title: Col-0,case,rep2,scRNA-seq

city: Baoding

first: Qing

last: LIU

state: Hebei

address: Lingyusi Street

department: College of Horticulture, College of Life Sciences

country: Afghanistan

institute: Hebei Agricultural University

data_processing:
Multiome matrices were generated using the 10x Cell Ranger ARC pipeline (2.0.2) with TAIR10 genome. We first prepared the raw FASTQ files from the sequencing library. The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library)
we used NormalizeData, FindVariableFeatures, ScaleData RunPCA for scRNA-seq performed by Seurat (4.3.0).
Clusters for RNA-seq and ATAC-seq data were achieved using RunUMAP function (Seurat)
We obtained 21 original clusters for RNA-seq data with resolution set to 0.6, min.dist to 0.3, umap.method to “uwot”, metric to “cosine”, and dims ranging from 1 to 30.
Differentially expressed genes (DEGs) for RNA-seq analysis were calculated using the functions FindAllMarkers or FindMarkers (Seurat) with the Wilcox test, using an average log2 fold-change threshold of 1 and an adjusted P value of less than 0.05.
Assembly: TAIR10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
The nuclei isolation procedure was modified from the product information sheet of the CelLyticTM PN Isolation/Extraction Kit (Sigma). Briefly, Arabidopsis root tips (5mm) were chopped and mixed into 1× NIBTA buffer (1× NIB, 1mM dithiothreitol, 1× ProtectRNATM RNase inhibitor, 1× cOmplete™, ethylenediaminetetraacetic acid-free Protease Inhibitor Cocktail, and 0.3% Triton X-100) on prechilled plates, and homogenates transferred to 15mL tubes. Tubes were then shaken for 5min on ice, after which lysates were passed through 40μm strainers, and flow-throughs were collected into new 15mL tubes. These were then centrifuged for 10min at 1,260 × g, supernatants decanted, and pellets resuspended in 4mL of 1× NIBTA buffer. In new 15mL tubes containing 80% Percoll® solution (4mL Percoll® plus 1mL NIBTA buffer), lysates were carefully overlaid onto Percoll® layers. Tubes were centrifuged for 30min at 800 × g, after which most of the nuclei had banded at the 1× NIBTA buffer and Percoll® interface. Nuclei bands were gently collected into new 15mL tubes, 10mL of 1× NIBTA buffer was added, and the tubes were recentrifuged for 5min at 1260 × g. Nuclei pellets were then washed twice in 1× NIBTA buffer, resuspended in diluted nuclei buffer (10× Genomics) to a final concentration of 3,000nuclei/uL, and then used as an input for single cell multiome ATAC plus gene expression library preparation (15,000 nuclei in 5uL).
The single cell multiome ATAC + gene expression libraries following the 10x Genomics Chromium Next GEM Single Cell ATAC Reagent Kits v2 protocol and sequenced on an Illumina NovaSeq 6000 paired-end sequencing run (2 × 150 bp).

value: Root

value: missing

value: osmotic stress


title: Col-0,control,rep2,scRNA-seq

status: Public on Apr 25 2024

type: SRA

library_source: transcriptomic single cell

molecule: polyA RNA

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: WT


title: Col-0,control,rep1,scRNA-seq


title: KI990s59_heart_nuclei

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

country: USA

institute: Cincinnati Children's Hospital Medical Center

description:
sce14111_2w_07-07-2023.rds
RT_barcode_sample_lookup.csv
Ligation_barcode_plate.csv
P7_barcode_PCR_plate.csv

data_processing:
Pre-processing of the single-nucleus RNA-seq data was performed using the published sci-RNA-seq3 pipeline  76, available in Github (https://github.com/JunyueC/sci-RNA-seq3_pipeline). The sci-RNA-seq3 pipeline takes fastq files separated by the P7 index as input, aligns reads to the genome, and returns a gene-by-cell read count matrix. First, raw reads were trimmed to remove poly A tails, aligned to the mm39 mouse reference genome using STAR, and filtered for MAPQ greater than or equal to 30. Duplicate reads were removed based on UMI. Read counts per gene were computed for each cell defined by the unique combination of the RT index, ligation index, and P7 index. The gene-by-cell count matrix produced by the sci-RNA-seq3 pipeline was further processed in the SingleCellExperiment package framework in R (Amezquita et al. 2020). We used the scDblFinder package for doublet detection and the scuttle package for mitochondrial RNA quantification in R. We obtained 14,111 cells after filtering for cells with the scDblFinder doublet score less than 0.25 and mitochondrial RNA contamination percentage less than 2% of total RNAs per cell. Read counts for a gene were normalized by per-cell read depth and then log-transformed to obtain normalized expression values (“logcounts”). Logcounts were used to plot expression values in graphs. Principal component analysis (PCA) was performed on logcounts for 2,000 highly variable genes across cells using the fixedPCA function in the scran package. The top 50 principal components were used in the runUMAP function in the scater package with n_neighbors=20 and min_dist=1 parameters to obtain UMAP dimensions. To cluster cells, logcounts were processed in the clusterCells function in the scran package using the top 50 principal components, with the number of nearest neighbors k=12. Cell clusters were annotated manually with cell type names based on marker gene expression.
Assembly: Mouse mm39/Gencode basic vM27
Supplementary files format and content: gene_by_cell normalized read coverage in SingleCellExperiment object
Supplementary files format and content: 96-well RT primer index sequences in text file
Supplementary files format and content: 96-well Ligation primer index sequences in text file

organism: Mus musculus

source_name: Adult heart

growth_protocol: We used wild-type (n=3) and LmnaCKO mice (n=3) at 2 weeks post tamoxifen.

extract_protocol:
Mice were anesthetized with isoflurane, euthanized by cervical dislocation, and then hearts were perfused with 100 mM KCl. Removed hearts were diced into small pieces in cold PBS containing Diethyl pyrocarbonate (DEPC, Sigma D5758). Fresh heart pieces were dounce-homogenized to liberate nuclei in Hypotonic lysis buffer B (7.7 mM Na2HPO4, 4.5 mM NaH2PO4, 1.8 mM KH2PO4, 2.7 mM KCl, 10.3 mM NaCl, 3 mM MgCl2, 0.08% BSA, 0.025% Igepal CA-630, 1% DEPC) and passed through cell strainers. Nuclei were fixed in 1 mg/mL dithiobis(succinimidyl propionate) (DSP, Thermo Fisher 22585) for 15 min on ice, washed, and stored at –80°C until use.
For each mouse, 50,000 nuclei were placed in each of 8 wells of a 96-well plate (total 48 wells for 6 mice). The remaining 48 wells were filled with similarly processed mouse heart nuclei with comparable sample quality from an unrelated project. Nuclei were subjected to reverse-transcription with 96-indexed poly-T RT primers that contained a unique molecular identifier (UMI) sequence. Nuclei from all wells were combined and redistributed evenly to 96 wells. Redistributed cells were subjected to ligation with 96-indexed ligation primers in 96 wells (Table SX). Nuclei from all wells were combined again and redistributed evenly to 96 wells at 1,000 nuclei per well. Redistributed cells underwent second strand synthesis, protease digestion, tagmentation using N7-loaded Tn5 transposase, and PCR-amplified using 96-indexed PCR P7 primers and the unindexed P5 primer, for 16 cycles. PCR amplicons were combined and size-selected for DNA fragments between 250 bp and 600 bp.
Combinatorial indexing-based single-nucleus RNA-seq (sci-RNA-seq3)

value: Adult heart

tag: pool id


title: Col-0,case,rep2,scATAC-seq

description: 10X genomics single cell multiome ATAC plus gene expression library sequencing

library_source: genomic single cell

data_processing:
Multiome matrices were generated using the 10x Cell Ranger ARC pipeline (2.0.2) with TAIR10 genome.
We then set the non_nuclear_contigs parameter to Mt and Pt in cellranger-arc mkref process to avoid peak calling on contigs without chromatin structure. Finally, quantification was achieved using cellranger-arc count.
We used the “reduce” function from R package GenomicRanges(1.44.0) to merge all intersecting peaks from different batches. ATAC assay for each cell was created using R package Signac  (1.7.0). The peaks were added to gene expression matrix using FeatureMatrix and CreateChromatinAssay function in Signac package. All intersected peaks were filtered with a width threshold of less than 10,000 bp and greater than 20 bp. Seurat  (4.3.0) was used to obtain nuclei with high qualities of both RNA-seq and ATAC-seq (nCount_ATAC < 100,000, nCount_RNA < 25,000, nCount_ATAC > 1,000, nCount_RNA > 1,000, nucleosome_signal < 2 and TSS.enrichment > 1).
scATAC-seq we applied RunTFIDF, FindTopFeatures (min.cutoff = "q0") and RunSVD. Reduction and clustering are performed by Seurat (4.3.0).  For ATAC-seq data, we obtained 9 original clusters using resolution of 1, min.dist of 0.1, umap.method of “umap-learn”, reduction of “lsi”, metric of “correlation”, and dims ranging from 2 to 30. Subclustering for RNA-seq cluster 0, 1, 8, and 12 are performed under resolution 0.25, 0.3, 0.1, and 0.3, respectively. Subclustering for ATAC-seq cluster 0 is performed under resolution 0.5.
scATAC-seq we applied RunTFIDF, FindTopFeatures (min.cutoff = "q0") and RunSVD. Reduction and clustering are performed by Seurat (4.3.0).  For ATAC-seq data, we obtained 9 original clusters using resolution of 1, min.dist of 0.1, umap.method of “umap-learn”, reduction of “lsi”, metric of “correlation”, and dims ranging from 2 to 30. Subclustering for RNA-seq cluster 0, 1, 8, and 12 are performed under resolution 0.25, 0.3, 0.1, and 0.3, respectively. Subclustering for ATAC-seq cluster 0 is performed under resolution 0.5. DACRs were calculated using the same functions with the LR test, an average log2fold-change threshold of 0.125, an adjustedPvalue less than 0.05, and ATAC-seq count as the latent variable.
Assembly: TAIR10
Supplementary files format and content: Filtered feature-barcode matrices containing only cellular barcodes corresponding to gene expression and chromatin accessibility

molecule: genomic DNA


title: Control 6

city: Amsterdam

first: Luuk

middle: Elard

last: de Vries

address: Meibergdreef 47

department: Neuroregeneration

country: Netherlands

institute: Netherlands Institute for Neuroscience

library_source: transcriptomic

data_processing:
Sequence reads were trimmed to remove possible adapter sequences using cutadapt v 2.10. Reads were aligned to the human genome (GRCh38.p13) using STAR (2.7.10a) with default settings. Feature counting was performed with HTSeq v0.11.0. Samples were sequenced in two batches, with a minimal batch effect between runs. Sequence reads were trimmed to remove possible adapter sequences using cutadapt v 2.10. Reads were aligned to the human genome (GRCh38.p13) using STAR (2.7.10a) with default settings. Feature counting was performed with HTSeq v0.11.0. Samples were sequenced in two batches, with a minimal batch effect between runs.
Assembly: GRCh38.p13
Supplementary files format and content: Raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Grey matter SFG

extract_protocol:
RNA was isolated with RNeasy Mini Kit RNA (Qiagen, Valencia, CA, USA) in combination with Trizol (3 ml Trizol per 100 mg tissue; Life Technologies, Grand Island, NY, USA).
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process 35 samples (GenomeScan, Leiden, The Netherlands). Briefly, rRNA was depleted from total RNA using the rRNA depletion kit (NEB #E6310). After fragmentation of the depleted rRNA, a cDNA synthesis was performed for ligation with the sequencing adapters and PCR amplification. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used. At least 15 Gb, yielding ~30-40 million read pairs, was generated per sample with a quality score of ≥30.

