title: 77CFARAging

source_name: Donor: 1318 Status: HIVPositive Age: OLD Timepoint: T1 Response: NonResponder


title: 75CFARAging

status: Public on Jan 19 2022

type: SRA

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

country: USA

institute: Case Western Reserve University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrices in CSV format containing raw as well as normalized Log2(n+3) CPM summarized reads

molecule: total RNA

organism: Homo sapiens

source_name: Donor: 758 Status: HIVNegative Age: Young Timepoint: T1 Response: Responder

growth_protocol: in vivo

extract_protocol:
RNA was extracted from 1 million PBMC using RNeasy Plus Mini Kit from QIAGEN
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded Total RNA - Globin kit.

tag: hiv status

value: HIVNegative

tag: donor id

tag: age

value: Young

tag: timepoint

tag: response

value: Responder

tag: tissue

value: PBMC


title: 76CFARAging

source_name: Donor: 1358 Status: HIVNegative Age: OLD Timepoint: T1 Response: Responder

value: OLD


title: 70CFARAging

source_name: Donor: 1118 Status: HIVPositive Age: Young Timepoint: T0 Response: Responder

value: HIVPositive


title: 6CFARAging

source_name: Donor: 2353 Status: HIVNegative Age: OLD Timepoint: T1 Response: Responder


title: 69CFARAging

source_name: Donor: 763 Status: HIVNegative Age: Young Timepoint: T0 Response: NonResponder

value: NonResponder


title: 68CFARAging

source_name: Donor: 763 Status: HIVNegative Age: Young Timepoint: T1 Response: NonResponder


title: 67CFARAging

source_name: Donor: 703 Status: HIVPositive Age: Young Timepoint: T1 Response: NonResponder


title: 62CFARAging

source_name: Donor: 1163 Status: HIVNegative Age: Young Timepoint: T0 Response: Responder


title: Hypoxia_Acriflavine_HUVEC_2 [Hyp_ACF_2]

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: E21_3141_Lib_Leisegang_ML1529-2_Probe_14

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (ensemble release 104) using STAR 2.7.9a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 2.0.2 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The Ensemble annotation was enriched with UniProt data based on Ensembl gene identifiers.
Genome_build: hg38
Supplementary_files_format_and_content: library size normalized counts

growth_protocol: Culturing of pooled human umbilical vein endothelial cells (HUVEC) purchased from PromoCell (C-12203, Lot No. 405Z013, 408Z014, 416Z042, Heidelberg, Germany) was performed at 37°C with 5% CO2. Dishes were coated with gelatin (Sigma-Aldrich, G1890-500G) prior to culturing. Endothelial growth medium (EGM) was prepared by supplementing endothelial basal medium (EBM) with human recombinant epidermal growth factor (EGF), EndoCGS-Heparin (PeloBiotech, Germany), 8% fetal calf serum (FCS) (S0113, Biochrom, Germany), penicillin (50 U/ml) and streptomycin (50 µg/ml) (15140-122, Gibco/ Lifetechnologies, USA). Biological replicates comprised at least three different batches from passage 3. For hypoxia treatment, cells were incubated for 16h in a SciTive Workstation (Baker Ruskinn, Leeds, UK) at 1% O2 and 5% CO2.

extract_protocol:
Total RNA Isolation was performed using the RNA Mini Kit (Bio&Sell).
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara) using manufactures protocols.

treatment_protocol: Hypoxia was performed for 16h (1% O2) with  DMSO or Acriflavine (10µM) treatment.

tag: cell line

tag: treatment

value: 16h (1% O2) with Acriflavine (10µM)


title: 51CFARAging

source_name: Donor: 1354 Status: HIVNegative Age: OLD Timepoint: T0 Response: Responder


title: 52CFARAging

source_name: Donor: 9101 Status: HIVPositive Age: OLD Timepoint: T0 Response: Responder


title: 44CFARAging

source_name: Donor: 1303 Status: HIVPositive Age: OLD Timepoint: T0 Response: Responder


title: 97CFARAging

source_name: Donor: 9003 Status: HIVPositive Age: Young Timepoint: T1 Response: Responder


title: 49CFARAging

source_name: Donor: 1318 Status: HIVPositive Age: OLD Timepoint: T0 Response: NonResponder


title: 48CFARAging

source_name: Donor: 1360 Status: HIVNegative Age: OLD Timepoint: T1 Response: Responder


title: 43CFARAging

source_name: Donor: 1307 Status: HIVPositive Age: OLD Timepoint: T0 Response: Responder


title: 47CFARAging

source_name: Donor: 855 Status: HIVNegative Age: OLD Timepoint: T1 Response: NonResponder


