title: Total_RNAseq_MCF7_sgControl_4hours_DMSO_Replicate1

city: La Jolla

data_processing:
For differential expression:
Transcript abundance was quantified using Salmon [v1.3.0] with GENCODE v37 annotation.
Gene level quantification was performed using tximeta [v1.8.4].
Differential gene expression was analyzed by DESeq2 [v1.30.1].
For splicing analysis, 22Rv1 data only:
RNA-seq reads were mapped to hg38 using STAR Aligner.
Alternative splicing (AS) analysis was completed using rMATs (v3.2.5).
Assembly: hg19
Supplementary files format and content: *.csv: Gene counts were used for differential expression.
Supplementary files format and content: *.xlsx: rMATs table was used for splicing analysis.

source_name: Breast carcinoma

tag: sg

value: sgControl

tag: treatment+dose

value: DMSO

value: 4 hours

tag: rna library prep

value: Total mRNA


title: O RNA-Seq replicate 2

status: Public on Mar 20 2023

type: SRA

city: Palo Alto

first: Jamie

middle: O.

last: Brett

state: CA

address: 3801 Miranda Avenue, Building 100, Room E4-216

department: Neurology and Neurological Sciences

country: USA

institute: Stanford University

description:
O2
PolyA-selected RNA
processed data file: Aging_MuSC_RNASeq.txt

library_source: transcriptomic

data_processing:
Reads were adapter- and quality-trimmed with trim_galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore) (quality cutoff 20, adapter stringency 1, final length filter 50). Trimmed reads were mapped to mm10 (Ensembl release 89, no patches) using transcript annotations from Ensembl with STAR (Dobin et al. 2013) along with the ERCC RNA sequences (mismatch cutoff 4% of read length, no non-canonical junction alignments). Exonic reads that mapped uniquely were summarized over genes with the featureCounts module of the Subread package (Liao et al. 2014).
Genes lacking an Entrez ID and ERCC reads were filtered out. Raw count data were then normalized using edgeR with the TMM method (Robinson et al. 2010).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Aging_MuSC_RNASeq.txt: Tab-delimited text file containing normalized FPKMs for each gene.

molecule: total RNA

organism: Mus musculus

source_name: Skeletal muscle stem cells

extract_protocol:
FACS-isolated MuSCs were snap-frozen. ERCC RNA (Invitrogen 4456740) was spiked in proportional to cell number: 10 mcL of 1:10,000 diluted ERCC RNA per 122,000 cells. RNA was extracted using the Nucleospin RNA XS kit (Machery-Nagel).
RNA (10 ng) was reverse-transcribed using oligo(dT) priming with the SMARTer Ultra Low Input system (Takara). The cDNA then sheared with a Covaris S2 ultrasonicator. End repair, multiplexed adapter ligation, and 6-9 cycles of library amplification were performed using the Ovation Ultralow Multiplex system (NuGEN). Libraries underwent paired-end 101-bp sequencing at the Stanford Genome Sequencing Service Center with an Illumina HiSeq 2000 to a depth of 26-37 million reads.

tag: strain

tag: Sex

value: Male

tag: age

value: 22 months

tag: cell type

value: Skeletal muscle stem cells


title: Basal_WT_HC-2

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Paired-end sequencing (101 x 2) was performed using a Hiseq (Illumina).
Illumina Casava1.7 software used for basecalling.
mapped to mm10 whole genome using STAR v2.5.1.
Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using an edgeR v.3.12.1. The CPM values are on log2 scale.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: Hippocampus from wild-type mouse

growth_protocol: Mice were bred and maintained at the SPF facility in the Korea Institute of Science and Technology (KIST).

extract_protocol:
Total RNA was isolated from the hippocampal tissues using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: Morris water maze original and reversal learning tasks were applied to wild-type and Ccny knockout mice. All experimental protocols were approved by the KIST Institutional Animal Care and Use Committee (approval number 2018-048)

tag: tissue

value: Mouse Hippocampal tissue

value: 8-10 weeks old


title: 106_hAd_MSC2_Dox_SIPS1

type: genomic

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

country: Italy

institute: Univeristy of Bologna

description: genomic DNA from Human adipose-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to doxorubicin from donor hAd_MSC2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infiniun MethylationEPIC v1.0 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged on Illumina iScan scanner using iScan Control Software (ICS) with standard recommended Illumina scanner settings

data_processing: R version 3.6.3

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from cell pellets using NucleoSpin Tissue kit (Macherey-Nagel, Düren, Germany) according to manufacturer’s instructions

tag: treatment

tag: donor

value: F


title: 107_hAd_MSC2_Dox_SIPS2

source_name: Human adipose-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to doxorubicin


title: 96_hAd_MSC1_Dox_SIPS1

description: genomic DNA from Human adipose-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to doxorubicin from donor hAd_MSC1


title: 97_hAd_MSC1_Dox_SIPS2


title: 102_hAd_MSC2_RS1

description: genomic DNA from Human adipose-derived mesenchymal stem cells, culture in replicative senescence from donor hAd_MSC2

value: Replicative sensescent


title: 103_hAd_MSC2_RS2

source_name: Human adipose-derived mesenchymal stem cells, culture in replicative senescence


title: 74_hBM_MSC1_IRR_SIPS1

description: genomic DNA from Human bone marrow-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to ionizing irradiation from donor hBM_MSC1


title: 105_hAd_MSC2_IRR_SIPS2

description: genomic DNA from Human adipose-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to ionizing irradiation from donor hAd_MSC2


title: 104_hAd_MSC2_IRR_SIPS1

source_name: Human adipose-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to ionizing irradiation


title: 94_hAd_MSC1_IRR_SIPS1

description: genomic DNA from Human adipose-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to ionizing irradiation from donor hAd_MSC1


title: 87_hBM_MSC2_Dox_SIPS2

description: genomic DNA from Human bone marrow-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to doxorubicin from donor hBM_MSC2


title: 93_hAd_MSC1_RS2

description: genomic DNA from Human adipose-derived mesenchymal stem cells, culture in replicative senescence from donor hAd_MSC1


title: 86_hBM_MSC2_Dox_SIPS1

source_name: Human bone marrow-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to doxorubicin


title: 77_hBM_MSC1_Dox_SIPS2

description: genomic DNA from Human bone marrow-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to doxorubicin from donor hBM_MSC1


title: 92_hAd_MSC1_RS1


title: 85_hBM_MSC2_IRR_SIPS2

description: genomic DNA from Human bone marrow-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to ionizing irradiation from donor hBM_MSC2


title: 100_hAd_MSC2_Young

description: genomic DNA from Human adipose-derived mesenchymal stem cells, early-passage culture from donor hAd_MSC2

value: Young


title: 83_hBM_MSC2_RS2

description: genomic DNA from Human bone marrow-derived mesenchymal stem cells, culture in replicative senescence from donor hBM_MSC2


title: 80_hBM_MSC2_Young

description: genomic DNA from Human bone marrow-derived mesenchymal stem cells, early-passage culture from donor hBM_MSC2


title: 72_hBM_MSC1_RS1

description: genomic DNA from Human bone marrow-derived mesenchymal stem cells, culture in replicative senescence from donor hBM_MSC1


title: 82_hBM_MSC2_RS1

source_name: Human bone marrow-derived mesenchymal stem cells, culture in replicative senescence


title: 81_hBM_MSC2_Middle_passaged

description: genomic DNA from Human bone marrow-derived mesenchymal stem cells, middle-passage culture from donor hBM_MSC2

value: Middle-passaged


title: 95_hAd_MSC1_IRR_SIPS2


title: 84_hBM_MSC2_IRR_SIPS1

source_name: Human bone marrow-derived mesenchymal stem cells, culture in stress-induced premature senescence after exposure to ionizing irradiation


title: 101_hAd_MSC2_Middle_passaged

description: genomic DNA from Human adipose-derived mesenchymal stem cells, middle-passage culture from donor hAd_MSC2


title: 76_hBM_MSC1_Dox_SIPS1


title: 73_hBM_MSC1_RS2


title: 91_hAd_MSC1_Middle_passaged

description: genomic DNA from Human adipose-derived mesenchymal stem cells, middle-passage culture from donor hAd_MSC1


title: 75_hBM_MSC1_IRR_SIPS2


title: 90_hAd_MSC1_Young

description: genomic DNA from Human adipose-derived mesenchymal stem cells, early-passage culture from donor hAd_MSC1


title: 71_hBM_MSC1_Middle_passaged

description: genomic DNA from Human bone marrow-derived mesenchymal stem cells, middle-passage culture from donor hBM_MSC1


title: grf10Δ mutant YPD Rep3

city: Washington

first: Ronda

middle: Joan

last: Rolfes

state: DC

address: 3700 O Street NW

department: Biology

institute: Georgetown University

description: arg4Δ/arg4Δ leu2Δ/leu2Δ his1Δ/his1Δ URA3/ura3Δ IRO1/iro1Δ grf10Δ::CdHIS1/grf10Δ::CmLEU2

data_processing:
FASTQ files were paired, trimmed using BBDuk
Mapping to the reference genome used the Geneious software and default settings.
Raw reads from the two alleles were combined and expression differences determined using DESeq2 (v1.30.1) in R
Assembly: Reference genome: the phased C_albicans_SC5314 Assembly 22 from Candida genome database (online)
Supplementary files format and content: The file "Expression Level Reads in High Copper" has the mapping to the phased genome for mutant and WT with and without copper sulfate
Supplementary files format and content: The file "allGenes_KOvWT_YPD_LFCshrink_padj" shows differential expression of the grf10 mutant compared with the WT in YPD medium
Supplementary files format and content: The file "allGenes_KOvWT_copper_LFCshrink_padj" shows differential expression of the grf10 mutant compared with the WT in 12 mM CuSO4 medium
Supplementary files format and content: The file "allGenes_COPPERvYPD_WT_LFCshrink_padj" shows differential expression for WT cells, comparing YPD to YPD+12 mM CuSO4
Supplementary files format and content: The file "allGenes_COPPERvYPD_KO_LFCshrink_padj" shows differential expression for grf10Δ mutant cells, comparing YPD to YPD+12 mM CuSO4

organism: Candida albicans

source_name: yeast

growth_protocol: Strains were grown overnight in 5 ml YPD at 30°C, inoculated into 100 ml of YDP medium at an OD600 of 0.2, and grown at 30°C with orbital shaking until an OD600 of ~1.

extract_protocol:
RNA was extracted using the Rneasy Plus Kit (Qiagen)
Samples were sent to NovoGene (Sacramento, CA) for cDNA synthesis and sequencing.

treatment_protocol: The 100 ml cultures were split into two 50 ml portions, 12 mM CuSO4 was added to one of the cultures, and both were grown at 30°C for 30 min, the cells were harvested by pelleting for 10 min, and stored at -80°C until RNA extraction.

