRPS1#1 +DOX DM rep3

description: TRPS1 knockdown 1


title: SHAM 16 weeks male Mice 3


title: RNA.MK_2

description: CAKIR;pT3Myc;sb13 HDTV


title: Treponema denticola infected 8 weeks female Mice 10

source_name: Infected 8 weeks

value: Treponema denticola infected 8 weeks

value: Female


title: WT_Cl13_3 [ATAC-seq]

value: WT P14


title: Treponema denticola infected 8 weeks female Mice 9


title: RD-i-shTRPS1#1 +DOX DM rep2

description: TRPS1 knockdown 1


title: WT_Cl13_2 [ATAC-seq]


title: Treponema denticola infected 8 weeks female Mice 8


title: shamA-cfMCC-SEQ

value: Serum

value: sham


title: RNA.K_1

description: CAKIR;pT3empty;sb13 HDTV


title: RD-i-shTRPS1#1 +DOX DM rep1

description: TRPS1 knockdown 1


title: Treponema denticola infected 8 weeks female Mice 7


title: RNA.K_2

description: CAKIR;pT3empty;sb13 HDTV


title: WT_Cl13_1 [ATAC-seq]


title: RNA.CTRL_2

description: livers without HDTV


title: Treponema denticola infected 8 weeks female Mice 6


title: RD-i-shNT +DOX DM rep3

description: control

value: shNT


title: RD-i-shNT +DOX DM rep1

description: control


title: RNA.CTRL_1

description: livers without HDTV


title: RNA-seq_posterior epiblast, E7.5, WT, rep2

city: Oeiras

first: Patrícia

last: Duarte

address: Rua da Quinta Grande

country: Portugal

institute: Instituto Gulbenkian Ciência

data_processing:
Reads were aligned to the reference mouse genome (mm10) using STAR
Read counts were normalized  using EdgeR
Assembly: mm10
Supplementary files format and content: excel file includes normalized CPM for each sample

source_name: posterior epiblast

extract_protocol:
Total RNA was isolated from pooled samples with TRI Reagent (Sigma-Aldrich) following the manufacturer’s protocol
Libraries were prepared from total RNA using the SMART-Seq2 protocol

value: posterior epiblast

tag: developmental stage

value: WT


title: ATAC.MK_4

description: CAKIR;pT3Myc;sb13 HDTV

data_processing:
Trimming of adapters and low quality bases was performed using Trim-Galore v0.4.0
Reads were mapped to the mouse mm10 genome using Bowtie v2.2.9 (PMID: 22388286). Reads with MAPQ lower than 10 were excluded from further analyses.
Accessible regions were identified using MACS v2 (PMID: 18798982) with the following parameters: callpeak --format=BAMPE --gsize=mm --nomodel --nolambda -p 0.00001 --call-summits
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: xls (MACS; list of peaks)

extract_protocol:
Three days after HDTV, livers were processed according to the Liver Dissociation Kit (Miltenyi Biotec). Immune cells were magnetically depleted using the MACS system and CD45 MicroBeads (Miltenyi Biotec). 40.000 RFP+ cells were facs sorted using a BD FACSAria™ III Cell Sorter.  Cells were washed in cold PBS and centrifuged (4000rpm, 5 min, 4 °C). Nuclei were isolated by resuspension of the cell pellet in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifugation. Nuclei were subjected to tagmentation in 50 µl reactions containing 1× TD buffer and 2.5 µl T5 transposase followed by incubation at 37 °C for 30 min. Tagmented DNA was recovered using a QIAGEN MinElute kit and eluted in 10 µl elution buffer (10 mM Tris-HCl, pH 8.0).
Libraries were amplified according to Buenrostro et al., 2015, purified using a QIAGEN PCR Cleanup kit and eluted in 20 µl elution buffer.


title: RD ChIP

description: Sample

data_processing:
Sequence information was extracted in FastQ format using the tool bcl2FastQ v2.20.0.422 (provided by Illumina).
High quality reads (Q>20) were identified and adapters were removed using cutadapt
Reads were aligned to the human genome (hg19) using bowtie2
Supplementary_files_format_and_content: bw

growth_protocol: RD cells were cultured in growth medium (DMEM + 10 % FBS + 1x P/S) at 37°C, 5 % CO2, and athmospheric O2 in a humidified incubator.

extract_protocol:
Chromatin preparation
NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and Dual Index Primers (NEBNext Multiplex Oligos for Illumina, NEB).

value: wildtype

tag: chip antibody

value: rabbit-anti-TRPS1 (selfmade)


title: RNA.K_3

description: CAKIR;pT3empty;sb13 HDTV


title: RNA-seq_posterior epiblast, E8.5, WT, rep2


title: Treponema denticola infected 8 weeks male Mice 3

value: Male


title: Treponema denticola infected 8 weeks male Mice 5

value: Left Mandibles


title: Treponema denticola infected 8 weeks male Mice 4


title: RD-TRPS1-KO ChIP

description: Negative control

value: Rhabdomyoblast


title: ATAC.MK_3

description: CAKIR;pT3Myc;sb13 HDTV


title: Treponema denticola infected 8 weeks male Mice 2


title: RNA-seq_posterior epiblast, E7.5, WT, rep1


title: posterior epiblast, E8.5, RAL, rep2

data_processing:
Fastq files were processed with GUAVA v1 (Divate and Cheung 2018), following the recommended guidelines.
ATAC-seq reads were trimmed with cutadapt, minimum read lenght >30
ATAC-seq reads were aligned to the mm10 genome using Bowtie2, minimum mapping quality >30
Peaks were called uing MACS2 with the significance cut-off q-value <=0.05
bigWig files were generated using deeptools and normalized  using 1x effective genome size.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Tissue samples were incubated with accutase for 30 minutes to dissociate into single cell suspension. After lysis and transposition reaction, genomic DNA was extracted with MinElute purification kit (Qiagen)
ATAC-seq libraries were prepared using NEBNext High-Fidelity 2× PCR Master Mix with custom-synthesized PCR primers (Buenrostro et al, 2013). Libraries were amplified using 8 cycles in the thermocycler. The amplified libraries were size selected using SPRIselect beads from Beckman Coulter.

value: Raldh2 Knockout


title: RD Input

description: Input


title: posterior epiblast, E8.5, RAL, rep1


title: Lysate_rep2

city: Martinsried

first: Fabien

last: Bonneau

address: Am Klopferspitz 18

department: Structural Cell Biology

institute: Max Planck Institute of Biochemistry

data_processing:
Reads were aligned with STAR (v 2.7.9a)
Read count extraction on sgdGene annotations was performed with featureCounts (Subread v 2.0.3) with parameters -p --countReadPairs -B -C
Normalized abundance measurements were obtained with DESeq2 (v 1.38.3)
BigWig files were generated with deeptools (v 3.5.1) using a bin size of 1 and scaling factors from DESeq2 output
Assembly: sacCer3
Supplementary files format and content: gene_counts.tsv is a tab-delimited text file of raw counts for each sample
Supplementary files format and content: Eluate_vs_Lysate_DESeq2.tsv is a tab-delimited text file of enrichment factors for each transcript in eluate vs. lysate samples
Supplementary files format and content: *_scaled.bw are bigWig files of scaled coverage with a 1 nt resolution