title: 42CFARAging

source_name: Donor: 855 Status: HIVNegative Age: OLD Timepoint: T0 Response: NonResponder


title: 82CFARAging

source_name: Donor: 2001 Status: HIVNegative Age: OLD Timepoint: T1 Response: NonResponder


title: 34CFARAging

source_name: Donor: 857 Status: HIVNegative Age: OLD Timepoint: T1 Response: NonResponder


title: 41CFARAging

source_name: Donor: 1281 Status: HIVNegative Age: OLD Timepoint: T1 Response: Responder


title: 40CFARAging

source_name: Donor: 1304 Status: HIVPositive Age: OLD Timepoint: T0 Response: Responder


title: 31CFARAging

source_name: Donor: 2303 Status: HIVPositive Age: OLD Timepoint: T0 Response: NonResponder


title: 2CFARAging

source_name: Donor: 2352 Status: HIVNegative Age: OLD Timepoint: T1 Response: NonResponder


title: 33CFARAging

source_name: Donor: 1281 Status: HIVNegative Age: OLD Timepoint: T0 Response: Responder


title: 32CFARAging

source_name: Donor: 2307 Status: HIVPositive Age: OLD Timepoint: T0 Response: NonResponder


title: 26CFARAging

source_name: Donor: 2012 Status: HIVPositive Age: OLD Timepoint: T0 Response: Responder


title: 28CFARAging

source_name: Donor: 851 Status: HIVNegative Age: OLD Timepoint: T0 Response: NonResponder


title: 189CFARAging

source_name: Donor: 3101 Status: HIVPositive Age: Young Timepoint: T1 Response: Responder


title: 19CFARAging

source_name: Donor: 859 Status: HIVNegative Age: OLD Timepoint: T0 Response: Responder


title: 65CFARAging

source_name: Donor: 1163 Status: HIVNegative Age: Young Timepoint: T1 Response: Responder


title: 187CFARAging

source_name: Donor: 1100 Status: HIVPositive Age: Young Timepoint: T0 Response: NonResponder


title: 186CFARAging

source_name: Donor: 1156 Status: HIVNegative Age: Young Timepoint: T1 Response: Responder


title: 24CFARAging

source_name: Donor: 1319 Status: HIVPositive Age: OLD Timepoint: T0 Response: Responder


title: 5CFARAging

source_name: Donor: 2001 Status: HIVNegative Age: OLD Timepoint: T0 Response: NonResponder


title: 57CFARAging

source_name: Donor: 1360 Status: HIVNegative Age: OLD Timepoint: T0 Response: Responder


title: 181CFARAging

source_name: Donor: 1200 Status: HIVPositive Age: Young Timepoint: T0 Response: NonResponder


title: 180CFARAging

source_name: Donor: 1165 Status: HIVNegative Age: Young Timepoint: T0 Response: NonResponder


title: 17CFARAging

source_name: Donor: 2352 Status: HIVNegative Age: OLD Timepoint: T0 Response: NonResponder


title: 178CFARAging

source_name: Donor: 9101 Status: HIVPositive Age: OLD Timepoint: T1 Response: Responder


title: 179CFARAging

source_name: Donor: 9001 Status: HIVPositive Age: Young Timepoint: T1 Response: Responder


title: 177CFARAging

source_name: Donor: 3102 Status: HIVPositive Age: Young Timepoint: T1 Response: NonResponder


title: 183CFARAging

source_name: Donor: 1102 Status: HIVPositive Age: Young Timepoint: T1 Response: NonResponder


title: 170CFARAging

source_name: Donor: 1179 Status: HIVNegative Age: Young Timepoint: T1 Response: Responder


title: 163CFARAging

source_name: Donor: 2307 Status: HIVPositive Age: OLD Timepoint: T1 Response: NonResponder


title: 169CFARAging

source_name: Donor: 1200 Status: HIVPositive Age: Young Timepoint: T1 Response: NonResponder


title: 160CFARAging

source_name: Donor: 2012 Status: HIVPositive Age: OLD Timepoint: T1 Response: Responder


title: 16CFARAging

source_name: Donor: 2309 Status: HIVPositive Age: OLD Timepoint: T0 Response: NonResponder


title: 176CFARAging

source_name: Donor: 1166 Status: HIVNegative Age: Young Timepoint: T0 Response: NonResponder


title: 155CFARAging

source_name: Donor: 1354 Status: HIVNegative Age: OLD Timepoint: T1 Response: Responder


title: 159CFARAging

source_name: Donor: 751 Status: HIVNegative Age: Young Timepoint: T0 Response: NonResponder


title: 158CFARAging

source_name: Donor: 766 Status: HIVNegative Age: Young Timepoint: T1 Response: NonResponder