value: Grey matter SFG

tag: condition

value: Control

tag: Sex

value: F

tag: batch

value: A


title: adult pancreas; PB2266-PAAD-T_S27_L007

city: Ulsan

first: Semin

last: Lee

address: 50, UNIST-gil

department: Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

data_processing:
The Cell Ranger pipeline was applied for pre-processing, including demultiplexing of sequencing results, barcode processing, read alignment, filtering of estimated droplets, and the generation of gene/barcode matrices. Reads were aligned to the GRCh38 human reference genome, and the UMI matrix of cell barcodes according to genes was generated for each sample.
Assembly: GRCh38
Supplementary files format and content: Raw_counts.txt.gz is a tab-delimited text file which includes UMI counts for all cells.

source_name: pancreas

extract_protocol:
All remaining tissues are collected in MACS® Tissue Storage Solution (Miltenyi Biotec., Auburn, CA, USA) on ice, and processed to the single cell dissociation immediately.
The sequenced libraries were processed using the HiSeqX platform from Illumina to obtain the requisite data for our study.

value: pancreas


title: KI990s58_heart_nuclei


title: KI990s61_heart_nuclei


title: KI990s62_heart_nuclei


title: adult pancreas; PB2266-PAAD-T_S26_L007


title: Control 5


title: KI990s57_heart_nuclei


title: Col-0,case,rep1,scRNA-seq


title: Control 4


title: Col-0,case,rep1,scATAC-seq


title: Col-0,control,rep2,scATAC-seq


title: adult pancreas; PB2266-PAAD-T_S25_L007


title: Control 2

value: M


title: Control 3


title: adult pancreas; PB2265-PAAD-T_S23_L006


title: KI990s54_heart_nuclei


title: KI990s55_heart_nuclei


title: adult pancreas; PB2265-PAAD-T_S24_L006


title: Col-0,control,rep1,scATAC-seq


title: P+ A14

city: Madrid

first: Leopoldo

last: González-Brusi

state: Madrid

address: Avda Puerta de Hierro, 12

department: Animal Reproduction

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

data_processing:
Paired-end read fastq files were quality checked with FastQC (Andrews, 2010) and preprocessed with fastp (Chen et al., 2018). Resulting files were pseudoaligned and quantified using kallisto (Bray et al., 2016) against the reference transcriptome of Homo sapiens hg38 (Ensembl release 102).
Assembly: Homo sapiens hg38 (Ensembl 102)
Supplementary files format and content: Tab-delimited text file with TPM normalized values for each Sample

source_name: cumulus cells associated to oocytes that developed to blastocysts and positive pregnancy outcome

extract_protocol:
Total RNA was extracted using MagMAX mirVana Total Isolation Kit (Applied Biosystems) following the manufacturer's instruction with minor modifications. Briefly 200 µl of Lysis Binding Mix were added to the sample, followed by gentle pipetting and 5 min incubation at room temperature. Then 20 µl of Binding Beads Mix were added and shaken gently for 5 min. Beads‐mRNA complexes were washed once in each Wash Solution 1 and 2. Following the washing step, samples were treated with 50 µl of Turbo DNAse treatment, 50 µl of Rebinding Buffer and 100 µl of Isopropanol were added to the sample and mixed gently. Finally, following a double wash in Wash Solution 2, total RNA was eluted in 20 µl of Elution Buffer and stored at −80°C until analysis.
RNA‐seq libraries were prepared with KAPA Stranded mRNA‐Seq Illumina Platforms Kit (Roche) following the manufacturer's recommendations. Briefly, 50–100 ng of total RNA was used for the poly‐A fraction enrichment with oligo‐dT magnetic beads, following the mRNA fragmentation. The strand specificity was achieved during the second strand synthesis performed in the presence of dUTP instead of dTTP. The blunt‐end double stranded cDNA was 3′ adenylated and Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on a HiSeq. 4000 system (Illumina) with a read length of 2 × 76 bp + 8 bp + 8 bp using the HiSeq. 4000 SBS kit (Illumina) obtaining >30 M reads/sample.

value: cumulus cells


title: adult pancreas; PB2265-PAAD-T_S21_L006


title: P+ A13


title: adult pancreas; PB2265-PAAD-T_S22_L006


title: KI990s53_heart_nuclei


title: KI990s52_heart_nuclei


title: AD 11

value: AD

value: B


title: adult pancreas; PB2264-PAAD-T_S20_L007


title: P+ A12


title: KI990s56_heart_nuclei


title: AD 10


title: KI990s51_heart_nuclei


title: adult pancreas; PB2264-PAAD-T_S20_L006


title: KI990s50_heart_nuclei


title: P+ A11


title: P- A10

source_name: cumulus cells associated to oocytes that developed to blastocysts but no pregnancy outcome


title: P+ A15


title: adult pancreas; PB2264-PAAD-T_S19_L007


title: Control 1


title: AD 12


title: AD 9


title: adult pancreas; PB2264-PAAD-T_S19_L006


title: AD 8


title: AD 7


title: adult pancreas; PB2264-PAAD-T_S18_L007


title: KI990s47_heart_nuclei


title: AD 6


title: adult pancreas; PB2264-PAAD-T_S18_L006


title: P- A8


title: KI990s46_heart_nuclei


title: AD 5


title: adult pancreas; PB2264-PAAD-T_S17_L007


title: KI990s49_heart_nuclei


title: AD 4


title: adult liver; PB2264-Livermeta-T_S8_L005

source_name: liver

value: liver


title: adult pancreas; PB2264-PAAD-T_S17_L006


title: P- A9


title: KI990s43_heart_nuclei


title: adult liver; PB2264-Livermeta-T_S7_L005


title: KI990s44_heart_nuclei


title: KI990s48_heart_nuclei


title: AD 3


title: Bl- A3

source_name: cumulus cells associated to oocytes that didn’t develop to blastocysts


title: KI990s41_heart_nuclei


title: KI990s45_heart_nuclei


title: KI990s42_heart_nuclei


title: P- A7


title: Bl- A4


title: AD 2


title: adult liver; PB2264-Livermeta-T_S6_L005


title: KI990s40_heart_nuclei


title: SW480-RSC (ROBO1neg), replicate 5

city: Irvine

first: Linzi

last: Hosohama

state: CA

address: 839 Health Sciences Court

institute: University of California Irvine

description: neg5 counts

data_processing:
Base Calling Software (Bcl2Fastq)
Paired-end sequencing reads were trimmed of adapter sequences and analyzed for quality using Fastqc using Base Calling Software (Bcl2Fastq v0.11.7).
Data was aligned to the human genome GRCh38 using STAR (v2.6.0c), converted to bam files and merged using samtools (v1.9).
Read count files were generated using Enthought Python (v7.3.2)
Differential gene expression analysis was performed in R studio (v1.1.423) with R (version v3.6.1) using default settings for the DESeq2 (v.1.24.0) pipeline for statistical analysis.
Normalized results were log2 transformed and filtered for padj value <0.01 using DESeq2 Wald P-value test for downstream DEG analyses.
Assembly: GRCh38
Supplementary files format and content: counts files per replicate

growth_protocol: SW480 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1X antimycotic-antibiotic (Lonza), 1X L-glutamine in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were collected in TRIzol Reagent (Invitrogen) and stored at -80˚C until all replicates were collected. RNA was isolated with the Direct-zol RNA Miniprep Kit (Zymo Research)
1µg of RNA was used for library generation using Illumina TruSeq Stranded mRNA Library Prep kit following manufacturer's protocols.

value: colorectal cancer epithelial cells

tag: subpopulation


title: Bl- A5


title: P- A6


title: Bl- A1


title: R2_4

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hanover Medical School

data_processing:
Alignment using HISAT2
Quantification using featureCounts
Assembly: Human reference (GRCh38) datasets
Supplementary files format and content: csv file containing raw counts

source_name: CRISPRi TERT hiPSCs

extract_protocol:
RNA was isolated using miRNeasy Mini Kit (Qiagen, 217004) according to the manufacturer’s guidelines
polyA-tail enrichment was performed. Subsequently mRNA was randomly fragmented and cDNA synthesis proceeds through the use of random hexamers and the reverse transcriptase enzyme. After synthesis of first chain teh second chain was synthesized with addition of an Illumina buffer along with dNTPs, RNAseH and polymerase I from E. coli by Nick translation. resulting products went through purification, end-repair, A-tailing and adapter ligation. Fragments of appropriate size are enriched by PCR where P5 and P7 primers are introduced and dinal products purified.

value: CRISPRi TERT hiPSCs

value: CRISPRi TERT hiPSCs reverse telomere

value: doxycyline treated for 5 passages then removed for 2 passages


title: AD 1


title: adult liver; PB2264-Livermeta-T_S5_L005


title: R2_3


title: adult liver; PB2264-Livermeta-T_S32_L008


title: Bl- A2


title: KI990s39_heart_nuclei


title: SW480-RSC (ROBO1neg), replicate 4

description: neg4 counts


title: adult liver; PB2264-Livermeta-T_S32_L001


title: R2_2


title: KI990s38_heart_nuclei


title: R2_1


title: SW480-RSC (ROBO1neg), replicate 3

description: neg3 counts


title: KI990s37_heart_nuclei


title: SW480-RSC (ROBO1neg), replicate 2

description: neg2 counts


title: D5_5

value: CRISPRi TERT hiPSCs short telomere

value: doxycyline treated for 5 passages


title: SW480-RSC (ROBO1neg), replicate 1

description: neg1 counts

value: WT


title: D5_4


title: adult liver; PB2264-Livermeta-T_S30_L008


title: KI990s36_heart_nuclei

value: Adult heart


title: adult liver; PB2264-Livermeta-T_S30_L001


title: adult liver; PB2264-Livermeta-T_S31_L008


title: adult liver; PB2264-Livermeta-T_S31_L001


title: KI990s35_heart_nuclei


title: SW480-CBC (ROBO1pos), replicate 5

description: pos5 counts


title: D5_2


title: SW480-CBC (ROBO1pos), replicate 4

description: pos4 counts


title: D5_1


title: KI990s33_heart_nuclei


title: SW480-CBC (ROBO1pos), replicate 3

description: pos3 counts


title: D2_5

value: CRISPRi TERT hiPSCs intermediate telomere

value: doxycyline treated for 2 passages


title: adult liver; PB2264-Livermeta-T_S29_L001


title: adult liver; PB2264-Livermeta-T_S29_L008


title: D2_4


title: KI990s32_heart_nuclei


title: adult pancreas; PB2256-PAAD-T_S52_L008


title: KI990s31_heart_nuclei


title: SW480-CBC (ROBO1pos), replicate 2

description: pos2 counts


title: SW480-CBC (ROBO1pos), replicate 1

description: pos1 counts


title: adult pancreas; PB2256-PAAD-T_S51_L008


title: D2_1


title: D2_3


title: KI990s30_heart_nuclei


title: HCT116 GFP-Transduced 3

city: Linköping

first: Johannes

middle: Artiaga

last: Gubat

address: Ing. 68 Campus US. Linköpings Universitet

department: Biomedical and Clinical Sciences

country: Sweden

institute: Linköping university

data_processing:
RNA-seq reads are aligned to hg19/GRC37,UCSC using Bowtie v2.2.9 and Tophat v2.0.14
Differential gene expression analysis was done using DESeq2 v1.40.3 with lfcThreshold parameter set to log2(1.2)
Assembly: hg19/GRC37,UCSC
Supplementary files format and content: tab delimited .txt file containing log fold change and p.values at the gene level

source_name: colon

growth_protocol: HCT116 cells were grown in McCoys 5A modified medium supplemented with 10%FBS and 100U of penicillin + streptomycin, maintained in 37C and 5% CO2

extract_protocol:
RNA was extracted from the cells using RNeasy plus mini (qiagen) using manufacturer protocols
library preparation is based on NEBNext Ultra II directional RNA library prep kit for Illumina

treatment_protocol: The cells were then transduced with either GFP-Cre or GFP lentiviral particles at a multiplicity of infection of 8, in medium containing 6µg/ul Polybrene. After 48 hours, fluorescence-activated cell sorting (FACS) with BD FACS Canto II (BD Biosciences) was done to separate GFP expressing cells.