value: yeast

tag: strain background

value: SN152-TF mutant

tag: genotype

value: arg4{delta}/arg4{delta} leu2{delta}/leu2{delta} his1{delta}/his1{delta} URA3/ura3{delta} IRO1/iro1{delta} grf10{delta}::CdHIS1/grf10{delta}::CmLEU2


title: grf10Δ mutant YPD Rep2


title: 65_DSF2_IRR_SIPS2

description: genomic DNA from Human diploid skin fibroblasts, culture in stress-induced premature senescence after exposure to ionizing irradiation from donor DSF2

value: M


title: grf10Δ mutant YPD Rep1


title: 67_DSF2_Dox_SIPS2

description: genomic DNA from Human diploid skin fibroblasts, culture in stress-induced premature senescence after exposure to doxorubicin from donor DSF2


title: 63_DSF2_RS2

description: genomic DNA from Human diploid skin fibroblasts, culture in replicative senescence from donor DSF2


title: WT YPD Rep3

description: arg4Δ/arg4Δ leu2Δ/leu2Δ::CmLEU2  his1Δ /his1Δ::CdHIS1 URA3/ura3Δ  IRO1/iro1Δ

value: arg4{delta}/arg4{delta} leu2{delta}/leu2{delta}::CmLEU2  his1{delta} /his1{delta}::CdHIS1 URA3/ura3{delta}  IRO1/iro1{delta}


title: 66_DSF2_Dox_SIPS1

source_name: Human diploid skin fibroblasts, culture in stress-induced premature senescence after exposure to doxorubicin


title: 62_DSF2_RS1

source_name: Human diploid skin fibroblasts, culture in replicative senescence


title: grf10Δ mutant +Cu Rep2

value: 12 mM CuSO4


title: WT YPD Rep1


title: 61_DSF2_Middle_passaged

description: genomic DNA from Human diploid skin fibroblasts, middle-passage culture from donor DSF2


title: grf10Δ mutant +Cu Rep1


title: WT +Cu Rep2


title: WT +Cu Rep1


title: 55_DSF3_IRR_SIPS2

description: genomic DNA from Human diploid skin fibroblasts, culture in stress-induced premature senescence after exposure to ionizing irradiation from donor DSF3


title: 52_DSF3_RS1

description: genomic DNA from Human diploid skin fibroblasts, culture in replicative senescence from donor DSF3


title: 51_DSF3_Middle_passaged

description: genomic DNA from Human diploid skin fibroblasts, middle-passage culture from donor DSF3


title: 54_DSF3_IRR_SIPS1

source_name: Human diploid skin fibroblasts, culture in stress-induced premature senescence after exposure to ionizing irradiation


title: grf10Δ mutant +Cu Rep3


title: 57_DSF3_Dox_SIPS2

description: genomic DNA from Human diploid skin fibroblasts, culture in stress-induced premature senescence after exposure to doxorubicin from donor DSF3


title: 56_DSF3_Dox_SIPS1


title: Genomic DNA from normal tongue tissue of patient 24

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

country: Spain

institute: Health Research Institute of Santiago (IDIS)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to human Infinium MethylationEPIC BeadChip (Illumina) using standard Infinium HD FFPE Methylation Protocol (Illumina).

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing: Methylation module (1.9.0) of GenomeStudio software (V2011.1)

source_name: Normal tongue tissue of patient 24

label_protocol: Standard Infinium HD FFPE Methylation Protocol from Illumina

extract_protocol: Genomic DNA was isolated from FFPE tissue sections of oral tongue squamous cell carcinoma (OTSCC) and normal tongue tissue using the AllPrep DNA/RNA FFPE Kit (Qiagen) and following the manufacturer’s instructions.

tag: gender

value: Female

tag: sample type

value: Formalin-fixed paraffin-embedded (FFPE)

value: Normal tongue tissue


title: ccrfer bio rep 1

city: Denton

first: Chang

last: Liu

address: 1155 Union Circle #311428

institute: University of North Texas

data_processing:
For each sample, RNA-seq raw reads were trimmed and filtered using in-house perl scrips.
Clean reads were mapped to the A. thaliana genome sequence and the reference-annotated genes (TAIR10) using Bowtie v2.3.2.0 (3) and TopHat v2.1.1 (4) with default parameters.
The gene expression levels for each sample were estimated by Cufflinks v2.2.1(5) based on the FPKM (fragments per kilobase of exon model per million mapped fragments) method.
Significantly differentially expressed genes were analyzed by Cuffdiff in the cufflinks package (6) using twofold change and multiple test p-value < 0.05.
Assembly: TAIR10
Supplementary files format and content: Excel files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Inflorescence stems

extract_protocol:
RNA was extracted from the main inflorescence stems of 2-month-old wild-type Col-0, ccr1-3, fer4, and ccr1-3/fer4 double mutant plants. Total RNA was isolated with Trizol reagent (Invitrogen, USA) and treated with TURBO DNA-free Kit (Ambion) to remove genomic DNA contaminants. RNA was cleaned using an RNA cleanup kit (Qiagen). Purified RNA was quantified using a Nanodrop ND-100 spectrophotometer (NanoDrop Technologies) and evaluated for purity with an Agilent 4200 TapeStation system (Agilent Technologies).
Libraries were constructed using a TruSeq stranded mRNAseq prep kit following the standard protocols and run on an Illumina Nextseq 500 platform (2 × 75 bp).

value: Inflorescence stems

value: ccr1-3/fer4 double mutant

value: 2- months -old


title: ccr bio rep 3

value: ccr1-3 mutant


title: fer bio rep 3

value: fer4 mutant


title: Genomic DNA from normal tongue tissue of patient 10

source_name: Normal tongue tissue of patient 10


title: Genomic DNA from normal tongue tissue of patient 21

source_name: Normal tongue tissue of patient 21

value: Male


title: ccr bio rep 2


title: Genomic DNA from oral tongue squamous cell carcinoma (OTSCC) of patient 24

source_name: Oral tongue squamous cell carcinoma (OTSCC) of patient 24


title: ccr bio rep 1


title: fer bio rep 2


title: fer bio rep 1


title: WT YPD Rep2


title: 60_DSF2_Young

description: genomic DNA from Human diploid skin fibroblasts, early-passage culture from donor DSF2

value: Young


title: WT +Cu Rep3


title: WT bio rep 3

value: Wild type


title: Genomic DNA from normal tongue tissue of patient 17

source_name: Normal tongue tissue of patient 17


title: WT bio rep 1


title: Genomic DNA from normal tongue tissue of patient 20

source_name: Normal tongue tissue of patient 20


title: 64_DSF2_IRR_SIPS1


title: Spleen RNA, PBS mock-infected C57BL/6 mice, Day0, replicate 3

type: RNA

city: Galveston

first: Lynn

last: Soong

state: TX

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

description: Total RNA isolated from spleens of PBS inoculated C57BL/6 mice. Replicate 3.

hyb_protocol: According to Nanostring's protocol; used commercially available kit catalog number XT-CSO-MIM1-12

data_processing: The raw data were submitted to ROSALIND for analysis. Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library1. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library2 that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library3, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro4, NCBI5, MSigDB6,7, REACTOME8, WikiPathways9. Enrichment was calculated relative to a set of background genes relevant for the experiment.

source_name: PBS-inoculated C57BL/6 mice mouse spleen

extract_protocol: Female C57BL/6J mice (8-12 weeks-old, purchased from the Jackson Laboratory #000664) were intravenously inoculated with a lethal dose (8 × 10e4 FFU, 200 µl) of bacteria or PBS (mock). Mice were sacrificed at from mock (D0) and D8 infected mice, and spleens were stored in RNALater (Ambion, Austin, TX) until extraction was performed. Total RNA was extracted by using the RNeasy Mini kit (Qiagen), and total RNA samples (3 mice/group, 200 ng/sample in ribonuclease-free water) were processed at the Baylor College of Medicine Genomic and RNA Expression Profiling Core (Houston, TX). We utilized the commercially available Mouse Immunology Panel NanoString Kit to analyzed our isolated total RNA.

value: Spleen

tag: mouse strain

tag: mouse age

value: 8-12 weeks

value: PBS

tag: timepoint


title: Spleen RNA, PBS mock-infected C57BL/6 mice, Day0, replicate 1

description: Total RNA isolated from spleens of PBS inoculated C57BL/6 mice. Replicate 1.

scan_protocol: According to Nanostring's protocol; used commercially available kit catalog number XT-CSO-MIM1-12


title: WT bio rep 2


title: Genomic DNA from oral tongue squamous cell carcinoma (OTSCC) of patient 18

source_name: Oral tongue squamous cell carcinoma (OTSCC) of patient 18


title: 70_hBM_MSC1_Young

description: genomic DNA from Human bone marrow-derived mesenchymal stem cells, early-passage culture from donor hBM_MSC1

value: F


title: VUILD99-MF

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

library_source: transcriptomic single cell

data_processing:
Reads with a read quality <3 were filtered and CellRanger Count v3.02 (10x Genomics) was used to align reads to the GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Matrix file containing counts
Supplementary files format and content: Tab-separated values file containing features
Supplementary files format and content: Tab-separated values file containing cell barcodes
Supplementary files format and content: Aggregated_expression.tar: Tar archive containing TSV files of aggregated expression for each cell population.
Supplementary files format and content: *_Seurat.rds: RDS files of Seurat objects for each major cell lineage.
Supplementary files format and content: limix_res_*.tar: Tar archives containing txt files of limix eQTL summary stats.
Supplementary files format and content: mashr_applied_*.tar: Tar archives containing TSV files of mashr eQTL summary stats.

source_name: Lung

extract_protocol:
Tissue samples were digested in either collagenase I/dispase II (1 μg/ml) or Miltenyi Multi-Tissue Dissociation Kit using a gentleMACS Octo Dissociator (Miltenyi Inc.). Tissue lysates were serially filtered through sterile gauze, 100- and 40-μm sterile filters (Fischer). The resulting suspensions then underwent cell sorting using serial columns (Miltenyi Microbeads, CD235a and CD45) or fluorescence-activated cell-sorting (FACS) at VUMC or FACSat the Translational Genomics Research Institute (TGen). CD45− and C45+ populations were mixed 2:1 in samples processed at VUMC and used to generate the scRNA-seq libraries. At TGen, calcein acetoxymethyl was used to stain live cells, and 10,000 to 15,000 live cells were sorted directly into the 10x reaction buffer and transferred to the 10x 5′ chip A (10x Genomics).
scRNA-seq libraries were generated using the 10x Chromium platform 3′ v2 or 5′ library preparation kits (10x Genomics) according to the manufacturer’s recommendations and targeting 5000 to 10,000 cells per sample.

value: Lung

tag: disease state/diagnosis

value: CTD-ILD

value: M

tag: tobacco status_(ever-smoker)

value: Y

tag: self-reported ethnicity

value: European

tag: tissue type


title: Spleen RNA, O. tsutsugamushi-infected C57BL/6 mice, Day8, replicate 2

description: Total RNA isolated from spleens of O. tsutsugamushi- lethally infected C57BL/6 mice on d8 post-infection. Replicate 2.

source_name: O. tsutsugamushi-infected C57BL/6 mice mouse spleen

label_protocol: According to Nanostring's protocol; used commercially available kit catalog number XT-CSO-MIM1-12

value: O. tsutsugamushi lethal dose


title: 50_DSF3_Young

description: genomic DNA from Human diploid skin fibroblasts, early-passage culture from donor DSF3

tag: Sex


title: HUVECs, SWG 25 nM treated sample 24 h, rep2

city: Helsinki

first: Juuso

last: Taskinen

address: Tukholmankatu 8

country: Finland

institute: Minerva Foundation Institue for Medical Research

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Pair ended reads were clipped with Triommatic (phred >= 30)
Aligned to the human genome with STAR
reads were counted using HTSeq
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include non-normalized transcript counts

source_name: Primary cell

growth_protocol: P6 HUVECs grown in media with either SWG 25 nM or DMSO 1:1000

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
NEB Next Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions

treatment_protocol: Cells were treated for 24 h with either SWG or DMSO

tag: cell line

value: Primary cell

value: Human umbilical vein endothelial cell

tag: passage

value: SWG 25 nM

tag: time


title: HUVECs, SWG 25 nM treated sample 24 h, rep4

tag: cell type

tag: treatment


title: HUVECs, DMSO 1:1000 treated sample 24 h, rep4


title: HUVECs, SWG 25 nM treated sample 24 h, rep3


title: HUVECs, DMSO 1:1000 treated sample 24 h, rep2


title: HUVECs, DMSO 1:1000 treated sample 24 h, rep3


title: HUVECs, SWG 25 nM treated sample 24 h, rep1


title: HUVECs, DMSO 1:1000 treated sample 24 h, rep1


title: ccrfer bio rep 3

tag: tissue

value: Inflorescence stems

value: ccr1-3/fer6 double mutant

tag: age

value: 2- months -old


title: 53_DSF3_RS2

value: Replicative sensescent

tag: donor


title: Spleen RNA, O. tsutsugamushi-infected C57BL/6 mice, Day8, replicate 3

description: Total RNA isolated from spleens of O. tsutsugamushi- lethally infected C57BL/6 mice on d8 post-infection. Replicate 3.

value: Spleen


title: Spleen RNA, O. tsutsugamushi-infected C57BL/6 mice, Day8, replicate 1

description: Total RNA isolated from spleens of O. tsutsugamushi- lethally infected C57BL/6 mice on d8 post-infection. Replicate 1.

