title: LCL_P4_EMA

city: Las Vegas

first: Łukasz

middle: J.

last: Sznajder

state: Nevada

address: 4505 S. Maryland Pkwy.

department: Chemistry and Biochemistry

institute: University of Nevada-Las Vegas (UNLV)

description: rRNA depleted total RNA

data_processing:
Basecalling was done using Illumina Real-Time Analysis (RTA) and demultiplexed fastq files were obtained from BaseSpace with BaseMount.
Reads were aligned to the genome assembly GRCh38 (hg38) using STAR.
Salmon was used for transcript expression quantification and differential gene expression analysis was performed using DESeq2.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data files contain the output from the Salmon.

source_name: Lymphoblastoid cell line (LCL)

growth_protocol: Lymphoblastoid cell lines were cultured in RPMI 1640 media supplemented with 15% FBS (ThermoFisher Scientific), 2 mM L-glutamine, Pen/Strep (100 IU/mL, 100 μg/mL), and 1 mM sodium pyruvate.

extract_protocol:
Total RNA from the lymphoblastoid cell lines was isolated using the hot TRIzol extraction protocol. Briefly, samples dissolved in TRIzol were incubated at thermomixer set to 55°C and 1,000 rpm for 10 min. After cooling to ambient temperature, RNA was isolated by using TRIzol Reagent and the Direct-zol RNA MiniPrep Kit with DNase treatment according to manufacturer’s provided protocol (Zymo Research). RNA was quantitated using Qubit RNA BR Assay Kit (Thermo Fisher Scientific).
Strand-specific, rRNA-depleted RNA-seq libraries were prepared using the KAPA Stranded RNA-seq Kit with RiboErase HMR (Kapa Biosystems) per manufacturer’s instructions, except for the use of custom Illumina-compatible index primers to allow multiplexing. Library size distribution was assessed using the High Sensitivity NGS Fragment Analysis Kit (DNF-747) on a Fragment Analyzer (Agilent). 2 × 150 paired-end sequencing was performed using an Illumina NextSeq 500.

value: Lymphoblastoid cell line (LCL)


title: SupT1 infected, RiboSeq, harr, 24hpi, rep2

status: Public on Nov 26 2024

type: SRA

city: Würzburg

first: Neva

last: Caliskan

address: Josef-Schneider-Str. 2/D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

library_source: transcriptomic

data_processing:
For PRICE analysis: (1) remove adapters cutadapt -a AGATCGGAAGAGCACACG -e 0.3 (2)  filter out short reads gedi -e FastqFilter -layout 2UI5U151 -min 18 (3) h.rRNA and mycoplasma removal  bowtie2 -un un --local -U (4) mapping reads STAR --runMode alignReads --alignIntronMax 1  --outSAMmode NoQS --outSAMtype BAM SortedByCoordinate --alignEndsType Extend5pOfRead1 --outSAMattributes nM MD NH (5) Convert BAM to CIT gedi -e BAM2CIT -umi (6) gedi -e CorrectCIT (7) deduplicate UMIs gedi -e DedupUMI (8) gedi -e MergeCIT (9) create report gedi -e Stats (10) P-site calling gedi -e Price
cutadapt 3.5, bowtie2 version 2.3.0, STAR version=2.7.10b, Gedi version 1.0.6, Price version 1.0.4
For differential gene expression analysis: (1) Count reads per genomic feature featureCounts -O (2) normalization and log2 fold change calculations by deltaTE/DTEG.R
featureCounts version 2.0.0, deltaTE (Chothani et al. 2019)
Assembly: GCF_000001405.36, AF324493
Supplementary files format and content: The PRICE codons BED files contain the genomic regions corresponding to predicted P-sites for each RiboSeq read. The "score" column equals to the read coverage at this position.
Supplementary files format and content: The countMatrix CSV files contain the read counts overlapping each genomic feature for every time point of infection for either cyclo RiboSeq or RNASeq.
Supplementary files format and content: The deltaTE text files contain the log2 fold changes (plus statistics) for each genomic feature, normalized by DESeq2 and calculated for each timepoint of infection against the 0h mock sample. This includes RiboSeq changes, RNASeq changes and  translation efficiency (TE) changes.
Supplementary files format and content: The DisomeSeq BED files contain the DisomeSeq reads that map to the HIV genome. The DisomeSeq text files contain the summed coverage per nucleotide for the HIV genome (column1: chromosome identifier; column2: genome position, column3: read coverage).
Supplementary files format and content: PRICE_report_harr_cyclo.tar contains quality control information for the RiboSeq PRICE pipeline, for both the cycloheximide and harringtonine treated samples. The index.html file allows interactive browsing through the different plots.
Supplementary files format and content: PRICE_report_disome.tar contains quality control information for the DisomeSeq PRICE pipeline. The index.html file allows interactive browsing through the different plots. Note that the p-site prediction is not valid for the DisomeSeq.
Supplementary files format and content: interactive_dTE_volcano_plots_DGE.tar contains interactive volcanoplots (translation efficiency) of the differential gene expression analysis with the deltaTE pipeline. Each infection timepoint was compared to the mock sample. Genes exceeding +/- 1 fold change and p_adj < 0.05 are colored based on consolidated gene ontology.
Supplementary files format and content: interactive_deltaTE_plots_DGE.tar contains interactive RiboSeq/RNASeq log2 fold change plots, of the differential gene expression analysis with the deltaTE pipeline. Each infection timepoint was compared to the mock sample. Only genes that are labelled as differentially expressed are plotted.
Library strategy: Ribo-seq

molecule: cytoplasmic RNA

organism:
Homo sapiens
Human immunodeficiency virus 1

growth_protocol: SupT1 cells (NIH HIV Reagent Program, Division of AIDS, NIAID, NIH: Sup-T1 Cells, ARP-100, contributed by Dr. Dharam Ablashi) were maintained in RPMI (Gibco) supplemented 10% FBS (Gibco), 1X L-Glutamine (Gibco), 100 μg/ml streptomycin and 100 U/ml penicillin. Cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Ribosome profiling samples were prepared as previously described (McGlincy and Ingolia., 2017) with modifications for suspension cell lines. Briefly, at each time point of infection, cells were treated with 100 μg/ml cycloheximide in DMSO at 37 °C for 5 min. For harringtonine treated samples, cells were treated with 2 μg/ml harringtonine in DMSO at 37 °C for 5 min, followed by cycloheximide treatment. Cells were immediately pelleted at 1000 RPM for 3 min at 4 °C, washed once with cold cycloheximide containing PBS and the cell pellet was snap-frozen in liquid nitrogen and stored at -80 °C, till further use. Cell pellet was thawed in the presence of ice-cold lysis buffer (20 mM Tris-Cl pH7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml cycloheximide, 1% Triton-X, 25U/ml Turbo DNase ) and triturated 10 times through a 26G needle. The lysate was centrifuged at 17000g for 10 min at 4 °C and the supernatant was recovered. Cell lysates were subjected to RiboSeq and RNASeq.
RiboSeq libraries: RNase I footprinting of ribosomes, ribosome purification by ultracentrifugation through a sucrose cushion, RNA extraction, polyacrylamide gel size selection for footprint fragments, preadenylylated linker ligation, reverse transcription, first-strand cDNA circularization. RNASeq libraries from these samples were constructed using CORALL Total RNA-Seq Library Prep Kit (Lexogen), according to manufacturer’s instructions.

treatment_protocol: For ribosome, disome and polysome profiling experiments, SupT1 cells were either mock treated (with PBS) or infected with 50 µl of virus suspension per 40 million cells by spinoculation at 1500 g for 30 min at 37 °C, in presence of 8 µg/ml polybrene (Sigma). Cells were pelleted at 1000 RPM for 3 min at 37 °C, washed once with warm media, resuspended in 40 ml RPMI medium and incubated at 37 °C.

tag: cell line

tag: cell type

value: T-cell

tag: treatment

value: harringtonine


title: SupT1 infected, DisomeSeq, cyclo, 24hpi, rep2

value: cycloheximide


title: RNAseq_SCd_1

city: Amsterdam

first: William

last: Faller

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Transcript quantifications were done with salmon version 1.1.0 using Gencode vM21 annotation.
mm10
"quant.sf" files are tab-seperated salmon outputs (includes transcript id, transcript length, effective length, TPM and raw_reads as columns).

molecule: polyA RNA

organism: Mus musculus

source_name: intestine

growth_protocol: Small intestinal organoids were generated from intestinal crypts. They were cultured in BME (Amsbio) plugs in ENR media: Advanced Dulbecco’s modified Eagle’s media (DMEM)/F12 (Thermo Fisher Scientific), supplemented with 10mM  HEPES (ThermoFisher Scientific), 1x GlutaMAXTM (Thermo Fisher Scientific), 100 U/ml penicillin, 100µg/ml streptomycin (Thermo Fisher Scientific), 0,1% BSA (Sigma Aldrich), 1x B27 (Thermo Fisher Scientific) and 1x N2 (Thermo Fisher Scientific), together with 10% (v/v) Noggin conditioned media, 10% (v/v) R-spondin conditioned media and 50ng/ml EGF (Peprotech). All organoid lines were kept at 37oC in a humidified atmosphere with 5% CO2.

extract_protocol:
For RNA extraction, cells were collected on ice, washed in PBS and centrifuged at 1000rpm for 5 minutes at 4oC. Pellets were lysed with TRIzolTM Reagent (Thermo Fisher Scientific). RNA was isolated by chloroform extraction followed by centrifugation, isopropanol precipitation, washing in 75% ethanol and resuspension in nuclease-free water.
Libraries were generated with the TrueSeq Stranded mRNA kit (Illumina).

treatment_protocol: Stem cell-depleted cultures (SCd) were obtained when culturing organoids in EN media (depleted of R-spondin) for 2 days.

tag: tissue

value: intestine

value: organoid

tag: genotype

value: stem cell depletion


title: ZH-32-B6

city: Louisville

first: Huang-Ge

last: Zhang

state: KY

address: 505 S Hancock Street

department: James Graham Brown Cancer Center

country: USA

institute: University of Louisville

description: 16s rRNA

data_processing:
3 μL of each library was pooled together into one tube.
The pooled library concentration was measured in ng/μL using the Qubit DNA HS assay.
Quality of the pooled library was checked using a Bioanalyzer. Size was measured at 636bp.
The pooled library was diluted to 10 nM using 10 mM Tris-HCl pH 8.5 0.1% Tween 20 buffer.
Sequencing was done on a Nano-300 cycle test chip (MS-103-1001) to confirm coverage of all libraries. Libraries with low reads were spiked in at higher concentrations to increase coverage. The re-pooled library was then ran on the MiSeq using an Illumina MiSeq Reagents kit v3 (600 cycles) (MS-102-3003) at 10 pM set at the below parameters according to kit instructions:
Supplementary files format and content: The 77 paired-end raw sequencing files (.fastq) representing two groups were generated in Genomics facility core, Univeristy of Louisville and downloaded from Illumina’s BaseSpace (https://basespace.illumina.com/) onto the KBRIN server for analysis using the script
Supplementary files format and content: The samples was further trimmed and analyzed using QIIME 2
Supplementary files format and content: The relative abundances of specific bacteria indicated in the file of 16s seq processing data Hu were generated by each toxonomic raw reads divided by whole reads on all samples
Library strategy: 16s rRNA sequencing

molecule: total RNA

organism: feces metagenome

source_name: Faeces

extract_protocol:
Fecal DNA extract from 5 g feces of human using the QIAamp DNA Stool Mini Kit (Qiagen) according the instruction of manufactory.
QIAseq 16S/ITS 96-Index I (384) (Cat# 333825) and QIAseq 16S/ITS Screening Panel (24) (Cat# 333812)

treatment_protocol: No treatment

tag: source

value: Mouse gut


title: ZH-31-B6

description: 16s rRNA


title: cut&tag,IgG

city: Nanjing

first: Hongzhen

last: Li

state: Jiangsu

address: No. 321 Zhongshan Road, Nanjing, Jiangsu, 210008, China

country: China

institute: The Affiliated Hospital of Nanjing University Medical School

library_source: genomic

data_processing:
Paired-end reads were aligned with Homo sapiens. GRCh38 genome using Bowtie2.
Peaks were called using MACS v2.2.6, and the bam files were converted to bigWiggle files using deeptools.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Panc1 cells were maintained in DMEM supplemented with 10% FBS and antibiotics atmosphere with 5% CO2 at 37℃.