value: colon

value: epithelial

value: USP14 floxed

value: GFP transduction


title: KI990s34_heart_nuclei


title: adult pancreas; PB2256-PAAD-T_S50_L008

value: pancreas


title: HCT116 GFP-Transduced 2


title: KI990s29_heart_nuclei


title: KI990s28_heart_nuclei


title: HCT116 GFP-Transduced 1


title: C2_4

value: CRISPRi TERT hiPSCs long telomere

value: untreated


title: C2_3


title: adult pancreas; PB2256-PAAD-T_S16_L007


title: KI990s27_heart_nuclei


title: adult pancreas; PB2256-PAAD-T_S49_L008


title: C2_2


title: HCT116 Cre-Transduced 3

value: Cre + GFP transduction


title: adult pancreas; PB2256-PAAD-T_S16_L005


title: HCT116 Cre-Transduced 2


title: adult pancreas; PB2256-PAAD-T_S15_L007


title: C2_1

value: CRISPRi TERT hiPSCs


title: KI990s25_heart_nuclei


title: adult pancreas; PB2256-PAAD-T_S15_L005


title: KI990s24_heart_nuclei


title: DRIP SCAN1#1 U2OS Rep2

city: Toulouse

first: Estelle

last: Nicolas

address: 118 route de Narbonne

country: France

institute: INSERM

description:
Instrument model: AVITI Element Biosciences
RNA-DNA hybrids
experiment # 2

library_source: genomic

data_processing:
Raw data quality was checked with FastQC (v0.11.5) and then aligned to the human hg38 reference genome with BWA-MEM (v0.7.17-r1188).
Supplementary alignments (flag 2048), reads with mapping quality lower than 25, and PCR duplicates were removed using the samtools suite (v1.9) and also for sorting and indexing BAMs.
BamCoverage from Deeptools (v3.5.1) was used to generate BigWig files with CPM normalization using the options: exactScaling, normalizeUsing CPM, binSize 1.
MACS3 callpeak (v3.0.0a6) with parameters -q 0.01 -f BAMPE were used on DRIP-seq BAM files and their input.
Assembly: hg38
Supplementary files format and content: Bigwig, narrowPeak
Library strategy: DRIP-seq

extract_protocol:
Non-crosslinked nuclei were isolated and genomic nucleic acids were extracted and sonicated. IPs were performed with the S9.6 antibody.
IP and Input samples were fragmented and libraries were performed using the NEBNext UltraTM II DNA Library Prep for Illumina (NEB) from 10 ng of samples. For IP samples only, a RNase H treatment to degrade the RNA in the RNA-DNA hybrids was performed before synthesis of second strand cDNA with dUTP mix.

value: TDP1 H493R (SCAN1)

tag: drip antibody

value: S9.6 antibody (MABE1095 Sigma-Aldrich (Merck), Mix of Lot#3695302 and #3774162)


title: adult pancreas; PB2256-PAAD-T_S14_L007


title: B6 WT Mouse Microglia-Macrophages 2.5 Month Timepoint

city: Chicago

first: Carla

middle: Marie

last: Cuda

state: IL

address: 240 E Huron St. M300

department: Medicine-Rheumatology

institute: Northwestern University

data_processing:
Processing of sequencing results to generate combined count matrices using the 10x genomics Cell Ranger pipeline version 6.0.0
Assembly: mm10-3.0.0
Supplementary files format and content: 10x Genomics filtered output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: brain

extract_protocol:
mice were transcardially perfused with ice cold HBSS. Brains were excised, meninges were removed and brains were placed in ice cold HBSS until processing. Brains were weighed, infused with digestion buffer (2.5 mg/mL Liberase TL [Roche, Basel, Switzerland] and 1 mg/mL DNase I in HBSS) using a 30g needle, cut into small pieces and placed into C-tubes (Miltenyi Biotec) containing 4 mL digestion buffer. C-tubes were placed on GentleMACS dissociator (m_brain_3_protocol; Miltenyi Biotec), incubated (30 minutes, 37°C, 200 rpm shaking) and placed on GentleMACS dissociator. Released cells were passed through 40 μm nylon mesh using a cell masher and washed with 100 ml autoMACS Running Buffer (Miltenyi Biotec). Microglia and infiltrating cells were isolated using 30/70-percoll gradient (Percoll Plus, GE Healthcare). Cells collected from gradient interphase were washed with HBSS and counted (Countess, Invitrogen); trypan blue discriminated dead cells. Cells were stained with live/dead Aqua viability dye (Invitrogen), incubated with Fc-Block (BD Biosciences) and stained with fluorochrome-conjugated antibodies. Live CD45+CD11b+ cells were sorted on a BD FACSAria into autoMACS Running Buffer, spun down, and counted with 16,000 cells loaded for partitioning.
Library preparation was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).  Chromium Single Cell v3 Reagent Kit and Controller (10X Genomics, Pleasanton, CA, USA)

value: brain

tag: library type

value: mRNA

value: C57BL/6J Wildtype

tag: age

value: 2.5 months

value: female


title: KI990s23_heart_nuclei

value: Adult heart


title: DRIP SCAN1#2 U2OS Rep2


title: pdz3cript_b2_wt_ctrl

city: Barcelona

first: Taraneh

last: Zarin

address: C/Dr. Aiguader 88

institute: Centre for Genomic Regulation

data_processing:
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Raw read files LTZ020_lib_04737AAD_RS2_GTCGATGC_R1_001.fastq.gz and LTZ020_lib_04737AAD_RS2_GTCGATGC_R2_001.fastq.gz were also used as technical replicates for cript2xa3_cis_input_biolrep1. Raw read files LTZ019_lib_04736AAD_RS2_TCAGATAC_R1_001.fastq.gz and LTZ019_lib_04736AAD_RS2_TCAGATAC_R2_001.fastq.gz were also used as technical replicates for cript2xa3_cis_input_biolrep2. These shared the same barcode with other samples (pdz3cript_b1_wt_ctrl and pdz3cript_b2_input_biolrep1) but contain different amplicons and therefore were further de-mutiplexed in data processing based on the specific designed sequences for each experiment.
Assembly: GRCh38
Supplementary files format and content: Tabular format with headers: aa_seq=amino acid sequence, WT=True if it is the wild type sequence, fitness=Average fitness/binding score of all replicates calculated by DiMSuM, sigma=standard error of the fitness measurement calculated by DiMSuM
Supplementary files format and content: For the processed files, the fitness estimates for the pdz3cript library were first normalized between block1 and block2 using a linear model between STOPs and synonymous substitutions in each block. Since all libraries shared common variants with the pdz3cript library and were strongly correlated (Pearson's r > 0.9), the common variants were used to linearly scale the fitness scores and sigma (error) associated with each variant.

organism: Saccharomyces cerevisiae

source_name: lab strain BY4741

growth_protocol: For each of the libraries of variants (cript_c, cript_n, pdz3cript [in 2 blocks, B1 and B2] and cript2xa3), each of the growth competitions were performed following transformation of yeast with each library in biological triplicates. After the first cycle of post-transformation plasmid selection, a second plasmid selection cycle (input) was performed by inoculating SD -URA/ADE at a starting OD600nm = 0.1 with the saturated culture. Cells were grown for 5 generations at 30ºC under constant agitation at 200 rpm. This allowed the pool of mutants to be amplified and enter the exponential growth phase. The competition cycle (output) was then started by inoculating cells from the input cycle into the competition media (SD -URA/ADE + 200 ug/mL Methotrexate) so that the starting OD600nm was 0.05. For that, the adequate volume of cells were collected, centrifuged at 3,000 rpm for 5 minutes and resuspended in the pre-warmed output media. Meanwhile, each input replicate culture was splitted in two and harvested by centrifugation for 5 min at 5,000g at 4ºC. Yeast cells were washed with water, pelleted and stored at -20ºC for later DNA extraction. After ~5 generations of competition cycle, each output replicate culture was splitted into two and harvested by centrifugation for 5 min at 5,000g at 4ºC, washed twice with water and pelleted to be stored at -20ºC

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 1 mL of DNA extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris-HCl pH8, 1mM EDTA pH8), frozen by dry ice-ethanol bath and incubated at 62ºC water bath twice. Subsequently, 1 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.1 mL of NaOAc 3M and 2.2 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC for 30 minutes. They were then centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was allowed to dry overnight at RT. DNA pellets were resuspended in 0.6 mL TE 1X and treated with 5 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (30 μL of QIAEX II beads). The samples were washed twice with PE buffer and eluted twice by 125 μL of 10 mM Tris-HCI buffer, pH 8.5 and then combined two elution. Finally, plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR using the primer pair oGJJ152-oGJJ153, that binds to the ori region of the plasmids.
We performed 2 consecutive PCR reactions for each sample (PCR1 and PCR2). In PCR1, we added frameshifting oligonucleotides and amplified the regions of interest (amplicon with constant region and mutated region) from the extracted DNA with 5 cycles. In PCR2 we added Illumina sequencing barcodes with PCR using the minimum number of cycles necessary to reach amplification plateau for each sample based on a qPCR run. The amplicon library pools were run on a 2% agarose gel and were purified using QIAEX II Gel Extraction Kit (QIAGEN) and using 30uL of QIAEX II beads for each sample. The purified amplicons were subjected to Illumina 150bp paired-end NextSeq sequencing.
PCR amplicon

value: yeast cells

tag: strain

value: lab strain BY4741

tag: variant

tag: group

value: ctrl

tag: block


title: DRIP WT U2OS Rep2

value: WT


title: KI990s22_heart_nuclei

tag: tissue


title: adult pancreas; PB2256-PAAD-T_S14_L005

value: pancreas


title: adult pancreas; PB2256-PAAD-T_S13_L007


title: KI990s21_heart_nuclei


title: INPUT SCAN1#2 U2OS Rep2

description:
Instrument model: AVITI Element Biosciences
experiment # 2

tag: cell line


title: adult pancreas; PB2256-PAAD-T_S13_L005


title: INPUT SCAN1#1 U2OS Rep2


title: KI990s20_heart_nuclei


title: pdz3cript_b2_output_biolrep3

tag: cell type

value: output


title: KI990s26_heart_nuclei


title: INPUT WT U2OS Rep2

tag: genotype


title: pdz3cript_b2_input_biolrep3

value: input


title: KI990s19_heart_nuclei


title: adult pancreas; PB2219-PAAD-T_S8_L007


title: KI990s18_heart_nuclei


title: pdz3cript_b2_output_biolrep2


title: adult pancreas; PB2219-PAAD-T_S8_L004


title: HCT116 Cre-Transduced 1

value: colon

value: epithelial

value: USP14 floxed

tag: treatment

value: Cre + GFP transduction


title: DRIP SCAN1#1 U2OS Rep1

description:
Instrument model: AVITI Element Biosciences
RNA-DNA hybrids
experiment # 1

value: TDP1 H493R (SCAN1)

value: S9.6 antibody (MABE1095 Sigma-Aldrich (Merck), Lot#3910138)


title: pdz3cript_b2_input_biolrep2


title: DRIP WT U2OS Rep1


title: adult pancreas; PB2219-PAAD-T_S7_L007


title: pdz3cript_b2_input_biolrep1

description:
Raw read files LTZ020_lib_04737AAD_RS2_GTCGATGC_R1_001.fastq.gz and LTZ020_lib_04737AAD_RS2_GTCGATGC_R2_001.fastq.gz were also used as technical replicates for cript2xa3_cis_input_biolrep1.
pdz3cript_sub.csv


title: adult pancreas; PB2219-PAAD-T_S7_L004


title: INPUT SCAN1#1 U2OS Rep1

description:
Instrument model: AVITI Element Biosciences
experiment # 1


title: KI990s17_heart_nuclei

tag: pool id


title: KI990s15_heart_nuclei


title: INPUT WT U2OS Rep1


title: KI990s16_heart_nuclei


title: KI990s14_heart_nuclei


title: adult pancreas; PB2219-PAAD-T_S6_L007


title: adult pancreas; PB2219-PAAD-T_S6_L004


title: pdz3cript_b1_output_biolrep2


title: pdz3cript_b1_output_biolrep3


title: pdz3cript_b2_output_biolrep1


title: pdz3cript_b1_output_biolrep1


title: hSFs, PvEVs stimulated

city: Badalona

first: Alberto

last: Ayllon-Hermida

state: Barcelona

address: Cami de les Escoles/Carretera de Can ruti s/n

department: PVREX

institute: ISGlobal

data_processing:
CellRanger V.7
Assembly: GRCh38
Supplementary files format and content: matrix.mtx / features.tsv / samples.tsv

source_name: Spleen

growth_protocol: 1.5 x 10^5 hSFs were seeded in a 6-well flat-bottom plate. Once 70-80% confluence was reached, EVs-depleted DMEM was introduced to each well. Subsequently, 100 µl of PvEVs was added to two wells, while 100 µl of PBS was added to two other wells. After 30 h of stimulation, cells were trypsinized and counted using a Neubauer chamber with Trypan Blue for viability assessment.