title: 164CFARAging

source_name: Donor: 1158 Status: HIVNegative Age: Young Timepoint: T1 Response: Responder


title: 153CFARAging

source_name: Donor: 1118 Status: HIVPositive Age: Young Timepoint: T1 Response: Responder


title: 152CFARAging

source_name: Donor: 758 Status: HIVNegative Age: Young Timepoint: T0 Response: Responder


title: 154CFARAging

source_name: Donor: 1102 Status: HIVPositive Age: Young Timepoint: T0 Response: NonResponder


title: 25CFARAging

source_name: Donor: 2006 Status: HIVPositive Age: OLD Timepoint: T0 Response: NonResponder


title: 20CFARAging

source_name: Donor: 1358 Status: HIVNegative Age: OLD Timepoint: T0 Response: Responder


title: 147CFARAging

source_name: Donor: 9003 Status: HIVPositive Age: Young Timepoint: T0 Response: Responder


title: 142CFARAging

source_name: Donor: 1319 Status: HIVPositive Age: OLD Timepoint: T1 Response: Responder


title: 141CFARAging

source_name: Donor: 1156 Status: HIVNegative Age: Young Timepoint: T0 Response: Responder


title: 13CFARAging

source_name: Donor: 857 Status: HIVNegative Age: OLD Timepoint: T0 Response: NonResponder


title: 145CFARAging

source_name: Donor: 1110 Status: HIVPositive Age: Young Timepoint: T1 Response: NonResponder


title: 146CFARAging

source_name: Donor: 9002 Status: HIVPositive Age: Young Timepoint: T0 Response: Responder


title: 143CFARAging

source_name: Donor: 1110 Status: HIVPositive Age: Young Timepoint: T0 Response: NonResponder


title: 139CFARAging

source_name: Donor: 766 Status: HIVNegative Age: Young Timepoint: T0 Response: NonResponder


title: 12CFARAging

source_name: Donor: 9302 Status: HIVNegative Age: OLD Timepoint: T0 Response: NonResponder


title: 138CFARAging

source_name: Donor: 2309 Status: HIVPositive Age: OLD Timepoint: T1 Response: NonResponder


title: 136CFARAging

source_name: Donor: 851 Status: HIVNegative Age: OLD Timepoint: T1 Response: NonResponder


title: 126CFARAging

source_name: Donor: 1303 Status: HIVPositive Age: OLD Timepoint: T1 Response: Responder


title: 134CFARAging

source_name: Donor: 754 Status: HIVNegative Age: Young Timepoint: T0 Response: Responder


title: 131CFARAging

source_name: Donor: 859 Status: HIVNegative Age: OLD Timepoint: T1 Response: Responder


title: 125CFARAging

source_name: Donor: 9302 Status: HIVNegative Age: OLD Timepoint: T1 Response: NonResponder


title: 121CFARAging

source_name: Donor: 3102 Status: HIVPositive Age: Young Timepoint: T0 Response: NonResponder


title: 114CFARAging

source_name: Donor: 2303 Status: HIVPositive Age: OLD Timepoint: T1 Response: NonResponder


title: 122CFARAging

source_name: Donor: 2006 Status: HIVPositive Age: OLD Timepoint: T1 Response: NonResponder


title: 110CFARAging

source_name: Donor: 703 Status: HIVPositive Age: Young Timepoint: T0 Response: NonResponder


title: 104CFARAging

source_name: Donor: 765 Status: HIVNegative Age: Young Timepoint: T1 Response: NonResponder


title: 107CFARAging

source_name: Donor: 1307 Status: HIVPositive Age: OLD Timepoint: T1 Response: Responder


title: 11CFARAging

source_name: Donor: 2353 Status: HIVNegative Age: OLD Timepoint: T0 Response: Responder


title: 119CFARAging

source_name: Donor: 1104 Status: HIVPositive Age: Young Timepoint: T1 Response: Responder


title: RNA-seq in MLL-AF4 patient derived xenograft cells - VEN_2

city: Warsaw

first: Malgorzata

last: Firczuk

state: masovian

address: Nielubowicza 5 Street

department: Department of Immunology

country: Poland

institute: Medical University of Warsaw

data_processing:
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using picard-tools MarkDuplicates
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: feature counts
Supplementary_files_format_and_content: contrast table

molecule: polyA RNA

source_name: MLL-AF4+ acute lymphoblastic leukemia, patient derived xenograft

growth_protocol: MLL-AF4+ ALL patient derived xenograft cells were injected intravenously to NSG mice (0.5 x 106/mouse)