extract_protocol:
50000 control or IGF1-treated panc1 cells were submitted for Cut&Tag analysis. c-JUN antibody was used to purify DNA fragments that bind to cjun. libraries were constructed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Nanjing, China, #TD903) according to the manufacturer’s protocol.
Paired-end libraries were prepared and sequenced on an Illumina NovaSeq6000 platform

treatment_protocol: Panc1 cells were serum-free starved for 12 hours and treated with or without IGF1 for 12 hours.

value: pancreatic cancer cells


title: LCL_P5_EM

description: rRNA depleted total RNA


title: SupT1 infected, RiboSeq, harr, 24hpi, rep1


title: WT_Input

city: 上海

first: 润华

last: 杜

address: 上海市浦东新区

institute: 上海药物所

data_processing:
ChIP-seq reads were mapped to reference genome of Illumina iGenomes UCSC hg38 using Bowtie (version 2.2.6), and only the uniquely mapped reads were retained
SAMtools (version 0.1.19) was then used to convert files to bam format, sort, and remove PCR duplicates
Peaks were called using MACS2 (version 2.1.1) with FDR = 0.01
Assembly: hg38
Supplementary files format and content: bigWig,broadPeak(except for Input sample)

source_name: brain

extract_protocol:
Two groups with 3 biological replicates were used for sample preparation, which is performed by SimpleChIP Enzymatic Chromatin IP Kit with magnetic beads
DNA fragments were repaired, A-tailed for DNA library construction using TruSeq ChIP Library Preparation Kit by Novogene company

value: brain

value: human glioblastoma

value: shSUCLG1 rSUCLG1 WT


title: LCL_P1_E

description: rRNA depleted total RNA


title: ZH-30-B6

description: 16s rRNA


title: ZH-29-B6

description: 16s rRNA


title: LCL_P3_EM

description: rRNA depleted total RNA


title: WT_ChIP_3

tag: antibody

value: L-Lactyl-Histone H3


title: WT_ChIP_2


title: SupT1 infected, RiboSeq, harr, 16hpi, rep2


title: LCL_WT1

description: rRNA depleted total RNA


title: SupT1 infected, RiboSeq, harr, 16hpi, rep1


title: SupT1 infected, RiboSeq, harr, 8hpi, rep2


title: cut&tag, Control,rep1

value: c-JUN


title: ZH-28-B6

description: 16s rRNA


title: WT_ChIP_1


title: LCL_P6_EMA

description: rRNA depleted total RNA


title: ZH-27-B6

description: 16s rRNA


title: K192R_Input

value: shSUCLG1 rSUCLG1 K192R


title: ZH-64-B6

description: 16s rRNA


title: SupT1 infected, RiboSeq, harr, 8hpi, rep1


title: LCL_P8_EA_der-Chr9

description: rRNA depleted total RNA


title: K192R_ChIP_3


title: LCL_P7_EA

description: rRNA depleted total RNA


title: ZH-61-B6

description: 16s rRNA


title: K192R_ChIP_2


title: ATAC siPKN1-DF_2

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus human genome version hg38 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 2.21.7 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 2.1.1 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Remaining peaks were unified to represent a common set of regions for all samples and counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.26.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 104.
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts of unified peaks.

source_name: umbilical cord

extract_protocol:
In brief, 50,000 cells were centrifuged at 500g for 5 min at 4°C and washed with PBS.
The Cell pellet was resuspended in 50µl Lysis/Transposition reaction (12.5µl THS-TD-Buffer, 2.5µl Tn5, 5µl 0.1% Digitonin and 30µl water) and incubated at 37°C for 30min with occasional snap mixing. Following purification of the DNA fragments was done by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing Primers was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced (Illumina).

value: umbilical cord

value: HUAEC

value: Human Umbilical Artery Endothelial Cells

value: Healthy

tag: sirna

tag: flow

value: Disturbed Flow


title: K192R_ChIP_1


title: SupT1 infected, RiboSeq, cyclo, 16hpi, rep2

value: T-cell

value: cycloheximide


title: SupT1 infected, RiboSeq, cyclo, 24hpi, rep1


title: ATAC siPKN1-DF_1


title: ZH-55-B6

description: 16s rRNA


title: ZH-88-Hu

description: 16s rRNA

value: Human gut


title: ATAC siPKN1-Static_2

value: Static


title: SupT1 infected, RiboSeq, cyclo, 8hpi, rep2


title: SupT1 infected, RiboSeq, cyclo, 16hpi, rep1


title: Control4

city: Shanghai

first: Jing

address: No.241, west huaihai road, Xuhui district

department: Department of Cardiovascular Surgery

institute: Shanghai Chest Hospital, Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each cell

source_name: Ascending aorta

extract_protocol:
Testicular immune cell were sorted CD45+ cells with BD FACS
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: Ascending aorta

tag: disease

value: normal control

tag: gender

value: Male

tag: age

tag: disease state

value: healthy donors for heart transplantation


title: ZH-87-Hu

description: 16s rRNA


title: SupT1 infected, RiboSeq, cyclo, 8hpi, rep1


title: ATAC siPKN1-Static_1


title: ATAC CTRL-DF_1

value: CTRL


title: pif4-2 npr1-1-R3-red

city: Peking

first: Zhou

last: yangyang

state: Peking

address: West Campus of China Agricultural University, Haidian District, Beijing

institute: China Agriculture University

data_processing:
The clean data were aligned to the Arabidopsis Col-0 genome (TAIR10) using the HISAT2 program with default parameters.
Differentially expressed genes (DEGs) were identified using the DESeq2 package in R.
Assembly: TAIR10.1
Supplementary files format and content: Comma-Separated Values file includes raw counts for each sample

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seeds were first surface-sterilized with 0.5% NaClO solution containing 0.02% Triton X-100 for 10 minutes, then washed six times with sterilized water, stratified at 4℃ for 2 days, and grown on MS plates containing 1% sucrose at 22°C under continuous blue (5 μmol m–2 s–1) or red (15 μmol m–2 s–1)  light.

extract_protocol:
100 mg 4-day-old seedlings collected in the dark (dim green light), Total RNA was extracted  using the TaKaRa MiniBEST Plant RNA Extraction Kit (Takara, Cat. # 9769) according to the manufacturer's instructions.
The library construction was carried out by BGI (Beijing Genomics Institute)

treatment_protocol: 4-day-old seedlings grown in continuous blue or red light

value: seedlings

tag: ecotype

value: pif4-2 npr1-1

value: grown in continuous red light


title: Control2


title: ZH-86-Hu

description: 16s rRNA


title: ATAC CTRL-Static_2

value: umbilical cord


title: K562 35Ab 5M

city: Pasadena

first: Isabel

last: Goronzy

state: CA

address: 1200 E California Blvd

department: Biology and Biological Engineering

institute: California Institute of Technology

data_processing:
Adapters were trimmed from raw paired-end fastq files using Trim Galore! v0.6.2 and assessed with Fastqc v0.11.9. The split-and-pool barcodes of trimmed reads were identified from Read 2 with Barcode ID v1.2.0 (https://github.com/GuttmanLab/sprite2.0-pipeline) and the ligation efficiency is assessed. Reads with a DPM barcode or an antibody-identifying oligonucleotide sequence were split into two separate files. Subsequently, the DPM and antibody-identifying oligonucleotide sequences are trimmed using Cutadapt v2.5 from the 5’ end of Read 1.
DNA reads were aligned to mm10 or hg38 using Bowtie2 v2.3.5, filtering out unmapped reads and reads with a low MapQ score (samtools view -bq 20).  Reads intersecting ENCODE blacklisted regions were filtered out using Bedtools v2.29.0.
Antibody-identifying oligonucleotide reads and mapped DNA reads were merged to generate a cluster file for all downstream analysis. MultiQC v1.6 was used to aggregate all reports.
Each cluster in the cluster file was assigned to a single antibody based on the antibody-identifying oligonucleotide reads within the cluster (minimum reads > 2, minimum proportion > 0.8). All DNA reads corresponding to clusters assigned to the same antibody were collected into a single alignment file.
Bigwig files were generated from individual antibody DNA alignment files using deeptools v3.4.3
Assembly: mm10, hg38
Supplementary files format and content: Bigwig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After cell lysis, chromatin was sonicated using a Branson needle-tip sonicator.
Prior to immunoprecipitation, Protein G beads were coupled with unique antibody identifying oligonucleotides and the corresponding antibodies. Protein-chromatin complexes were isolated from prepared chromatin with a heterogenous pool of these oligonucleotide-labeled, antibody-coupled Protein G beads.  After immunoprecipitation, DNA ends were repaired and dA-tailed to generate a protruding 3’ A. Split-and-pool barcoding was performed to associate IP'd DNA molecules with the antibody-identifying oligonucleotide on the same Protein G bead. Crosslinks were reversed, the DNA was isolated and the DNA was amplified 8-12 cycles using standard Illumina library prep (dual index). The PCR products were purified using SPRI beads and gel cut.

value: Human lymphoblastic cells

tag: chip antibody

value: See supplemental file


title: ZH-85-Hu

description: 16s rRNA


title: ATAC CTRL-Static_1

value: HUAEC

value: Human Umbilical Artery Endothelial Cells

value: Healthy


title: ZH-58-B6

description: 16s rRNA

value: Mouse gut


title: Control3


title: Control1


title: SupT1 infected, RiboSeq, cyclo, 24hpi, rep2

value: T-cell

value: cycloheximide


title: pif4-2 npr1-1-R1-red


title: ZH-84-Hu

description: 16s rRNA

value: Human gut


title: ZH-83-Hu

description: 16s rRNA


title: siPKN1-DF_2

data_processing:
Raw data were checked for quality, adapter content and duplication rates using FastQC.
Trimmomatic version 0.39 was used to trim reads after a drop in quality below a mean value of Q15 in a window of 5 nucleotides. Only reads above 15 nucleotides were released for further analysis.
Trimmed and filtered reads were aligned with STAR 2.6.1d against the Ensembl human genome version hg38 (Ensembl release 104), using STAR 2.7.3a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10 %.
Multi-mapping reads were excluded.
The number of reads aligned to genes was counted using featureCounts 1.6.4 from the subread package. Only reads that map at least partially within exons were allowed and aggregated per gene. Reads overlapping with multiple genes or aligned to multiple regions were excluded.
The raw count matrix was normalized with DESeq2 version 1.18.1.
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

extract_protocol:
RNA was extracted from HUAECs using the miRNeasy Micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen). RNA and library preparation integrity were verified using the LabChip Gx Touch 24 (Perkin Elmer).
3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina). Sequencing was performed on NextSeq500 instrument (Illumina).