extract_protocol:
Next GEM Single Cell 3’ Reagents kits v3.1 (10x Genomics), following the manufacturer’s instructions. A total of 1.6 x 10^5 hSFs, from both the stimulated and non-stimulated groups, were independently loaded onto the Chromium Controller instrument (10X Genomics) to generate single-cell gel bead-in-emulsions (GEMs).
Chromium Controller instrument (10X Genomics) to generate single-cell gel bead-in-emulsions (GEMs)

treatment_protocol: 100 µl of PvEVs was added to each well, while 100 µl of PBS was added as a control in separated wells

value: Spleen

value: Human Spleen Fibroblast


title: adult pancreas; PB2219-PAAD-T_S5_L004


title: Normal plasma cell differentiation, replicat 2

city: Montpellier

first: Elina

last: Alaterre

address: 141 Rue de la Cardonille

institute: Institute of Human Genetics

description:
Rhapsody WTA+Stag
concat_NPCD_rep1_rep2.csv

data_processing:
Raw sequencing data were processed using the BD RhapsodyTM WTA Analysis pipeline on the online SevenBridges platform.
Reads were aligned to the hg19 reference human genome.
The demultiplexing of single-cell data was done using the Lex plugin (version 1.1) in the SeqGeq software (version 1.6.0).
Assembly: hg19
Supplementary files format and content: Comma-separated values files

source_name: Plasma cells

extract_protocol:
The four populations were tagged and pooled using the BD® Single-Cell Multiplexing Kit (Cat No: 633781). Tagged cells were subjected to scRNA-seq using the BD RhapsodyTM platform. Briefly, we aimed to capture ~2,500 cells per population in a BD RhapsodyTM cartridge composed of >200,000 microwells. Beads with oligonucleotide barcodes were added to saturation. Cell lysis leaded to the hybridization of RNA molecules to the beads. After reverse transcription, each cDNA molecule was then tagged on the 5’ end (3’ end of the mRNA molecule) with a unique molecular identifier and cell label indicating its cell of origin.
Whole transcriptome and sample tag libraries were prepared using the mRNA whole transcriptome analysis and sample tag library preparation workflow from BD RhapsodyTM.

value: Plasma cells


title: KI990s13_heart_nuclei

value: Adult heart


title: KI990s12_heart_nuclei


title: Normal plasma cell differentiation, replicat 1


title: pdz3cript_b1_input_biolrep3

value: yeast cells


title: adult pancreas; PB2219-PAAD-T_S28_L006


title: pdz3cript_b1_wt_ctrl

description:
Raw read files LTZ019_lib_04736AAD_RS2_TCAGATAC_R1_001.fastq.gz and LTZ019_lib_04736AAD_RS2_TCAGATAC_R2_001.fastq.gz were also used as technical replicates for cript2xa3_cis_input_biolrep2. These shared the same barcode with other samples (pdz3cript_b1_wt_ctrl and pdz3cript_b2_input_biolrep1) but contain different amplicons and therefore were further de-mutiplexed in data processing based on the specific designed sequences for each experiment.
pdz3cript_sub.csv

value: lab strain BY4741


title: KI990s11_heart_nuclei


title: adult pancreas; PB2219-PAAD-T_S27_L006


title: PC, scATACseq

description: SureCell ATAC-seq BioRad

data_processing:
The resulting sequencing data was performed using the Bio-Rad ATAC-Seq Analysis Toolkit.
Bead barcodes were parsed out of the R1 reads and appended to the R1 and R2 read names for all reads with valid barcodes. Debarcoded reads were aligned to the reference genome using BWA.
The peak calling was performed using MACS2 on the bulk ATAC-Seq alignment file and calculates fixed-width peaks around the summits of those peaks.
Assembly: hg19
Supplementary files format and content: BioRad toolkit: count_matrix.csv, peak_names_out.csv, fragments.sorted.tsv.gz

extract_protocol:
The SureCell ATAC-seq Library Preparation kit (BioRad) in combination with the indexes from the SureCell ATAC-seq Index kit (BioRad) were used. Cells viability and cell counting were performed using a TC20 automated cell counter (Biorad). Following filtration on a cell strainer (40μm pore size), 300k cells were used for nuclei isolation with lysis buffer. Following lysis, nuclei were counted and transposed for 30min at 37° following the aforementioned kit manual. A range of 3000-5000 cells/sample was used for droplet generation on a ddSEQ Single-cell Insulator (BioRad).
Fragments were barcoded and amplified on a C1000 Thermal Cycler (BioRad). Emulsion was broken and DNA samples were purified using Agencourt® AMPure® XP (Beckman Coulter). A second amplification of barcoded fragments was carried out for 7 or 9 cycles. Library clean-up was performed with Ampure beads and quantification with Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854).


title: KI990s10_heart_nuclei


title: hSFs, PBS stimulated


title: pdz3cript_b1_input_biolrep1


title: adult pancreas; PB2219-PAAD-T_S5_L007


title: adult pancreas; PB2219-PAAD-T_S26_L006


title: adult pancreas; PB2219-PAAD-T_S25_L006


title: cript2xa3_cis_output_biolrep3


title: PB, scATACseq

description: SureCell ATAC-seq BioRad

source_name: Plasmablasts

value: Plasmablasts


title: KI990s09_heart_nuclei


title: KI990s08_heart_nuclei


title: prePB, scATACseq

description: SureCell ATAC-seq BioRad

source_name: prePlasmablasts

value: prePlasmablasts


title: adult pancreas; PB2218-PAAD-T_S44_L008

value: pancreas


title: MBC, scATACseq

description: SureCell ATAC-seq BioRad

source_name: Memory B cells

value: Memory B cells


title: KI990s07_heart_nuclei


title: KI990s06_heart_nuclei


title: cript2xa3_cis_output_biolrep2

value: output


title: cript2xa3_cis_output_biolrep1


title: cript2xa3_cis_input_biolrep3

value: input


title: HL60_sgmir-663a_REP_C

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

data_processing:
The libraries were sequenced as paired-end 50bp reads on an Illumina NovaSeq6000 (Illumina) with a sequencing depth of approximately 25 million clusters per sample.
Raw data QC and processing was performed using the nf-core/rnaseq v1.4.2 workflow.
Reads were trimmed using Trim Galore! v0.6.4 and aligned using STAR v2.6.1d
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw read counts for each replicate.

source_name: tumor, blood

growth_protocol: Cells were grown under optimized conditions in RPMI supplemented with 10% FCS (PC9, HL60), DMEM supplemented with 10% FCS (MCF7), or McCoy's supplemented with 10% FCS (HT29).

extract_protocol:
RNA was isloated using RNeasy mini plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
mRNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit

value: tumor, blood

value: acute myeloid leukemia


title: pdz3cript_b1_input_biolrep2


title: KI990s05_heart_nuclei

source_name: Adult heart


title: HL60_sgmir-663a_REP_B


title: adult pancreas; PB2218-PAAD-T_S42_L008


title: cript2xa3_cis_input_biolrep2


title: HL60_sgmir-663a_REP_A


title: adult pancreas; PB2218-PAAD-T_S41_L008


title: KI990s04_heart_nuclei


title: cript2xa3_cis_input_biolrep1


title: KI990s03_heart_nuclei


title: adult pancreas; PB2218-PAAD-T_S4_L007


title: HL60_sgmir-483_REP_B


title: cript_c_output_biolrep3


title: HL60_sgmir-483_REP_C


title: adult pancreas; PB2218-PAAD-T_S4_L004


title: cript_c_output_biolrep2


title: KI990s02_heart_nuclei


title: HL60_sgmir-483_REP_A


title: adult pancreas; PB2218-PAAD-T_S3_L007


title: KI990s01_heart_nuclei


title: cript_c_output_biolrep1


title: HL60_empty_REP_C

value: empty control for lentiCRISPRv2


title: adult pancreas; PB2218-PAAD-T_S3_L004


title: adult pancreas; PB2218-PAAD-T_S43_L008


title: AE020_mRNA_heart_80863

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

data_processing:
High-throughput sequencing reads were aligned to the mouse mm39 reference genome with the Gencode vM27 basic annotation using STAR version 2.7.9 73 with the default alignment parameters except “clip3pAdapterSeq AGATCGGAAGAGCACACGTCTGAACTCCAGTCA”. From raw read counts per transcript, TPM (transcripts per million) was calculated in R as follows: TPM=106 x RPK/sum(RPK), where RPK=read count/transcript length in kp and sum(RPK) is the sum of RPKs of all transcripts.
Assembly: Mouse mm39/Gencode basic vM27
Supplementary files format and content: Counts or TPMs in a text file

extract_protocol:
Hearts were perfused with 100 mM KCl and removed for RNA extraction. Total RNAs were extracted with Trizol LS (Invitrogen, 10296010), treated with DNaseI, and purified.
For tamoxifen time course experiments, mRNA sequencing libraries were generated using the poly-A selection module in the NEBNext UltraII Directional RNA Library Prep Kit (NEB E7760) and sequenced on the Illumina HiSeq 2500 sequencer with single-end 50 cycles. For cGas/Lmna double knockout experiments, libraries were generated using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, K01596) and sequenced on the Illumina NovaSeq 6000 sequencer with single-end 100 cycles.

treatment_protocol: All mice used in experiments were administered with tamoxifen (Sigma, T5648) at 6-8 weeks of age via intraperitoneal injections (100 μL of 4 mg/mL solution per day for 4 consecutive days) dissolved in corn oil (Sigma, C8267).