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were grown in YPD to an absorbance around 1 at 600 nm

extract_protocol:
Total RNA was extracted with the hot-phenol method and subsequently treated with DNase
Library was prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina after ribosomal RNA depletion using riboPOOLs kit from siTOOLS

treatment_protocol: Two-step affinity purification using Sub2 and Hpr1 as baits

tag: fraction

value: total lysate


title: ATAC.MK_2

description: CAKIR;pT3Myc;sb13 HDTV

tag: tissue

value: Liver


title: RD-i-shNT +DOX DM rep2

description: control

value: differentiation medium with doxycycline


title: SHAM 8 weeks female Mice 10

source_name: Control Mice 8 weeks

value: Sham group 8 weeks


title: RNA-seq_posterior epiblast, E8.5, WT, rep1


title: posterior epiblast, E8.5, WT, rep2


title: ATAC.K_3

description: CAKIR;pT3empty;sb13 HDTV


title: Treponema denticola infected 8 weeks male Mice 1

value: Treponema denticola infected 8 weeks


title: ATAC.K_2

description: CAKIR;pT3empty;sb13 HDTV


title: Lysate_rep1


title: posterior epiblast, E8.5, WT, rep1


title: SHAM 8 weeks female Mice 8

value: Female


title: ATAC.K_1

description: CAKIR;pT3empty;sb13 HDTV


title: Eluate_rep2

value: eluted particles


title: posterior epiblast, E7.5, WT, rep2


title: SHAM 8 weeks female Mice 7


title: ATAC.CTRL_1

description: livers without HDTV


title: Eluate_rep1


title: ATAC.CTRL_2

description: livers without HDTV


title: day 4, cKO, replicate 2

city: Bunkyo-ku

first: Akari

last: Nakamura

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

library_source: transcriptomic single cell

data_processing:
Read mapping and counting were processed with the 10x Genomics Cell Ranger 6.0.1. with the mm10 reference genome assembly and gene annotation provided by 10x Genomics.
Assembly: mm10
Supplementary files format and content: Tab-separated barcodes files
Supplementary files format and content: Tab-separated features files
Supplementary files format and content: Tab-separated matrix files

source_name: Cerebral cortex

extract_protocol:
Four days after stroke onset, brains were removed and sliced in ice-cold artificial cerebrospinal fluid. Peri-infarct area was trimmed and treated with pronase (Sigma-Aldrich) for 75 minutes at room temperature. Enzyme-treated tissue was dissociated by gentle pipetting with a Pasteur pipette. Neuron enriched cell populations (Thy1+/ACSA2-/CD31-/CD45-/O4-/CD140a-/CD140b-) were collected by fluorescence-activated cell sorting (BD FACS Aria III).
RNA libraries for scRNA-seq were prepared using Chromium Next GEM Single-cell 3' Reagent Kits v3.1 (10x Genomics) according to the manufacturer’s protocol.

treatment_protocol: Mice were subjected to transient brain ischemia (middle cerebral artery occlusion: MCAO) for 60 min or sham operation.

value: Cerebral cortex

value: male

value: Neurons

value: Slc17a7-Cre; Slc32a1-Cre; Padi4 flox/flox

value: transient brain ischemia (middle cerebral artery occlusion:MCAO)


title: day 4, cKO, replicate 1


title: day 5 replicate 1, lane 4, scATAC-seq

city: Saint Louis

first: Samantha

last: Morris

state: Missouri

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: 10x Genomics

data_processing:
Single-cell barcoded bam files were generated using CellRanger-ATAC (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)
lineage barcodes were processed using our in house pipeline (https://github.com/morris-lab/newCloneCalling)
Assembly: mm10
Supplementary files format and content: H5 files for single-cell peak matrices

source_name: adult mouse bone marrow

extract_protocol:
FACS sorting
10x Genomics scATAC-seq library prep, with modifications to capture CellTags

value: LSK cells

value: adult mouse bone marrow

tag: timepoint

value: day 5


title: SHAM 8 weeks male Mice 5

value: Left Mandibles

value: Male


title: SHAM 8 weeks male Mice 4


title: day 4, control, replicate 2

value: Padi4 flox/flox


title: day 5 replicate 1, lane 2, scATAC-seq

description: 10x Genomics


title: SHAM 8 weeks female Mice 9


title: day 4, control, replicate 1


title: SHAM 8 weeks male Mice 3


title: SHAM 8 weeks male Mice 2


title: day 5 replicate 1, lane 1, scATAC-seq

description: 10x Genomics


title: sham, control, replicate 1

value: sham operation


title: day 2.5, scATAC-seq

description: 10x Genomics

value: day 2.5


title: SHAM 8 weeks male Mice 1

value: Sham group 8 weeks


title: WT rep1

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

country: France

institute: Institut Curie

data_processing:
Sample demultiplexing, alignment, UMI counting, and cell calling are performed using CellRanger v3.0.2 with default parameters, except for the expected number of recovered cells (--expect-cells 6000)
Doublets are predicted by running DoubletDetection 50 times with a p-value threshold of 1E-7 at each iteration; a barcode is labeled as doublet if it is detected as such in at least 40 iterations
Gene-cell expression matrices are imported with Seurat v3.0.0 for each sample separately. Expression values are normalized and log-transformed (log((xij+1)/nj) where x is the UMI count of gene j in cell i and nj is the total UMI count for cell j); cells with <200 detected genes (UMI>0) and genes detected in <2 cells are filtered out
Filtered and normalized gene-cell expression matrices for the four samples are concatenated; gene expression is centered and scaled (z-score)
Gene expression dispersion is computed with mean.var.plot method from Seurat v3.0.0; highly variable genes are defined as those with average expression in [0.1,10] and scaled dispersion >1.5
PCA is computed on the highly variable genes
Clustering is performed on the top 20 PCs with Waltman and van Eck algorithm using k=30 neighbors and resolution r=0.7
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files containing the gene/cell expression matrices (UMI counts)
Supplementary_files_format_and_content: h5ad files containing the gene-cell expression matrix for the concatenated samples (raw counts and normalized counts) and the cell-associated metadata

source_name: Lung CD45+ cells

extract_protocol:
Live, CD45.2+ immune cells were sorted from the lungs of 2 WT vand 2 Lmna-flox/flox Vav1-cre+/- mice at 10 weeks of age.
Approximately 9600 cells were processed using the Chromium Single Cell 3' Reagents Kits v3 and sequenced using 25,000 reads per cell (NovaSeq).