value: 8-12 weeks


title: Genomic DNA from oral tongue squamous cell carcinoma (OTSCC) of patient 10

source_name: Oral tongue squamous cell carcinoma (OTSCC) of patient 10

tag: gender

value: Female

tag: sample type

value: Formalin-fixed paraffin-embedded (FFPE)


title: VUILD99-LF

value: Lung


title: VUILD87-MF

value: IPF

value: F

value: Former smoker


title: VUHD101

value: Control

value: M

value: N


title: VUILD89-MF

value: CWP

value: Caucasian


title: VUILD87-LF

value: European


title: TILD111-LF


title: VUILD108-LF

value: NSIP


title: TILD113-LF


title: TILD111-MF


title: TILD113-MF


title: Genomic DNA from oral tongue squamous cell carcinoma (OTSCC) of patient 21

source_name: Oral tongue squamous cell carcinoma (OTSCC) of patient 21

value: Male


title: TILD109-LF


title: VUILD108-MF


title: TILD109-MF


title: VUILD102-LF

value: Y


title: VUILD104-MF


title: VUILD102-MF


title: VUHD115


title: VUHD0076


title: ccrfer bio rep 2

value: Inflorescence stems

tag: genotype

value: ccr1-3/fer5 double mutant

value: 2- months -old


title: VUHD113


title: VUHD112


title: Genomic DNA from oral tongue squamous cell carcinoma (OTSCC) of patient 17

source_name: Oral tongue squamous cell carcinoma (OTSCC) of patient 17

value: Female

value: Formalin-fixed paraffin-embedded (FFPE)


title: Genomic DNA from oral tongue squamous cell carcinoma (OTSCC) of patient 20

source_name: Oral tongue squamous cell carcinoma (OTSCC) of patient 20


title: Genomic DNA from normal tongue tissue of patient 18

source_name: Normal tongue tissue of patient 18

value: Normal tongue tissue


title: VUHD109

value: Lung


title: TILD136-MF

value: ILD


title: TILD136-LF


title: TILD123-LF


title: VUILD104-LF

value: IPF


title: VUILD100-MF

value: IPAF

value: M


title: THD0023

value: Control

value: F


title: THD0022


title: TILD126-MF


title: THD0021


title: VUHD114


title: TILD126-LF


title: TILD103-LF


title: THD0019


title: TILD103-MF


title: THD0020


title: VUILD92-MF

value: N

value: Caucasian


title: THD0017


title: THD0016


title: TILD116-LF


title: VUILD91-MF


title: VUILD90

value: CTD-ILD

value: Unknown


title: VUILD88-LF


title: VUILD84-MF


title: VUILD84-LF


title: VUILD83-LF

value: Y

value: European


title: VUILD83-MF


title: VUILD88-MF


title: TILD123-MF


title: VUHD107

value: Former Smoker


title: THD0026


title: VUILD82-LF


title: VUHD104

value: Yes


title: TILD080-MF


title: TILD102-MF

value: ILD/HP


title: THD0015


title: TILD060-MF


title: TILD102-LF


title: VUHD095


title: TILD084-MF


title: TILD084-LF


title: VUILD97-MF


title: THD0014


title: VUILD97-LF


title: TILD074-LF


title: TILD074-MF


title: VUILD96-LF

value: Sarcoidosis


title: VUILD82-MF

value: Lung


title: VUILD93-MF

value: Former smoker


title: VUILDD95-MF


title: TILD080-LF

value: ILD


title: WT_UT_1

city: Tucson

first: Andrew

last: Paek

state: Arizona

address: Life Sciences South, 1007 E. Lowell Stre, PO Box 210106

department: Molecular and Cellular Biology

institute: University of Arizona

description:
WT_UT_1
SampleFileAll.txt
W50vUT_deseq.csv

data_processing:
Bam files were generated by Novogene, aligned using reference genome hg38 and HISAT2 after quality control.
Counts were extracted from .bam files by the featureCounts function (with annot.inbuilt = "hg38", isPairedEnd = TRUE) in the Rsubread package (v. 2.10.4)
Features were combined into one matrix, and those features with less than 10 counts across all rows were dropped. TPM normalized counts were also calculated.
Counts were run through DESeq2 (v. 1.36.0) with design based on group, with results chosen based on alpha of 0.05 for the following comparisons: J14 50 vs J14 UT, SFRX 50 vs SFRX UT, WT 50 vs WT UT, SFRX 50 vs J14 50/J14 50 vs SFRX 50. A ranked list of differentially expressed genes was then used for GSEA analysis.
Results from DESeq2 were then run through apeglm for LFC shrinkage based on effect size using the lfcShrink function from DEseq2 for visualization. Genes with adjusted p-values  of NA were removed.
Assembly: hg38
Supplementary files format and content: bam and bai files: Aligned bam files using reference genome hg38 used for further processing, along with index files.
Supplementary files format and content: Comma-separated value files: sample_counts_unnormalized.csv contains output from featureCounts for each sample with features with less than 10 counts removed. tpm_counts_all.csv contains tpm-normalized counts generated with information from featureCounts.  JvS50_deseq.csv, SvJ50_deseq.csv, S50vUT_deseq.csv, J50vUT_deseq.csv, W50vUT_deseq.csv all contain LFC and padj values, along with other statistics for each gene for comparisons used.
Supplementary files format and content: NRF2List.txt and p53List.txt contain lists of target genes used for GSEA and DE analysis. SampleFileAll.txt contains tab-separated annotations for each sample.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Cat. No. 74104) from Qiagen
Novogene constructed cDNA library. They performed Poly (A) Capture/ rRNA removal. RNA fragmentation followed by cDNA reverse transcription

value: Breast epithelia, adenocarcinoma

value: WT

value: PBS Control


title: WT_UT_2

description:
WT_UT_2
SampleFileAll.txt
W50vUT_deseq.csv


title: MCF7 cells 75 uM H2O2 5 hours

description:
All_75
All_75

library_source: other

data_processing:
library strategy: scATAC-seq and scRNA-seq
Fragment and matrix files were generated from fastq files by the Cell Ranger ATAC pipeline by 10x genomics.
ArchR (v. 1.0.1) was used to extract features from fragment files.  Arrow files were created from fragments via the createArrowFiles function (minTSS = 4, minFrags = 1000)
Doublets were processed and removed via the addDoubletScores function (k = 10, knnMethod = "UMAP", LSIMethod = 1) and filterDoublets function.
The iterativeLSI function was applied for dimensionality reduction with default arguments except for resolution = c(0.2), clustering with addClusters with default parameters and resolution 0.16.
Peaks were called using MACS2 and the addReproduciblePeakSet function, grouping by Clusters.
Gene integration information was generated using scRNAseq data using the addGeneIntegrationMatrix function, grouping by sample.
Assembly: hg38
Supplementary files format and content: Motifs, peaks, gene score, and gene integration matrices are included as R Data Serialization (.rds) files in ArchRMatrices.tar
Supplementary files format and content: Fragment files are in tsv format. These contain scATAC data post-processing. Filtered barcodes and features for scRNAseq and scATACseq are in tsv format, while filtered matrices are in .mtx format.

molecule: other

extract_protocol:
Nuclei were then isolated using the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expresssion protocol (CG000365)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (Product code: 1000285) from 10X Genomics was used for transposition, GEM generation and Barcoding, ATAC Library Construction, cDNA Amplication, Gene expression and library construction (CG000338).

value: 75 uM H2O2

tag: molecule type

value: genomic DNA and total RNA


title: MCF7 cells PBS Control

description:
All_UT
All_UT

value: PBS


title: WT_75_3

description:
WT_75_3
SampleFileAll.txt


title: WT_UT_3

description:
WT_UT_3
SampleFileAll.txt
W50vUT_deseq.csv


title: WT_50_3

description:
WT_50_3
SampleFileAll.txt
W50vUT_deseq.csv

value: 50 uM H2O2


title: WT_75_1

description:
WT_75_1
SampleFileAll.txt


title: MCF7 cells 50 uM H2O2 5 hours

description:
All_50
All_50


title: WT_50_2

description:
WT_50_2
SampleFileAll.txt
W50vUT_deseq.csv


title: WT_75_2

description:
WT_75_2
SampleFileAll.txt


title: WT_50_1

description:
WT_50_1
SampleFileAll.txt
W50vUT_deseq.csv


title: SFRX_75_3

description:
SFRX_75_3
SampleFileAll.txt

value: SRXN1 Overexpression


title: SFRX_UT_2

description:
SFRX_UT_2
SampleFileAll.txt
S50vUT_deseq.csv


title: SFRX_75_2

description:
SFRX_75_2
SampleFileAll.txt


title: SFRX_75_1

description:
SFRX_75_1
SampleFileAll.txt


title: SFRX_UT_1

description:
SFRX_UT_1
SampleFileAll.txt
S50vUT_deseq.csv


title: SFRX_UT_3

description:
SFRX_UT_3
SampleFileAll.txt
S50vUT_deseq.csv


title: VUILD96-MF

tag: disease state/diagnosis

value: F

value: N


title: SFRX_50_3

description:
SFRX_50_3
SampleFileAll.txt
S50vUT_deseq.csv
JvS50_deseq.csv
SvJ50_deseq.csv


title: SFRX_50_2

description:
SFRX_50_2
SampleFileAll.txt
S50vUT_deseq.csv
JvS50_deseq.csv
SvJ50_deseq.csv


title: THD0010

value: Control

value: M

tag: tobacco status_(ever-smoker)

value: Hispanic


title: J14_UT_3

description:
J14_UT_3
SampleFileAll.txt
J50vUT_deseq.csv

value: J14 20 uM, PBS Control


title: J14_UT_1

description:
J14_UT_1
SampleFileAll.txt
J50vUT_deseq.csv


title: J14_75_3

description:
J14_75_3
SampleFileAll.txt


title: J14_UT_2

description:
J14_UT_2
SampleFileAll.txt
J50vUT_deseq.csv


title: J14_50_1

description:
J14_50_1
SampleFileAll.txt
J50vUT_deseq.csv
JvS50_deseq.csv
SvJ50_deseq.csv


title: J14_50_2

description:
J14_50_2
SampleFileAll.txt
J50vUT_deseq.csv
JvS50_deseq.csv
SvJ50_deseq.csv


title: J14_75_2

description:
J14_75_2
SampleFileAll.txt


title: J14_75_1

description:
J14_75_1
SampleFileAll.txt


title: J14_50_3

description:
J14_50_3
SampleFileAll.txt
J50vUT_deseq.csv
JvS50_deseq.csv
SvJ50_deseq.csv


title: SFRX_50_1

description:
SFRX_50_1
SampleFileAll.txt
S50vUT_deseq.csv
JvS50_deseq.csv
SvJ50_deseq.csv


title: Oxaliplatin reolicate 2 (OXA2)

city: Montpellier

first: Alexandre

last: Djiane

address: 208 rue des apothicaires

department: IRCM

country: France

institute: Inserm

description: Novaseq full FC S1 2x100

data_processing:
Adapter trimming using Trimmomatic v0.32
Mapping using STAR v2.7.5b
Expression estimation using RSEM v1.3.3
Normalization and comparison using DESeq2 v2.13
Assembly: Ensembl GRCh38
Supplementary files format and content: Table with raw and normalized gene counts for every gene and every sample

growth_protocol: Cells were cultured in RPMI media supplemented with 10% bovine fetal serum and 1% Pen/Strep to a confluency of 60-70%

extract_protocol:
1 Million HCT116 cells per replicate. Total RNA extracted using QIAGEN kit. Genomic DNA was removed using Ambion's DNA-free kit.
Illumina TruSeq stranded mRNA Sample Prep Kit was used on PolyA purified from 0.5 µg of total RNA

treatment_protocol: Oxaliplatin at 0.5 µM (IC50) for 24 hours

value: Oxaliplatin 0.5 µM


title: Oxaliplatin reolicate 3 (OXA3)

description: Novaseq full FC S1 2x100


title: Spleen RNA, PBS mock-infected C57BL/6 mice, Day0, replicate 2

description: Total RNA isolated from spleens of PBS inoculated C57BL/6 mice. Replicate 2.