tag: treatment 1

value: 2 weeks post tamoxifen

value: Lmna F/F; cGas null/null; Myh6MCM Tg/0

value: M


title: AE019_mRNA_heart_80605

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Lmna F/F; cGas +/+; Myh6MCM Tg/0

tag: Sex

value: F

value: QuantSeq 3’ mRNA-Seq Library Prep Kit FWD


title: adult pancreas; PB2218-PAAD-T_S2_L007


title: AE018_mRNA_heart_80601

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Adult heart


title: HL60_empty_REP_A


title: adult pancreas; PB2218-PAAD-T_S2_L004


title: PC9_sgmir-663a_REP_C

source_name: tumor, lung

value: tumor, lung

value: lung adenocarcinoma


title: HL60_empty_REP_B


title: AE017_mRNA_heart_80597

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Lmna F/+; cGas +/+; Myh6MCM Tg/0


title: adult pancreas; PB2218-PAAD-T_S1_L007

source_name: pancreas

value: pancreas


title: AE016_mRNA_heart_80393

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: cript_c_input_biolrep1

value: yeast cells

value: lab strain BY4741


title: adult pancreas; PB2218-PAAD-T_S1_L004


title: cript_n_output_biolrep2

value: output


title: PC9_sgmir-663a_REP_B


title: cript_n_output_biolrep3


title: PC9_sgmir-663a_REP_A


title: AE015_mRNA_heart_80387

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: cript_n_output_biolrep1


title: cript_c_input_biolrep3

value: input


title: adult pancreas; PB2203-PAAD-N_S1_L001


title: AE014_mRNA_heart_80744

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Lmna F/+; cGas null/null; Myh6MCM Tg/0


title: PC9_sgmir-483_REP_B


title: AE013_mRNA_heart_80742

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: PC9_sgmir-483_REP_C


title: cript_c_input_biolrep2


title: cript_n_input_biolrep3


title: adult pancreas; PB2191-PAAD-T_S1_L001


title: adult pancreas; PB2191-PAAD-N_S1_L001


title: cript_n_input_biolrep2


title: AE012_mRNA_heart_80603

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: adult liver; PB2191-Livermeta-T_S1_L001

value: liver


title: PC9_empty_REP_C

value: empty control for lentiCRISPRv2


title: cript_n_input_biolrep1


title: SPL4

city: xi'an

first: yujing

last: xiong

state: Shaanxi

address: Xinyi Road, Baqiao District

department: Obstetrics and Gynecology

country: China

institute: Tangdu Hospital of Air Force Medical University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: GRCh38
Supplementary files format and content: excel,expression profiles

source_name: circulating exosomes

extract_protocol:
Serum exosomes were extracted using Plasma/Serum Exosome Purification Kit (Norgen Biotek, Canada), total RNA was extracted using Exosomal RNA Isolation Kit (Norgen Biotek, Canada) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: sporadic pregnancy loss

tag: exosome source

value: serum

tag: type

value: pregnant woman

tag: pregnancy days


title: PC9_empty_REP_B


title: AE010_mRNA_heart_80602

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: 2 weeks post tamoxifen

value: M

tag: library type


title: adult pancreas; PB2203-PAAD-T_S1_L001


title: AE009_mRNA_heart_80385

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Adult heart

value: Lmna F/F; cGas +/+; Myh6MCM Tg/0

value: F

value: QuantSeq 3’ mRNA-Seq Library Prep Kit FWD


title: SPL3


title: PC9_empty_REP_A

value: tumor, lung

value: lung adenocarcinoma


title: adult pancreas; PB2155-PAAD-T_S1_L003

value: pancreas


title: SPL2


title: HT29_sgmir-663a_REP_C

source_name: tumor, colon

value: tumor, colon

value: colorectal adenocarcinoma


title: adult pancreas; PB2155-PAAD-T_S1_L002


title: SPL1


title: AE008_mRNA_heart_81195

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Lmna F/F; cGas null/null; Myh6MCM Tg/0


title: HT29_sgmir-663a_REP_B


title: RPL4

value: recurrent pregnancy loss


title: AE007_mRNA_heart_80371

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Lmna F/+; cGas +/+; Myh6MCM Tg/0


title: AE006_mRNA_heart_80739

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: adult pancreas; PB2155-PAAD-T_S1_L001


title: PC9_sgmir-483_REP_A


title: RPL3


title: adult pancreas; PB2155-PAAD-N_S1_L004


title: AE011_mRNA_heart_80370

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: AE005_mRNA_heart_80862

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Lmna F/+; cGas null/null; Myh6MCM Tg/0


title: HT29_sgmir-483_REP_C


title: adult pancreas; PB2155-PAAD-T_S1_L004


title: adult pancreas; PB2155-PAAD-N_S1_L003


title: RPL2

value: serum


title: HT29_sgmir-483_REP_B


title: adult pancreas; PB2155-PAAD-N_S1_L002


title: AE004_mRNA_heart_80389

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: HT29_empty_REP_C

value: empty control for lentiCRISPRv2


title: OP5

value: ongoing pregnancy

value: pregnant woman


title: AE003_mRNA_heart_80386

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Adult heart

value: 2 weeks post tamoxifen

value: M


title: adult liver; PB2155-Livermeta-T_S1_L004

source_name: liver

value: liver


title: adult pancreas; PB2155-PAAD-N_S1_L001


title: RPL1


title: AE002_mRNA_heart_80374

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: QuantSeq 3’ mRNA-Seq Library Prep Kit FWD


title: HT29_empty_REP_B


title: HT29_sgmir-663a_REP_A


title: adult liver; PB2155-Livermeta-T_S1_L003


title: OP3


title: OP2


title: adult liver; PB2155-Livermeta-T_S1_L002


title: HT29_empty_REP_A


title: MFC7_sgmir-663a_REP_C

source_name: tumor, breast

value: tumor, breast

value: breast adenocarcinoma


title: Edited Dmdmdx; Pax7-nGFP myoblasts line 72

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
bcl2Fastq v2.20 software used for demultiplexing + basecalling.
fastp v0.20 used for trimming adapter sequences and low quality reads.
Pseudocounts generated with kallisto v0.46.1, options: -t 8 --bias --bootstrap-samples 10 --seed 42 --single --fragment-length 180 --sd 50
Assembly: GRCm39
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts and TPMs.

source_name: Myoblasts derived from intraspecies mouse chimeras

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

value: Dmdmdx; Pax7-nGFP

value: CRISPR/Cas9 gene editing to correct mdx mutation


title: adult liver; PB2155-Livermeta-T_S1_L001


title: Edited Dmdmdx; Pax7-nGFP myoblasts line 67

value: Myoblasts derived from intraspecies mouse chimeras


title: OP1


title: MFC7_sgmir-663a_REP_B


title: HT29_sgmir-483_REP_A

value: tumor, colon

value: colorectal adenocarcinoma


title: Edited Dmdmdx; Pax7-nGFP myoblasts line 66


title: CON_5

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

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: Skin or mucosa

extract_protocol:
Tissue were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CA means specimen of condyloma acuminatum, CON means the adjcent mucocal tissues

value: adjcent mucocal tissues


title: adult pancreas; PB2151-PAAD-T_S1_L004

value: pancreas


title: MFC7_sgmir-663a_REP_A


title: 18DIV cortical neurons, KIS shRNA, replica B3

first: Carme

last: Gallego

state: Catalonia

address: Baldiri Reixac 15 3-A16

institute: IBMB-CSIC

data_processing:
Reads were aligned to the mm10 mouse genome using HISAT2 in the Galaxy platform. Assignment to transcriptional units, standard filtering steps and basic statistical analysis of triplicate samples was done using Rsubread (version 3.6) in Bioconductor and custom R scripts.
Assembly: mm10
Supplementary files format and content: CSV files containing raw read counts per gene or exon

source_name: cortical neurons

extract_protocol:
Total RNA was obtained using EZNA total RNA purification kit (Omega, R6834-01).
PolyA+ enriched libraries were prepared for paired-end (2x100 bp) sequencing (BGI DNBSEQ platform).

value: cortical neurons

value: KIS knockdown


title: adult pancreas; PB2151-PAAD-T1_S1_L002

data_processing:
The Cell Ranger pipeline was applied for pre-processing, including demultiplexing of sequencing results, barcode processing, read alignment, filtering of estimated droplets, and the generation of gene/barcode matrices. Reads were aligned to the GRCh38 human reference genome, and the UMI matrix of cell barcodes according to genes was generated for each sample.
Assembly: GRCh38
Supplementary files format and content: Raw_counts.txt.gz is a tab-delimited text file which includes UMI counts for all cells.

extract_protocol:
All remaining tissues are collected in MACS® Tissue Storage Solution (Miltenyi Biotec., Auburn, CA, USA) on ice, and processed to the single cell dissociation immediately.
The sequenced libraries were processed using the HiSeqX platform from Illumina to obtain the requisite data for our study.


title: CON_4


title: OP4

value: ongoing pregnancy

value: serum

value: pregnant woman


title: MFC7_sgmir-483_REP_C


title: adult pancreas; PB2151-PAAD-T_S1_L003


title: AE001_mRNA_heart_80372

first: Kohta

last: Ikegami

address: 240 Albert Sabin Way, Cincinnati, OH 45229

institute: Cincinnati Children's Hospital Medical Center

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Adult heart

value: 2 weeks post tamoxifen

value: Lmna F/+; cGas null/null; Myh6MCM Tg/0

value: M


title: CON_3


title: MFC7_sgmir-483_REP_B

value: tumor, breast

value: breast adenocarcinoma


title: adult pancreas; PB2151-PAAD-T_S1_L002


title: 18DIV cortical neurons, KIS shRNA, replica B1


title: CON_2


title: 18DIV cortical neurons, KIS shRNA, replica B2


title: 18DIV cortical neurons, ctrl shRNA, replica A3

value: wt


title: adult pancreas; PB2151-PAAD-T_S1_L001


title: MFC7_empty_REP_C

value: empty control for lentiCRISPRv2


title: 18DIV cortical neurons, ctrl shRNA, replica A2


title: 18DIV cortical neurons, ctrl shRNA, replica A1


title: adult pancreas; PB2151-PAAD-N_S1_L003


title: MFC7_empty_REP_B


title: MFC7_sgmir-483_REP_A


title: CA_4

value: specimen of condyloma acuminatum


title: adult pancreas; PB2151-PAAD-N_S1_L002


title: CA_3


title: MFC7_empty_REP_A


title: CA_2


title: adult pancreas; PB2151-PAAD-N_S1_L001


title: muscle, 30d, ScRNA-seq

city: Wuhan City

first: Qi

last: Liu

address: Huazhong Agricultural University, Hongshan District, Wuhan City, Hubei Province

institute: Huazhong Agricultural University

description: 10x Genomics

data_processing:
The demultiplexing,barcoded processing,gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
Assembly: ASM1881202v1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Megalobrama amblycephala

source_name: dorsal skeletal muscle

extract_protocol:
Dorsal skeletal muscle tissue was obtained from Megalobrama amblycephala. Place a sterile RNase-free culture dish containing an appropriate amount of calcium-free and magnesium-free 1 × PBS on ice, the tissue was transferred into the culture dish and cut it into 0.5 mm2 pieces, the tissues were washed with 1 × PBS, and remove as many non-purpose tissues as possible such as blood stains and fatty layers. Tissues were dissociated into single cells in dissociation solution in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum , then pipetting 5-10 times with a Pasteur pipette. The resulting cell suspension was filtered by passing through 40μm stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added with 2-3 ml 1× red blood cell lysis buffer（Invitrogen, 00-4333） and incubated at room temperature for 2-4 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. Then the suspension was resuspended in 1× PBS (0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C (repeat twice).The cell pellet was resuspended in appropriate volume of 1× PBS (0.04% BSA).
Library was performed according to the manufacter's instructions (single cell 3'v3.1 protocol,10x Genomics). A Chromium Single Cell 3’ Library & Gel Beads Kit v3.1 (10x Genomics) was used to generate oligo-dT-primed cDNA libraries according to the manufacturer’s protocol. Subsequently, they were sequenced on an Illumina NovaSeq 6000 platform with a paired-end 150 read length.