value: lung

value: CD45+ immune cells

value: Lmna-flox/flox Vav1-cre-/-

tag: age

value: 10 weeks


title: Lmna-KO rep2

tag: strain

value: Lmna-flox/flox Vav1-cre+/-


title: WT rep2


title: Hnf1b, ChIP-seq

status: Public on Jul 23 2023

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

data_processing:
RNA-sequencing data was analyzed using the seq2science pipeline (https://vanheeringen-lab.github.io/seq2science/content/workflows/rna_seq.html). Briefly, reads were aligned with to the pre-indexed mm10 transcript assembly from UCSC. Samtools was used to filter reads with a quality score lower than 20, and PCR duplicates were removed. Reads per gene were counted with the htseq-count script from the Hisat2 software suite using the GTF file corresponding to the transcript assembly. Read counts were analyzed with DESeq2 to identify significant dynamics.
Base calling was performed with CASAVA version 1.4 burrows-wheeler transformation, 0.710 -r789 , default Peak calling was executed with Macs2, q-value (False discovery rate, FDR) 0.001. BigWig files were generated using a custom bam to bigwig script.
Genome_build: RNA-seq: mm10; ChIP-seq mm9
Supplementary_files_format_and_content: RNA-seq: read counts per transcript; ChIP-seq: Bigwig and Bed files

growth_protocol: Murine distal convoluted tubule cells (mpkDCT) clone 4a were grown in DMEM/F-12 containing 2% (v/v) fetal calf serum (FCS) (Biowest, Kansas City, MO, USA), 90 nm sodium selenate; 5 μg/ml transferrin; 2 mM glutamine; 50 nM dexamethasone; 1 nM triiodothyronine; 10 ng/ml epidermal growth factor; 5 μg/ml insulin; 20 mM d-glucose; and 20 mM HEPES, pH 7.4. Cells were grown at 37 °C in a humidity-controlled incubator with 5% (v/v) CO2.

extract_protocol:
RNA was isolated using the NucleoSpin RNA plus kit following the manufacturer’s protocol (Macherey Nagel, Dueren, Germany). ChIP: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Total RNA was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, Wilmington, MA, USA). In short, oligo hybridization and rRNA depletion, rRNA depletion cleanup, DNase digestion, DNase digestion cleanup, and RNA elution were performed according to protocol. Fragmentation and priming were performed at 94 °C for 6 min. First strand synthesis, second strand synthesis and A-tailing were performed according to protocol. For the adaptor ligation, a 1.5 mM stock was used (NextFlex DNA barcodes, Bioo Scientific, Austin, Tx, USA). First and second post-ligation cleanup was performed according to protocol. A total of 11 PCR cycles were performed for library amplification. The library amplification cleanup was done using a 0.8 x followed by a 1.0 x bead-based cleanup. Library size was determined using the High Sensitivity DNA bioanalyzer kit, and the library concentration was measured using the dsDNA High Sensitivity Assay (DeNovix, Wilmington, DE, USA). Paired-end sequencing reads of 50 bp were generated using an Illumina NextSeq 500. ChIP-sequencing: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: MpkDCT4a cells were seeded in a 12 well plate and transiently transfected with 100 pmol of a SMARTpool of siRNAs targeting Hnf1b (Dharmacon, Lafayette, CO, USA), or non-targeting siRNAs using 3 μL RNAiMAX transfection reagent (ThermoFisher Scientific). 48 hours after transfection cells were harvested for RNA isolation using the NucleoSpin RNA plus kit following the manufacturer’s protocol (Macherey Nagel, Dueren, Germany). For ChIP-seq mpkDCT4a cells were untreated.

tag: treatment

value: rabbit anti-Hnf1β (Santa Cruz, H-85, SC-22840)

tag: icu admission


title: Mycelium, DMSO, rep3

city: MALAGA

first: DAVID

last: VELA-CORCIA

address: CAMPUS DE TEATINOS

department: MICROBIOLOGIA

institute: UNIVERSIDAD DE MALAGA

data_processing:
Raw reads were preprocessed by NextSeq System Suite v.2.2.0. using specific NGS technology configuration parameters. This preprocessing removes low-quality, ambiguous and low-complexity stretches, linkers, adapters, vector fragments and contaminated sequences, and preserves the longest informative parts of the reads. SeqTrimNext also discarded sequences shorter than 25 bp.
Clean reads of the BAM files were aligned and annotated by Bowtie2 using the Botrytis cinerea B05.10 genome v.109.3 as the reference; these data were then sorted and indexed using SAMtools v.1.484110.
Uniquely localized reads were used to calculate the read number values for each gene by Sam2counts (https://github.com/vsbuffalo/sam2counts).

organism: Botrytis cinerea

source_name: Fungal mycleium

growth_protocol: B. cinerea isolate B05.10 was cultured on potato dextrose agar (PDA, Oxoid) in a controlled-environment chamber at 20ºC under illumination with fluorescent light at a photo fluency rate of 12 μmol m-2 s-1 and 12/12 h photoperiod.

extract_protocol:
RNA from B. cinerea B05.10 was extracted from clumps after 24 h growth on PDB supplemented with 0.25 mg mL-1 of Cyclo (Pro-Tyr), and DMSO as control, at 28ºC 150rpm, using NucleoSpin RNA Plant and Fungi kit (Macherey-Nagel), according to the manufacturer’s instructions.
For RNA sequencing analysis, 200-500 bp single-end read libraries were prepared using a TruSeq stranded total RNA kit (Illumina). The libraries were sequenced using a NextSeq550 instrument (Illumina).

value: Fungal mycleium

tag: cell line

value: WT

value: DMSO


title: Mycelium, 0.25mg/mL Cyclo (Pro-Tyr), rep2

value: Cyclo (Pro-Tyr)


title: Mycelium, 0.25mg/mL Cyclo (Pro-Tyr), rep3


title: Mycelium, DMSO, rep1


title: Mycelium, 0.25mg/mL Cyclo (Pro-Tyr), rep1


title: day 5 replicate 1, lane 3, scATAC-seq

description: 10x Genomics

tag: cell type

value: LSK cells

value: adult mouse bone marrow

value: day 5


title: SHAM 8 weeks female Mice 6

value: Left Mandibles

value: Female


title: Worm, 0.25mg/mL Cyclo (Pro-Tyr), rep2

data_processing:
Raw reads were preprocessed by NextSeq System Suite v.2.2.0. using specific NGS technology configuration parameters. This preprocessing removes low-quality, ambiguous and low-complexity stretches, linkers, adapters, vector fragments and contaminated sequences, and preserves the longest informative parts of the reads. SeqTrimNext also discarded sequences shorter than 25 bp.
Clean reads of the BAM files were aligned and annotated by Bowtie2 using the C. elegans N2 genome as reference; these data were then sorted and indexed using SAMtools v.1.484110.
Uniquely localized reads were used to calculate the read number values for each gene by Sam2counts (https://github.com/vsbuffalo/sam2counts).

organism: Caenorhabditis elegans

source_name: Entire worm

growth_protocol: C. elegans N2 was cultured at 20ºC under standard growth conditions on an NGM agar plates seeded with E. coli OP50.

extract_protocol:
RNA from synchronized C. elegans N2 was extracted as previously described with slight modifications. Briefly, C. elegans N2 was incubated on M9 buffer supplemented with 0.25 mg mL-1 of Cyclo (Pro-Tyr), and DMSO as control, for 24 h at 19ºC with gentle shaking. After that, worms were centrifuged and supernatant was discarded, worm pellet was resuspended in TRI-Reagent (Simga-Aldrich) with 0.1 mm glass beads and worms were lysate in TissueLyser II (Qiagen) at 30 cycles sec-1 for 20 min. After worm lysis, RNA was extracted using NucleoSpin RNA Plant and Fungi kit (Macherey-Nagel), according to the manufacturer’s instructions.
For RNA sequencing analysis, 200-500 bp single-end read libraries were prepared using a TruSeq stranded total RNA kit (Illumina). The libraries were sequenced using a NextSeq550 instrument (Illumina).