value: Disturbed Flow


title: ATAD4

value: Ascending aorta

value: acute thoracic aortic dissection

value: Male

value: acute thoracic aortic dissection patients


title: npr1-1-R3-red

value: seedlings


title: pif4-2 npr1-1-R2-red

value: pif4-2 npr1-1

value: grown in continuous red light


title: siPKN1-DF_1

value: umbilical cord


title: ATAD5


title: ZH-82-Hu

description: 16s rRNA


title: ATAD3


title: siPKN1-Static_2

value: Static


title: ZH-81-Hu

description: 16s rRNA


title: npr1-1-R1-red


title: ATAD2


title: npr1-1-R2-red


title: siPKN1-Static_1

value: HUAEC


title: ZH-07-Hu

description: 16s rRNA


title: pif4-2-R3-red


title: ATAD1


title: CTRL-DF_2

value: Human Umbilical Artery Endothelial Cells

value: CTRL


title: pif4-2-R2-red


title: CTRL-DF_1

value: Healthy


title: pif4-2-R1-red


title: ZH-04-Hu

description: 16s rRNA


title: HT22_NR3C1_2nd

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2 Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: NR3C1 overexpression in HT22 cell

growth_protocol: HT22 cells (CL-0595, Procell Life Science & Technology Co., Ltd.,China) were cultured at 37 ℃ in DMEM with 5% CO2, 10% fetal bovine serum (164210, Procell Life Science & Technology Co., Ltd.,China), 100 µg/mL streptomycin, and 100 U/mL penicillin (SV30010, Hyclone).

extract_protocol:
TRIzol Reagent (Invitrogen, US) was used to extract total RNA from cells. To remove the residual DNA, total RNA samples was treated with RQ1 DNase (Promega). The purity and concentration of the resulting RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1 μg of total RNA was used to prepare RNA-seq library via KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (#KK8544). Polyadenylated mRNAs were purified by VAHTS mRNA capture Beads (N401-01) and fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726). Products corresponding to 300-500bps were amplified, purified, quantified, and stored at -80 ℃, followed by sequencing. The strand marked with dUTP (the 2nd cDNA strand) was not amplified, allowing strand-specific sequencing.

treatment_protocol: HT22 cells were transfected with pIRES-hrGFP-1a-NR3C1 and empty vectors (control) by Lipofectamine 2000 (11668019, Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48h for RT-qPCR analysis. The overexpression of NR3C1 in HT22 cells via plasmid transfection was verified RT-qPCR. Briefly, standard procedures were followed to obtain the cDNA and RT-qPCR was performed on the Bio-Rad S1000 with Bestar SYBR Green RT-PCR Master Mix (DBI Bioscience, Shanghai, China).

value: NR3C1 overexpression


title: CTRL-Static_2


title: HT22_Ctrl_3rd

source_name: HT22 cell (control plasmid)

value: control plasmid


title: Col-0-R2-red

tag: developmental stage

value: 4-day-old seedlings

value: wildtype


title: HT22_NR3C1_1st


title: ZH-03-Hu

description: 16s rRNA

value: Human gut


title: Col-0-R3-red


title: ZH-02-Hu

description: 16s rRNA


title: Col-0-R1-red


title: CTRL-Static_1


title: SupT1 mock, RNASeq, 0hpi, rep1

data_processing:
For PRICE analysis: (1) remove adapters cutadapt -a AGATCGGAAGAGCACACG -e 0.3 (2)  filter out short reads gedi -e FastqFilter -layout 2UI5U151 -min 18 (3) h.rRNA and mycoplasma removal  bowtie2 -un un --local -U (4) mapping reads STAR --runMode alignReads --alignIntronMax 1  --outSAMmode NoQS --outSAMtype BAM SortedByCoordinate --alignEndsType Extend5pOfRead1 --outSAMattributes nM MD NH (5) Convert BAM to CIT gedi -e BAM2CIT -umi (6) gedi -e CorrectCIT (7) deduplicate UMIs gedi -e DedupUMI (8) gedi -e MergeCIT (9) create report gedi -e Stats (10) P-site calling gedi -e Price
cutadapt 3.5, bowtie2 version 2.3.0, STAR version=2.7.10b, Gedi version 1.0.6, Price version 1.0.4
For differential gene expression analysis: (1) Count reads per genomic feature featureCounts -O (2) normalization and log2 fold change calculations by deltaTE/DTEG.R
featureCounts version 2.0.0, deltaTE (Chothani et al. 2019)
Assembly: GCF_000001405.36, AF324493
Supplementary files format and content: The PRICE codons BED files contain the genomic regions corresponding to predicted P-sites for each RiboSeq read. The "score" column equals to the read coverage at this position.
Supplementary files format and content: The countMatrix CSV files contain the read counts overlapping each genomic feature for every time point of infection for either cyclo RiboSeq or RNASeq.
Supplementary files format and content: The deltaTE text files contain the log2 fold changes (plus statistics) for each genomic feature, normalized by DESeq2 and calculated for each timepoint of infection against the 0h mock sample. This includes RiboSeq changes, RNASeq changes and  translation efficiency (TE) changes.
Supplementary files format and content: The DisomeSeq BED files contain the DisomeSeq reads that map to the HIV genome. The DisomeSeq text files contain the summed coverage per nucleotide for the HIV genome (column1: chromosome identifier; column2: genome position, column3: read coverage).
Supplementary files format and content: PRICE_report_harr_cyclo.tar contains quality control information for the RiboSeq PRICE pipeline, for both the cycloheximide and harringtonine treated samples. The index.html file allows interactive browsing through the different plots.
Supplementary files format and content: PRICE_report_disome.tar contains quality control information for the DisomeSeq PRICE pipeline. The index.html file allows interactive browsing through the different plots. Note that the p-site prediction is not valid for the DisomeSeq.
Supplementary files format and content: interactive_dTE_volcano_plots_DGE.tar contains interactive volcanoplots (translation efficiency) of the differential gene expression analysis with the deltaTE pipeline. Each infection timepoint was compared to the mock sample. Genes exceeding +/- 1 fold change and p_adj < 0.05 are colored based on consolidated gene ontology.
Supplementary files format and content: interactive_deltaTE_plots_DGE.tar contains interactive RiboSeq/RNASeq log2 fold change plots, of the differential gene expression analysis with the deltaTE pipeline. Each infection timepoint was compared to the mock sample. Only genes that are labelled as differentially expressed are plotted.

value: T-cell

value: cycloheximide


title: ZH-01-Hu

description: 16s rRNA


title: HT22_Ctrl_1st


title: huh7,Cas9,NTC,day3, scRNA-seq

first: Leilei

last: Wu

address: RD215 FuTe south

institute: Epigenic Therapeutics, Inc

description:
Library name: huh7_Cas_NTC
huh7_Cas_NTC
10X Genomics

library_source: transcriptomic single cell

data_processing:
The scRNA-seq reads were aligned to the GRCh38 reference genome and quantified using cellranger count (10× Genomics, v7.1.0). A filtered and qualified feature matrix was generated (provide process data), which only included barcodes with unique molecular identifier (UMI) counts surpassing the threshold for cell detection. The raw expression matrix was processed using the scanpy packages in Python. A total of 217,033 cells were detected initially. After cellranger, applying quality control metrics (total counts <50,000, mitochondrial ratio <10, and detected gene numbers between 500 and 8,000), 209,469 cells remained for further analysis. The qualified raw count data was log-normalized per cell with a size factor of 10,000. The top 3,000 genes with the highest variations across all cells were selected as "highly variable genes". A subset of the expression matrix was extracted and scaled using these highly variable genes. Principal component analysis (PCA) was then applied to derive meaningful features from the scaled data. The elbow point in the variance ratio distributions of PCA was used to select fifty principal components for computing the neighboring cluster graph. To further reduce dimensionality, Uniform Manifold Approximation Projection (UMAP) with the leiden algorithm was applied (resolution = 1.2). For ABE8.8, a total of 19 clusters were obtained and visualized using UMAP. We removed cluster 13 based on the marker genes specifically expressed in MT-related genes. For high-fidelity ABE, a total of 19 clusters were obtained and visualized using UMAP. Next, we performed differential expression analysis in each cluster using the Wilcoxon rank sum-test method. The top differentially expressed genes in each cluster, as determined by ranking, were defined as marker genes and used for subsequent cell type annotations.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Cryopreserved PBMCs were then retrieved from a liquid nitrogen tank, thawed in a 37°C water bath, and transferred into the cabinet after removing any remaining ice clumps. The outer surface of the container was sterilized with 5% ethanol, dried, and transferred into the cabinet. The cells were then transferred into 9 mL of T cell medium and centrifuged at 400g for 5 minutes at room temperature. After discarding the supernatant, the cells were resuspended in 5 mL of medium and counted using a ThermoFisher Attune NxT flow cytometer. Subsequently, the cells were seeded at a density of 1e6 cells/mL in plates or culture flasks. After 6 hours of PBMC revival, CD3/28 dynabeads were added for activation. Following 3 days of cell activation, the activation beads were removed using a magnet and the culture was continued for 24 hours. For electroporation, 24-well plates were prepared by adding 900 μL of PBMC complete medium per well and incubating at 37°C for 10 minutes. The Lonza 4D Nucleofector System with the P3 Primary Cell 4D kit was used, following the kit instructions for electroporation. Each electroporation reaction consisted of 1E6 cells, 1.2 pmol of EPIREG mRNA, and 40 pmol of sgRNA for each target gene. Immediately after electroporation, 100 μL of cell-free medium was added to each well, followed by a 1-hour incubation at 37°C. The cells were then transferred to 24-well plates for further culture.
The cell suspension was loaded into Chromium microfluidic chips with 3' (v2 or v3, depending on the project) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries were constructed using reagents from a Chromium Single Cell 3' v2 (v2 or v3, depending on the project) reagent kit (10X Genomics) according to the manufacturer's instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq, depending on the project) according to the manufacturer's instructions (Illumina). The same library construction process was used in Huh7 cells.

value: liver

tag: time point


title: HT22_NR3C1_3rd

tag: cell line


title: ZH-06-Hu

description: 16s rRNA


title: ZH-05-Hu

description: 16s rRNA


title: T5_2

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0 [2]. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/),Gene ontology (GO)(http://www.geneontology.org), SwissProt(http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG)(http://www.genome.jp/kegg/) and eggNOG(http://eggnogdb.embl.de/) databases using DIAMOND [3] with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR.
Supplementary_files_format_and_content: xls include TPM values for each Sample

organism: Dugesia japonica

source_name: Worm

growth_protocol: Freshwater planarian Dugesia japonica (clonal strain NH, called Dj-NH) were collected from Nanhe stream in Qi County, China (35°43′05″N, 114°06′31″E) and asexually reproduced at laboratory.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA)

treatment_protocol: Planarians were exposed to 64 mg L−1 glyphosate (1/2 LC50). On the exposure of 1, 3 and 5 day, individuals were randomly sampled, immediately frozen in liquid nitrogen,  and then kept at −80℃ until RNA extraction.