value: Spleen

tag: mouse strain

tag: mouse age

value: 8-12 weeks

tag: timepoint


title: PMA_PTX3

city: Tainan

first: Feng-Wei

last: Chen

address: No. 1 University Rd., Department of Biotechnology and Bioindustry Sciences

department: Institute of Basic Medical Sciences

country: Taiwan

institute: National Cheng Kung University

data_processing:
FastQC, MultiQC, and ReSeqTools were used for analysis of quality and Trimmomatic (v.0.38) was used to remove poor quality reads and adaptors.
The reads were aligned to reference genome GRCh38 (Homo sapiens) by using HISAT2 software.
The normalization of gene expression was performed by using DESeq method and the differential gene expression was analyzed by using R (DESeq)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: tab-delimited text files include original read counts for each Sample

growth_protocol: THP-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin in humidified atmosphere with 5% CO2 at 37oC

extract_protocol:
RNA was harvested using Trizol® Reagent (Invitrogen, USA) according to manufacturer instructions. The quantification of purified RNA was measured by using SimpliNano™ - Biochrom Spectrophotometers (Biochrom, MA, USA) and 1μg total RNA were used for library construction.
RNA libraries for RNA-seq were prepared using g KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer's protocols. The purification of PCR products was performed by using KAPA Pure Beads system and the library quality was determined by using the Qsep 100 DNA/RNA Analyzer (BiOptic Inc., Taiwan). The library was then sequenced on an illumina NovaSeq6000.

treatment_protocol: Macrophage differentiation was induced by treatment with 320 nM PMA for 6 h. THP-1 macrophages were then stimulated with or without 50 ng/ml PTX3 recombinant protein for 18 h.

tag: cell line

value: monocyte

value: 320 nM PMA for 6 h

value: 50 ng/ml PTX3 for 18 h


title: Non Treated replicate 3 (NT3)

description: Novaseq full FC S1 2x100


title: PMA

value: WT

value: 0 ng/ml PTX3 for 18 h


title: Oxaliplatin reolicate 1 (OXA1)

description: Novaseq full FC S1 2x100


title: Non Treated replicate 2 (NT2)

description: Novaseq full FC S1 2x100


title: Arch, ASD line CTNNB1 mutation corrected, Passage7, rep2

city: Cleveland

first: Shuai

last: Fu

state: OH

address: 10900 Euclid Avenue

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Paired-end RNA sequencing reads were pseudoaligned to the human reference transriptome GRCh38.p13 release 103 using Kallisto version 0.46.2  for transcript abundance quantification.
Tximport R package was used to summarize transcript quantification data to genes followed by the R package edgeR TMM method for normalization
Genes with <1 CPM among 9 sample replicates, were filtered out.
Assembly: GRCh38.p13 release 103
Supplementary files format and content: tsv file for log2 normalized cpm value for each sample in passage 5,6 and 7

molecule: polyA RNA

source_name: Arch

growth_protocol: Neural progenitor cells were maintained in Neural Expansion Medium (Neurbasal (catalog: 21103049) /Advanced DMEM/F12(catalog: 12634028) 50:50, 1X neural induction supplement (catalog: A1647801))  with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Direct-zol RNA Miniprep Plus Kit (Zymo Research). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNextUltra™II RNA Library Prep Kit following manufacturer's protocols.

value: Arch

value: neural progenitor cells

value: CTNNB1 WT/WT

tag: passage


title: Non Treated replicate 1 (NT1)

description: Novaseq full FC S1 2x100


title: Chap, control, Passage7, rep3

source_name: Chap

value: Chap


title: Arch, ASD line CTNNB1 mutation corrected, Passage7, rep1


title: Arch, ASD line CTNNB1 mutation corrected, Passage7, rep3


title: Chap, control, Passage6, rep3


title: Chap, control, Passage6, rep1


title: Chap, control, Passage6, rep2


title: Arch, ASD line CTNNB1 mutation corrected, Passage5, rep2


title: Chap, control, Passage7, rep1


title: Arch, ASD line CTNNB1 mutation corrected, Passage6, rep3


title: Chap, control, Passage7, rep2


title: Arch, ASD line CTNNB1 mutation corrected, Passage6, rep1


title: Arch, ASD line CTNNB1 mutation corrected, Passage5, rep3


title: Arch, ASD line CTNNB1 mutation corrected, Passage6, rep2


title: Chap, control, Passage5, rep3


title: Arch, ASD line CTNNB1 mutation corrected, Passage5, rep1


title: Chap, control, Passage5, rep2


title: Chap, control, Passage5, rep1


title: Arch, ASD line, CTNNB1 mutation CRISPR-corrected, week 10

description: 10x Genomics Single Cell 3' Kit v3.1

data_processing:
Raw demultiplexed fastq files were uploaded into the 10x genomics cloud, and reads were aligned to Human (GRCh38) 2020-A using Cell Ranger v7.0.1 with default settings.
Assembly: Human (GRCh38) 2020-A
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format

extract_protocol:
Cortical organoids were dissociated into single-cell suspension with the Papain dissociation system (Worthington Biochemical, LK003150). Cells were then loaded onto the Chromium Next GEM Chip G Single Cell Kit, (10x Genomics, 1000120), and were processed with Chromium Controller to generate single-cell gel beads in emulsion.
The Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics, 1000268) was used for all scRNA-seq library preparations.

tag: time

value: week 10


title: Clay, control, week 10

description: 10x Genomics Single Cell 3' Kit v3.1

source_name: Clay

value: Clay


title: CD3D Mock 0877 FB

city: Los Angeles

first: Gay

middle: M

last: Crooks

address: 610 CHARLES E. YOUNG DRIVE EAST

department: Department of Pathology & Lab Medicine

institute: University of California, Los Angeles (UCLA)

description:
10X Genomics
M0877

data_processing:
Sequenced libraries were demultiplexed and used FASTQ were genereated by the UCLA Technology Center for Bioinformatics and Genomics core. Sequenced libraries for 5' Gene Expression. (5' GEX), VDJ, and Feature Barcoding (ADT) libraries were processed  and count matrices were generated using the CellRanger software v7.0.0 Multi pipeline (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/multi).
Count matrices for 5' GEX and ADT librariers are combined, and fully reconstructed TCR (VDJ) chains are included as filtered_contig_annotations.csv
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: ADT-seq

source_name: Bone Marrow HSPC (CD34+)

growth_protocol: Bone Marrow ATOs were generated as previously described (PMID: 28369043). MS5-hDLL4 cells were harvested by trypsinization and resuspended in serum free ATO culture medium (“RB27”) composed of RPMI 1640 (Corning, Manassas, VA), 4% B27 supplement (ThermoFisher Scientific, Grand Island, NY), 30 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, St. Louis, MO) reconstituted in PBS, 1% penicillin/streptomycin (Gemini Bio-Products, West Sacramento, CA), 2% Glutamax (ThermoFisher Scientific, Grand Island, NY), 5 ng/ml rhFLT3L and 2.5 ng/ml rhIL-7 (Peprotech, Rocky Hill, NJ). RB27 was made fresh weekly. 1.5×105 MS5-hDLL1 cells were combined with 1.5×103 CD34+ cells per ATO in 1.5 ml Eppendorf tubes (up to 12 ATOs per tube) and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended in 6 µl RB27 per ATO and mixed by brief vortexing. ATOs were plated on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) placed in a 6-well plate containing 1 ml RB27 per well. Medium was changed completely every 3–4 days by aspiration from around the cell insert followed by replacement with 1 ml with fresh RB27/cytokines. ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer.

extract_protocol:
ATOs were harvested at week 8 (as above) and subjected to MACs Dead Cell Removal Kit (Miltenyi, Cat. 130–090-101), and ~5 x 105 cells were stained with TotalSeq-C Human Universal Cocktail, V1.0 (Biolegend, Cat. 399905) per the manufacturer's protocol.
Labeled cells were submitted to the UCLA Technology Center for Bioinformatics and Genomics for unique molecular identifier (UMI) tagging and generation of gene expression (GEX), human TCR repertoire (VDJ), and Feature Barcoding libraries using the 10X Chromium Next GEM Single Cell 5’ Kit v2 (10X Genomics, Pleasanton, CA). Fully constructed libraries for all samples were run in one S4 flowcell on the Illumina Novaseq platform.
5' Gene Expression (GEX), VDJ, and Feature Barcoding libraries were constructed according to the manufacturer's instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2, 10X Genomics).

treatment_protocol: Mock cells were electroporated and edited cells were electroporated with mRNA encoding ABEmax-NRTH and sgRNA

value: Bone Marrow HSPC (CD34+)

value: CD3D SCID (c.202C>T)

tag: cell type

value: Mature Hematopoeitic cells, derived in vitro from CD34+ Bone Marrow HSPCs

value: Mock

tag: culture method

value: artificial thymic organoid

value: 8 weeks


title: CD3D Edited 0877 FB

description:
10X Genomics
E0877

tag: tissue

tag: treatment

value: Base-Edited


title: Apex, PTEN KO/KO, week 21

description: 10x Genomics Single Cell 3' Kit v3.1

data_processing:
Raw demultiplexed fastq files were uploaded into the 10x genomics cloud, and reads were aligned to Human (GRCh38) 2020-A using Cell Ranger v6.1.2 with default settings.
Assembly: Human (GRCh38) 2020-A
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format

source_name: cortical organoids

value: cortical organoids

value: Apex

value: PTEN KO/KO

value: week 21


title: CD3D Mock 0721 5' GEX

description:
10X Genomics
M0721

data_processing:
Sequenced libraries were demultiplexed and used FASTQ were genereated by the UCLA Technology Center for Bioinformatics and Genomics core. Sequenced libraries for 5' Gene Expression. (5' GEX), VDJ, and Feature Barcoding (ADT) libraries were processed  and count matrices were generated using the CellRanger software v7.0.0 Multi pipeline (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/multi).
Count matrices for 5' GEX and ADT librariers are combined, and fully reconstructed TCR (VDJ) chains are included as filtered_contig_annotations.csv
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files


title: CD3D Mock 0721 VDJ

description:
10X Genomics
M0721_filtered_contig_annotations.csv

data_processing:
Sequenced libraries were demultiplexed and used FASTQ were genereated by the UCLA Technology Center for Bioinformatics and Genomics core. Sequenced libraries for 5' Gene Expression. (5' GEX), VDJ, and Feature Barcoding (ADT) libraries were processed  and count matrices were generated using the CellRanger software v7.0.0 Multi pipeline (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/multi).
Count matrices for 5' GEX and ADT librariers are combined, and fully reconstructed TCR (VDJ) chains are included as filtered_contig_annotations.csv
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scVDJ-seq


title: CD3D Edited 0721 5' GEX

description:
10X Genomics
E0721


title: CD3D Edited 0877 5' GEX

description:
10X Genomics
E0877


title: CD3D Mock 0721 FB

description:
10X Genomics
M0721


title: CD3D Mock 0877 5' GEX

description:
10X Genomics
M0877


title: CD3D Edited 0877 VDJ

description:
10X Genomics
E0877_filtered_contig_annotations.csv


title: CD3D Mock 0877 VDJ

description:
10X Genomics
M0877_filtered_contig_annotations.csv


title: Apex, PTEN WT/I135L, week 21

description: 10x Genomics Single Cell 3' Kit v3.1

value: PTEN WT/I135L


title: Apex, PTEN WT/I135L, week 10

description: 10x Genomics Single Cell 3' Kit v3.1


title: Chap, PTEN WT/I135L, week 21

description: 10x Genomics Single Cell 3' Kit v3.1


title: Chap, PTEN KO/KO, week 21

description: 10x Genomics Single Cell 3' Kit v3.1


title: Chap, PTEN WT/WT, week 21

description: 10x Genomics Single Cell 3' Kit v3.1

value: PTEN WT/WT


title: Apex, PTEN KO/KO, week 10

description: 10x Genomics Single Cell 3' Kit v3.1


title: Apex, PTEN WT/WT, week 21

description: 10x Genomics Single Cell 3' Kit v3.1


title: Apex, PTEN KO/KO, Passage5, rep3 [A_KO_5_3]