value: dorsal skeletal muscle


title: muscle, 45d, ScRNA-seq

description: 10x Genomics


title: adult pancreas; PB2032-PAAD-T2_S20_L007

first: Semin

last: Lee

address: 50, UNIST-gil

institute: Ulsan National Institute of Science and Technology


title: adult pancreas; PB2032-PAAD-T2_S20_L003


title: cth1Δcth2Δ mutant Ribo-seq, 6H, replicate 3

city: Boston

first: Vyacheslav

last: Labunskyy

state: MA

address: 609 Albany St

department: Department of Dermatology

institute: Boston University School of Medicine

data_processing:
Library strategy: Ribo-Seq
De-multiplexing and base-calling was performed by Harvard University Bauer Center Sequencing Core
Sequence reads were trimmed for 3' adaptor sequence with cutadapt v.3.4
rRNA sequences were removed using alignment with bowtie v1.1.2
Sequence reads were mapped to the yeast genome with STAR 2.7.9a
Quantitation of reads was performed with Rsubread v.1.22.2
Genome_build: R64-2-1
Supplementary_files_format_and_content: Tab-delimited txt files with 3 columns: 1. SGD ORF name, 2. transcript length, 3. counts

source_name: Whole cells

growth_protocol: Cells were grown in 500 mL of Kaiser SC media at 30°C for at least 15 hours to reach early exponential phase (OD600=0.2). Wild-type (W303a) and cth1Δcth2Δ mutant strains were treated with 100 μM of the Fe2+-specific chelator bathophenanthroline disulfonic acid (BPS) for 3h and 6h and collected using 0.45 µm PVDF membrane. Cells were flash frozen in liquid nitrogen and stored at -80C. As a control we collected wild-type (W303a) and cth1Δcth2Δ mutant cells that were grown in Fe-sufficient conditions (0h). Each sample was collected in triplicates (biological replicates) for each deletion strain and wild-type controls.

extract_protocol:
Lysates were subjected to ribosome footprinting by RNAse I treatment. After sucrose density gradient fractionation ribosome-protected fragments were purified from 80S peak fractions. In parallel, mRNA was isolated with Dynabeads mRNA Purification Kit (Life technologies) and subjected to alkaline hydrolysis. Fragments of 50-75 nt were used for library preparation.
The RNA-seq and Ribo-seq libraries were prepared using ARTseq Ribosome Profiling kit (Illumina)

treatment_protocol: Yeast extracts were prepared by cryogrinding with BioSpec cryomill. Extracts were resuspended in buffer containging cycloheximide, and aliquots of cell lysates were used for footprint extraction and isolation of total RNA.

value: cth1deltacth2delta mutant

tag: hours in fe-deficient conditions


title: Sample 26_HeLa cells, mRNA, eIF3h KD, rep2

city: Prague

first: Anna

last: Herrmannová

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Microbiology of the Czech Academy of Sciences

description: Raw data were originally paired-end but only read 1 was analysed and is provided here

data_processing:
Sample1 -Sample12:
Adapter sequence “CTGTAGGCACCATCAAT” and all sequences 3’ of the adapter were trimmed from the 3’ end of each read; flanking Ns were trimmed from both 5' and 3' ends of each read; and reads without adapter sequence and reads shorter than 15 nt after trimming were discarded by Cutadapt v. 3.5
rRNA and tRNA reads were discarded after alignment with Bowtie2 v. 2.4.4. Used sequences rRNA: RNA5S1, RNA5-8SN5, RNA18SN5 and RNA28SN5 from NCBI, and ENSG00000211459 and ENSG00000210082 from Ensembl. Used sequences tRNA: human tRNA sequences from tRNAdb and all high confidence hg38 tRNA sequences from GtRNAdb.
Reads were aligned to genome and transcriptome from Ensembl (GRCh38.p13, annotation release 104) by the STAR aligner v. 2.7.9a_2021-06-25 using local alignment with 10% mismatches, and with indels and soft clipping allowed for transcriptomic alignment
Alignments were indexed using Samtools index v. 1.13
Read counts within CDS region were counted with Htseq-count v. 0.13.5
Sample13-Sample28:
First 3 nucleotides on the 5’ end were removed, and poly(A) sequence (10xA) was trimmed from the 3’end; flanking Ns were trimmed from both 5' and 3' ends of each read; and reads without adapter sequence and reads shorter than 15 nt after trimming were discarded by Cutadapt v. 3.5
rRNA and tRNA reads were discarded after alignment with Bowtie2 v. 2.4.4. Used sequences rRNA: RNA5S1, RNA5-8SN5, RNA18SN5 and RNA28SN5 from NCBI, and ENSG00000211459 and ENSG00000210082 from Ensembl. Used sequences tRNA: human tRNA sequences from tRNAdb and all high confidence hg38 tRNA sequences from GtRNAdb.
Reads were aligned to genome and transcriptome from Ensembl (GRCh38.p13, annotation release 104) by the STAR aligner v. 2.7.9a_2021-06-25 using local alignment with 10% mismatches, and with indels and soft clipping allowed for transcriptomic alignment
Alignments were indexed using Samtools index v. 1.13
Read counts within CDS region were counted with Htseq-count v. 0.13.5
Assembly: GRCh38.p13, annotation release 104
Supplementary files format and content: Ensembl gene identifiers and gene counts in tab-separated values file format

source_name: HeLa

growth_protocol:
Sample1 -Sample12:
HeLa cells were grown at 37 °C and 5% CO2 in Ø 15 cm dishes in DMEM supplemented with 10% FBS.
Sample13-Sample28:
HeLa cells were grown at 37 °C and 5% CO2 in Ø 15 cm dishes in DMEM supplemented with 10% FBS.

extract_protocol:
Sample1 -Sample12:
For footprint libraries cycloheximide was added to a final concentration of 100 µg/ml 1 min prior to harvesting. Cells were washed with ice cold 1x PBS and lysed in buffer A (10 mM HEPES [pH 7.5], 62.5 mM KCl, 2.5 mM MgCl2, 1 mM DTT, 1mM PMSF, 1 µg/ml Aprotinin, 1 µg/ml Leupeptin, 1 µg/ml Pepstatin, Complete Mini EDTA-free [Roche] – 1 tablet/5 ml, 1% Triton X-100, 100 µg/ml Cycloheximide) on the dish. The resulting lysate was collected and cleared by centrifugation. Aliquots of twelve absorbance units (AU) OD260 of WCE were flash frozen in liquid nitrogen and used for footprint isolation. One aliquot of 12 AU OD260 was thawed on ice, digested with 5 µl RNAseI (Ambion) for 30 min at 24 °C with mild shaking (300 rpm) and inactivated with SuperaseIN (Ambion). 80S ribosomes were separated by high-velocity sedimentation through a 5% to 45% sucrose gradient at 39,000 rpm for 2.5 h using the SW41Ti rotor. The gradients were scanned at 254 nm to visualize the ribosomal species and fractions containing 80S ribosomes were collected and mixed with RNA Blue (TopBio). RNA was isolated according to vendor’s instructions, FP RNA was size selected on 15% TBE-Urea PAGE (Biorad) in range 20-40 nt.
Sample13-Sample28:
For mRNA libraries the growth media was aspirated and cells were harvested into 5 ml of RNA Blue per Ø 15 cm dish. RNA was isolated according to vendor’s instructions. mRNA was isolated from the total RNA using Poly(A)purist MAG kit (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and size selected on 15% TBE-Urea PAGE in range 50-100 nt.
Sample1 -Sample12:
According to Ingolia et al., 2010, Methods Enzymology
Sample13-Sample28:
library was prepared using SMARTer smRNA-Seq Kit (TAKARA) according to vendor’s instructions

treatment_protocol:
Sample1 -Sample12:
Twenty-four hours after seeding, cells were transfected with the ON-TARGETplus siRNA cocktail system from Dharmacon at a final concentration of 5 nM. INTERFERin (Polyplus) was used as a transfection reagent, 100 ul were used per dish. Cells were harvested 72 hours after transfection at approximately 80% confluency.
Sample13-Sample28:
Twenty-four hours after seeding, cells were transfected with the ON-TARGETplus siRNA cocktail system from Dharmacon at a final concentration of 5 nM. INTERFERin (Polyplus) was used as a transfection reagent, 100 ul were used per dish. Cells were harvested 72 hours after transfection at approximately 80% confluency.

value: HeLa

value: human epithelial cell

value: EIF3H knock down

value: eIF3h siRNA, 72 hours


title: NEM316 WT Replicate 2

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 2.10. Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 2.5.1, with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 2.0.0 from Subreads package (parameters: -t locus_tag -g ID -s 1).
Count data were analyzed using R version 4.0.5 and the Bioconductor package DESeq2 version 1.30.1. The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed with(out) applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the biological condition. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially  expressed.
Assembly: Streptococcus agalactiae BM110 (from NCBI id=318722, NCBI RefSeq reference NZ_LT714196)
Assembly: Streptococcus agalactiae NEM316 (from NCBI id=165229, NCBI RefSeq reference NC_004368)
Supplementary files format and content: DESeq 2 output matrix

organism: Streptococcus agalactiae NEM316

source_name: bacterial cell

growth_protocol: Bacterial cultures in rich media (THY) incubated at 37°C in static condition are harvested in exponential growth phase (OD600 = 0.5).

extract_protocol:
Total RNA are extracted after cell wall mechanical lysis with 0.1 µm beads (Precellys Evolution, Bertin Technologies) in RNApro reagent (MP Biomedicals), and purified by chloroform extraction and ethanol precipitation.
Depletion of rRNA (FastSelect Bacterial, Qiagen) and libraries construction ((TruSeq Stranded mRNA, Illumina) are done following manufacturer instructions.

treatment_protocol: Bacterial pellets are washed with cold PBS containing RNA stabilization reagents (RNAprotect, Qiagen) before flash freezing and storage at -80°C.

value: bacterial cell

value: WT


title: Sample 25_HeLa cells, mRNA, eIF3h KD, rep1


title: CON_1

value: adjcent mucocal tissues


title: NEM316 WT Replicate 3


title: Sample 27_HeLa cells, mRNA, eIF3h KD, rep3


title: adult pancreas; PB2151-PAAD-N_S1_L004

city: Ulsan

value: pancreas


title: CA_5


title: cth1Δcth2Δ mutant Ribo-seq, 6H, replicate 1

tag: strain


title: cth1Δcth2Δ mutant Ribo-seq, 6H, replicate 2


title: NEM316 ∆gdpP Replicate 3

value: {delta}gdpP


title: Sample 28_HeLa cells, mRNA, eIF3h KD, rep4


title: adult pancreas; PB2032-PAAD-T2_S18_L007


title: adult pancreas; PB2032-PAAD-T2_S18_L003


title: Sample 22_HeLa cells, mRNA, eIF3e KD, rep2

value: EIF3E knock down

value: eIF3e siRNA, 72 hours


title: cth1Δcth2Δ mutant Ribo-seq, 3H, replicate 2


title: cth1Δcth2Δ mutant Ribo-seq, 3H, replicate 3


title: NEM316 ∆gdpP Replicate 1


title: cth1Δcth2Δ mutant Ribo-seq, 3H, replicate 1


title: NEM316 ∆gdpP Replicate 2


title: adult pancreas; PB2032-PAAD-T2_S17_L007


title: adult pancreas; PB2032-PAAD-T2_S19_L007


title: NEM316 ∆busR Replicate 3

value: {delta}busR


title: cth1Δcth2Δ mutant Ribo-seq, 0H, replicate 3


title: NEM316 ∆busR Replicate 2


title: NEM316 WT Replicate 1


title: adult pancreas; PB2032-PAAD-T2_S17_L003


title: NEM316 ∆busR Replicate 1


title: cth1Δcth2Δ mutant Ribo-seq, 0H, replicate 1


title: Sample 24_HeLa cells, mRNA, eIF3e KD, rep4


title: Sample 23_HeLa cells, mRNA, eIF3e KD, rep3


title: adult pancreas; PB2032-PAAD-T_S4_L007


title: Sample 20_HeLa cells, mRNA, eIF3d KD, rep4

value: EIF3D knock down

value: eIF3d siRNA, 72 hours


title: Sample 19_HeLa cells, mRNA, eIF3d KD, rep3


title: Seed maturation stage MATURE biol rep 2

city: Zaragoza

first: Miguel

last: Alfonso

state: Aragón

address: Avda. Montañana 1005

department: Plant Biology

institute: CSIC

data_processing:
Original image data file from high-throughput sequencing was transformed to sequenced reads by CASAVA.
Raw data were stored in FASTQ(fq) files, containing sequences of reads and corresponding base quality. For each library, raw reads, clean reads, quality parameters as Q20 (%), Q30 (%) and QC (%), as well as the mapped percentage were first monitored. The results are available in Supplementary Table S2. Once raw reads were cleaned, alignments were performed with HISAT2 (Mortazavi et al., 2008).
Once raw reads were cleaned, alignments were performed with HISAT2 (Mortazavi et al., 2008).
Assembly: www.ncbi.nl.gov/assembly/GCA_91186555.2
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files includes FPKM values for each sample