value: Worm

tag: treat

value: exposed to glyphosate 5 day

tag: time

value: 5 day


title: pif4-2 npr1-1-R2-blue

tag: tissue

value: seedlings

value: pif4-2 npr1-1

tag: treatment

value: grown in continuous blue light


title: New1-HTP in hel2-deletion background at 20°C, replicate 2

city: Mainz

first: Marie-Luise

last: Winz

address: Staudingerweg 5

institute: Johannes Gutenberg-University Mainz

library_source: other

data_processing:
pyCRAC pipeline; additional analyses as described in manuscript
adapters were cut with: flexbar (-n 3 -ao 4 -qt 30 -u 3 -g)
reads were aligned with: novoalign-c 55 -s 1 -r Random -o Native -l 17
hittables were generated with:pyCRAC package: pyReadCounters.py  --rpkm
Assembly: Saccharomyces cerevisiae (Ensembl releaseEF4.74)
Supplementary files format and content: .txt files containing hittables of raw (non-collapsed) data. Collapsing was avoided to allow for adquate representation of tRNA and rRNA, which is prone to over-collapsing

molecule: other

organism: Saccharomyces cerevisiae

growth_protocol: grow in SD-Trp media at 20 or 30°C, as indicated, until an OD600 of about 0.5

extract_protocol:
bead-beating, as described in manuscript
CRAC, as described in manuscript

treatment_protocol: UV-crosslinking

tag: genotype

value: New1-HTP::URA3, hel2-delta::KanMX6

value: 20°C, SD-Trp, OD600 about 0.5


title: huh7,Cas9,B2M,day3, scRNA-seq

description:
Library name: huh7_Cas_B2M
huh7_Cas_B2M
10X Genomics


title: New1-HTP in wt background at 20°C, replicate 2


title: Hel2-HTP in new1-deletion background at 20°C, replicate 2

value: Hel2-HTP::URA3, new1-delta::KanMX6


title: T5_1


title: SupT1 mock, RNASeq, 0hpi, rep2

tag: cell type


title: pif4-2 npr1-1-R1-blue


title: pif4-2-R3-blue


title: Hel2-HTP in wt background at 20°C, replicate 2


title: pif4-2-R2-blue


title: pif4-2-R1-blue


title: HT22_Ctrl_2nd


title: non-tagged control at 20°C, replicate 2

value: wt


title: T5_3


title: pif4-2 npr1-1-R3-blue


title: huh7,ABE,NTC,day3, scRNA-seq

description:
Library name: huh7_ABE_NTC
huh7_ABE_NTC
10X Genomics

value: ABE,NTC


title: T3_2

value: exposed to glyphosate 3 day

value: 3 day


title: ABEe8,NTC,day3, scRNA-seq

description:
Library name: ABEe8_NTC
ABEe8_NTC
10X Genomics

source_name: blood

value: blood

value: human T cells


title: ABEe8,PD1,day3, scRNA-seq

description:
Library name: ABEe8_PD1
ABEe8_PD1
10X Genomics


title: New1-HTP in hel2-deletion background at 20°C, replicate 1


title: T1_3

value: exposed to glyphosate 1 day

value: 1 day


title: Cas9,PD1,day21, scRNA-seq

description:
Library name: Casq_PD1
Casq_PD1
10X Genomics


title: npr1-1-R2-blue

value: 4-day-old seedlings


title: npr1-1-R3-blue


title: T3_1

value: Worm


title: huh7,ABE,B2M,day3, scRNA-seq

description:
Library name: huh7_ABE_B2M
huh7_ABE_B2M
10X Genomics

value: liver


title: npr1-1-R1-blue

value: seedlings


title: T1_2


title: New1-HTP in wt background at 20°C, replicate 1


title: T3_3


title: Cas9,B2M,day21, scRNA-seq

description:
Library name: Casq_B2M
Casq_B2M
10X Genomics


title: Cas9,NTC,day21, scRNA-seq

description:
Library name: Casq
Casq
10X Genomics


title: T1_1


title: Hel2-HTP in new1-deletion background at 20°C, replicate 1


title: CK_3

value: Untreated

value: control


title: ABE,PD1,day21, scRNA-seq

description:
Library name: ABE_PD1
ABE_PD1
10X Genomics


title: Hel2-HTP in wt background at 20°C, replicate 1


title: ABE,B2M,day7, scRNA-seq

description:
Library name: ISC_SCRNA019
ISC_SCRNA019
10X Genomics


title: Col-0-R3-blue

value: wildtype

value: grown in continuous blue light


title: Col-0-R2-blue


title: Hel2-HTP in new1-deletion background at 30°C, replicate 2

value: Hel2-HTP::URA3, new1-delta::KanMX6

value: 30°C, SD-Trp, OD600 about 0.5


title: CK_1


title: CK_2


title: ABE,PD1,day7, scRNA-seq

description:
Library name: ISC_SCRNA018
ISC_SCRNA018
10X Genomics


title: Col-0-R1-blue


title: non-tagged control at 20°C, replicate 1

value: wt

value: 20°C, SD-Trp, OD600 about 0.5


title: Mpmri-1, replicate C

city: Sophia Antipolis

first: Aurélien

last: Boisson-Dernier

address: 400 route des Chappes, BP 167

department: SPE

country: France

institute: INRAE

data_processing:
Galaxy Web server
Read quality was assessed using the FastQC package. Adapter sequences were trimmed, and the reads were quality-filtered using the fastp package with default settings.
Transcript count was then determined from the resulting preprocessed FASTQ files using the KallistoQuant package with default settings and sequence-based bias correction (42 bootstraps)
Differentially expressed genes (DEGs) were determined using the DESeq2 package with default settings.
All transcripts were mapped to the Marchantia polymorpha genome (MpTakv6.1) obtained from the MarpolBase website (https://marchantia.info).
Assembly: MpTakv6.1
Supplementary files format and content: Tab-delimited text file includes raw counts for each of the 12 samples.

organism: Marchantia polymorpha

source_name: Thalli and Rhizoids

growth_protocol: Marchantia polymorpha gemmae were cultivated for 3 weeks under axenic conditions on sterilized cellophane membranes placed over solid Johnson’s medium (0.8 % micro agar). Conditions  were : 16 h light/8 h darkness cycle, with white light irradiation (60 µmol m-1 s-1) at 21°C and 60 % humidity.

extract_protocol:
Total RNA was extracted using TRI reagent (Ambion Life Technologies). Two μg of DNaseI-treated total RNA was used for generating the sequencing libraries.
RNA libraries for RNA-seq were prepared at the Cologne Center for Genomics using the TruSeq stranded mRNA Kit (Illumina) according to manufacturer's instructions. ERCC spike-ins controls (ERCC RNA Spike-In Mix; Thermo Fischer) were used.

value: Thalli and Rhizoids

value: All

value: MpMRI Knockdown

tag: Sex

value: female


title: Hel2-HTP in wt background at 30°C, replicate 2


title: ABE,NTC,day7, scRNA-seq

description:
Library name: ISC_SCRNA017
ISC_SCRNA017
10X Genomics

value: blood

value: human T cells

value: ABE,NTC


title: Mpmri-1, replicate B


title: Cas9,B2M,day7, scRNA-seq

description:
Library name: ISC_SCRNA016
ISC_SCRNA016
10X Genomics


title: Mpmri-1, replicate A


title: Hel2-HTP in new1-deletion background at 30°C, replicate 1


title: Cas9,PD1,day7, scRNA-seq

description:
Library name: ISC_SCRNA015
ISC_SCRNA015
10X Genomics


title: Cas9,NTC,day7, scRNA-seq

description:
Library name: ISC_SCRNA014
ISC_SCRNA014
10X Genomics


title: Tak-2, replicate C

value: WT


title: Hel2-HTP in wt background at 30°C, replicate 1


title: Tak-2, replicate B


title: ABE,B2M,day3, scRNA-seq

description:
Library name: ISC_SCRNA010
ISC_SCRNA010
10X Genomics


title: Mpfer-1, replicate C

value: MpFER Knockdown

value: male


title: Tak-2, replicate A


title: ABE,PD1,day3, scRNA-seq

description:
Library name: ISC_SCRNA009
ISC_SCRNA009
10X Genomics


title: ABE,NTC,day3, scRNA-seq

description:
Library name: ISC_SCRNA008
ISC_SCRNA008
10X Genomics


title: normal RNA seq of of liver of P. jordani

city: Guangzhou

first: Xidong

last: Mu

address: No.1 Xingyu Road

institute: Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke (version 2.1.0) (parameters -lowQual=20, -nRate=0.005 and -qualRate=0.5).
The clean RNA-Seq reads were assembled using Trinity (version 2.8.5) and then aligned to the assembled genome using HISAT2 (version 2.2.1).
Read count extraction and normalization were performed using RSEM (version 1.3.3) (default parameter).
Assembly: JBGFUG000000000
Supplementary files format and content: txt file includes FPKM values for each Sample

organism: Ptychidio jordani

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen, MA, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated from the purified mRNA using the V AHTS Universal V6 RNA-seq Library Kit for MGI (V azyme, Nanjing, China) following the manufacturer's recommendations with unique index codes.

value: liver


title: normal RNA seq of of Kidney of P. jordani

source_name: Kidney

value: Kidney


title: Mpfer-1, replicate A


title: non-tagged control at 30°C, replicate 2


title: normal RNA seq of of spleen of P. jordani

source_name: spleen

value: spleen


title: normal RNA seq of of muscle of P. jordani

source_name: muscle

value: muscle


title: Cas9,B2M,day3, scRNA-seq

description:
Library name: ISC_SCRNA007
ISC_SCRNA007
10X Genomics


title: Tak-1, replicate C


title: Cas9,PD1,day3, scRNA-seq

description:
Library name: ISC_SCRNA006
ISC_SCRNA006
10X Genomics


title: non-tagged control at 30°C, replicate 1

value: 30°C, SD-Trp, OD600 about 0.5


title: KRT3C84

type: genomic

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.10.1.1).

data_processing: Bioconductor package MANOR was used for loess normalisation and quality filtering of data followed by copy number calling using the R packages CGHcall and CGHregions.

source_name: pancreas

label_protocol: 250 ng of genomic DNA were labelled with Cy3 (test) or Cy5 (reference) using the Enzo Oligo Array CGH Labelling Kit

growth_protocol: Mice were housed in specific pathogen free (SPF) conditions at 22 ± 2 °C, with a humidity of 55 ± 10% and on a 12 h light-dark cycle.

extract_protocol: Genomic DNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue sections using the DNAeasy FFPE kit. DNA extracted from 4 normal pancreatic tissues was pooled and used as reference DNA.

treatment_protocol: Due to the genetic modifications, the mice show a spontaneous pancreas phenotype, which leads to ADM and PanIn formation. No further treatment of the animals was done.