data_processing:
Paired-end RNA sequencing reads were pseudoaligned to the human reference transriptome GRCh38.p13 release 103 using Kallisto version 0.46.2  for transcript abundance quantification.
Tximport R package was used to summarize transcript quantification data to genes followed by the R package edgeR TMM method for normalization
Genes with <1 CPM among 3 sample replicates, were filtered out.
Assembly: GRCh38.p13 release 103
Supplementary files format and content: tsv files for log2 normalized cpm value for each sample in passage 3
Supplementary files format and content: tsv files for log2 normalized cpm value for each sample in passage 4
Supplementary files format and content: tsv files for log2 normalized cpm value for each sample in passage 5

source_name: Apex

value: neural progenitor cells


title: Apex, PTEN WT/WT, week 10

description: 10x Genomics Single Cell 3' Kit v3.1


title: Apex, PTEN KO/KO, Passage5, rep2 [A_KO_5_2]


title: CD3D Edited 0721 FB

description:
10X Genomics
E0721


title: Chap, PTEN WT/I135L, week 10

description: 10x Genomics Single Cell 3' Kit v3.1

value: Chap


title: CD3D Edited 0721 VDJ

description:
10X Genomics
E0721_filtered_contig_annotations.csv


title: Apex, PTEN WT/I135L, Passage5, rep3 [Apex_5_3]


title: Chap, PTEN WT/WT, week 10

description: 10x Genomics Single Cell 3' Kit v3.1

value: week 10


title: Apex, PTEN KO/KO, Passage5, rep1 [A_KO_5_1]


title: Apex, PTEN WT/I135L, Passage5, rep2 [Apex_5_2]


title: Apex, PTEN WT/I135L, Passage5, rep1 [Apex_5_1]


title: Apex, PTEN WT/WT, Passage5, rep2 [A_PC_5_2]


title: Apex, PTEN WT/WT, Passage5, rep1 [A_PC_5_1]


title: Chap, PTEN KO/KO, Passage5, rep3 [C_KO_5_3]


title: Chap, PTEN WT/I135L, Passage5, rep2 [Ch_P_5_2]


title: Chap, PTEN KO/KO, Passage5, rep1 [C_KO_5_1]


title: Chap, PTEN WT/I135L, Passage5, rep1 [Ch_P_5_1]


title: Chap, PTEN WT/I135L, Passage5, rep3 [Ch_P_5_3]


title: Chap, PTEN WT/WT, Passage5, rep3 [Chap_5_3]


title: Chap, PTEN KO/KO, Passage5, rep2 [C_KO_5_2]


title: Chap, PTEN KO/KO, week 10

description: 10x Genomics Single Cell 3' Kit v3.1


title: Chap, PTEN WT/WT, Passage5, rep2 [Chap_5_2]


title: Apex, PTEN KO/KO, Passage4, rep3 [A_KO_4_3]


title: Chap, PTEN WT/WT, Passage5, rep1 [Chap_5_1]


title: Apex, PTEN WT/I135L, Passage4, rep3 [Apex_4_3]


title: Apex, PTEN KO/KO, Passage4, rep1 [A_KO_4_1]


title: Apex, PTEN KO/KO, Passage4, rep2 [A_KO_4_2]


title: Apex, PTEN WT/I135L, Passage4, rep2 [Apex_4_2]


title: Apex, PTEN WT/I135L, Passage4, rep1 [Apex_4_1]


title: Chap, PTEN KO/KO, Passage4, rep2 [C_KO_4_2]


title: Apex, PTEN WT/WT, Passage4, rep1 [A_PC_4_1]


title: Chap, PTEN KO/KO, Passage4, rep1 [C_KO_4_1]


title: Chap, PTEN WT/I135L, Passage4, rep2 [Ch_P_4_2]


title: Apex, PTEN WT/WT, Passage4, rep2 [A_PC_4_2]


title: Chap, PTEN WT/I135L, Passage4, rep3 [Ch_P_4_3]


title: VUILD98-MF

value: Lung

value: IPF

tag: age

tag: Sex

value: M

value: Y

tag: self-reported ethnicity

value: European

tag: tissue type


title: Apex, PTEN WT/WT, Passage4, rep3 [A_PC_4_3]

tag: genotype


title: Apex, PTEN WT/WT, Passage5, rep3 [A_PC_5_3]


title: Chap, PTEN KO/KO, Passage4, rep3 [C_KO_4_3]


title: Chap, PTEN WT/WT, Passage4, rep3 [Chap_4_3]


title: Apex, PTEN WT/I135L, Passage3, rep3 [Apex_3_3]


title: Apex, PTEN WT/I135L, Passage3, rep2 [Apex_3_2]


title: Apex, PTEN WT/I135L, Passage3, rep1 [Apex_3_1]


title: Chap, PTEN WT/I135L, Passage4, rep1 [Ch_P_4_1]


title: Apex, PTEN WT/WT, Passage3, rep3 [A_PC_3_3]


title: Apex, PTEN KO/KO, Passage3, rep1 [A_KO_3_1]


title: Apex, PTEN KO/KO, Passage3, rep2 [A_KO_3_2]


title: Chap, PTEN WT/WT, Passage4, rep1 [Chap_4_1]


title: E192

city: Nanchang

first: Biao

address: Zhimin street, Jingkai district

country: China

institute: Jiangxi Agricultural University

data_processing:
Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Bowtie and Tophat2 were used to map reads to the genome of Anas platyrhynchos. Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion.
CIRCExplorer2  and CIRI  was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion.
All samples were generated unique circular RNAs.
Circular RNA expressions from different groups (E13 and E19) were caculated by scripts in house. Only the comparisons with “p value”less than 0.05 were regarded as showing differential expression by R package.
Genome_build: IASCAAS_PekingDuck_PBH1.5 (GCF_003850225.1)
Supplementary_files_format_and_content: abundance measurements

organism: Anas platyrhynchos

source_name: Breast muscle

growth_protocol: A total of 120 hatching eggs of Shanma ducks with same genetical background were obtained from Jiangxi Tianyun duck breeding farm (Nanchang, Jiangxi), and incubated in the incubator (Keyu, Shandong, China) at 37.2 °C, with 60 ± 10% humidity.

extract_protocol:
Total RNAs of six samples were extracted and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.  All samples were kept at -80 °C.
circRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Breast muscle samples of 15 ducks were collected every 3 days during E10 to 1-day post hatch (E10, E13, E16, E19, E22 and 1-day post hatch), quick-frozen by liquid nitrogen and stored at -80 °C until RNA extraction.

tag: strain

value: Shanma duck

tag: phenotype

value: most myoblasts have differentiated

value: embryo 19 days

tag: group


title: E193


title: Chap, PTEN KO/KO, Passage3, rep3 [C_KO_3_3]


title: E191


title: E133

value: myoblasts didn't differentiated

value: embryo 13 days


title: Apex, PTEN WT/WT, Passage3, rep2 [A_PC_3_2]

value: Apex


title: Apex, PTEN WT/WT, Passage3, rep1 [A_PC_3_1]


title: Chap, PTEN KO/KO, Passage3, rep2 [C_KO_3_2]

value: PTEN KO/KO


title: Chap, PTEN KO/KO, Passage3, rep1 [C_KO_3_1]


title: Chap, PTEN WT/I135L, Passage3, rep3 [Ch_P_3_3]

value: PTEN WT/I135L


title: Chap, PTEN WT/I135L, Passage3, rep2 [Ch_P_3_2]


title: E132


title: Chap, PTEN WT/I135L, Passage3, rep1 [Ch_P_3_1]


title: E131


title: #42 adjancent normal tissue

city: beijing

first: Wang

last: Yan

address: 16# Lincui street,Chaoyang

institute: CAS

description: miRNA-seq

data_processing:
Raw sequencing reads were filtered with FASTQ to remove those that were low-quality, adapter contaminated, or shorter than 16 nt. Clean reads were mapped to the reference genome using anchor alignment-based small annotation (AASRA). Those reads that matched with rRNAs and tRNAs were excluded.
The unremoved reads were aligned against the miRBase (v21)  using Bowtie and allowing for one mismatch. Unaligned sequences were pooled together to identify novel miRNAs with miRDeep (v2.0.0.5) software using the default parameters.
To determine the miRNA expression profiles, miRNA counts were normalized to tags per million (TPM) using the following formula: normalized expression = actual miRNA read count /total clean read count × 106
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Total RNA was extracted from the frozen tissues using the TIANamp DNA/RNA Isolation Kit (TIANGEN) and treated with RNase-free DNase I (Ambion) for 30 minutes at 37°C to remove contaminating DNA.
RNA (1µg) from the tumor and paired adjacent tissues of 32 HCC patients were used to generate a miRNA sequencing library. RNA segments (18–30nt) were separated and recovered using a PAGE gel.
The miRNA DNBs were loaded onto patterned nanoarrays and the 50 bp single-end reads were read using the BGISEQ-500 platform at Beijing Genomics Institute (BGI; Shenzhen, China).

value: liver

tag: disease

value: hepatocellular carcinoma


title: #43 tumor tissue

description: miRNA-seq


title: #43 adjancent normal tissue

description: miRNA-seq


title: Chap, PTEN WT/WT, Passage3, rep1 [Chap_3_1]

value: Chap

value: neural progenitor cells

value: PTEN WT/WT


title: Chap, PTEN WT/WT, Passage3, rep3 [Chap_3_3]


title: Apex, PTEN KO/KO, Passage3, rep3 [A_KO_3_3]


title: Chap, PTEN WT/WT, Passage4, rep2 [Chap_4_2]


title: #40 tumor tissue

description: miRNA-seq


title: #38 adjancent normal tissue

description: miRNA-seq


title: #42 tumor tissue

description: miRNA-seq


title: #40 adjancent normal tissue

description: miRNA-seq


title: #37 adjancent normal tissue

description: miRNA-seq


title: #36 adjancent normal tissue

description: miRNA-seq


title: #36 tumor tissue

description: miRNA-seq


title: #37 tumor tissue

description: miRNA-seq


title: Chap, PTEN WT/WT, Passage3, rep2 [Chap_3_2]


title: #35 tumor tissue

description: miRNA-seq


title: #38 tumor tissue

description: miRNA-seq


title: #35 adjancent normal tissue

description: miRNA-seq


title: #34 adjancent normal tissue

description: miRNA-seq


title: ADhu-15_S15

city: ABINGDON

first: Adit

last: Dhummakupt

state: MD

address: 349 SPRUCE PINE ROAD,

institute: Johns Hopkins University, School of Medicine

data_processing:
Base calling was done using Illumina bcl2fastq2 version 1.37.0
Sequenced reads were mapped to human reference genome hg38 usinng HISAT2 v2.2.1.
Transcripts per million (TPM) were obtained usinng StringTie v1.3.6.

source_name: CD4+ T cells

extract_protocol:
Cells were lysed and stored in Trizol (Thermo Fisher). RNA was extracted according to manufacturer instructions.
Library was constructed using TruSeq Stranded mRNA kit (Illumina)

treatment_protocol: PBMCs were isolated from whole blood using Ficoll centrifugation (GE Healthcare). CD4+ T cells were isolated from PBMCs using a negative enrichment bead system (Miltenyi Biotec).

value: CD4+ T cells


title: ADhu-7_S7


title: ADhu-5_S5


title: ADhu-2_S2


title: ADhu-16_S16


title: ADhu-9_S9


title: ADhu-6_S6


title: ADhu-4_S4


title: ADhu-8_S8


title: #34 tumor tissue

description: miRNA-seq


title: #32 adjancent normal tissue

description: miRNA-seq


title: ADhu-14_S14


title: ADhu-12_S12


title: #32 tumor tissue

description: miRNA-seq


title: #31 adjancent normal tissue

description: miRNA-seq


title: #31 tumor tissue

description: miRNA-seq


title: ADhu-11_S11


title: ADhu-10_S10


title: ADhu-3_S3


title: #30 adjancent normal tissue

description: miRNA-seq


title: #30 tumor tissue

description: miRNA-seq


title: RH4, si-YTHDC1, replicate3 [RH4siYC13_S34]