extract_protocol:
Following the last dose, spleens were harvested and CD19+ leukemic cells were isolated using EasySep™ Human CD19 Positive Selection Kit II (STEMCELL, cat. # 17854). RNA was isolated from Trizol preserved cells according to manufacturer’s protocol (Ambion, Life Technologies) followed by loading the ethanol-precipitated sample into an RNeasy column (RNeasy Mini Kit; QIAGEN)  and DNase digestion with an RNase-Free DNase Set (QIAGEN).
RNA sequencing was performed using TruSeq Stranded mRNA Library Prep (Illumina) according to the manufacturers' protocol. 1 μg of RNA was purified, fragmented and transcribed into cDNA, then samples were indexed with TruSeq RNA CD Index Plate (cat. no 20019792) and amplified. Quantification of DNA libraries using DNA 1000 chip on an Agilent Technologies 2200 TapeStation System was performed, then DNA libraries were normalized to 4 nM and then pooled in equal volumes.

treatment_protocol: Mice were treated with vehicle (60% Phosal 50PG; 30% PEG400; 10% Ethanol) or with 100 mg/kg of venetoclax for 3 weeks (5 days on/2 says off schedule)

tag: cell type

value: lymphoblasts (CD19+) - patient derived xenograft cells

value: spleen

value: 100 mg/kg of venetoclax (oral gavage) for 3 weeks


title: RNA-seq in MLL-AF4 patient derived xenograft cells - control_3

value: vehicle (60percent Phosal 50PG; 30percent PEG400; 10percent Ethanol – by oral gavage) for 3 weeks


title: 115CFARAging

source_name: Donor: 1104 Status: HIVPositive Age: Young Timepoint: T0 Response: Responder


title: 109CFARAging

source_name: Donor: 9001 Status: HIVPositive Age: Young Timepoint: T0 Response: Responder


title: RNA-seq in MLL-AF4 patient derived xenograft cells - control_1


title: 118CFARAging

source_name: Donor: 1165 Status: HIVNegative Age: Young Timepoint: T1 Response: NonResponder


title: RNA-seq in MLL-AF4 patient derived xenograft cells - VEN_3


title: RNA-seq in MLL-AF4 patient derived xenograft cells - VEN_1


title: RNA-seq in MLL-AF4 patient derived xenograft cells - control_2


title: Parental HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 1

city: Seattle

first: Sudarshan

last: Pinglay

state: WA

address: 3720 15th Ave NE

institute: University of Washington

data_processing:
Basecall conversion to fastq files was performed using Picard
Alignment: Fastq files were aligned to the genome (mm10_synHoxA or mm10_synHoxA_delHoxA custom genomes) using HISAT2, using options: -p 20 -q --rna-strandness F.
Computing Abundance: Mapped reads were assigned to annotated genes using the featureCount function in Rsubread, using options -s 2.
Differential gene expression analysis: Read counts were normalized using the ‘rlog’ or regularized log transformation in DESeq2 and used as inputs for the Principal Component Analysis (PCA). The log2 fold change (FC) and adjusted p-value in gene expression levels between 24h, 48h, and 96h vs. 0h was estimated using DESeq2 and plotted using ggplot. Normalized counts from DESeq2 were used to generate transgene/endogenous ratio plots, with the counts from endogenous locus being reduced by half to normalize the copy number between HoxA clusters. RNAseq track visualization was performed using combine tracks tool in IGV on bigwigs generated with deeptools bamCoverage and subsequent editing in Adobe Illustrator.
Initial comparison between HoxA-/- differentiation RNAseq and all others from this manuscript revealed distinct differences between the mutant line and others. However, after comparison with several other, more recently sequenced but unrelated differentiations from our lab, the difference appears to be correlated with recency of differentiation and sequencing, and not any other known variable (differentiation batch, researcher performing differentiation or library prep, library kit type, sequencing machine, genotype either at the endogenous HoxA locus or at Hprt). Thus, we used batch correction to eliminate this unrelated variance in the data (Zhang et al., NAR Genomics and Bioinformatics, 2020), and the batch corrected data from all samples clusters well by differentiation time.
Genome_build: mm10_synHoxA custom genome
Supplementary_files_format_and_content: Tab Separated Text File: Unnormalized Read Counts at annotated genes