source_name: FFPE sections

value: pooled reference


title: normal RNA seq of of gill of P. jordani

description: normal RNA seq of of gill of P. jordani

source_name: gill

value: gill


title: KRT3C83


title: KRT3C81


title: Cas9,NTC,day3, scRNA-seq

description:
Library name: ISC_SCRNA005
ISC_SCRNA005
10X Genomics


title: KRT3C82


title: Tak-1, replicate B

value: Thalli and Rhizoids


title: KRT3C85


title: K4

value: KRAS-mutant


title: K5


title: Mpfer-1, replicate B

value: All


title: blank, scRNA-seq

description:
Library name: ISC_SCRNA001
ISC_SCRNA001
10X Genomics


title: normal RNA seq of of heart of P. jordani

source_name: heart

value: heart


title: mDC 25Ab

source_name: Mouse dendritic cells

treatment_protocol: Cells were stimulated for 0 hours (unstimulated), 6 hours or 24 hours with LPS (100ng/ml, rough, ultra-pure E. coli K12 strain, Invitrogen).

value: Mouse dendritic cells

value: See supplemental file


title: Tak-1, replicate A


title: normal RNA seq of of fin of P. jordani

description: normal RNA seq of of fin of P. jordani

source_name: fin

value: fin


title: WT_S40_Rep1, miRNA-seq

status: Public on Nov 25 2024

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

data_processing:
Reads were trimmed using cutadapt (with -u 1 option)
Trimmed reads were mapped to the Maize Genome v4 miRNA precursors using bowtie2 with default parameters.
Assembly: Zea_mays.AGPv4.dna.toplevel.fa
Supplementary files format and content: microRNA haipin mapping count files in txt format (the identifiers come from miRBase).

organism: Zea mays

source_name: Leaf

growth_protocol: Z. mays seedlings were grown under controlled temperature and humidity conditions throughout with a 16 h light and 8 h dark cycle. U. maydis sporidia were grown at 28ºC under constant shaking at 200 rpm till OD600 of the culture reached 0.8. At this stage the cells were harvested and used for infection.

extract_protocol:
RNA was extracted from all the different samples using TRIzol method following the manufacturer’s protocol.
We used the commertial kit RealSeq_v2
small RNAseq following manufacturer instructions with RealSeq v2

treatment_protocol: The Z. mays seedlings were infected with a suspension of U. maydis sporidia in sterile water using a syringe infection method.

value: Leaf

tag: u. maydis_strain

value: WT

tag: fraction


title: WT_S40_Rep2, miRNA-seq


title: WT_S40_Rep5, miRNA-seq


title: WT_P40_Rep5, miRNA-seq


title: WT_P40_Rep2, miRNA-seq


title: WT_P40_Rep1, miRNA-seq


title: WT_LSW_Rep2, miRNA-seq

value: LSW


title: WT_LSW_Rep5, miRNA-seq


title: K2


title: UI_S40_Rep3, miRNA-seq

value: UI


title: WT_LSW_Rep1, miRNA-seq


title: UI_S40_Rep1, miRNA-seq


title: UI_S40_Rep2, miRNA-seq


title: striatal nuclei, Dlx5/6-Cre;Zswim6 c/c, Mouse ID#497

city: Philadelphia

first: Nathan

middle: Thomas

last: Henderson

state: PA

address: 415 Curie Blvd., Room 778

institute: University of Pennsylvania

description: Library name: KO497

data_processing:
For ATAC-seq analysis, alignments were performed with Bowtie2 (2.1.0), using the mm10 genome with the pipeline at https://github.com/shenlab-sinai/chip-seq_preprocess. Reads were mapped using NGS plot. 3 biological replicates per condition were sequenced and each replicate yielded greater than 60 million reads. Replicates were merged to generate average profile plots.
Assembly: mm10
Supplementary files format and content: TDF files

source_name: striatum

extract_protocol:
tissue was homogenized in homogenization buffer (0.32M Sucrose, 5mM CaCl2, 10mM Tris-Cl pH 8, 3mM MgAc2, 0.1% Triton X-100, 0.1mM EDTA), pippetted onto a sucrose cushion, then centrifuged for 90 min at 100,000g. . Nuclei were resuspended in cold lysis buffer (100 µl per 100,000 cells; 10 mM Tris-Cl (pH 7.5), 10 mM NaCl, 3 mM MgCl2, 0.1% (vol/vol) NP-40, 0.1% (vol/vol) Tween-20 and 0.01% (vol/vol) digitonin) and washed in wash buffer (10 mM Tris-Cl (pH 7.5), 10 mM NaCl, 3 mM MgCl2 and 0.1% (vol/vol) Tween-20). Transposition was performed with Tagment DNA TDE1 (Illumina, 15027865). Transposition reactions were cleaned with AMPure XP beads (Beckman, A63880).
libraries were generated by PCR with NEBNext High-Fidelity  2× PCR Master Mix (NEB, M0541).

value: striatum

value: Dlx5/6-Cre; Zswim6 c/c


title: striatal nuclei, Dlx5/6-Cre;Zswim6 c/c, Mouse ID#410

description: Library name: KO410


title: UI_P40_Rep1, miRNA-seq


title: UI_LSW_Rep2, miRNA-seq


title: striatal nuclei, Dlx5/6-Cre;Zswim6 c/c, Mouse ID#408

description: Library name: KO408


title: UI_LSW_Rep1, miRNA-seq


title: striatal nuclei, Dlx5/6-Cre;WT, Mouse ID#475

description: Library name: WT475


title: UI_LSW_Rep3, miRNA-seq


title: UI_P40_Rep3, miRNA-seq


title: UI_P40_Rep2, miRNA-seq


title: striatal nuclei, Dlx5/6-Cre;WT, Mouse ID#402

description: Library name: WT402


title: K3


title: K1


title: nuc3_S40_Rep2, miRNA-seq


title: nuc3_S40_Rep1, miRNA-seq


title: nuc3_P40_Rep4, miRNA-seq


title: nuc3_LSW_Rep4, miRNA-seq

description: nuc3_LSW_Rep4.fq.Zma_hp.sam.count.txt is empty.  This is expected.


title: nuc3_LSW_Rep2, miRNA-seq

description: nuc3_LSW_Rep2.fq.Zma_hp.sam.count.txt is empty.  This is expected.


title: nuc3_S40_Rep4, miRNA-seq


title: nuc3_P40_Rep2, miRNA-seq


title: nuc3_P40_Rep1, miRNA-seq


title: nuc3_LSW_Rep1, miRNA-seq

description: nuc3_LSW_Rep1.fq.Zma_hp.sam.count.txt is empty.  This is expected.


title: NUC1-nuc2_S40_Rep2, miRNA-seq


title: striatal nuclei, Dlx5/6-Cre;WT, Mouse ID#403

description: Library name: WT403


title: NUC1-nuc2_S40_Rep1, miRNA-seq


title: Whole larvae, fyn model, day5, rep4

city: Ames

first: Sahiba

last: Siddiqui

state: IA

address: 2213 Pammel Dr

department: Genetics, Development, and Cell Biology

institute: Iowa State University

description: M4_5dpf_biol rep 4

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads
Clean data (clean reads) were obtained by removing reads containing adapter, reads 1 containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tool
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gen
Assembly: GRCz11, Danio rerio

organism: Danio rerio

source_name: Whole larvae

growth_protocol: The zebrafish larvae for these experiments were maintained in E3 embryo media at 28.5 °C with a 14-hour light/10-hour dark light/dark cycle.

extract_protocol:
RNA was extracted using the Zymo RNA extraction kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: At 3dpf and 5dpf, larvae were stored at -20°C in DNA/RNA shield solution from Zymo Research, or processed same day for RNA extraction.

value: Whole larvae

value: Neuronal expression of constitutive fyn


title: Whole larvae, fyn model, day5, rep3

description: M3_5dpf_biol rep 3


title: Whole larvae, fyn model, day5, rep1

description: M1_5dpf_biol rep 1


title: NUC1-nuc2_S40_Rep4, miRNA-seq


title: Whole larvae, huC Control, day5, rep3

description: H3_5dpf_biol rep 3

value: Neuronal gal4 driver


title: NUC1-nuc2_P40_Rep4, miRNA-seq


title: Whole larvae, WT Control, day5, rep3

description: C3_5dpf_biol rep 3

value: No genetic mutation


title: NUC1-nuc2_P40_Rep2, miRNA-seq


title: Whole larvae, huC Control, day5, rep2

description: H2_5dpf_biol rep 2


title: Whole larvae, WT Control, day5, rep4

description: C4_5dpf_biol rep 4


title: Whole larvae, WT Control, day5, rep2

description: C2_5dpf_biol rep 2


title: NUC1-nuc2_LSW_Rep4, miRNA-seq


title: NUC1-nuc2_P40_Rep1, miRNA-seq


title: Whole larvae, fyn model, day3, rep4

description: M4_3dpf_biol rep 4


title: Whole larvae, fyn model, day5, rep2

description: M2_5dpf_biol rep 2


title: Whole larvae, fyn model, day3, rep3

description: M3_3dpf_biol rep 3


title: Whole larvae, WT Control, day5, rep1

description: C1_5dpf_biol rep 1


title: NUC1-nuc2_LSW_Rep2, miRNA-seq


title: Whole larvae, fyn model, day3, rep2

description: M2_3dpf_biol rep 2


title: Whole larvae, huC Control, day5, rep1

description: H1_5dpf_biol rep 1


title: NUC1-nuc2_LSW_Rep1, miRNA-seq


title: Whole larvae, fyn model, day3, rep1

description: M1_3dpf_biol rep 1


title: Whole larvae, huc Control, day3, rep4

description: H4_3dpf_biol rep 4


title: Whole larvae, huc Control, day3, rep3

description: H3_3dpf_biol rep 3


title: Whole larvae, huc Control, day3, rep2

description: H2_3dpf_biol rep 2


title: Peritoneum, CHX, 3

city: Madrid

first: Vanessa

last: Marchant

state: Madrid

address: Avda. Reyes Católicos, 2

department: IIS-FJD

country: Spain

institute: Universidad Autónoma de Madrid

data_processing:
Read cleaning was performed with PrinSeq.
Mapping and alignments to mouse genome were made with TopHat (v2.1.1).
Differential expression analysis and statistics were carried out with CuffDiff.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw fragment counts and FPKM values for each sample and gene

source_name: Parietal peritoneum (includes abdominal muscle)

extract_protocol:
Mechanical disruption in a TissueLyser apparatus (QIAGEN) and RNeasy Mini Kit (QIAGEN) with DNase treatment were used for total RNA extraction. Total RNA quality and concentration were assessed on 4200 TapeStation (Agilent), confirming all samples had RIN > 7.
Library preparation was performed with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs) following manufacturer recommendations for Poly(A) mRNA protocol. Libraries were validated and quantified by TapeStation and an equimolecular pool was made, purified using AMPure XP beads (Beckman Coulter), and titrated by PicoGreen.