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

institute: Sapienza University of Rome

description: Ribo minus

data_processing:
Trimmomatic (Bolger et al., 2014) and Cutadapt (Martin, 2011) were used to remove adapter sequences and poor quality bases; minimum read length after trimming was set to 35.
Reads were then aligned to the human reference genome (GRCh38) using BWA-MEM (Li, 2013) with -T 19 option.
CircRNA detection in each sample was then carried out using CIRI2 software (Gao, Zhang and Zhao, 2018) (see methods for further explanation about linear junction quantification).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include counts values for each Sample

source_name: RH4 (ARMS)

growth_protocol: Wild-type human primary myoblasts (Telethon Biobank) were cultured in growth medium (GM): DMEM high glucose (Sigma-Aldrich, Saint Louis, MO, USA), 10% FBS (Sigma-Aldrich), L-glutammine (Sigma-Aldrich) 2 mM, insulin (Sigma-Aldrich) 50 mg/ml, FGFb (Millipore-Merck) 25 ng/ml, EGF (Corning, Corning, NY, USA) 1 ng/ml, penicillin-streptomycin 1 × (Sigma-Aldrich). Human ERMS RD cell line (embryonal rhabdomyosarcoma cell line from a female patient) and ARMS RH4 cells line (alveolar rhabdomyosarcoma cell line from a female patient) cells were cultured in DMEM high glucose (Sigma-Aldrich) supplemented with 10% FBS (Sigma-Aldrich), L-glutammine (Sigma-Aldrich) 2 mM and penicillin-streptomycin 1 × (Sigma-Aldrich). All cells were cultured at 37°C in a humidified atmosphere of 5% CO2. All cell lines were tested for mycoplasma contamination.

extract_protocol:
RNA was harvested using Direct-zol RNA Miniprep (Zymo Research) kit according to the manufacturer’s specifications.
RNA libraries for RNA-seq were prepared using Stranded Total RNA Prep with Ribo-Zero Plus (Illumina) following manufacturer's protocols. Three biological replicates of each condition were used for sequencing.

treatment_protocol: Cells (150-200x103) were plated in 35mm plates and transfected 12hrs later with the siRNA against the target selected or the negative control (final concentration 30nM) using 5μl of Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific) and 300μl of Opti-MEM (Thermo Fisher Scientific). The medium was replaced 5-12hrs later. Cells were harvested 48hrs later.

value: RH4 (ARMS)

value: rhabdomyosarcoma ARMS


title: RH4, si-YTHDC1, replicate2 [RH4siYC12_S22]

description: Ribo minus


title: RH4, si-YTHDC1, replicate1 [RH4siYC11_S10]

description: Ribo minus


title: ADhu-1_S1


title: RH4, si-DDX5, replicate3 [RH4siDDX53_S36]

description: Ribo minus


title: #28 adjancent normal tissue

description: miRNA-seq


title: #29 tumor tissue

description: miRNA-seq


title: RH4, si-DDX5, replicate1 [RH4siDDX51_S12]

description: Ribo minus


title: RH4, si-SCR, replicate3 [RH4scr3_S33]

description: Ribo minus

value: si-SCR


title: #27 tumor tissue

description: miRNA-seq


title: #27 adjancent normal tissue

description: miRNA-seq


title: RH4, si-DDX5, replicate2 [RH4siDDX52_S24]

description: Ribo minus


title: #25 adjancent normal tissue

description: miRNA-seq


title: ADhu-13_S13


title: #28 tumor tissue

description: miRNA-seq


title: #25 tumor tissue

description: miRNA-seq


title: #24 adjancent normal tissue

description: miRNA-seq


title: RD, si-YTHDC1, replicate3 [RDsiYC13_S30]

description: Ribo minus

source_name: RD (ERMS)

value: RD (ERMS)

value: rhabdomyosarcoma ERMS


title: #24 tumor tissue

description: miRNA-seq


title: #23 adjancent normal tissue

description: miRNA-seq


title: RD, si-YTHDC1, replicate2 [RDsiYC12_S18]

description: Ribo minus


title: #29 adjancent normal tissue

description: miRNA-seq


title: #22 adjancent normal tissue

description: miRNA-seq


title: #23 tumor tissue

description: miRNA-seq


title: RD, si-DDX5, replicate2 [RDsiDDX52_S20]

description: Ribo minus

value: adipogenic differentiation


title: #20 adjancent normal tissue

description: miRNA-seq


title: #20 tumor tissue

description: miRNA-seq


title: RD, si-SCR, replicate1 [RDscr1_S5]

description: Ribo minus


title: #19 adjancent normal tissue

description: miRNA-seq


title: #19 tumor tissue

description: miRNA-seq


title: RH4, si-SCR, replicate1 [RH4scr1_S9]

description: Ribo minus


title: Myoblast, si-SCR, replicate3 [MYOscr3_S25]

description: Ribo minus

source_name: human primary myoblasts

value: human primary myoblasts


title: Myoblast, si-SCR, replicate2 [MYOscr2_S13]

description: Ribo minus


title: Myoblast, si-SCR, replicate1 [MYOscr1_S1]

description: Ribo minus

value: transfection with siRNA


title: #15 adjancent normal tissue

description: miRNA-seq


title: 29siTAZ-MDA-MB-231

city: Rehovot

first: Benjamin

last: Geiger

address: POB 26

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
RNA sequencing analysis was done using the user-friendly Transcriptome Analysis Pipeline (UTAP v1.10) transcriptome analysis pipeline (Kohen, Barlev et al. 2019). Reads were trimmed to remove adapters and low quality bases using cut adapt (-a “A (10)” -a “T (10)” –times 2 -q 20 -m 25) (Martin 2011) and mapped to the human genome (GRCh38, GENECODE version 34) using STAR v2.4.2a (Dobin, Davis et al. 2013) (using –alignEndsType EndToEnd, –outFilterMismatchNoverLmax. 0.05, –two pass Mode Basic). Reads were counted using STAR, and genes having minimum of five reads in at least one sample were considered. Normalized counts and detection of differential expression were performed using DESeq2 (Love, Huber et al. 2014) (betaPrior, cooksCutoff, and independent filtering parameters set to False). Differentially expressed genes were selected with absolute fold change (log2)≥1 and adjusted multiple testing p-value ≤0.05 (Benjamini and Hochberg 1995).
Assembly: GRCh38, GENECODE version 34
Supplementary files format and content: Tab-delimited text file contains raw and normalized counts, and DESeq2 analysis for genes after filtering based on expression levels (sum normalized count in all samples greater than 5)

growth_protocol: MDA-MB-231  cells (0.7 ×106) were seeded on 10 cm culture dishes and incubated for 24 h. Subsequently, the cells were transfected with SMARTpool siRNA for siControl, siYAP, siTAZ, and siYAPTAZ and incubated for a further 48 h for the knockdown. After the incubation, the knockdown cells were seeded on non-labeled gelatin-coated 10 cm plates and cultured for 5-6 h in an incubator. Subsequently, the culture medium was aspirated, and the cells were given a wash with DPBS.  One ml of DPBS was added to the plate, and the cells were then scraped using a cell scraper. Then the cells were centrifuged at 3000 rpm at 4C. The supernatant was aspirated, and the RNA was extracted from the cell pellet.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Catalog Nos; 74104, 74106 Qiagen) according to the manufacturer’s instructions.
Libraries were prepared using the INCPM-mRNA-seq protocol. Briefly, the polyA fraction was purified from the 500ng of total RNA, followed by fragmentation and generation of double-stranded cDNA, Agencourt Ampure XP beads cleanup (Beckman Coulter, USA), end repair, A base addition, adapter ligation, and PCR amplification.

value: TAZ knockdown

value: Transfection with  TAZ siRNA


title: 30siYAPTAZ-MDA-MB-231

value: YAP+TAZ knockdown

value: Transfection with  YAP+TAZ siRNA


title: #15 tumor tissue

description: miRNA-seq

value: liver

value: hepatocellular carcinoma


title: RH4, si-SCR, replicate2 [RH4scr2_S21]

description: Ribo minus


title: RD, si-YTHDC1, replicate1 [RDsiYC11_S6]

description: Ribo minus


title: RD, si-DDX5, replicate3 [RDsiDDX53_S32]

description: Ribo minus


title: 27siControl-MDA-MB-231

value: WT

value: Transfection with control siRNA


title: #13 adjancent normal tissue

description: miRNA-seq


title: RD, si-SCR, replicate3 [RDscr3_S29]

description: Ribo minus


title: #22 tumor tissue

description: miRNA-seq


title: #13 tumor tissue

description: miRNA-seq


title: 28siYAP-MDA-MB-231

value: YAP knockdown

value: Transfection with  YAP siRNA


title: 24siTAZ-MDA-MB-231


title: RD, si-DDX5, replicate1 [RDsiDDX51_S8]

description: Ribo minus


title: #18 adjancent normal tissue

description: miRNA-seq


title: 23siYAP-MDA-MB-231


title: #18 tumor tissue

description: miRNA-seq


title: #14 tumor tissue

description: miRNA-seq


title: #12 tumor tissue

description: miRNA-seq


title: 26Control-MDA-MB-231

value: Untransfected Control


title: RD, si-SCR, replicate2 [RDscr2_S17]

description: Ribo minus

value: si-SCR


title: 25siYAPTAZ-MDA-MB-231


title: #10 tumor tissue

description: miRNA-seq


title: #9 adjancent normal tissue

description: miRNA-seq


title: 21Control-MDA-MB-231


title: 22siControl-MDA-MB-231


title: #14 adjancent normal tissue

description: miRNA-seq


title: 20siYAPTAZ-MDA-MB-231


title: 19siTAZ-MDA-MB-231


title: #9 tumor tissue

description: miRNA-seq


title: #8 tumor tissue

description: miRNA-seq


title: 17siControl-MDA-MB-231


title: 18siYAP-MDA-MB-231


title: #8 adjancent normal tissue

description: miRNA-seq


title: #12 adjancent normal tissue

description: miRNA-seq


title: #4 adjancent normal tissue

description: miRNA-seq


title: 16Control-MDA-MB-231


title: #5 adjancent normal tissue

description: miRNA-seq


title: #5 tumor tissue

description: miRNA-seq


title: T21, HTP0706A

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description: globin-depleted, poly(A)+ RNA from whole blood

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (FPKM).

source_name: whole blood

extract_protocol:
Whole blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX/Qiagen) and RNA purified using a PAXgene Blood RNA Kit (Qiagen). RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Globin RNA depletion, poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a GlobinClear kit, NEBNext® Poly(A) mRNA Magnetic Isolation Module, and NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by Novogene Co., Ltd.

value: whole blood

tag: karyotype

value: Female

tag: sample source

value: A

tag: library type

value: strand-specific


title: T21, HTP0676A


title: T21, HTP0708A

value: Male


title: Control, HTP0669B

value: Control

value: D


title: #4 tumor tissue

description: miRNA-seq


title: T21, HTP0672A


title: #2 tumor tissue

description: miRNA-seq


title: #2 adjancent normal tissue

description: miRNA-seq


title: #10 adjancent normal tissue

description: miRNA-seq


title: #1 adjancent normal tissue

description: miRNA-seq


title: #1 tumor tissue

description: miRNA-seq


title: NB18_4

city: Ithaca

first: Vimal

last: Selvaraj

state: NY

address: 204 Morrison Hall

department: Animal Sciences

institute: Cornell University

data_processing:
The quality of raw reads was checked using FastQC before aligning to bovine reference genome (ARS UCD 1.2) using R package STAR
Differentially expressed genes were identified using R package EdgeR
Genome_build: ARS UCD 1.2
Supplementary_files_format_and_content: Raw Reads

organism: Bos taurus

source_name: Day 18 bovine endometrium

extract_protocol:
Total RNA was isolated using RNAqueous Micro Total RNA isolation kit.
mRNA was captured using poly (A) and cDNA libraries were prepared using TruSeq stranded total RNA sample preparation kit (Illumina)

treatment_protocol: Cattle (Holstein virgin heifers) at least 7 months of age, sexually mature, non-lactating and weighing at least 340 kg (750 lbs) were subjected to estrous cycle synchronization, five-day Co-synch. In brief, a GnRH analog (100 μg intra-muscular, Fertagyl, MWI Animal Health) and progesterone (1.38g in a controlled intra-vaginal drug release device, Eazi-Breed, Zoetis) were administered. After 96 hours, a prostaglandin F2α analog Estrumate (500 μg intra-muscular, Cloprostenol, MWI Animal Health) was administered, followed by a second dose of Estrumate (500 μg intra-muscular, Cloprostenol, MWI Animal Health) and removal of the Eazi-Breed device at 120 hours. The synchronized animals were randomly selected for one of five estrous cycle timepoints [day 0 (estrus), 5,10,14 and 18; n=4/timepoint] for endometrial biopsies.