organism: Mus musculus

source_name: ES-derived embryoid bodies with variant synthetic Hox clusters

growth_protocol: mESCs were cultured on plastic tissue culture plates coated with 0.1% gelatin (EMD Millipore ES-006-B) at 37°C and 5% CO2 in ‘80/20’ medium comprising 80% 2i medium and 20% mESC medium. mESCs were grown at 37°C and 8% CO2 before differentiation experiments.  2i medium was made from a 1:1 mix of Advanced DMEM/F12 (Gibco 12634010) and Neurobasal-A (Gibco 10888022), containing 1X N-2 supplement (Gibco 17502048), 1X B-27 supplement (Gibco 17504044), 2mM Glutamax (Gibco 35050061), 0.1mM Beta-Mercaptoethanol (Gibco 31350010), 103 units/mL LIF (Millipore, ESG1107), 1 μM MEK1/2 inhibitor (Stemgent, PD0325901), and 3 μM GSK3 inhibitor (R&D Systems, CHIR99021). mESC medium was made from Knockout DMEM (Gibco 10829018), containing 15% Fetal Bovine Serum (Gemini), 0.1 mM Beta-Mercaptoethanol (Gibco 31350010), 1X MEM Non Essential Amino Acids (Gibco 11140050), Glutamax (Gibco 35050061), 1X Nucleosides (Millipore ES-008-D) and LIF (Millipore ESG1107).

extract_protocol:
Cells were collected at 0h or 24h, 48h, or 96h after RA/SAG treatment. RNA was extracted with the TRIzol LS Reagent (Life Technologies) followed by purification with the RNAeasy mini kit (Qiagen). RNA integrity was checked with the Agilent High Sensitivity RNA Screentape (Agilent, 5067-5579).
500 ng of RNA was used to prepare libraries and spiked-in with ERCC Exfold Spike-in mixes (Thermo Fisher 4456739). The TruSeq Stranded mRNA Library Preparation kit (Illumina 20020594) was used to prepare RNA-seq libraries. Library size was checked on the High Sensitivity DNA ScreenTape (Agilent 5067-5584). The KAPA library amplification kit was used to quantify libraries on the Bio-Rad CFX96 or the Roche Lightcycler 480 before pooling libraries. Libraries were sequenced on the Illumina NextSeq 500 using V2.5 chemistry (75 cycles, single-end 75 bp) or on the Illumina NovaSeq 6000 using the SP Reagent Kit (100 cycles, single-end 100bp) at the Genomics Core Facility at NYU.

treatment_protocol: Trypsinized (Gibco) mESCs were plated in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco)) to induce formation of embryoid bodies (EBs), at 37°C, 5% CO2. 3.5x105 cells were plated in 100 mm suspension plates (Corning) for RNA-seq experiments, while 3.5x106 cells were plated in 245 mm x 245 mm square plates (Corning) for ChIP-seq experiments. After 2 days (0h timepoint), the EBs were split 1:2 and plated in fresh AK medium supplemented with 1 μM all-trans retinoic acid (RA) and 0.5 μM smoothened agonist (SAG) (Millipore 566660). For CHIR differentiation, in place of RA/SAG, CHIR99021 was added at 3 µM concentration

tag: strain

value: Parental HoxA -/- mESCs

value: 96h of RA+SAG differentiation

value: Embryoid Bodies


title: 116CFARAging

source_name: Donor: 2302 Status: HIVPositive Age: OLD Timepoint: T1 Response: NonResponder


title: 137CFARAging

source_name: Donor: 765 Status: HIVNegative Age: Young Timepoint: T0 Response: NonResponder


title: Parental HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 2


title: Parental HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 3

value: 48h of RA+SAG differentiation


title: Parental HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1


title: 124CFARAging

source_name: Donor: 754 Status: HIVNegative Age: Young Timepoint: T1 Response: Responder


title: Parental HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 2

value: 24h of RA+SAG differentiation


title: Parental HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 3


title: Parental HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2

value: 0h of RA+SAG differentiation


title: Parental HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 1


title: Parental HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1


title: Izu1RCKO.skin#2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Whole skin

extract_protocol:
1,000 Cells were double-sorted by Moflo into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). For whole tissue RNAseq extraction was completed using Trizol reagent manufacturer protocol.
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: For the IMQ treated, dorsal and ventral sides of the ear were treated with 125ug of 5% Imiquimod cream until indicated date. All other data are from untreated mice at indicated age.