organism: Thlaspi arvense

source_name: seed

growth_protocol: Pennycress (Thlaspi arvense L.) seeds from the SPRING32 germline were germinated in plates on wet Whatman paper without addition of any other supplement. For germination, seeds were vernalized for 3 days at 4 ºC and then moved to a growth chamber for additional 10-14 days. No vernalization treatment was required for fully development of flowers and seeds in this germline. Once germinated, seeds were transferred to pots containing a 75:25 mixture of substrate (peat moss, Kekkilä White 420W: vermiculite) and grown in a bioclimatic chamber under a light intensity of 120-150 mmol m-2 s-1, with a 16h/8h light/dark photoperiod at 22 ºC and a relative humidity of 45%.

extract_protocol:
Total RNA was isolated from 0.1 g of Thlaspi arvense seeds from the five maturation stages analyzed using the CTAB-LiCl extraction method of Gasic et al. (2004). RNA concentration and integrity were measured in a Nanodrop 2000 UV-Vis Spectrophotometer (Thermo Scientific).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. 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. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced.

treatment_protocol: Seeds separated from the pods, corresponding to these different maturation stages,were harvested, frozen in liquid nitrogen, and stored at -80 ºC for further analysis

value: seed

value: Spring 32

value: Seed maturation stage MATURE


title: Sample 18_HeLa cells, mRNA, eIF3d KD, rep2

value: HeLa


title: adult pancreas; PB2032-PAAD-T_S4_L006


title: Sample 17_HeLa cells, mRNA, eIF3d KD, rep1

value: human epithelial cell


title: adult pancreas; PB2032-PAAD-T2_S19_L003


title: wild-type Ribo-seq, 6H, replicate 3

value: wild-type (W303a)


title: wild-type Ribo-seq, 6H, replicate 2


title: Sample 16_HeLa cells, mRNA, NT control, rep4

value: non-targeting siRNA, 72 hours


title: Seed maturation stage MATURE biol rep 1


title: Sample 21_HeLa cells, mRNA, eIF3e KD, rep1


title: Seed maturation stage YELLOW biol rep 2

value: Seed maturation stage YELLOW


title: wild-type Ribo-seq, 6H, replicate 1


title: adult pancreas; PB2032-PAAD-T_S4_L005


title: adult pancreas; PB2032-PAAD-T_S4_L008


title: adult pancreas; PB2032-PAAD-T_S4_L004


title: wild-type Ribo-seq, 3H, replicate 3


title: cth1Δcth2Δ mutant Ribo-seq, 0H, replicate 2

value: cth1deltacth2delta mutant


title: Sample 15_HeLa cells, mRNA, NT control, rep3

value: WT


title: adult pancreas; PB2032-PAAD-T_S4_L003

value: pancreas


title: wild-type Ribo-seq, 3H, replicate 2


title: Seed maturation stage YELLOW biol rep 1


title: Sample 14_HeLa cells, mRNA, NT control, rep2


title: wild-type Ribo-seq, 0H, replicate 3


title: Seed maturation stage GREENYELLOW biol rep 2

value: Seed maturation stage GREENYELLOW


title: Seed maturation stage GREENYELLOW biol rep 1


title: adult pancreas; PB2032-PAAD-T_S4_L002


title: Seed maturation stage YELLOWGREEN biol rep 2

value: Seed maturation stage YELLOWGREEN


title: Sample 13_HeLa cells, mRNA, NT control, rep1


title: Seed maturation stage YELLOWGREEN biolo rep 1


title: wild-type Ribo-seq, 0H, replicate 2


title: adult pancreas; PB2032-PAAD-T_S3_L007


title: wild-type Ribo-seq, 0H, replicate 1


title: wild-type Ribo-seq, 3H, replicate 1


title: Sample 9_HeLa cells, 80S footprints, eIF3e KD, rep3

library_source: other

data_processing:
library strategy: Ribo-seq
Sample1 -Sample12:
Adapter sequence “CTGTAGGCACCATCAAT” and all sequences 3’ of the adapter were trimmed from the 3’ end of each read; flanking Ns were trimmed from both 5' and 3' ends of each read; and reads without adapter sequence and reads shorter than 15 nt after trimming were discarded by Cutadapt v. 3.5
rRNA and tRNA reads were discarded after alignment with Bowtie2 v. 2.4.4. Used sequences rRNA: RNA5S1, RNA5-8SN5, RNA18SN5 and RNA28SN5 from NCBI, and ENSG00000211459 and ENSG00000210082 from Ensembl. Used sequences tRNA: human tRNA sequences from tRNAdb and all high confidence hg38 tRNA sequences from GtRNAdb.
Reads were aligned to genome and transcriptome from Ensembl (GRCh38.p13, annotation release 104) by the STAR aligner v. 2.7.9a_2021-06-25 using local alignment with 10% mismatches, and with indels and soft clipping allowed for transcriptomic alignment
Alignments were indexed using Samtools index v. 1.13
Read counts within CDS region were counted with Htseq-count v. 0.13.5
Sample13-Sample28:
First 3 nucleotides on the 5’ end were removed, and poly(A) sequence (10xA) was trimmed from the 3’end; flanking Ns were trimmed from both 5' and 3' ends of each read; and reads without adapter sequence and reads shorter than 15 nt after trimming were discarded by Cutadapt v. 3.5
rRNA and tRNA reads were discarded after alignment with Bowtie2 v. 2.4.4. Used sequences rRNA: RNA5S1, RNA5-8SN5, RNA18SN5 and RNA28SN5 from NCBI, and ENSG00000211459 and ENSG00000210082 from Ensembl. Used sequences tRNA: human tRNA sequences from tRNAdb and all high confidence hg38 tRNA sequences from GtRNAdb.
Reads were aligned to genome and transcriptome from Ensembl (GRCh38.p13, annotation release 104) by the STAR aligner v. 2.7.9a_2021-06-25 using local alignment with 10% mismatches, and with indels and soft clipping allowed for transcriptomic alignment
Alignments were indexed using Samtools index v. 1.13
Read counts within CDS region were counted with Htseq-count v. 0.13.5
Assembly: GRCh38.p13, annotation release 104
Supplementary files format and content: Ensembl gene identifiers and gene counts in tab-separated values file format

molecule: other

value: EIF3E knock down

value: eIF3e siRNA, 72 hours

tag: molecule subtype

value: 80S RNA footprints


title: Sample 12_HeLa cells, 80S footprints, eIF3h KD, rep3

value: EIF3H knock down

value: eIF3h siRNA, 72 hours


title: Sample 8_HeLa cells, 80S footprints, eIF3e KD, rep2


title: adult pancreas; PB2032-PAAD-T_S4_L001


title: cth1Δcth2Δ mutant RNA-seq, 6H, replicate 2

data_processing:
De-multiplexing and base-calling was performed by Harvard University Bauer Center Sequencing Core
Sequence reads were trimmed for 3' adaptor sequence with cutadapt v.3.4
rRNA sequences were removed using alignment with bowtie v1.1.2
Sequence reads were mapped to the yeast genome with STAR 2.7.9a
Quantitation of reads was performed with Rsubread v.1.22.2
Genome_build: R64-2-1
Supplementary_files_format_and_content: Tab-delimited txt files with 3 columns: 1. SGD ORF name, 2. transcript length, 3. counts


title: adult pancreas; PB2032-PAAD-T_S3_L008


title: Sample 11_HeLa cells, 80S footprints, eIF3h KD, rep2


title: Sample 10_HeLa cells, 80S footprints, eIF3h KD, rep1


title: adult pancreas; PB2032-PAAD-T_S3_L004


title: cth1Δcth2Δ mutant RNA-seq, 6H, replicate 1


title: Sample 6_HeLa cells, 80S footprints, eIF3d KD, rep3

value: EIF3D knock down

value: eIF3d siRNA, 72 hours


title: adult pancreas; PB2032-PAAD-T_S3_L003


title: cth1Δcth2Δ mutant RNA-seq, 3H, replicate 3


title: cth1Δcth2Δ mutant RNA-seq, 3H, replicate 2


title: Sample 4_HeLa cells, 80S footprints, eIF3d KD, rep1

value: HeLa


title: Seed maturation stage GREEN biol rep 2

value: seed

value: Spring 32

value: Seed maturation stage GREEN


title: adult pancreas; PB2032-PAAD-T_S3_L001


title: Seed maturation stage GREEN biol rep 1


title: cth1Δcth2Δ mutant RNA-seq, 6H, replicate 3


title: LymphNode_MutantToxin_2

type: RNA

city: Oklahoma City

first: Kaylee

middle: M

last: Norman

state: OK

address: 940 Statond L Young Blvd

department: Microbiology and Immunology

description:
D versus P baseline: no significant genes from 654 hits. T versus D: 3 significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
D2

scan_protocol: RNA analysis was performed by the OUHSC core facility using a NanoString nCounter SPRINT profilerTM (NanoString, Seattle, WA) in conjunction with the nCounter Myeloid Innate Immunity PanelTM.

data_processing:
Data were analyzed with nSolver 4.0 Advanced Analysis SoftwareTM (Version 2.0.134, NanoString, Seattle, WA). Analysis was performed by normalizing the raw transcript counts utilizing negative synthetic sequences to account for background noise and positive synthetic sequences to account for technical variations.
Data summarizes the log2 fold change, raw p values, and adjusted p values (Benjamin-Yekutieli method) for each two-way comparison in the experiment: TcdB2 versus PBS, TcdB2 versus D270N, and D270N versus PBS.

source_name: Inguinal and axillary lymph nodes

growth_protocol: Female C57BL/6 mice (C57BL/6NCr) at 8 weeks of age were purchased from Charles River Laboratories (Bethesda, MD, Cat # model 027). All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Oklahoma Health Sciences Center (OUHSC) (original protocol 20-020-AHI, renewed as 22-082-CHI). Procedures were performed under inhalational anesthesia using a 4% isoflurane / 96% medical air mixture dispersed through a precision vaporizer. This study was performed in accordance with the recommendations of the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health.

extract_protocol: The aLNs and iLNs were isolated after 7 days. Lymph nodes were placed immediately in DNA / RNA Shield (Zymo Research, Irvine, CA). RNA was purified from the lymph nodes using Zymo Quick-RNA Miniprep Plus Kit (Zymo Research, Irvine, CA). Purified RNA was stored at -80°C until needed.