tag: breed

value: holstein

value: endometrium

tag: time

value: Day 18


title: T21, HTP0668A


title: NB18_3

tag: cell type


title: NB18_2


title: T21, HTP0665A

tag: tissue


title: T21, HTP0664A


title: T21, HTP0666A


title: NB18_1


title: NB14_4

source_name: Day 14 bovine endometrium

value: Day 14


title: NB14_3


title: T21, HTP0662A


title: T21, HTP0661A


title: NB14_2


title: NB14_1


title: T21, HTP0659A


title: NB10_4

source_name: Day 10 bovine endometrium

value: Day 10


title: T21, HTP0658A


title: T21, HTP0667A


title: NB10_3


title: T21, HTP0657A


title: NB5_4

source_name: Day 5 bovine endometrium

value: Day 5


title: NB10_1


title: NB10_2


title: NB5_1


title: NB5_2


title: T21, HTP0651A


title: T21, HTP0650A


title: NB0_3

source_name: Day 0 bovine endometrium

value: Day 0


title: T21, HTP0663A


title: T21, HTP0652A


title: T21, HTP0654A


title: Control, HTP0653B


title: NB0_4


title: Control, HTP0649B


title: NB0_2


title: Control, HTP0648B


title: NB0_1


title: T21, HTP0647A


title: T21, HTP0660A


title: T21, HTP0646A


title: Control, HTP0655B


title: NB5_3


title: T21, HTP0644A


title: T21, HTP0645A


title: T21, HTP0642A


title: T21, HTP0641A


title: folr-1(syb4116) rep2

first: Olli

last: Matilainen

address: Viikinkaari 9C

department: Faculty of Biological and Environmental Sciences

institute: University of Helsinki

description:
gene_id N2_EV1 N2_EV2 N2_EV3 FR_EV1 FR_EV2 FR_EV3
FR_EV2

data_processing:
To obtain clean reads, raw data (raw reads) of FASTQ format were firstly processed through fastp.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
FeatureCounts was used to count the read numbers mapped of each gene. Consequently, RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by Trimmed Mean of M- values (TMM) through one scaling normalized factor. Data processing was done by Novogene.
Assembly: WBcel235
Supplementary files format and content: fpkm_sample.txt, content: FPKM values
Supplementary files format and content: readcount.txt, content: read counts

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: N2 and folr-1(syb4116) strains were synchronized by bleaching and plated as L1 larvae on RNAi plates seeded with HT115 bacteria carrying empty vector (control vector for RNAi). Animals were collected at L4 stage (three biological replicates for both strains) and freezed in liquid nitrogen.

extract_protocol:
Total RNA was extracted with TRIzol Reagent (ThermoFisher Scientific)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Library construction and sequencing was done by Novogene.

value: whole animal

tag: developmental stage

value: L4 larvae

tag: temperature

value: 20 degree celcius

tag: treatment

value: empty vector (control) RNAi


title: folr-1(syb4116) rep1

description:
gene_id N2_EV1 N2_EV2 N2_EV3 FR_EV1 FR_EV2 FR_EV3
FR_EV1


title: N2 rep1

description:
gene_id N2_EV1 N2_EV2 N2_EV3 FR_EV1 FR_EV2 FR_EV3
N2_EV1

value: N2 (wild-type)


title: N2 rep3

description:
gene_id N2_EV1 N2_EV2 N2_EV3 FR_EV1 FR_EV2 FR_EV3
N2_EV3


title: folr-1(syb4116) rep3

description:
gene_id N2_EV1 N2_EV2 N2_EV3 FR_EV1 FR_EV2 FR_EV3
FR_EV3


title: N2 rep2

description:
gene_id N2_EV1 N2_EV2 N2_EV3 FR_EV1 FR_EV2 FR_EV3
N2_EV2


title: T21, HTP0643A

value: whole blood

tag: Sex

tag: age


title: Gr5a_SD+OSMI-6

city: Ann Arbor

first: Monica

last: Dus

state: Michigan

address: 1105 N University, 4224

institute: University of Michigan

description: Ribosome associated RNA

data_processing:
Reads were aligned using STAR  (version: 020201). --quantMode GeneCounts
Convert .sam files to .bam files using samtools (version 1.4).
HTSeq counts, text format, gene ID, union, intersection_strict, intersection_nonempty
Determine differential RNA abundance using DeSeq2 (version 1.18.0). dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition)
Genome_build: BDGP6

organism: Drosophila melanogaster

source_name: Gr5a sensory neurons

growth_protocol: Male flies were collected 2 days after eclosure and housed in vials of 35. Flies were placed on their specific dietary condition at day 5 until day 12 when samples were collected.

extract_protocol:
2-3 biological replicates were used for each condition, and each replicate consisted of 300 heads. For tissue collections, briefly heads were collected using pre-chilled sieves in liquid nitrogen on dry ice. Frozen heads were then lysed. From the lysate total RNA was extracted by TRIzol LS Reagent and used as input. The remainder of the lysate was incubated with Dynabeads protein G  to preclear samples for 2 hours and subsequently incubated with Dynabeads protein G coated with an anti-Flag antibody. The lysate-beads mixture was incubated at 4°C with rotation for 2 hours, then washed in buffer. RNA was extracted from ribosomes bound to the beads by TRIzol Reagent.
Samples were ribo-depleted, DNase treated, and libraries were prepared using the Nugen Ovation SoLo RNA-Seq System for Drosophila (0502) by the University of Michigan sequencing core facility. Library concentrations were determined by qPCR.
RNA-seq illumina Next-seq500

treatment_protocol: Flies were placed either on a control diet (5% sucrose) or sugar diet (30% sucrose). Both diets were supplemented with 10 uM OSMI-1 dissolved in 10 % DMSO

value: Gr5a sensory neurons

tag: dietary condition

value: Sugar diet + 10uM OSMI-1

tag: genotype


title: T21, HTP0634A

value: Male

value: strand-specific


title: T21, HTP0637A

value: Female

value: D


title: Gr5a_CD+OSMI-3

description: Ribosome associated RNA

value: Control diet + 10uM OSMI-1


title: Gr5a_SD+OSMI-5

description: Ribosome associated RNA


title: T21, HTP0633A


title: Gr5a_SD+OSMI-4

description: Ribosome associated RNA


title: T21, HTP0638A


title: Gr5a_CD+OSMI-2

description: Ribosome associated RNA


title: T21, HTP0630A


title: Gr5a_DamPcl_SD+OSMI-1

description:
sonicated DNA
processed by converting normalized log2(Dam-Pcl/Dam) ratio files to bigwig

library_source: genomic

data_processing:
Reads were aligned using Bowtie2
Reads are extended to 300bp or closest GATC
Bam output is used to generate the ratio file between Dam::Pcl and Dam in bedgraph format
Ratio files were converted to bigwig normalized to 1X genome
Peaks were identified from log2(Dam::Pcl/Dam) ratio files using find_peaks (FDR<0.01)
Genome_build: BDGP6

growth_protocol: Flies were grown at 19-20C. Male and feamle age-matched flies were collected 2 days after eclosure and housed in vials of 35. Flies were placed on their specific dietary condition in 20C. At day 5 flies were mover to 28C until day 6 afor an additional day to induce Dam. Samples were collected and DNA isolated.

extract_protocol:
Three biological replicates were used for each condition, and each replicate consisted of 300 heads. For tissue collections, briefly heads were collected using pre-chilled sieves in liquid nitrogen on dry ice. Frozen heads were then lysed. DNA was extracted from frozen heads following kit instructions. For identification of methylated regions briefly, purified DNA was digested by DpnI followed by PCR purification of digested sequences. TaDa adaptors were ligated by T4 DNA ligase . Adapter ligated DNA was PCR amplified according to protocol, and subsequently purified. Purified DNA was digested with DpnII followed by sonication to yield fragments averaging 200-300bp. TaDa adaptors were removed from sonicated DNA by digestion.
Libraries were generated using the Takara ThruPlex kit (cat #022818) using 3ng input and 10 cycles of PCR. All libraries were sequenced on the Illumina NextSeq platform (High-output kit v2 75 cycles).
DNA-seq


title: Gr5a_DamPcl_SD+OSMI-2

value: Sugar diet + 10uM OSMI-2


title: T21, HTP0632A


title: T21, HTP0631A


title: Gr5a_CD+OSMI-1

description: Ribosome associated RNA


title: Gr5a_DamPcl_CD+OSMI-2


title: T21, HTP0629A


title: T21, HTP0627A


title: Gr5a_DamPcl_CD+OSMI-1


title: T21, HTP0639A


title: Control, HTP0628B

value: Control


title: Gr5a_Dam_SD+OSMI-2

description:
sonicated DNA
processed as BAM to bigwig by normalizing to 1X genome size


title: T21, HTP0623A


title: Gr5a_Dam_SD+OSMI-1


title: T21, HTP0624A


title: T21, HTP0626A


title: T21, HTP0625A


title: Gr5a_Dam_CD+OSMI-2


title: Gr5a_Dam_CD+OSMI-3


title: Gr5a_Dam_CD+OSMI-1


title: Gr5a_DamOGT_SD 1

value: Sugar diet


title: Gr5a_Dam_SD+OSMI-3


title: Gr5a_DamOGT_CD 3

value: Control diet


title: Gr5a_DamOGT_SD 2


title: T21, HTP0621A


title: T21, HTP0618A


title: Gr5a_DamOGT_CD 1


title: T21, HTP0620A


title: T21, HTP0619A


title: Gr5a_Dam_SD 2


title: T21, HTP0617A


title: T21, HTP0616A


title: Control, HTP0615B


title: Gr5a_Dam_SD 1


title: T21, HTP0612A


title: T21, HTP0613A


title: T21, HTP0622A


title: Gr5a_Dam_CD 2


title: Gr5a_Dam_CD 3


title: T21, HTP0611A


title: T21, HTP0609A


title: T21, HTP0610A


title: Gr5a_Dam_CD 1


title: T21, HTP0608A


title: T21, HTP0607A


title: Repressible rne strain in the presence of ATc at 32 minutes after rifampicin treatment replicate 3

city: Worcester

first: Scarlet

last: Shell

state: MA

address: 60 Prescott Street

department: Biology & Biotechnology

institute: Worcester Polytechnic Institute

data_processing:
For mRNA degradation profiling, reads were aligned to the reference genome using BWA-MEM v0.7.17 with default parameters.
For mRNA degradation profiling, the alignments were processed for each strand using SAMtools v1.10.
For mRNA degradation profiling, raw coverage of each coordinate was calculated using BEDTools v2.29.1.
For mRNA degradation profiling, the coverage for each gene was calculated as the summation of the coverage of its coordinates using custom Python script.
For mRNA degradation profiling, the raw coverage were nomalized by the library size, relative qPCR expression levels and gene length using custom Python script.
For RNaseE cleavage site analysis, reads were filtered using Trimmomatic v0.39 with the parameters "SLIDINGWINDOW:4:20 MINLEN:25".
For RNaseE cleavage site analysis, the filtered reads aligned to tRNA and rRNA were removed using Bowtie2 v2.4.5 with the parameter "--very-sensitive".
For RNaseE cleavage site analysis, the remaining reads were aligned to genome using Bowtie2 v2.4.5 with the parameter "--very-sensitive".
For RNaseE cleavage site analysis, the alignments were filtered using SAMtools v1.16.1 with the parameter "-q 10 -F 260".
For RNaseE cleavage site analysis, raw strand specific coverage of each coordinate was calculated using SAMtools v1.16.1 and BEDTools v2.30.0.
For RNaseE cleavage site analysis, the single-nucleotide coverage for each gene was normalized by the summed coverage of that gene.
Assembly: NC_008596.1
Supplementary files format and content: mRNA_halfLife_normalized_log2_coverage.txt is a text file including log2 normalized gene coverage for all replicates of all time points and conditions.
Supplementary files format and content: RNaseE_cleavageSite_normalized_coverage.txt is a text file including normalized single-nucleotide coverage and log2 coverage ratio between rne knockdown and control for qualified nucleotide coordinates, along with the annotations for each coordinate.