value: Entire worm

value: Bristol N2

tag: genotype

value: 0.25mg/mL Cyclo (Pro-Tyr), rep1


title: Lmna-KO rep1

value: lung

value: CD45+ immune cells


title: Worm, DMSO, rep2


title: Worm, 0.25mg/mL Cyclo (Pro-Tyr), rep1


title: traditional breeding [TB-3]

city: Wu han

first: Li

last: Zhang

state: Hu bei

address: No. 29, Nanhu Avenue, Shizishan Street, Hongshan District, Wuhan City, Hubei Pro

country: China

institute: Institute of Animal Husbandry and Veterinary Medicine, Hubei Academy of Agricultural Sciences

description: apla intestine

data_processing:
Illumina Casava1.8 software used for basecalling.
After removing the adaptors, low quality tags and contaminants reads, the clean reads were aligned with the duck genome
The expressions of miRNAs were normalized by Fragments per Kilobase of Transcript per Million Fragments Mapped (FPKM)
Supplementary files format and content: FPKM

organism: Anas platyrhynchos

source_name: duodenum

extract_protocol:
Total RNA of each sample was extracted with Trizol (Invitrogen, USA). Using a Novex 15% TBE-Urea gel, 20–30-nt long RNA fragments were isolated and purified from 10 μg of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: duodenum

value: Intestinal epithelial cells

tag: group

value: traditional breeding


title: cage raring [CR-2]

description: apla intestine

value: cage raring


title: traditional breeding [TB-2]

description: apla intestine


title: cage raring [CR-1]

description: apla intestine


title: cage raring [CR-3]

description: apla intestine


title: traditional breeding [TB-1]

description: apla intestine


title: Mycobacterium smegmatis, RNAseq library by HieffNGS kit repeat3

city: wuhan

first: zaiqiao

last: sun

institute: wuhan university

data_processing:
Raw reads from sequencing were firstly subjected to Trimmomatic (v0.39) for quality control and adaptor trimming
reads were mapped to genome using STAR (v2.7.10a)
gene counts was statisticed with featurecount
Genes with FPKM >0.5 were considered to be expressed
Assembly: Homo_sapiens.GRCh38, Mus_musculus.GRCm39, Mycobacterium_smegmatis.NZ_CP054795.1
Supplementary files format and content: tab-delimited text file includes raw counts for each
Supplementary files format and content: Sampletab-delimited text files include FPKM values for each Sample mRNA Fragmentation and cDNA synthesis.

organism: Mycolicibacterium smegmatis

source_name: Mycobacterium smegmatis

growth_protocol: HEK293T cells and Hepa1-6 cells were maintained in DMEM medium (Gibco, Cat #11965092) + 10% FBS (Gibco, Cat#16000044) and 1% penicillin/streptomycin (Gibco, Cat#15140122) at 37°C with 5%CO2, Mycobacterium smegmatis was maintained in Middlebrook 7H9 broth base medium

extract_protocol:
Total RNA was extracted from mouse tissue with TRIzol, Total RNA from Cell line or bacterium was extracted by MolPure® Cell/Tissue Total RNA Kit
RNA libraries for RNA-seq were prepared using DADCSeq, HieffNGS kit and SHERRY following manufacturer's protocols

treatment_protocol: No special treatment

value: Mycobacterium smegmatis

value: WT

value: RNAseq library by HieffNGS kit


title: Mycobacterium smegmatis, RNAseq library by DADCSeq repeat3

value: RNAseq library by DADCSeq


title: Mycobacterium smegmatis, RNAseq library by HieffNGS kit repeat1


title: Mycobacterium smegmatis, RNAseq library by HieffNGS kit repeat2


title: Mycobacterium smegmatis, RNAseq library by DADCSeq repeat1


title: Mycobacterium smegmatis, RNAseq library by DADCSeq repeat2


title: posterior epiblast, E7.5, WT, rep1

value: posterior epiblast


title: Mycelium, DMSO, rep2

value: Fungal mycleium

value: DMSO


title: LoVo cells, shNSD2#2 biol rep 1

city: Wuhan

first: da

last: song

state: Hubei

address: Jiefang Avenue 1095

department: tongji hospital

institute: huazhong university of science and technology

description: Colume-H

data_processing:
The raw  paired end reads were trimmed and quality controlled by fastp with default parameters
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach
To identify DEGs between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads method
Differential expression analysis was performed using the DESeq2. DEGs with |log2Fc|>=1 and FDR <=0.05 were considered to be significantly expressed genes
Assembly: hg18
Supplementary files format and content: Excel includede raw counts for all samples
Supplementary files format and content: Excel includede TPM for all samples

source_name: LoVo

growth_protocol: LoVo CRC cells were maintained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from the cells using TRIzol Reagent according to the mamufacture's instructions (Invitrogen) and genomic DNA was removed using Dnase I (Takara)
The RNA-seq transcriptome library was prepared following Illumina NovaSeq Reagent Kit

treatment_protocol: LoVo CRC cells were infected with lentivirus containing shRNA against NSD2 or control lentivirus

value: LoVo

value: CRC cells

value: NSD2 knockdown


title: LoVo cells, shNSD2#2 biol rep 2

description: Colume-I


title: LoVo cells, shNSD2#2 biol rep 3

description: Colume-J


title: LoVo cells, shNSD2#1 biol rep 3

description: Colume-G


title: LoVo cells, shNSD2#1 biol rep 2

description: Colume-F


title: Worm, DMSO, rep1

value: Entire worm

value: Bristol N2


title: LoVo cells, shNC biol rep 3

description: Colume-M


title: LoVo cells, shNC biol rep 2

description: Colume-L


title: LoVo cells, shNSD2#1 biol rep 1

description: Colume-E


title: LoVo cells, shNC biol rep 1

description: Colume-K


title: PdCSC_2

city: Cleveland

first: Qian

last: Huang

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

data_processing:
RNA-seq data were analyzed by Galaxy project (usegalaxy.org). The genes were counted by htseq package in galaxy project, and the differentially expressed genes were compared by edgR package in galaxy project.
Assembly: homo sapiens hg38
Supplementary files format and content: txt format, contain gene ensg number and normalized expression

source_name: lung

growth_protocol: CD44+ CSCs and Pd-CSCs were cultured in neurobasal medium contaning 1% penicillin/streptomycin in a humidified chamber under 5% CO2 at 37 °C. Cd-pericytes were cultured in pericyte special medium contaning 1% penicillin/streptomycin in a humidified chamber under 5% CO2 at 37 °C.

extract_protocol:
Total RNA samples were extracted from cells by using the PureLinkTM RNA Kit (ThermoFisher, 12183020)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: primary lung ADC cell

value: lung adenocarcinoma


title: Cdpericyte_2


title: CSC_1


title: PdCSC_1


title: Cdpericyte_1


title: CSC_2


title: shGPR124_2

data_processing:
RNA-seq data were analyzed by Galaxy project (usegalaxy.org). The genes were counted by htseq package in galaxy project, and the differentially expressed genes were compared by edgeR package in galaxy project.
Assembly: homo sapiens hg38
Supplementary files format and content: txt format, contain gene ensg number and expression

growth_protocol: Cells were cultured in pericyte special medium contaning 1% penicillin/streptomycin in a humidified chamber under 5% CO2 at 37 °C.