treatment_protocol: TcdB2 and D270N were expressed in Bacillus megaterium (MoBiTec, Göttingen, Germany) and purified by nickel affinity chromatography (GE Life Sciences, Boston, MA) as previously described. Purity and integrity were confirmed by SDS-PAGE and each batch of TcdB2 was tested for toxicity using a CHO cell killing assay. Mice were injected s.c. with 10 ng TcdB2 in PBS (controls were given PBS or 10 ng D270N in PBS).

value: Inguinal and axillary lymph nodes

value: C. difficile glucotransferase null mutant toxin B2

value: Female

tag: age

value: 8 weeks


title: LymphNode_MutantToxin_3

institute: University of Oklahoma Health Sciences Center

description:
D versus P baseline: no significant genes from 654 hits. T versus D: 3 significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
D3


title: LymphNode_MutantToxin_4

description:
D versus P baseline: no significant genes from 654 hits. T versus D: 3 significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
D4


title: Male pupal forewing, 24h APF, scRNAseq

city: Sheffield

first: Anupama

last: Prakash

address: Firth Court

country: United Kingdom

institute: University of Sheffield

description: 10X Genomics

data_processing:
Barcode and UMI trimming, demultiplexing, and quality assessment of the reads was performed using the scPipe R package (Tian et al., 2018). The workflow was as follows: The FASTQ files containing the reads were first reformatted to trim the barcodes and UMI sequences and move it to the header. Reads were then aligned to the Bicyclus anynana genome (v1.2) and mapped to exons using an annotation file - Bicyclus_anynana_v1.2.gff3 downloaded from Lepbase (Challi et al., 2016). Demultiplexing was done based on barcodes. Of the 346,685,500 initial reads, 72.36% had a barcode match. The generated gene count matrix consisted of 13631 genes and 9986 cells, with a mean count per cell of ~10700 reads and mean number of genes per cell of ~1400.   We next discarded low-quality cells, empty droplets with no cells, and potential doublets from the gene count matrix. Cells with counts per cell>100000 were removed and genes with less than 10 counts summed across all cells were discarded. The DropletUtils R package (Griffiths et al., 2018; Lun et al., 2019) was used to filter our empty droplets using a FDR <=0.001. The detect_outlier function in scPipe was then used to detect outliers (both low quality cells and potential doublets) using a Gaussian mixture model. Additionally, we removed 18 histone and 53 ribosomal protein genes because an initial analysis of the data indicated unsupervised clustering based on these genes, masking underlying patterns (Table S2 in the manuscript). This led to a gene count matrix of 5268 cells and 10743 genes used in the initial exploratory analysis. A Seurat object (Stuart et al., 2019) was created using the count matrix with min.cells = 5 i.e., keeping features that were present in at least 5 cells. The count matrix for the Seurat analysis comprised 5268 cells and 10696 genes.
Assembly: Bicyclus_anynana_v1.2; GenBank  GCA_900239965.1
Supplementary files format and content: Bany_MFW_24h_unprocessed.rds; A SingleCellExperiment R Data Object of 13631 genes and 9986 cells. This is the unprocessed gene count matrix without quality control and normalization.
Supplementary files format and content: Bany_MFW_24h_QC_norm.rds; A SingleCellExperiment R Data Object of 10743 genes and 5268 cells. This is the processed data matrix after quality control and normalization.

organism: Bicyclus anynana

source_name: Pupal forewing

growth_protocol: Bicyclus anynana caterpillars were maintained in temperature, light and humidity controlled growth chambers and fed on corn plants. Pupation times were captured on camera.

extract_protocol:
The preparation of a single-cell suspension from 22.5-25-hour male pupal forewings of Bicyclus anynana butterflies has been documented in-depth in a protocol paper (Prakash and Monteiro, Methods Protoc, 2020). Briefly, 14 male pupal forewings were dissected into multiple tubes with sterile PBS, washed, then dissociated in warm 5X TrypLE with continuous trituration for a total of 15-20 minutes. The dissociated cell mixture was filtered with a 41 µm filter and collected by centrifuging at 300 g, 4 ˚C for 5 minutes. Samples were pooled and gently resuspended into 1mL of cold 1X PBS + 0.01% BSA. Cells were counted in a Countess Automated cell counter by mixing 5 µl of sample with 5 µl of 0.4% trypan blue and loading it into a Countess cell counting chamber. Before going for fluorescence-activated cell sorting (FACS), 5 µl of a 300 µM intermediate concentration of DAPI (Invitrogen by Thermo Fisher Scientific, Cat. no.: D1306) was added per mL of sample. Cells larger than 6 µm in diameter were sorted using FACS and collected in a 1.5 mL LoBind Eppendorf tube pre-filled with 50 µl of cold 1X PBS + 0.01% BSA. Around 104,000 cells were collected and precipitated by centrifuging at 900g, 4 ˚C for 3 minutes. Cells were resuspended in 30 µl of cold 1X PBS + 0.01% BSA, with a final cell count of 1650 cells/µl and 88% viability.
Cells were processed via the 10X Genomics microfluidics system at the Genome Institute of Singapore. Single-cell libraries were generated using the Chromium Single cell 3’ Library Kit V3 with a targeted cell recovery of 7000 cells. The quality of the generated cDNA library was quantified using an Agilent Bioanlyzer and sequenced on one lane of HiSeq4K 2x151bp (multiplex) at the Genome Institute of Singapore.

value: Pupal forewing

value: Large cells (>6 um)

value: Male

tag: developmental stage

value: 22.5-25 hours after pupation


title: adult pancreas; PB2032-PAAD-T_S3_L005

tag: tissue

value: pancreas


title: Sample 5_HeLa cells, 80S footprints, eIF3d KD, rep2

tag: cell line

value: human epithelial cell

value: 80S RNA footprints


title: adult pancreas; PB2032-PAAD-T_S3_L002


title: adult pancreas; PB2032-PAAD-T_S2_L007


title: cth1Δcth2Δ mutant RNA-seq, 0H, replicate 2

value: cth1deltacth2delta mutant


title: Sample 7_HeLa cells, 80S footprints, eIF3e KD, rep1

tag: cell type

value: EIF3E knock down

value: eIF3e siRNA, 72 hours


title: adult pancreas; PB2032-PAAD-T_S3_L006


title: cth1Δcth2Δ mutant RNA-seq, 3H, replicate 1


title: Sample 3_HeLa cells, 80S footprints, NT control, rep3

value: HeLa

tag: genotype

value: WT

value: non-targeting siRNA, 72 hours


title: adult pancreas; PB2032-PAAD-T_S2_L006


title: LymphNode_Toxin_4

description:
T versus P baseline: 18 significant genes from 649 hits. T versus D: 3 significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
T4

value: Inguinal and axillary lymph nodes

tag: treatment

value: C. difficile toxin B2


title: LymphNode_Toxin_3

description:
T versus P baseline: 18 significant genes from 649 hits. T versus D: 3 significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
T3

value: Female


title: cth1Δcth2Δ mutant RNA-seq, 0H, replicate 3


title: adult pancreas; PB2032-PAAD-T_S2_L008


title: Sample 2_HeLa cells, 80S footprints, NT control, rep2


title: wild-type RNA-seq, 6H, replicate 3

value: wild-type (W303a)


title: LymphNode_MutantToxin_1

description:
D versus P baseline: no significant genes from 654 hits. T versus D: 3 significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
D1

value: C. difficile glucotransferase null mutant toxin B2

value: 8 weeks


title: Sample 1_HeLa cells, 80S footprints, NT control, rep1


title: LymphNode_Vehicle_4

description:
T versus P baseline: 18 significant genes from 649 hits. D versus P baseline: no significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
P4

value: Vehicle control


title: wild-type RNA-seq, 6H, replicate 2


title: CON_4_IP

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
ABLIRC strategy was used to identify the binding regions of RBP on genome (Xia et al., 2017a). Reads with at least 1 bp overlap were clustered as peaks. For each gene, computational simulation was used to randomly generated reads with the same number and lengths as reads in peaks. The outputting reads were further mapped to the same genes to generate random max peak height from overlapping reads. The whole process was repeated for 500 times. All the observed peaks with heights higher than those of random max peaks (p-value < 0.05) were selected. The IP and input samples were analyzed by the simulation independently, and the IP peaks that have overlap with Input peaks were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak data

value: adjcent mucocal tissues

tag: rip antibody

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)


title: wild-type RNA-seq, 6H, replicate 1


title: adult pancreas; PB2032-PAAD-T_S2_L005

value: pancreas


title: CON_5_IP


title: LymphNode_Toxin_2

description:
T versus P baseline: 18 significant genes from 649 hits. T versus D: 3 significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
T2


title: adult pancreas; PB2032-PAAD-T_S2_L002


title: CON_5_input


title: LymphNode_Vehicle_3

description:
T versus P baseline: 18 significant genes from 649 hits. D versus P baseline: no significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
P3


title: adult pancreas; PB2032-PAAD-T_S2_L003


title: cth1Δcth2Δ mutant RNA-seq, 0H, replicate 1


title: CON_4_input


title: LymphNode_Toxin_1

description:
T versus P baseline: 18 significant genes from 649 hits. T versus D: 3 significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
T1


title: wild-type RNA-seq, 3H, replicate 3


title: adult pancreas; PB2032-PAAD-T_S2_L001


title: CON_3_IP


title: adult pancreas; PB2032-PAAD-T_S1_L008


title: wild-type RNA-seq, 3H, replicate 2


title: Mb231-ctrl-2

city: Long Island City

first: Alyssa

last: Fronk

state: NY

address: 30-02 48th Avenue, Suite 140

institute: Envisagenics

data_processing:
Sequencing reads were trimmed with fastq-mcf
Trimmed reads were mapped to hg38 using STAR-2.7.10a
Read counts were generated using featureCounts v2.0.0, normalization, and differential gene expression were performed using DESeq2
Assembly: hg38
Supplementary files format and content: FeatureCount files are txt files containing the read counts for the indicated samples
Supplementary files format and content: DESeq2 output files are txt files containing the results of differential expression analysis performed on the indicated samples.

extract_protocol:
Trizol Extraction as per manufacturers protocol
Illumina Truseq library protocol with Illumina adapters

treatment_protocol: Lipofectamine mediated SSO transfection, 400 nM for 48 hrs

value: mammary cancer


title: LymphNode_Vehicle_2

description:
T versus P baseline: 18 significant genes from 649 hits. D versus P baseline: no significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
P2


title: adult pancreas; PB2032-PAAD-T_S2_L004


title: CON_2_IP


title: CON_3_input


title: wild-type RNA-seq, 3H, replicate 1


title: Mb231-ctrl-1


title: adult pancreas; PB2032-PAAD-T_S1_L007


title: LymphNode_Vehicle_1

description:
T versus P baseline: 18 significant genes from 649 hits. D versus P baseline: no significant genes from 654 hits. Myeloid Innate Immunity Panel with total of 754 genes.
P1


title: wild-type RNA-seq, 0H, replicate 3


title: adult pancreas; PB2032-PAAD-T_S1_L006


title: Mb231-LF-2


title: CON_1_IP


title: wild-type RNA-seq, 0H, replicate 2


title: Mb231-LF-1


title: adult pancreas; PB2032-PAAD-T_S1_L005


title: CON_1_input


title: wild-type RNA-seq, 0H, replicate 1


title: CA_5_IP

value: specimen of condyloma acuminatum


title: adult pancreas; PB2032-PAAD-T_S1_L003


title: BM110 WT Replicate 2

organism: Streptococcus agalactiae

tag: isolate

value: bacterial cell


title: Mb231-2-5-1


title: CA_5_input


title: CA_4_IP


title: adult pancreas; PB2032-PAAD-T_S1_L001


title: Mb231-2-2-2


title: Mb231-2-2-1


title: CA_4_input


title: BM110 ∆gdpP Replicate 3

value: {delta}gdpP


title: BM110 ∆gdpP Replicate 2