value: Skin

tag: genotype

value: Foxp3Cre+ Izumo1R fl

value: 10 weeks


title: Izu1CRKO.skin#3


title: KOSkinTcon#1

source_name: Tcon


title: KOSkinTcon#3


title: Parental HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 3


title: CtlSkinTcon#3


title: KOSkinTcon#2


title: gamma.delta.T.C.10w.m.skin#3

source_name: Gamma delta T cell


title: CtlSkinTcon#2


title: gamma.delta.T.KO.10w.m.skin#1


title: CtlSkinTcon#1


title: Ctl.skin#2


title: Parental HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2


title: gamma.delta.T.C.10w.m.skin#1


title: Ctl.skin#3


title: Izu1CRKO.ear#3


title: Izu1CRKO.ear#2


title: Parental HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 3


title: Izu1CRKO.ear#1


title: Ctl.ear#3


title: D3IMQKO.10w.m.ear#2


title: D3IMQCtl.10w.m.ear#2


title: Ctl.ear#2


title: Ctl.ear#1


title: D3IMQKO.10w.m.ear#1


title: gamma.delta.T.KO.10w.m.skin#2


title: gamma.delta.T.C.10w.m.skin#2


title: D1IMQKO.10w.m.ear#2


title: Izu1RCKO.skin#1


title: Ctl.skin#4


title: Izu1RCKO.skin#5


title: KO.56dm.skin#1

value: 8 weeks


title: Izu1RCKO.skin#4


title: KO.28dm.skin#3

value: 4 weeks


title: Ctl.56dm.skin#2


title: D1IMQKO.10w.m.ear#1


title: KO.28dm.skin#2


title: D1IMQCtl.10w.m.ear#2


title: D1IMQCtl.10w.m.ear#1


title: KO.56dm.skin#2


title: Ctl.28dm.skin#2


title: Ctl.28dm.skin#3


title: Ctl.skin#1


title: Ctl.56dm.skin#1


title: KO.28dm.skin#1


title: Ctl.28dm.skin#1


title: KO.14dm.skin#2

value: 2 weeks


title: KO.14dm.skin#1


title: Ctl.14dm.skin#2


title: Ctl.14dm.skin#1


title: KO.7dm.skin#3

value: 1 week


title: KO.7dm.skin#2


title: D3IMQCtl.10w.m.ear#1


title: Ctl.7dm.skin#2


title: Ctl.7dm.skin#3


title: Ctl.7dm.skin#1


title: Izu1RCKO.Treg#3

source_name: Treg

value: Spleen


title: Izu1RCKO.Treg#2


title: Izu1RCKO.Treg#1


title: Ctl.Treg#1


title: Ctl.Treg#2


title: Ctl.Treg#3


title: KZ2crePlus1

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

institute: University of Oklahoma Health Sciences Center

data_processing:
CellRanger version 5.0.1 mkfastq tool was used for basecalling, which created 4 fastq files per samples from the 4 lanes of the flowcell. So, R1 has 4 fastq files; R2 has 4 fastq files; and I (index) has 4 fastq files.
CellRanger version 5.0.1 count was used to create the matrix table for further processing.
The matrix was then loaded into Seurat version 3.1.5 for normalization, clustering and visualization.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing gene symbols with their respective expression for each cell/barcode.

source_name: Kidney

extract_protocol:
After digestion, kidney tissue from both groups was individually passed through 70-µm cell-strainers (Falcon; BD Biosciences) yielding single-cell suspensions. Cells were centrifuged at 1300rpm for 5 minutes at 4ºC, resuspended in ACK red blood cell lysis buffer, and incubated at 37ºC for 5 minutes.  After 5 minutes, 10 ml RPMI was added to each tube, cells were spun at 1300 rpm for 5 minutes at 4C, and cells were resuspended in 1% BSA with FC blocking solution (1:200, BioXcell; catalog #: BE0307) for 30 minutes on ice. After blocking, cells were spun and incubated with the following antibodies in 1% BSA for 30 minutes: FITC conjugated Lotus tetragonolobus agglutinin (LTA) (catalog number FL-1321; Vector Laboratories), PE rat anti-mouse CD45 (catalog no. 12–0451, 30-F11; eBioscience), and Fixable Aqua Dead Cell Stain (catalog no. L34957; Invitrogen). After staining for 30 minutes, cells were spun, washed with 1% BSA, and sorted using a Becton–Dickenson FACSAriaII.  For subsequent experiments involving single cell RNA sequencing, we sorted ~25,000 live, CD45+, LTA+, and CD45-/LTA- cells into individual BSA coated tubes. Cells were counted and approximately 3,300 cells from each of the three groups (CD45+, LTA+, CD45-/LTA-) were combined into a single tube followed by performing bead emulsion and 10X genomics. This was done for N=2 animals from each experimental group; all animals were female.
10xChromium single cell libraries were prepared according to the standard protocol outlined in the manual. Briefly, sorted single cell suspension, 10x barcoded gel beads, and oil were loaded into Chromium™ Single Cell Chip B to capture single cells in nanoliter-scale oil droplets by Chromium™ Controller and to generate Gel Bead-In-EMulsions (GEMs). We used “Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3” and chip B for these experiments.  Full length cDNA libraries were prepared by incubation of GEMs in a thermocycler machine. GEMs containing cDNAs were broken and all single cell cDNA libraries were pooled together, cleaned using DynaBeads MyOne™ Silane beads (Fisher PN 37002D), and pre-amplified by PCR to generate sufficient mass for sequencing library construction. Sequencing libraries were constructed by following the steps: cDNA fragmentation, end repair & A-tailing, size selection by SPRIselect beads (Beckman Coulter, PN B23318), adaptor ligation, sample index PCR amplification, and a repeat of SPRIselect beads size selection. The final constructed single cell libraries were sequenced by Illumina Nextseq machine with total reads per cell targeted for a minimum of 25,000.
single cell RNA-Seq