treatment_protocol: Cells were transduced with non-targeting shRNA or shRNA targeting GPR124

value: GPR124 knockdown

value: pericyte differentiation


title: shGPR124_1


title: shNT_1


title: shNT_2


title: HEK293T cell mRNA by HieffNGS kit repeat1

source_name: kidney

value: kidney

value: embryonic kidney cell

value: HEK293T cell mRNA by HieffNGS kit


title: HEK293T cell mRNA by SHERRY repeat3

value: WT

value: HEK293T cell mRNA by SHERRY


title: HEK293T cell mRNA by HieffNGS kit repeat3


title: HEK293T cell mRNA by HieffNGS kit repeat2


title: Phi29 DNA ploymerance I extension enzyme repeat4


title: Phi29 DNA ploymerance I extension enzyme repeat2


title: HEK293T cell mRNA by SHERRY repeat2


title: HEK293T cell mRNA by SHERRY repeat1


title: RNA  fragment, new Random octamer and 18 cycle PCR repeat2


title: RNA  fragment, new Random octamer and 18 cycle PCR repeat4


title: RNA  fragment, new Random octamer and 18 cycle PCR repeat3


title: Phi29 DNA ploymerance I extension enzyme repeat1


title: RNA  fragment, new Random octamer and 20 cycle PCR repeat3


title: RNA  fragment, new Random octamer and 20 cycle PCR repeat2


title: RNA  fragment, new Random octamer and 20 cycle PCR repeat1


title: RNA  fragment, new Random octamer and 20 cycle PCR repeat4


title: RNA  fragment and new Random octamer primer repeat3


title: RNA  fragment, new Random octamer and 18 cycle PCR repeat1


title: RNA  fragment and new Random octamer primer repeat4


title: RNA  fragment and Random octamer primer repeat3

value: RNA  fragment and Random octamer primer


title: RNA  fragment and new Random octamer primer repeat1


title: RNA  fragment and new Random octamer primer repeat2


title: RNA  fragment and Random octamer primer repeat2


title: RNA  fragment and Random octamer primer repeat1


title: Phi29 DNA ploymerance I extension enzyme repeat3


title: RNA no fragment and Random hexamer primer repeat4


title: RNA no fragment and Random octamer primer repeat2


title: RNA no fragment and Random octamer primer repeat3


title: RNA no fragment and Random octamer primer repeat4


title: Bsu DNA ploymerance I extension enzyme repeat4

value: Bsu DNA ploymerance  extension enzyme


title: no Rnase H treatment repeat3

value: no Rnase H treatment


title: Bsu DNA ploymerance I extension enzyme repeat3


title: no Rnase H treatment repeat1


title: Bsu DNA ploymerance I extension enzyme repeat1

description: HS_DADCvsSHERRYvsHieff_matrix.txt/HS_optimize_matrix.txt


title: RNA no fragment and Random hexamer primer repeat1


title: RNA no fragment and Random octamer primer repeat1


title: no Rnase H treatment repeat4


title: E.coli DNA ploymerance I extension enzyme repeat3


title: E.coli DNA ploymerance I extension enzyme repeat1


title: RNA  fragment and Random octamer primer repeat4


title: WGBS_HEK293_TNRC18_MUT_W2858A_rep1

city: CHAPEL HILL

first: Gang

middle: Greg

last: Wang

state: North Carolina

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: UNC chapel hill

data_processing:
Raw reads were mapped using the DRAGEN Methylation app with duplicate read detection enabled. Simultaneously, MethylKit compatible Cytosine Report was produced for each sample. All the Dragen stats were aggregated into a single MultiQC report using Dragen FastQC+MultiQC App. The report includes stats for FastQC, mapping, duplicate reads, and M-bias. For each pair of samples in each group, the differential methylation analysis was performed by extracting relevant cytosine context CpG from the genome-wide cytosine report. From the resulting files, the reads with coverage of less than 10 were filtered out to retain high confidence, and methylation counts. The counts were then normalized. For further analysis bases covered in all the samples were retained.
Assembly: hg19
Supplementary files format and content: Cytosine Report (The cytosine report contains methylation status for every cytosine in the genome, including both strands.)

growth_protocol: HEK293 cells were cultured and maintained in the DMEM base medium supplemented with 10% of FBS and 1% of antibiotics (penicillin and streptomycin). A routine examination of cell lines in culture for any possible mycoplasma contamination was performed every month with MycoAlert PLUS Mycoplasma Detection Kit (Lonza, #LT27-286). Cells at a passage of less than ten were used in this study.

extract_protocol:
Genomic DNA was purified using PureLink Genomic DNA kit (Invitrogen).
DNA bisulfite treatment was performed using an EZ DNA Methylation-Gold kit (Zymo Research #D5005) according to the manufacturer’s instructions. The recovered bisulfite-converted single-stranded DNA was processed for library construction using an Accel-NGS@Methyl-seq DNA Library kit (Swift BioSciences #30024) per the manufacturer’s instructions. DNA was then enriched using PCR with primers compatible with Illumina sequencing. The quantity and molecular size of the library were confirmed with a Qubit HS DNA assay (ThermoFisher) and a Tapestation 2200 system coupled with High Sensitivity D1000 ScreenTapes (Agilent).

treatment_protocol: HEK293 cells used in this work included parental cells and those carrying the CRISPR-cas9-based KI mutation (W2858A) at TNRC18’s H3K9me3-binding BAH domain. Cell lines with homozygous mutation were validated at both DNA and RNA levels by Sanger sequencing of PCR products that cover the mutation site.

value: Human embryonic kidney

value: TNRC18 BAH mutant, W2858A

value: CRISPR-Cas9 knock-in, TNRC18 W2858A


title: WGBS_HEK293_TNRC18_MUT_W2858A_rep2


title: WGBS_HEK293_TNRC18_MUT_W2858A_rep3


title: WGBS_HEK293_TNRC18_WT_rep1

value: TNRC18 WT


title: WGBS_HEK293_TNRC18_WT_rep3


title: WGBS_HEK293_TNRC18_WT_rep2


title: HT29_TNRC18KO_rep3

description: total RNA, rRNA depletion

data_processing:
The fastq files of RNA-seq data were aligned to the GRCh38 human genome (GRCh38.d1.vd1.fa) by using STAR v2.4.2 with the following parameters: --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM. Then, transcript abundance for each sample was estimated with salmon V1.4.0 to quantify the transcriptome defined by Gencode v22. QC was performed using the Picard 2.22.4 CollectRnaSeqMetric and FastQC 0.11.9. Gene level counts were summed across isoforms, and genes with low counts (maximum expression < 10) were filtered out from the downstream analyses. We tested genes for differential expression in DESeq2 v1.38.2 in R and gene set enrichment analysis (GSEA) on Molecular Signatures Database (MsigDB) C2 curated genesets was conducted with GSVA v1.30.1 in R.  To comprehensively quantify expression by all repetitive elements including transposable elements (TEs) in RNA-seq data, we used REdiscoverTE (v1.0.1) which annotates the genes defined in Gencode and all RepeatMasker sequences in the human genome down to the TE sub-family level after the repetitive element expression quantification by salmon. TE count matrix was appended to gene expression data matrix for differential expression analysis using DESeq2 and the TE showing significant differential expression is defined by the adjusted p-value less than 0.05 and a log2 value of fold-change greater than 1 in the experimental versus control group (with a basemean value greater than 10).
Assembly: hg38
Supplementary files format and content: normalized abundance measurements