tag: strain

value: Male

value: Wildtype

value: CHX


title: Whole larvae, huc Control, day3, rep1

description: H1_3dpf_biol rep 1


title: Peritoneum, CHX, 4

value: Parietal peritoneum (includes abdominal muscle)


title: Whole larvae, WT Control, day3, rep3

description: C3_3dpf_biol rep 3


title: Whole larvae, huC Control, day5, rep4

description: H4_5dpf_biol rep 4


title: Whole larvae, WT Control, day3, rep4

description: C4_3dpf_biol rep 4


title: Peritoneum, CHX, 1


title: Whole larvae, WT Control, day3, rep2

description: C2_3dpf_biol rep 2


title: Peritoneum, CHX, 2


title: Whole larvae, WT Control, day3, rep1

description: C1_3dpf_biol rep 1


title: Peritoneum, Control, 2

value: Control


title: Peritoneum, Control, 1


title: Peritoneum, Control, 3


title: Saliomycin_Sen_A549_R1_biological replicate 3

city: Amsterdam

first: gabriele

last: casagrande raffi

address: Plesmanlaan 121

institute: Netherlands cancer institute

data_processing:
Sequencing data was demultiplexed into FastQ files using BCLConvert version 4.1.5 (Illumina). The paired-end reads were trimmed for adapter sequences using SeqPurge version 2019_0939  and aligned to the human reference genome using HiSat2version 2.1.0 with the pre-built grch38_snp_tran reference.40 After alignment, UMI aware duplicates were marked using Rumidup. The de-duplicated gene counts were determined by GenSum using Ensembl release 102 transcript GTF as a reference
Assembly: Sequencing data was demultiplexed into FastQ files using BCLConvert version 4.1.5 (Illumina). The paired-end reads were trimmed for adapter sequences using SeqPurge version 2019_0939  and aligned to the human reference genome using HiSat2version 2.1.0 with the pre-built grch38_snp_tran reference.40 After alignment, UMI aware duplicates were marked using Rumidup. The de-duplicated gene counts were determined by GenSum using Ensembl release 102 transcript GTF as a reference
Supplementary files format and content: GSEA_Analysis, Gene counts

extract_protocol: Cells were harvested and lysed using 750 µL of RLY buffer

value: NSCLC


title: Brain_11

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

hyb_protocol: Bisulfite-converted DNA samples were randomly assigned to a chip well on the Human Imprintome array BeadChip (Illumina, Inc., San Diego, CA), amplified, hybridized onto the array, stained, washed, and imaged with the Illumina iScan SQ instrument (Illumina, Inc., San Diego, CA) to obtain raw image intensities.

data_processing: To preprocess the DNA methylation values, we utilized the sesame package  due to its compatibility with custom arrays. Specifically, we employed the readIDATpair followed by the getBetas functions, which require the IDAT file locations and the custom manifest to generate a beta value matrix. To visualize the distribution of beta values we employed the densityPlot function from the minfi package

label: Cy3, Cy5

source_name: Brain

extract_protocol: For the preparation of samples, 200 ng of DNA were bisulfite converted using the EZ DNA Methylation kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions.

treatment_protocol: We used 16 brain samples from Alzheimer’s cases and controls. These samples were classified into 4 controls and 4 cases of NHBs and 4 controls and 4 cases of NHWs. To correctly assess the correlations between the Human Imprintome array and WGBS, we combined the 4 samples from each group by averaging the DNA methylation levels in the Human Imprintome array. We collapsed the probes that were targeting the same CpG site in the Human Imprintome array.

value: Brain

tag: race

value: white

tag: disease


title: Brain_12

scan_protocol: Bisulfite-converted DNA samples were randomly assigned to a chip well on the Human Imprintome array BeadChip (Illumina, Inc., San Diego, CA), amplified, hybridized onto the array, stained, washed, and imaged with the Illumina iScan SQ instrument (Illumina, Inc., San Diego, CA) to obtain raw image intensities.


title: Brain_13

label_protocol: Bisulfite-converted DNA samples were randomly assigned to a chip well on the Human Imprintome array BeadChip (Illumina, Inc., San Diego, CA), amplified, hybridized onto the array, stained, washed, and imaged with the Illumina iScan SQ instrument (Illumina, Inc., San Diego, CA) to obtain raw image intensities.

value: Alzheimer Disease


title: Salinomycin_Sen_A549_R1_biological replicate 1


title: Untreated_Sen_A549_R1_biological replicate 3


title: Brain_7

value: black


title: Brain_9


title: Brain_14


title: Untreated_Sen_A549_R1_biological replicate 2


title: Brain_10


title: Brain_6


title: Untreated_Sen_A549_R1_biological replicate 1


title: Brain_15


title: Peritoneum, Control, 4


title: Brain_3


title: Brain_4


title: Brain_1


title: Cord_Blood_7_rep2

source_name: Cord Blood

treatment_protocol: NEST is an ongoing prospective birth cohort study with 2,681 pregnant women recruited in two waves between 2005 and 2011; enrollment of participants is described in detail elsewhere. Briefly, pregnant women were recruited from prenatal clinics serving Duke University Hospital and Durham Regional Hospital obstetrics facilities in Durham, NC. Eligible participants were: (1) pregnant, (2) at least 18 years of age, (3) English-speaking, and (4) intending to deliver at one of two obstetric facilities. Women with HIV or intending to give up custody of their offspring were excluded. At delivery, umbilical cord blood was obtained. For the current study, we used 8 umbilical cord blood samples, and processed them twice with the Human Imprintome Array to assess the reliability of the array.

value: Cord Blood


title: Cord_Blood_8_rep2


title: Cord_Blood_8_rep1


title: Brain_16


title: Brain_2


title: Salinomycin_Sen_A549_R1_biological replicate 2


title: Cord_Blood_7_rep1


title: Brain_8


title: Brain_5


title: BT-549, ZEB1, replicate 2

city: Cleveland

first: Noah

middle: Matthew

last: Chernosky

state: Ohio

address: 2103 Cornell Road

department: Pathology

institute: Case Western Reserve University

data_processing:
Prepared paired-end 42 base-pair sequencing reads were generated by Illumina sequencing
using NextSeq 500.
Sequencing reads were mapped to genome build hg38 using the STAR RNA-seq aligner
2.5.2b mapping algorithm with default parameters.
Assembly: hg38
Supplementary files format and content: Excel file provided as a supplementary file. File contains fold change values of all genes from OSM, TGF-B1, SNAI1, and ZEB1 cells compared to Vec control cells.

extract_protocol:
RNA was harvested using RNeasy Plus kit (QIAGEN). 3 ug of total RNA was used for the construction of sequencing libraries.
Libraries were generated by Active Motif, Inc. using the supplied RNA.


title: Cord_Blood_6_rep1


title: BT-549, SNAI1, replicate 2


title: BT-549, ZEB1, replicate 1


title: 3LL IFNG

type: RNA

city: Tokushima

first: atsushi

last: mitsuhashi

address: 3-18-15 Kuramoto-cho

department: Department of Respiratory Medicine and Rheumatology

country: Japan

institute: Tokushima university

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Gene Expression 4 × 44 K ver. 2.0 Micro Arrays for 17 hours at 65℃in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: LLC, IFN-gamma, 24hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.15 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color  (Agilent, 5190-2305) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: lung carcinoma


title: BT-549, SNAI1, replicate 1


title: Cord_Blood_6_rep2


title: Cord_Blood_4_rep2


title: Cord_Blood_3_rep1


title: AB1-HA IFNG

source_name: AB1-HA, IFN-gamma, 24hr

value: mesothelioma

value: BALB/c


title: BT-549, TGF-B1, replicate 1


title: BT-549, TGF-B1, replicate 2


title: Cord_Blood_5_rep1


title: Cord_Blood_2_rep1


title: Cord_Blood_5_rep2


title: BT-549, OSM, replicate 2

value: OSM


title: 3LL con

source_name: LLC, vehicle, 24hr


title: Cord_Blood_1_rep1


title: Cord_Blood_1_rep2


title: BT-549, OSM, replicate 1


title: Blood_AD173_Imprintome_rep2

source_name: Peripheral Whole Blood

treatment_protocol: A pilot case control study of 50 cases and 50 controls was also conducted at the Duke Memory Clinic. Peripheral whole blood was collected by the lancet and capillary method into lysis buffer and DNA extracted. In total, DNA samples from 17 individuals were randomly selected. Among them, 10 were Alzheimer’s disease cases and 7 were controls. All the samples were processed twice using the Human Imprintome array to assess the performance of the array. Moreover, three more controls were randomly selected to process them with the Human Imprintome array and the EPICv2 array

value: Peripheral Whole Blood

value: M

value: AA


title: AB1-HA con

source_name: AB1-HA, vehicle, 24hr


title: Blood_AD174_Imprintome_rep2

value: F

value: EA


title: Cord_Blood_3_rep2


title: Blood_AD163_Imprintome_rep2


title: Blood_AD154_Imprintome_rep2


title: Blood_AD198_Imprintome_rep2


title: BT-549, Vec, replicate 2

value: Vec


title: Blood_AD161_Imprintome_rep2

value: Control


title: Blood_AD169_Imprintome_rep2


title: Cord_Blood_4_rep1


title: BT-549, Vec, replicate 1


title: Blood_AD124_Imprintome_rep2


title: Blood_AD202_Imprintome_rep2


title: OPC_monos_scRNAseq

city: Manhasset

first: Vincent

middle: R

last: Bonagura

state: New York

address: 350 Community Drive

department: Pediatric Immunology

institute: Northwell Health

description: 10X genomics

data_processing:
Demultiplexing and barcode processing were performed using a custom pipeline using the Seurat (v 5.0.3) package in R.
Assembly: hg38
Supplementary files format and content: Tab-separated values for barcodes, features and matricies for each experimental condition.

source_name: primary monocytes

growth_protocol: SCC-25 and SCC-154 OPC cell lines were maintained in E-media supplemented with 10% FCII (E10) plus growth factors. During CM generation, cells were plated in E10 and when approximately 60-70% confluent, media was replaced with E-media supplemented with 2% FCII for 48 hours. Monocytes used during stimulation were isolated from both individuals in parallel and stimulated for 18 hours immediately after confirmation of purity.

extract_protocol:
Monocytes were isolated from 30mL of blood from a single healthy and OPC-diagnosed individuals. Briefly, leukocytes were enriched by Ficoll separation and isolated by negative selection (Miltenyi). Conditioned media was generated by incubating sub confluent SCC-25 or SCC-154 cell lines in E-media supplemented with 2% FCII. Monocytes were incubated for 18 hours in E2 media (control) or in E2 media diluted 1:2 with SCC-25, SCC-154 CM or E-media containing recombinant human IL1α to a final concentration of 200 pg/mL. Cells were incubated for 18 hours.
Cells from each stimulation condition (4) were multiplexed for each individual and libraries prepared accoding to manufacturer's protocols (10X Genomics)

treatment_protocol: Monocytes from either individual were plated at 2 million per mL in 12 well plates. Equivelent volumes of either fresh E2 media (control), recombinant IL1α (to a final concentration of 200pg/mL), SCC-25 CM or SCC-154 CM were added to appropriate wells. Cells were incubated for 18 hours prior to single cell library preparation.