treatment_protocol: After perfusion of the mouse with PBS, the left kidney (sham, injured, or aged) was removed and put into RPMI 1640 on ice. For the initial comparison of digestion methods, kidneys were minced and digested in either 1) 1 ml of RPMI 1640 containing 1mg/ml collagenase type I (Sigma-Aldrich) and 100U/ml DNase I (Sigma-Aldrich) for 30 minutes at 37 º C with mixing or 2) 1ml of 2.5 mg/ml type II collagenase (Worthington, cat No; LS004176), 7.5 mg/ml B. licheniformis cold activated protease (Creative enzymes, Cat no: NATE-0633), and 125 U/ml DNase in D-PBS for ~45 minutes at 12C.

tag: group

value: CM

value: aged


title: KZ1creMinus1

value: cont


title: KZ4

value: IR


title: KZ3

value: sham


title: KZ5


title: KZ6


title: HSC-5-FU_6_days-1

city: Kumamoto

first: Terumasa

last: Umemoto

address: 2-2-1, Honjo, Chuo-Ku

country: Japan

institute: Kumamoto University

library_source: genomic

data_processing:
Library strategy: CUT&Tag
Deep sequencing was performed by Illumina Next-Seq 500
Trimming, alignment, peak calling, and Quantification were performed by Trimmomatic, Bowtie2, MACS2, and HOMER, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: peak files

molecule: genomic DNA

source_name: hematopoietic stem cells

extract_protocol:
To isolate nuclei, 12500 sorted cells were lysed with NE buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM Spermidine, 1x Roche Complete Protease Inhibitor).
After the transposase reactions following the immunoprecipitation reaction, tagmented fractions were amplified by PCR with indexed primers. CUT&Tag libraries were cleaned with SPRIselect beads (Beckman Coulter) and subjected to sequencing using Illumina NextSeq 500 Platform with 75 bps single-end reads

value: Bone marrow

value: 8-10 weeks


title: HSC-5-FU_10_days-1


title: KO.7dm.skin#1


title: CD48+HPC-5-FU_10_days-1


title: HSC-5-FU_10_days-2


title: KZ3crePlus2


title: KZ2


title: CD48+HPC-5-FU_10_days-2


title: HSC-5-FU_6_days-2


title: KZ1


title: HSC-Untreated-1

value: untreated


title: HSC-Untreated-2


title: CD150+CD48+HPC-4  (10 days)

data_processing:
mRNA profile generated by deep sequencing using Illumina Next-Seq 500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using CLC genomic workbench v.11.0.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by CLC genomic workbench v.12.0.4
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM, RPKM, and Read number for each Sample.

source_name: hematopoietic progenitor cells

extract_protocol:
After 100 cells were sorted, first strand cDNA were synthesized followed by generating 2nd strand by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9) .
Using Nextera XT DNA sample Prep Kit (Illumina Inc., San Diego, CA), libraries were prepared by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9) .

tag: strain background

value: hematopoietic progenitor cells

tag: cell subtype


title: CD150+CD48+HPC-2  (10 days)


title: CD150+CD48+HPC-3  (10 days)


title: Ctl.skin#5

value: Skin


title: CD150+CD48+HPC-1  (10 days)


title: CD150+CD48-HSC-4  (10 days)

value: hematopoietic stem cells


title: CD150+CD48-HSC-3  (10 days)


title: CD150+CD48-HSC-2  (10 days)


title: CD150+CD48-HSC-1 (10 days)


title: EPCR-Low 2-4

description: 2_EPCR-Low_scATAC_mm10_uniqnorm_signal.bw

data_processing:
Deep sequencing was performed by Illumina Next-Seq 500
Trimming, alignment, peak calling, and Quantification were performed by Cell Ranger ATAC software and MACS2, respectively.
Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Signal maps and peak locations were used as input data to the Active Motif’s proprietary analysis program.
Genome_build: mm10
Supplementary_files_format_and_content: peak files

extract_protocol:
According to the manufacturer’s instructions, sorted HSCs were resuspended in lysis buffer and incubated on ice for 5 minutes. Lysed cells were washed, strained, and nuclei were resuspended. Isolated nuclei were then used as input following the 10X Genomics Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 manual (10X Genomics, Pleasanton, CA).
With a target of 5,000 nuclei recovery, samples were added to the tagmentation reaction, loaded into the Chromium Controller for nuclei barcoding, and prepared for library construction following the manufacturer’s protocol