organism: Mycolicibacterium smegmatis

source_name: Mycolicibacterium smegmatis mc2155

growth_protocol: Strains were growth in 7H9 supplemented with ADC, glycerol, and Tween-80.

extract_protocol:
Pellets were resuspended in Trizol and lysed by bead-beating. RNA was extracted with a Zymo Direct-zol kit, treated with DNase, and purified with a Zymo Clean and Concentrate kit.
Libraries were constructed by the Broad Institute Microbial 'Omics Core using the protocol described in https://doi.org/10.1038/nmeth.3313
Ligation of 3' and 5' adapters to sheared RNA to construct paired-end Illumina RNAseq libraries with TruSeq-style adapters

treatment_protocol:
For hypoxia, cultures were diluted to OD 0.01, sealed in bottles with a 1:1 airspace:culture ratio, and incubated with shaking for 18 hours. Rifampicin was then injected by a syringe to a final concentration of 150 µg/mL and cultures were harvested by freezing in liquid nitrogen at the indicated timepoints.
For non-hypoxic samples, strains were grown to OD 0.8-0.9, with or without addition of ATc 8 hrs prior as indicated. Rifampicin was then added to a final concentration of 150 µg/mL and cultures were harvested by freezing in liquid nitrogen at the indicated timepoints.

tag: cell line

value: Mycolicibacterium smegmatis mc2155

value: The rne promoter and 5' UTR were replaced with the P766(8G) promoter and 5' UTR, and a hygromycin resistance gene was inserted upstream and divergent from the rne locus.

value: Rifampicin

value: 32 minutes


title: Gr5a_DamOGT_CD 2


title: T21, HTP0605A


title: Repressible rne strain in the presence of ATc at 32 minutes after rifampicin treatment replicate 1


title: T21, HTP0604A


title: Repressible rne strain in the presence of ATc at 16 minutes after rifampicin treatment replicate 2

value: 16 minutes


title: Repressible rne strain in the presence of ATc at 16 minutes after rifampicin treatment replicate 3


title: T21, HTP0600A

value: whole blood


title: Repressible rne strain in the presence of ATc at 16 minutes after rifampicin treatment replicate 1


title: T21, HTP0603A


title: T21, HTP0602A


title: Repressible rne strain in the presence of ATc at 4 minutes after rifampicin treatment replicate 3

value: 4 minutes


title: Repressible rne strain in the presence of ATc at 8 minutes after rifampicin treatment replicate 2

value: 8 minutes


title: Repressible rne strain in the presence of ATc at 8 minutes after rifampicin treatment replicate 3


title: T21, HTP0598A


title: T21, HTP0599A


title: Repressible rne strain in the presence of ATc at 4 minutes after rifampicin treatment replicate 2


title: Repressible rne strain in the presence of ATc at 32 minutes after rifampicin treatment replicate 2


title: T21, HTP0596A


title: Control, HTP0595B


title: Repressible rne strain in the presence of ATc at 2 minutes after rifampicin treatment replicate 2

value: 2 minute


title: Repressible rne strain in the presence of ATc at 2 minutes after rifampicin treatment replicate 1


title: Repressible rne strain in the presence of ATc at 2 minutes after rifampicin treatment replicate 3


title: T21, HTP0594A

value: Male

value: strand-specific


title: Repressible rne strain in the presence of ATc at 4 minutes after rifampicin treatment replicate 1


title: Repressible rne strain in the presence of ATc at 0 minutes after rifampicin treatment replicate 3

value: 0 minute


title: T21, HTP0592A

value: Female

value: D


title: T21, HTP0591A


title: T21, HTP0590A


title: T21, HTP0593A


title: Repressible rne strain in the presence of ATc at 8 minutes after rifampicin treatment replicate 1


title: T21, HTP0589A


title: T21, HTP0597A


title: Repressible rne strain in the presence of ATc at 0 minutes after rifampicin treatment replicate 1


title: Repressible rne strain in the absence of ATc at 16 minutes after rifampicin treatment replicate 2


title: Repressible rne strain in the presence of ATc at 0 minutes after rifampicin treatment replicate 2


title: Repressible rne strain in the absence of ATc at 16 minutes after rifampicin treatment replicate 3


title: T21, HTP0588A


title: T21, HTP0586A


title: Repressible rne strain in the absence of ATc at 8 minutes after rifampicin treatment replicate 3


title: T21, HTP0585A


title: Repressible rne strain in the absence of ATc at 16 minutes after rifampicin treatment replicate 1


title: Repressible rne strain in the absence of ATc at 8 minutes after rifampicin treatment replicate 2


title: Repressible rne strain in the absence of ATc at 8 minutes after rifampicin treatment replicate 1


title: T21, HTP0584A


title: Repressible rne strain in the absence of ATc at 4 minutes after rifampicin treatment replicate 3


title: T21, HTP0583A


title: Repressible rne strain in the absence of ATc at 4 minutes after rifampicin treatment replicate 2


title: Control, HTP0582B

value: Control


title: Repressible rne strain in the absence of ATc at 4 minutes after rifampicin treatment replicate 1


title: Repressible rne strain in the absence of ATc at 2 minutes after rifampicin treatment replicate 3

value: 2 minutes


title: Repressible rne strain in the absence of ATc at 2 minutes after rifampicin treatment replicate 2


title: T21, HTP0580A


title: T21, HTP0578A


title: T21, HTP0587A


title: T21, HTP0577A


title: Repressible rne strain in the absence of ATc at 1 minute after rifampicin treatment replicate 3

value: 1 minute


title: T21, HTP0575A


title: Repressible rne strain in the absence of ATc at 1 minute after rifampicin treatment replicate 1

value: Mycolicibacterium smegmatis mc2155


title: Control, HTP0576B


title: Repressible rne strain in the absence of ATc at 2 minutes after rifampicin treatment replicate 1

value: The rne promoter and 5' UTR were replaced with the P766(8G) promoter and 5' UTR, and a hygromycin resistance gene was inserted upstream and divergent from the rne locus.


title: Repressible rne strain in the absence of ATc at 0 minutes after rifampicin treatment replicate 3

value: Rifampicin


title: Control, HTP0573B


title: Repressible rne strain in the absence of ATc at 1 minute after rifampicin treatment replicate 2


title: T21, HTP0574A


title: T21, HTP0570A


title: T21, HTP0571A


title: Repressible rne strain in the absence of ATc at 0 minutes after rifampicin treatment replicate 2


title: Control strain in hypoxia at 60 minutes after rifampicin treatment replicate 2

value: A hygromycin resistance gene was inserted upstream of, and divergent from, the rne promoter.

value: Rifampicin. Hypoxia

value: 60 minutes


title: Repressible rne strain in the absence of ATc at 0 minutes after rifampicin treatment replicate 1


title: T21, HTP0572A

value: whole blood


title: T21, HTP0569A


title: Control strain in hypoxia at 60 minutes after rifampicin treatment replicate 1


title: Control strain in hypoxia at 60 minutes after rifampicin treatment replicate 3


title: T21, HTP0581A


title: Control strain in hypoxia at 30 minutes after rifampicin treatment replicate 3

value: 30 minutes


title: Control, HTP0567B


title: T21, HTP0566A


title: T21, HTP0565A


title: Control strain in hypoxia at 30 minutes after rifampicin treatment replicate 1


title: Control strain in hypoxia at 15 minutes after rifampicin treatment replicate 2

value: 15 minutes


title: Control strain in hypoxia at 30 minutes after rifampicin treatment replicate 2


title: Control strain in hypoxia at 15 minutes after rifampicin treatment replicate 3


title: Control, HTP0559B

value: Male


title: T21, HTP0563A

value: strand-specific


title: Control strain in hypoxia at 15 minutes after rifampicin treatment replicate 1


title: T21, HTP0561A


title: Control, HTP0557B


title: Control strain in hypoxia at 9 minutes after rifampicin treatment replicate 2

value: 9 minutes


title: Control strain in hypoxia at 9 minutes after rifampicin treatment replicate 3


title: T21, HTP0556A


title: Control strain in hypoxia at 3 minutes after rifampicin treatment replicate 2

value: 3 minutes


title: Control strain in hypoxia at 3 minutes after rifampicin treatment replicate 3


title: Control strain in hypoxia at 6 minutes after rifampicin treatment replicate 3

value: 6 minutes


title: Control strain in hypoxia at 6 minutes after rifampicin treatment replicate 2


title: T21, HTP0554A

value: D


title: T21, HTP0560A


title: T21, HTP0552A


title: Control strain in hypoxia at 6 minutes after rifampicin treatment replicate 1


title: Control strain in hypoxia at 3 minutes after rifampicin treatment replicate 1


title: T21, HTP0553A

value: Female


title: T21, HTP0564A


title: T21, HTP0550A


title: Control strain in hypoxia at 0 minutes after rifampicin treatment replicate 3

value: 0 minute


title: Control, HTP0551B

value: Control


title: Control strain in hypoxia at 9 minutes after rifampicin treatment replicate 1

value: Mycolicibacterium smegmatis mc2155


title: T21, HTP0548A


title: T21, HTP0568A


title: T21, HTP0547A


title: T21, HTP0546A


title: Control strain in hypoxia at 0 minutes after rifampicin treatment replicate 1


title: Control strain in the presence of ATc at 16 minutes after rifampicin treatment replicate 2

value: Rifampicin

value: 16 minutes


title: Control strain in the presence of ATc at 16 minutes after rifampicin treatment replicate 3

value: A hygromycin resistance gene was inserted upstream of, and divergent from, the rne promoter.


title: T21, HTP0544A


title: Control strain in the presence of ATc at 16 minutes after rifampicin treatment replicate 1


title: T21, HTP0549A


title: T21, HTP0545A


title: Control strain in the presence of ATc at 8 minutes after rifampicin treatment replicate 3

value: 8 minutes


title: T21, HTP0543A

value: whole blood


title: Control strain in the presence of ATc at 8 minutes after rifampicin treatment replicate 2


title: Control strain in the presence of ATc at 8 minutes after rifampicin treatment replicate 1


title: T21, HTP0542A


title: Control, HTP0555B


title: Control strain in the presence of ATc at 4 minutes after rifampicin treatment replicate 1

value: 4 minutes


title: Control strain in the presence of ATc at 4 minutes after rifampicin treatment replicate 3


title: T21, HTP0539A


title: T21, HTP0540A


title: Control strain in the presence of ATc at 4 minutes after rifampicin treatment replicate 2


title: Control strain in the presence of ATc at 2 minutes after rifampicin treatment replicate 3

value: 2 minutes


title: Control strain in hypoxia at 0 minutes after rifampicin treatment replicate 2

value: Rifampicin. Hypoxia


title: T21, HTP0538A

value: Male

value: strand-specific


title: Control strain in the presence of ATc at 2 minutes after rifampicin treatment replicate 2


title: T21, HTP0537A


title: Control strain in the presence of ATc at 2 minutes after rifampicin treatment replicate 1


title: Control strain in the presence of ATc at 1 minute after rifampicin treatment replicate 2

value: 1 minute


title: T21, HTP0534A

value: A


title: T21, HTP0535A


title: T21, HTP0530A


title: T21, HTP0541A

value: D


title: T21, HTP0531A

value: Female