growth_protocol: HEK293 cells were maintained in DMEM base medium supplemented with 10% of FBS and 1% of antibiotics (penicillin and streptomycin). SNU-1 cells were maintained in RPMI1640 base medium supplemented with 10% of FBS and 1% of antibiotics (penicillin and streptomycin). HT-29 cells were maintained in McCoy's 5A base medium supplemented with 10% of FBS and 1% of antibiotics (penicillin and streptomycin). A routine examination of cell lines in culture for any possible mycoplasma contamination was performed every month with MycoAlert PLUS Mycoplasma Detection Kit (Lonza, #LT27-286). Cells at a passage of less than ten were used in this study.

extract_protocol: For RNA-seq, total RNA was extracted using the RNeasy Mini Kit (Qiagen #74106). RNA was first subjected for the on-column digestion by DNase (Qiagen #79254) for 0.5 hours and next prepared by using the NEBNext rRNA Depletion Kit (NEB #E6310L).

treatment_protocol: The Alt-R CRISPR-Cas9 System (purchased from IDT Inc.) in combination with two crRNAs was used to introduce TNRC18 partial deletion or knockout (KO) in cells. The same Alt-R CRISPR-Cas9 System in combination with one crRNA and one single-stranded oligodeoxynucleotide donor (ssODN) was used to introduce TNRC18 knockin (KI) mutation to cells. Preparation and delivery of the CRISPR–Cas9 ribonucleoprotein (RNP) complex (Alt-R CRISPR-Cas9 crRNA:tracrRNA and S.p. HiFi Cas9 Nuclease) and electroporation enhancer (with additional ssODN for introducing the KI mutation) into cells were performed according to the manufacturer’s user guide. Cell lines with TNRC18 KO or homozygous KI mutation were validated at both DNA and RNA levels by Sanger sequencing of PCR products that cover the mutation/deletion site.

value: Human colon adenocarcinoma


title: RNA no fragment and Random hexamer primer repeat3


title: RNA no fragment and Random hexamer primer repeat2


title: HT29_TNRC18KO_rep2

description: total RNA, rRNA depletion


title: no Rnase H treatment repeat2


title: HT29_WT_rep1

description: total RNA, rRNA depletion


title: HT29_WT_rep2

description: total RNA, rRNA depletion


title: HT29_WT_rep3

description: total RNA, rRNA depletion


title: HT29_TNRC18KO_rep1

description: total RNA, rRNA depletion


title: E.coli DNA ploymerance I extension enzyme repeat2


title: Bsu DNA ploymerance I extension enzyme repeat2


title: SNU1_TNRC18KO_rep2

description: total RNA, rRNA depletion

value: Human gastric carcinoma


title: SNU1_TNRC18KO_rep3

description: total RNA, rRNA depletion


title: SNU1_TNRC18KO_rep1

description: total RNA, rRNA depletion


title: E.coli DNA ploymerance I extension enzyme repeat4


title: SNU1_WT_rep3

description: total RNA, rRNA depletion


title: wild type, 40 min, rep2

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description:
TrAEL-seq adaptor 3, Pool 6
T2 - wt (2)

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.47, truncated to a single base and 2kb windows were defined and quantified by correcting for total read counts per million reads mapped.
Assembly: S. cerevisiae (R64-1-1)
Supplementary files format and content: Processed file contains a Probe Report counting the number of TrAEL-seq reads within 2 Kb windows spaced at 200 bp intervals.
Library strategy: TrAEL-seq

source_name: yeast cell

growth_protocol: Yeast Cells were grown in YPD, scynchronized to G1 phase in YPD with alpha factor. Cells were washed with YPD and released into YPD with 200 mM hydroxyurea.

extract_protocol:
Half an agarose plug of 2x10^6 cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µlof indicated TrAEL-seq adaptor (eg. TrAEL-seq adaptor 1 [App]NNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTUGCGCAGGCCATTGGCC[BtndT]GCGCUACACTCTTTCCCTACACGACGCT)) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs with different TrAEL-seq adaptors were pooled into one eppendorf tube (as indicated in Sample description), equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. One third of this solution from ascynhronously dividing wild type cells were spiked into each pool (i.e. T0, T1 and T2 pools). DNA was then ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5 µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2 µl 10 mM dNTPs and 1 µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined.An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

treatment_protocol: T0 timepoint contains cells that are maintained in hydroxyurea. T1 timepoint contains cells 20 min, and T2 timepoint contains cells 40 min after removal of hydroxyurea. Asynchrounously growing wild type yeast cells were collected to be used as a spike in during library preparation.

value: yeast cell

value: wild type

value: HU release (40 min)


title: pol1-1A, 40 min, rep2

description:
TrAEL-seq adaptor 6, Pool 6
T2 - pol1-1A (2)


title: HEK293_TNRC18L760A_rep3

description: total RNA, rRNA depletion


title: SNU1_WT_rep2

description: total RNA, rRNA depletion


title: SNU1_WT_rep1

description: total RNA, rRNA depletion


title: HEK293_TNRC18L760A_rep2

description: total RNA, rRNA depletion


title: Asynchronous wild type, Spike-in for 40 min, rep2

description:
TrAEL-seq adaptor 5, Pool 6
T2 - Asynchronous wt (2)

value: Spike-in


title: mrc1-AQ cdc45-2A pol1-1A, 20 min, rep2

description:
TrAEL-seq adaptor 8, Pool 5
T1 - pol1-1A mrc1-AQ cdc45-2A (2)

value: mrc1-AQ cdc45-2A pol1-1A

value: HU release (20 min)


title: mrc1-AQ cdc45-2A, 20 min, rep2

description:
TrAEL-seq adaptor 7, Pool 5
T1 - mrc1-AQ cdc45-2A (2)

value: mrc1-AQ cdc45-2A


title: wild type, 20 min, rep2

description:
TrAEL-seq adaptor 3, Pool 5
T1 - wt (2)


title: HEK293_TNRC18L760A_rep1

description: total RNA, rRNA depletion


title: pol1-1A, 20 min, rep2

description:
TrAEL-seq adaptor 6, Pool 5
T1 - pol1-1A (2)


title: HEK293_TNRC18KO_rep3

description: total RNA, rRNA depletion


title: HEK293_TNRC18KO_rep2

description: total RNA, rRNA depletion


title: Asynchronous wild type, Spike-in for 20 min, rep2

description:
TrAEL-seq adaptor 5, Pool 5
T1 - Asynchronous wt (2)


title: mrc1-AQ cdc45-2A pol1-1A, 0 min, rep2

description:
TrAEL-seq adaptor 8, Pool 4
T0 - pol1-1A mrc1-AQ cdc45-2A (2)