value: primary monocytes


title: control_monos_scRNAseq

description: 10X genomics


title: GSTT1-3

city: Goyang

first: JAE YEON

last: MOON

address: Dongguk-ro 32

country: South Korea

institute: Dongguk university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: adipose-derived stromal/stem cells

growth_protocol: The transfected hASCs were seeded onto 100 mm dishes at density of 1 × 106 cells per dish in αMEM supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin 100X for 3 days after transfection.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Two groups: pAcGFP1-C1 control vector (Control) and pAcGFP1-C1_GSTT1 vector (GSTT1)-transfected ASCs

tag: tansfection

tag: passages

value: lipoaspirate


title: GSTT1-1


title: Blood_AD136_Imprintome_rep2


title: Blood_AD126_Imprintome_rep2


title: Blood_AD111_Imprintome_rep2


title: Blood_AD125_Imprintome_rep2


title: Blood_AD127_Imprintome_rep2


title: Blood_AD112_Imprintome_rep2


title: Blood_AD100_Imprintome_rep2


title: Blood_AD114_Imprintome_rep2


title: Control-2

value: pAcGFP1-C1 control


title: Blood_AD163_Imprintome_rep1


title: Blood_AD127_Imprintome_rep1


title: Control-1


title: Blood_AD161_Imprintome_rep1


title: Blood_AD154_Imprintome_rep1

value: Alzheimer Disease


title: Control-3


title: Blood_AD136_Imprintome_rep1


title: Blood_AD174_Imprintome_rep1


title: Blood_AD202_Imprintome_rep1


title: Blood_AD198_Imprintome_rep1


title: Blood_AD169_Imprintome_rep1


title: Blood_AD173_Imprintome_rep1


title: GSTT1-2


title: Blood_AD126_Imprintome_rep1


title: Blood_AD124_Imprintome_rep1


title: Blood_AD114_Imprintome_rep1


title: Blood_AD125_Imprintome_rep1


title: J1165_SCN

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

address: 450 Technology Drive

institute: University of Pittsburgh

data_processing:
FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of the data. Per base sequence quality was high (Quality score generally > 30) indicating good data quality. HISAT2 (HISAT2v2.1.0) was used to align reads to the reference (Mus musculus Ensembl GRCm38) using default parameters.
Assembly: GRCm38
Supplementary files format and content: mouse_filteredCounts_NACPFC.csv; mouse_filteredCounts_SCN.csv

source_name: SCN

extract_protocol:
Mice exposed to adolescent CRD and adult CRD, as well as matching controls, were euthanized approximately 4 wks after the CRD or control paradigm ended by cervical dislocation and rapid decapitation at ZT6. Brains were flash frozen on dry ice and stored at –80 °C until used for punching.
Libraries were prepared with 10 ng of RNA from each sample using the Smartseq HT ultra-low input sample preparation kits (Illumina).

value: SCN


title: J1198_SCN


title: J1141_SCN


title: J1162_SCN


title: J1140_SCN


title: J1160_SCN


title: J1158_SCN


title: SAMPLE 2_Test_Trichoderma infestation

city: wuhan

first: jiaxin

last: song

address: No. 1, Shizishan Street, Hongshan District, Wuhan City, Hubei Province

department: College of Plant Science & Technology

institute: Huazhong Agricultural University

data_processing: Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR green

organism: Lentinula edodes

source_name: mycelium cell

label_protocol: cDNA

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: stress

value: Trichoderma infestation

value: Lentinula edoes strain w1


title: SAMPLE 1_Control_normal

value: normal


title: J1178_SCN


title: UTX_CD8+ Progenitor_2

city: Los Angeles

first: Ho Chung

last: Chen

address: 609 Charles E Young Dr E

department: MIMG

institute: University of California, Los Angeles

data_processing:
sequence reads were passed the QC test and were trimmed for adaptor sequence/low quality seuqence.
Trimmed sequence reads were mapped to mm10 using HISAT2 (2.2.1) on Galaxy to generate the bam file.
raw count table was generated by using featureCounts.
Raw count table was analzyed by Deseq2 to generate the normalized count table.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized count with p-value and fold change for each sample

source_name: pancreatic lymph node

extract_protocol:
total RNA was isolated using Quick-RNA MicroPrep (Zymo)
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit following manufacturer's protocols

value: pancreatic lymph node

value: CD8+ T cells


title: WT_CD8+ Progenitor_3

value: WT


title: UTX_CD8+ Progenitor_3


title: UTX_CD8+ Progenitor_1


title: SAMPLE 6_Test_Heat

value: Heat


title: Blood_AD100_Imprintome_rep1

value: Peripheral Whole Blood

value: AA


title: J1159_SCN


title: Blood_AD112_Imprintome_rep1

value: F


title: WT_CD8+ Progenitors_2


title: HTC116 cells, Mutant, 3

city: Bethesda

first: Hernan

middle: A

last: Lorenzi

state: Maryland

address: 8 Center Dr, Bldg 8A

department: National Institutes of Diabetes and Digestive and Kidney Diseas

institute: National Institutes of Health

data_processing:
bam files containing mapped read were converted to bed format with the bamtobed tool from the bedtools suite (v2.31.0)
Quantification of transposition events per predicted insertion site from bed files was performed with a Perl custom script bed2histogram.pl (https://github.com/TriLab-bioinf/PBAT_MANUSCRIP_2023/tree/main/supplementary_scripts)
Transposition event quantitative data were formatted as bed files with the Perl custom script histogram2bed.pl (https://github.com/TriLab-bioinf/PBAT_MANUSCRIP_2023/tree/main/supplementary_scripts)
Assembly: GCA_000001405.15
Supplementary files format and content: bed
Supplementary files format and content: tab-delimited file with the following columns: chromosome id, pBAT insertion site 5' coordinate, pBAT insertion site 3' coordinate, insertion site id (chromosome:5' and 3' coordinates of flanking genomic region spanning insertion site), read counts supporting insertion site, strand.

source_name: colon

extract_protocol:
Total RNA was extracted from HCT116 cells using NucleoSpin RNA Plus (Macherey-Nagel) and reversed transcribed targetting polyA RNA with primer SMART-dT18VN, 5’-AAGCAGTGGTATCAACGCAGAGTACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN-3’
cDNAs were PCR amplified with four primers located in transposon areas, SRT-PAC-F1, 5’-CAACCTCCCCTTCTACGAGC-3’, SRT-Seq P1, 5’-CGGTGCCTGATAACAACTCG-3’, SRT-Seq P2, 5’-GGTTCAGCAGGAATGCCGAG-3’, and SRT-Seq P3 5’-CTCAGTGTCCATAGCGACGC-3’ and one primer located in Smart-dT18VN, Smart: 5’-AAGCAGTGGTATCAACGCAGAGT-3’
Amplicons were fragmented with and tagged with Illumina DNA Prep (Illumina).
Tagged DNA fragments were further PCR amplified using Read1-TnME, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTAGATGTGTATAAGAGACA*G-3’, and Read2-Pbat, 5’-GACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTCGTTTCCCGCAATCCAAGTG -3’, containing sequencing adapters, to enrich for fragments carrying the LE end of the transposon and downstream genomic insertion site
PCR amplicons were 100-500bp size selected with 2% agarose gel before sequencing library preparation
NEBNext Ultra II Q5 Master Mix (NEB, M0544S) was used to barcode size-selected amplicons for Illumina sequencing (NEB, E7780S). The amplified fragments were purified and size selected using AMPure XP beads (Beckman Coulter, A63881) at 0.9x bead/sample ratio.

value: colon

value: colon carcinoma

value: Mutant

value: pTpBat SRT Puro LE88RE100  (Mutant reporter transposon) + pCF2-pFV4a-MLT pBat Mutant S8A, S24A, S32A, S37A 2XCRD (Mutant pBAT transposase)


title: WT_CD8+ Progenitors_1


title: J1021_SCN


title: Cord_Blood_2_rep2

value: Cord Blood


title: SAMPLE 3_Test_Cd2+


title: SAMPLE 4_Test_Light

value: Light


title: J1177_SCN

value: SCN


title: HTC116 cells, WT, 3

value: pTpBat SRT Puro LERE (WT reporter transposon) + pCF2-pFV4a-MLT (WT pBAT transposase)


title: J1199_SCN


title: SAMPLE 5_Test_Cold

value: Cold

value: Lentinula edoes strain w1


title: Blood_AD111_Imprintome_rep1

value: M

value: EA

value: Control


title: HTC116 cells, WT, 1

value: WT


title: HTC116 cells, Mutant, 2


title: HTC116 cells, WT, 2


title: striatal nuclei, Dlx5/6-Cre;Zswim6 c/c, Mouse ID#494, , UPenn NGSC ID#110291

description: Library name: KO494

data_processing:
Initial data processing was carried out using the CellRanger v6.1.2 pipeline. Briefly, raw base call (BCL) files were de-multiplexed using the mkfastq command, generating FASTQ files. Extracted and quality control passed FASTQ reads were aligned to the GRCm38/mm10 genome and single cell nucleus count data was generating using the count command.
Assembly: GRCm38/mm10
Supplementary files format and content: feature and barcode data (tsv) and sparse gene expression matrices (mtx)

molecule: nuclear RNA

extract_protocol:
P8 male and female mice were deeply anesthetized with isoflurane, then decapitated. Brains were quickly removed and transferring to sucrose cutting solution (26 mM NaHCO3, 1 mM NaH2PO4, 2.5 mM KCl, 228 mM sucrose, 11 mM glucose, 7 mM MgSO4, and 0.5 mM CaCl2). 400 µm sections were cut on a vibratome (VT1200s, Leica), then transferred to artificial cerebrospinal fluid (ACSF; 119 mM NaCl, 26.2 mM NaHCO3, 1 mM NaH2PO4, 2.5 mM KCl, 11 mM glucose, 1.3 mM MgSO4, and 2.5 mM CaCl2). Sucrose and ACSF solutions were both bubbled with a 95% O2, 5% CO2 mixture at all times. With the slices in ACSF, striatum was then dissected from each slice (4 slices per animal) then snap frozen in liquid nitrogen and stored at -80. Nuclei extraction was carried out using a protocol optimized by the Macosko Lab (dx.doi.org/10.17504/protocols.io.7xchpiw). FACs capture was omitted, as no fluorophores were present and minimal nuclei clumping was observed.
Nuclei capture, 10X sequencing, read alignment, and initial quality control steps were carried out by the Next Generation Sequencing Core (NGSC) at the Perelman School of Medicine (University of Pennsylvania), using the 10x Genomics Chromium Single Cell Controller and Chromium Next GEM Single Cell 3ʹ Kit v3 (Cat. # 1000268).

value: striatum

value: Dlx5/6-Cre; Zswim6 c/c


title: striatal nuclei, Dlx5/6-Cre;Zswim6 c/c, Mouse ID#397, , UPenn NGSC ID#108054

description: Library name: KO397


title: J1020_SCN


title: striatal nuclei, Dlx5/6-Cre;Zswim6 c/c, Mouse ID#12, UPenn NGSC ID#110290

description: Library name: KO12


title: J1157_SCN


title: J1017_SCN


title: striatal nuclei, Dlx5/6-Cre;WT, Mouse ID#438, UPenn NGSC ID#110287

description: Library name: WT438


title: striatal nuclei, Dlx5/6-Cre;WT, Mouse ID#433, UPenn NGSC ID#110286

description: Library name: WT433


title: J1011_SCN


title: striatal nuclei, Dlx5/6-Cre;WT, Mouse ID#401, UPenn NGSC ID#108053

description: Library name: WT401


title: KE6_KO_DMSO

city: Ithaca

first: Joeva

last: Barrow

address: 244 Garden Ave

institute: Cornell University

data_processing:
reads were trimmed for low quality and adaptor sequences with TrimGalore v0.6.0, a wrapper for cutadapt and fastQC.
reads were mapped to the reference genome/transcriptome GRCm38/mm10 using STAR v2.7.0e.Parameters: --outReadsUnmapped Fastx
SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: Primary murine myoblasts

growth_protocol: Ham's F-10 media with 20% horse serum and 1% penicillin/ streptomycin, cells cultured at 37C, 5% CO2

extract_protocol:
Total RNA was purified using the Trizol method (Thermo Fisher) according to the commercial protocol. 2ug of total RNA was used for the construction of RNA sequencing libraries
RNA libraries for RNAseq were prepared using the NEBNext Ultra II Directional RNA kit according to manufacturers protocol

treatment_protocol: Cells were seeded in T75 flasks at 4*10^5 cells, 72hrs after adenoviral cre/gfp treatment. 24hrs post seeding cells were treated with 7.5uM of oxy (equal volume DMSO for controls) and cultured for 5days

value: Primary murine myoblasts

value: uqcrfs1 -/- (KO)


title: KE8_KO_OXY

value: Myoblast Proliferation under oxybutynin treatment


title: KE9_KO_OXY


title: KE7_KO_OXY


title: KE4_KO_DMSO


title: J1018_SCN


title: J965_SCN


title: J1199_NAC

source_name: NAC

value: NAC


title: HTC116 cells, Mutant, 1

value: colon

value: colon carcinoma

value: Mutant

value: pTpBat SRT Puro LE88RE100  (Mutant reporter transposon) + pCF2-pFV4a-MLT pBat Mutant S8A, S24A, S32A, S37A 2XCRD (Mutant pBAT transposase)


title: J1165_NAC


title: striatal nuclei, Dlx5/6-Cre;WT, Mouse ID#555, UPenn NGSC ID#110288

description: Library name: WT555

source_name: striatum


title: bleomycin, lung mesenchymal, adult, ATAC-seq

city: San Diego

first: Le

last: Xu

address: 8018 Regents Road Atp. 301

department: Pediatrics

institute: University of California, San Diego

description: scRNA-seq

library_source: genomic single cell

data_processing:
For data analysis, reads alignment (mouse genome mm10) and cell barcode demultiplex were conducted by using 10x Genomics Cell Ranger ATAC (version 2.1) with default settings. Quality control, TSS enrichment, data normalization, dimensional reduction and UMAP-based cell clustering were performed by Signac82. Analysis of differentially accessible peaks was performed by FindAllMarkers. ChromVAR44 was used to analyze differential TF binding motif activities between groups of cells. The expression features of marker genes, as well as the projection of motif enrichment scores, was profiled and visualized by R package ggplot2 (version 3.3.2).
Assembly: mouse mm10
Supplementary files format and content: For scATACseq, h5 files from cellranger and integrated Seurat object

growth_protocol: All mice were in B6 background. All mice were housed in facilities accredited by American Association for Accreditation of Laboratory Animal Care (AAALAC) at University of California San Diego. All animal husbandry and experiments were approved by Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
The lungs were perfused with 12 ml of cold DPBS (Life Technology) and then inflated with dissociation buffer (PRMI1640 (Thermo Scientific) with 10% FBS, 1mM HEPES (Life Technology), 1mM MgCl2(Life Technology), 1mM CaCl2 (Sigma-Aldrich), 0.525mg/ml collagenase D (Roche), 5unit/ml Dispase (Stemcell Technologies) and 0.05 mg/ml DNase I (Roche)). Minced lung was placed in dissociation buffer for 30 min at 37°C, and cell solution was filtered through 70μm and 40μm strainers. Ammonium-Chloride-Potassium (ACK) lysis was used to remove blood cells, and cell pellets were resuspended in FACS buffer. Antibodies used for flow cytometry include BV510-CD45, PE-Epcam, PE-CD31, APC-PDGFRa (all from BioLegend), and DAPI to label dead cells. 18,000 cells from each group were subjected to scATAC-seq following standard protocol by Center for Epigenomics at the University of California, San Diego.
Sample preparation and library construction were performed according published protocol doi:10.7554/eLife.62522

treatment_protocol: 8-week-old C57BL/6 wildtype mice were intratracheally administered with 1 unit/kg bleomycin or saline after anesthesia with ketamine (100 mg/kg) and xylazine (10 mg/kg). At day 14, the lungs were harvested.

value: mesenchymal cells, 14 days post BLM

value: wild type

value: single dose bleo (1.0U/kg)


title: KE5_KO_DMSO


title: striatal nuclei, Dlx5/6-Cre;Zswim6 c/c, Mouse ID#3, UPenn NGSC ID#110289

description: Library name: KO3


title: J1013_SCN

value: SCN


title: KE3_GFP_DMSO

value: uqcrfs1 +/+ (floxed)


title: control, lung mesenchymal, adult, ATAC-seq

description: scRNA-seq

value: mesenchymal cells, 14 days post Saline

value: Saline


title: Tmem cells, HP1g WT, R4

city: Toulouse

first: Olivier

last: Joffre

address: CHU Purpan

department: Infinity UMR1291

institute: Inserm

data_processing:
nf-core RNAseq pipeline v.3.9
Sequence reads were trimmed for adapter/low-quality sequence using nf-core/rnaseq pipeline (default parameters)
Trimmed sequence reads were mapped to the GRCm39/mm39 genome using nf-core/rnaseq pipeline (STAR aligner with default parameters)
Read count extraction was performed using nf-core/rnaseq pipeline (Salmon with default parameters)
Assembly: GRCm39 v.107
Supplementary files format and content: raw_counts.tsv: tab-delimited text file with length of each gene and their raw count values for each sample
Supplementary files format and content: tpm_counts.tsv: tab-delimited text file with TPM values for each sample

source_name: Spleen

growth_protocol: Treg were isolated from B6 Foxp3-Thy1.1 mice and cultured in complete medium (RPMI 1640 with 10% Fetal Calf Serum (FCS), 1 IU/mL penicillin, 1 μg/mL streptomycin, non-essential amino acids, 50 μM 2-Mercaptoethanol, 2 mM glutamine and 1 μM HEPES) supplemented with 500 IU/mL recombinant human IL-2, 0.1 ng/mL recombinant human TGFb 1 and anti-CD3/CD28 coated Dynabeads (1 bead per cell). After three days of culture, TCR stimulation was removed and cells were further cultured in fresh medium for 5 to 7 additional days.

extract_protocol:
RNA was harvested using Rneasy micro kit. 50 to 100 ng of total RNA was used for the constructio of the librairies.
RNA librairies for RNA-seq were prepared using Illumina Stranded mRNA Prep Ligation Kit following manufacturer's protocols.

value: Spleen

value: Tmem

value: HP1g WT

value: Treg transferred with HP1a KO Tconv


title: J1198_NAC


title: KE2_GFP_DMSO

value: Primary murine myoblasts


title: KE1_GFP_DMSO


title: td+, Saline

city: New York

first: Yinshan

last: Fang

address: 650W 168th Street

institute: Columbia University Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: matrix files

source_name: lung

extract_protocol:
To obtain single cell suspension, lung tissues were dissected, washed with PBS and then minced with a razor blade followed by digesting in a digestion buffer (2 mg/ml collagenase-IV, 2 mg/ml dispase II and 10 U/ml DNase I) for 30 min at 37°C. DMEM containing 10% FBS was added to stop digestion and then the cells were filtered through 100-μm and 40-μm strainers. After centrifuged at 300g for 5 min, the cell pellet was resuspended in red blood cell lysis buffer (Sigma), incubated for 2 min at 37°C, washed with HBSS containing 10% FBS and then centrifuged at 300g for 5 min to obtain cell pellet.  Cells were incubated with PE-Cy7-CD45 (Biolegend, 103114), APC-EpCAM (Biolegend, 118214) and BV711-CD31 (Biolegend, 102449) antibodies in FACS buffer (5% FBS with 0.5mM EDTA in PBS) for one hour at 4°C, and then incubated with Live/Dead stain dye for 10 min at room temperature to exclude dead cells. Live Tdtomato+CD45-EpCAM-CD31- mesenchymal cells were sorted by using BD Influx cell Sorter for single cell RNA sequencing (scRNA-seq).
Single Cell 3’ V3 chemistry kit (10x Genomics) was used to produce single-cell barcoded droplets and libraries according to the manufacturer's protocol.

value: lung

tag: age

value: 8-10 weeks

value: td+ lung mesenchymal cells

value: saline


title: J1160_NAC

value: NAC


title: Tmem cells, HP1a WT, R4

value: HP1a WT


title: J1159_NAC


title: Tmem cells, HP1g WT, R3


title: J1178_NAC


title: Tmem cells, HP1a KO, R3

value: HP1a KO


title: td+, bleomycin

description: 10x Genomics

value: bleomycin


title: Tmem cells, HP1a WT, R3


title: Tmem cells, HP1a KO, R2

value: Treg transferred with HP1a WT Tconv


title: J1177_NAC


title: J1141_NAC


title: J1164_NAC


title: Tmem cells, HP1a WT, R1


title: Tmem cells, HP1g KO, R4

value: HP1g KO


title: J1163_NAC


title: Tmem cells, HP1g WT, R1


title: Tmem cells, HP1g KO, R1


title: Tmem cells, HP1g KO, R3


title: J1140_NAC


title: Tmem cells, HP1a WT, R2


title: Tmem cells, HP1g KO, R2


title: WT2 LP Second

city: London

first: Patricia

last: Barral

address: Great Maze Pond

department: CIBCI

country: United Kingdom

institute: King's College London

data_processing:
Sample quality was assessed with FastQC with MultiQC used to inspect all samples together. Fastq files were trimmed using Cutadapt with a quality threshold of 10
Trimmed sequence reads were mapped to GRCm38.p6 mouse reference genome using RSEM/Bowtie2
QC of alignment was performed with Picard Tools (MarkDuplicates, CollectAligmentSummaryMetrics and CollectRnaSeqMetrics tools) to generate alignment metrics that were then inspected with MultiQC
FeatureCounts program from the subread package was used to aggregate the total read counts for each gene or exon. The raw count data was then imported into R and analysed using DESeq to identify differentially expressed genes (false discovery threshold(FDR) of 0.05) between tissues.
Assembly: Grcm38.p6
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: Small intestine lamina propria

extract_protocol:
RNA was harvested using Rneasy mini kit (QIAGEN). RNA was then quantified using with Nanodrop and submitted for RNA-sequencing.
Library preparation and whole transcriptome profiling was performed by The Francis Crick Institute Advanced sequencing facility. Sequencing libraries were prepared with 100ng total RNA with RN integrity (RIN) values of more than 7. The Nugen Ovation ultralow kit was used to prepare the sequencing libraries following manufacturer’s instructions. Libraries were barcoded and run on an Illumina HiSeq 2500system with paired-end read lengths of 101 bp

value: Small intestine lamina propria

value: iNKT cell


title: Tmem cells, HP1a KO, R4

value: Spleen


title: Tmem cells, HP1g WT, R2

value: Tmem