value: HU block


title: mrc1-AQ cdc45-2A pol1-1A, 40 min, rep2

description:
TrAEL-seq adaptor 8, Pool 6
T2 - pol1-1A mrc1-AQ cdc45-2A (2)


title: HEK293_TNRC18KO_rep1

description: total RNA, rRNA depletion


title: mrc1-AQ cdc45-2A, 40 min, rep2

description:
TrAEL-seq adaptor 7, Pool 6
T2 - mrc1-AQ cdc45-2A (2)


title: HEK293_WT_rep3

description: total RNA, rRNA depletion


title: pol1-1A, 0 min, rep2

description:
TrAEL-seq adaptor 6, Pool 4
T0 - pol1-1A (2)


title: HEK293_WT_rep2

description: total RNA, rRNA depletion


title: mrc1-AQ cdc45-2A, 0 min, rep2

description:
TrAEL-seq adaptor 7, Pool 4
T0 - mrc1-AQ cdc45-2A (2)


title: wild type, 0 min, rep2

description:
TrAEL-seq adaptor 3, Pool 4
T0 - wt (2)


title: mrc1-AQ cdc45-2A pol1-1A, 40 min, rep1

description:
TrAEL-seq adaptor 6, Pool 3
T2 - pol1-1A mrc1-AQ cdc45-2A (1)


title: Asynchronous wild type, Spike-in for 0 min, rep2

description:
TrAEL-seq adaptor 5, Pool 4
T0 - Asynchronous wt (2)


title: HEK293_WT_rep1

description: total RNA, rRNA depletion


title: FF8FCF.M0.PAX

city: Durham

first: Matthew

middle: Scott

last: Kelly

state: NC

address: 3 Genome Court, MSRB3, Room 4200

department: Pediatrics

institute: Duke University

data_processing:
Raw sequencing reads were checked for quality using FastQC v0.11.9 and trimmed using Trimmomatic v0.39 with the following parameters in the command line: PE; threads 16; phred33; path/sampleid_R1.fastq.gz path/sampleid_R2.fastq.gz; ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True; LEADING:3; TRAILING:3; SLIDINGWINDOW:4:15; MINLEN:36
Genome index files were generated using STAR v2.7.1b with parameters in the command line: runMode: genomeGenerate; runThreadN: 16; genomeDir: path/index; genomeFastaFiles: path/GRCh38.primary_assembly.genome.fa; sjdbGTFfile: path/gencode.v43.basic.annotation.gtf; sjdbOverhang 100
Reads were mapped to the genome using STAR v2.7.1b with parameters in the command line: quantMode: GeneCounts; genomeDir: path/index; runThreadN: 16; readFilesIn: path/sampleid_R1.fastq.gz path/sampleid_R2.fastq.gz; outFileNamePrefix: path/sampleid; readFilesCommand: gunzip -c; outSAMtype BAM SortedByCoordinate; outSAMunmapped Within; outSAMattributes Standard
Assembly: Homo_sapiens.GRCh38 (https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/GRCh38.primary_assembly.genome.fa.gz and https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.basic.annotation.gtf.gz)
Supplementary files format and content: csv file containing raw read counts

source_name: Whole blood

extract_protocol:
Total RNA was extracted from nasal and nasopharyngeal swabs using QIAsymphony RNA kits and from peripheral blood preserved in PAXgene Blood RNA tubes using QIAGEN PAXgene miRNA Extraction Kits according to manufacturer's instructions.
Libraries were prepared using TECAN Universal Plus mRNA-seq with AnyDeplete Globin Kits according to manufacturer's instructions.
Libraries were sequenced on an Illumina NovaSeq 6000 instrument as 100 bp PE reads.

value: Whole blood

tag: subject id

tag: batch

tag: sample timing

value: acute

tag: Sex

value: Female

tag: covid

value: Negative

tag: covid cat

tag: research pcr

tag: vl copies

tag: hospitalized

value: No

tag: year

tag: vaccine doses

tag: timing sx

tag: timing dx


title: FF27EC.M0.PAX

tag: tissue

tag: age

value: Male

value: Positive


title: FE81C5.M0.PAX

value: healthy

value: Not Tested


title: mrc1-AQ cdc45-2A, 40 min, rep1

description:
TrAEL-seq adaptor 5, Pool 3
T2 - mrc1-AQ cdc45-2A (1)

tag: cell type

value: yeast cell

tag: genotype

tag: treatment


title: FDE02B.M0.PAX

tag: subject id

tag: batch


title: FB394D.M0.PAX

tag: sample timing

tag: Sex


title: Asynchronous wild type, Spike-in for 40 min, rep1

description:
TrAEL-seq adaptor 7, Pool 3
T2 - Asynchronous wt (1)

value: wild type


title: F9170E.M0.PAX

tag: covid

tag: covid cat


title: wild type, 40 min, rep1

description:
TrAEL-seq adaptor 1, Pool 3
T2 - wt (1)

value: HU release (40 min)


title: pol1-1A, 40 min, rep1

description:
TrAEL-seq adaptor 3, Pool 3
T2 - pol1-1A (1)


title: F126CE.M0.PAX

tag: research pcr

tag: vl copies


title: mrc1-AQ cdc45-2A pol1-1A, 20 min, rep1

description:
TrAEL-seq adaptor 6, Pool 2
T1 - pol1-1A mrc1-AQ cdc45-2A (1)


title: mrc1-AQ cdc45-2A, 20 min, rep1

description:
TrAEL-seq adaptor 5, Pool 2
T1 - mrc1-AQ cdc45-2A (1)


title: pol1-1A, 20 min, rep1

description:
TrAEL-seq adaptor 3, Pool 2
T1 - pol1-1A (1)


title: EE435A.M0.PAX

tag: hospitalized

tag: year


title: EB2A47.M0.PAX

tag: vaccine doses

tag: timing sx


title: wild type, 20 min, rep1

description:
TrAEL-seq adaptor 1, Pool 2
T1 - wt (1)


title: Asynchronous wild type, Spike-in for 20 min, rep1

description:
TrAEL-seq adaptor 7, Pool 2
T1 - Asynchronous wt (1)

value: Spike-in


title: E674EB.M0.PAX

tag: tissue

tag: timing dx


title: E60E94.M0.PAX

tag: age


title: mrc1-AQ cdc45-2A pol1-1A, 0 min, rep1

description:
TrAEL-seq adaptor 6, Pool 1
T0 - pol1-1A mrc1-AQ cdc45-2A (1)

tag: cell type

tag: genotype

value: mrc1-AQ cdc45-2A pol1-1A


title: E48FF4.M0.PAX

tag: subject id


title: E410D2.M0.PAX

tag: batch


title: E24969.M0.PAX

tag: sample timing


title: DA8A0E.M0.PAX

tag: Sex


title: mrc1-AQ cdc45-2A, 0 min, rep1

description:
TrAEL-seq adaptor 5, Pool 1
T0 - mrc1-AQ cdc45-2A (1)

tag: treatment


title: Asynchronous wild type, Spike-in for 0 min, rep1

description:
TrAEL-seq adaptor 7, Pool 1
T0 - Asynchronous wt (1)


title: wild type, 0 min, rep1

description:
TrAEL-seq adaptor 1, Pool 1
T0 - wt (1)


title: pol1-1A, 0 min, rep1

description:
TrAEL-seq adaptor 3, Pool 1
T0 - pol1-1A (1)


title: D48DAF.M0.PAX

tag: covid

tag: covid cat


title: D95609.M0.PAX

tag: research pcr

tag: vl copies


title: D30537.M0.PAX

tag: hospitalized

tag: year


title: D11595.M0.PAX

tag: vaccine doses

tag: timing sx


title: C6A33E.M0.PAX

tag: tissue

tag: timing dx


title: C795F1.M0.PAX

tag: age


title: C1F457.M0.PAX


title: C5190E.M0.PAX


title: D47359.M0.PAX


title: B33581.M6.PAX


title: B480DD.M0.PAX


title: B2905A.M0.PAX


title: ADAF6C.M0.PAX


title: B1FE00.M0.PAX


title: ABD53F.M0.PAX


title: A97D5B.M0.PAX


title: AB9A75.M0.PAX


title: A8FD53.M0.PAX


title: 9FAB68.M0.PAX


title: 9C0AA4.M0.PAX


title: 990CA3.M0.PAX


title: 9E259D.M0.PAX


title: 8FDB69.M0.PAX


title: 8F0016.M0.PAX


title: 88732B.M0.PAX


title: 8867DF.M0.PAX


title: 85F0AB.M0.PAX


title: C9EEEA.M0.PAX


title: 8655BF.M0.PAX


title: 830937.M0.PAX


title: 7D880A.M0.PAX


title: 6AA2F7.M0.PAX


title: 58A568.M0.PAX


title: 71549F.M0.PAX


title: 496933.M0.PAX


title: 826E5F.M0.PAX


title: 3B441F.M0.PAX


title: 5217A5.M0.PAX


title: 3501A9.M0.PAX


title: 234BBF.M0.PAX


title: 322088.M0.PAX


title: 1AC6B8.M0.PAX


title: 22D142.M0.PAX


title: 88B192.M0.PAX


title: 12CE1E.M0.PAX


title: 18EF5E.M0.PAX


title: 8CF0CC.M0.PAX


title: 1E06CA.M0.PAX


title: 17A783.M0.PAX


title: 150B4B.M0.PAX


title: 0BF51C.M6.PAX


title: 0E1ECA.M0.PAX


title: 025CBE.M0.PAX


title: 0719FA.M0.PAX


title: ZY4788.M0.PAX


title: 72C971.M0.PAX


title: 7400BF.M0.PAX


title: 0BF51C.M0.PAX


title: ZQ4859.M0.PAX


title: ZS4446.M0.PAX


title: ZQ3518.M0.PAX


title: ZO9902.M1.PAX


title: ZF0029.M0.PAX


title: ZO9902.M0.PAX


title: ZD3287.M0.PAX


title: ZC8626.M0.PAX


title: ZC2922.M0.PAX


title: YQ1674.M0.PAX


title: YX3199.M0.PAX


title: YH5235.M0.PAX


title: YH1847.M0.PAX


title: YD8439.M0.PAX


title: XW2354.M0.PAX


title: YF5006.M0.PAX


title: XT5859.M0.PAX


title: XU1619.M0.PAX


title: XM2821.M0.PAX


title: WQ7051.M0.PAX


title: VZ0734.M0.PAX


title: WB1507.M0.PAX


title: WM7261.M0.PAX


title: ZG9202.M0.PAX


title: VV9796.M0.PAX


title: VT3754.M0.PAX


title: VI0592.M0.PAX


title: LAS256A1716

city: London

first: Vassilis

last: Pachnis

address: 1 Midland Rd

department: Development and Homeostasis of the Nervous System Laboratory

institute: The Francis Crick Institute

data_processing:
Reads were aligned to the Ensembl GRCm38 genome using Tophat2.
Transcript counts, including counts for spliced and unspliced reads were obtained using the program Velocyto.
Quality control, normalisation and downstream analysis were performed using the software SCANPY.
Cells expressing more than 2000 genes and less than 10 percent mitochondrial genes were retained for further analysis. Contaminating epithelial cells (n = 9) were filtered from the data based on Cdh1 counts (>= 10 counts). Likewise, mesenchymal cells (n = 39) were filtered based on the expression of the marker Meis2 (>= 10 counts) and macrophages (n = 6) were filtered using expression of the marker Cd14 (>= 10 counts). After filtering 904 cells were retained, 143 cells (E13.5), 20 cells (E12.5 → E15.5), 129 cells (E17.5), 432 cells (P1), 11 cells (P26) and 169 cells (P61).
Genes detected in fewer than 3 cells or with total counts < 10 were omitted from further analysis (23299 genes were retained). Counts were normalised to counts per million (CPM) and log transformed (after the addition of a pseudocount of 1).
Counts were normalized to 1 million counts per cell, natural-log transformed using log1p, and scaled.
2954 genes identified as taking part in gene modules identified using the Antler algorithm were used as input for PCA analysis in SCANPY. The first 15 PCs were selected for dimensionality reduction and clustering using the Louvain algorithm (resolution 1.5). The resulting clustering was manually curated and those clusters with similar transcriptional profiles that separated purely based on the expression of cell-cycle associated markers were merged.
Assembly: GrCM38
Supplementary files format and content: Scanpy object containing normalised data and UMAP. Matrices containing spliced and unspliced counts (CSV format). Gene and cell metadata (CSV format).

source_name: Enteric nervous system

growth_protocol: Mice used in this study were maintained according to standard practices and all procedures were approved by The Francis Crick Institute Animal Ethics Committee and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.

extract_protocol:
Tissue was incubated with Collagenase I (1 mg/ml, Sigma, C0130) for 30-45 min and enzyme activity was terminated by rinsing cells with ice cold PBS. The cell suspension was centrifuged and filtered through 40 μm nylon cell strainers (Falcon, 352340). tdT+ cells were isolated by flow cytometry (BD Biosciences Aria Fusion sorter equipped with Diva V8 software) with a 100 μm nozzle and collected in 2% FBS in OptiMEM without phenol red (Thermo Fisher Scientific, 11058021). Dead cells were excluded by labelling with the cell viability dye Zombie Aqua (2 ng/ml, BioLegend, 423101) that was added to the single cell suspension before sorting. For the P0 stage, we also sorted the cells directly into 96-well plates to increase the yield.
The SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System, IFCs was used to reverse transcribe and amplify cDNA. cDNA was quantified using the Glomax (Promega). Libraries were prepared from cDNA generated from single cells using the Nextera XT kit from Illumina. Final libraries were pooled and sequenced on the HiSeq 4000.

treatment_protocol: All mice were injected with tamoxifen 24 hours prior to single cell isolation apart from E12.5_E15.5 time points (these were injected with tamoxifen 72 hours prior to single cell isolation).

tag: sample type

tag: Stage

tag: strain


title: VF7018.M1.PAX

tag: subject id

tag: batch

tag: sample timing


title: LAS256A1711


title: VF7018.M0.PAX

tag: Sex

tag: covid


title: VB2611.M0.PAX

tag: covid cat

tag: research pcr