title: KZ4creMinus2


title: EPCR-Low 2-3


title: EPCR-Low 2-2


title: EPCR-High 1-4

description: 1_EPCR-High_scATAC_mm10_uniqnorm_signal.bw


title: EPCR+++(1) RNA-seq


title: EPCR+++(3) RNA-seq


title: EPCR++(3) RNA-seq


title: EPCR++(1) RNA-seq


title: EPCR+(3) RNA-seq


title: EPCR+(2) RNA-seq


title: EPCR-High 1-3


title: EPCR-High 1-1


title: EPCR+++(2) RNA-seq


title: EPCR-Low 2-1


title: +mOSM Replicate 2

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatoc version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (ensemble release 101) using STAR 2.7.7a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% .
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package [54]. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The Ensemble annotation was enriched with UniProt data based on Ensembl gene identifiers.
Genome_build: mm10
Supplementary_files_format_and_content: library-size normalized counts

source_name: Primary cardiomyocytes

growth_protocol: Murine cardiomyocytes were isolated and cultured in 6-well dishes according to standard protocols.

extract_protocol:
RNA of cardiomyocytes was isolated by using RNeasy Micro Kit (Qiagen).
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).

treatment_protocol: Thereafter, all recombinant proteins were added to a final concentration of 25ng ml-1. Administration of equivalent volumes of steriles PBS served as controls. Stimulation period was 24 hours under normoxic conditions.

value: Adult (12 weeks of age)

tag: Sex

value: Male


title: EPCR++(2) RNA-seq


title: EPCR+(4) RNA-seq


title: EPCR+++(4) RNA-seq


title: EPCR+(1) RNA-seq


title: +mOSM Replicate 1


title: +mOSM Replicate 3


title: +hlOSM Replicate 3


title: +hlOSM Replicate 2


title: +mLIF Replicate3


title: +hlOSM Replicate 1


title: +mLIF Replicate2


title: +mLIF Replicate1


title: +PBS (Control/Reference) Replicate 2


title: 1-day_culture-2 RNA-Seq


title: 1-day_culture-1 RNA-Seq


title: 1-day_culture-4 RNA-Seq


title: 1-day_culture-3 RNA-Seq


title: EPCR-High 1-2


title: EPCR++(4) RNA-seq


title: Uncultured-1 RNA-Seq


title: 5-FU_6_days-4 RNA-Seq


title: 5-FU_10_days-2 RNA-Seq


title: 5-FU_10_days-1 RNA-Seq


title: Acriflavine_mLEC_1

data_processing:
Trimmomatic was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (nt) (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads between 30 and 150 nt were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (ensemble release 101) using STAR 2.7.7a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
For mLECs, Ensembl mouse genome version mm10 (GRCm38.p5) and STAR 2.6.0c was used.
The number of reads aligning to genes was counted with featureCounts tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes in HUVEC were identified using DESeq2 version 1.30.0 (for mLEC version 1.18.1 was used).
The Ensembl annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt))
Genome_build: hg38 / mm10
Supplementary_files_format_and_content: library size normalized counts

source_name: murine lung endothelial cells

growth_protocol: Culturing of pooled human umbilical vein endothelial cells (HUVEC) purchased from PromoCell (C-12203, Lot No. 405Z013, 408Z014, 416Z042, Heidelberg, Germany) was performed at 37°C with 5% CO2. Dishes were coated with gelatin (Sigma-Aldrich, G1890-500G) prior to culturing. Endothelial growth medium (EGM) was prepared by supplementing endothelial basal medium (EBM) with human recombinant epidermal growth factor (EGF), EndoCGS-Heparin (PeloBiotech, Germany), 8% fetal calf serum (FCS) (S0113, Biochrom, Germany), penicillin (50 U/ml) and streptomycin (50 µg/ml) (15140-122, Gibco/ Lifetechnologies, USA). Biological replicates comprised at least three different batches from passage 3. Murine lung endothelial cells (mLEC) were isolated as described previously (DOI: 10.1242/jcs.02541). Briefly, the tissue was minced and digested with dispase at 37°C for 60 min. After washing and filtering, mLEC separation was done with CD144 coated Dynabeads. mLECs were cultured in DMEM/F12 supplemented with 20% FCS, penicillin (50 U/ml) and streptomycin (50 µg/ml) and ECGF Bovine + Heparin (PeloBiotech) at 37°C with 5% CO2.

extract_protocol:
Total RNA Isolation was performed using the RNA Mini Kit (Bio&Sell).
). 1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).

treatment_protocol: Acriflavine (10µM) or DMSO for 16h.

value: mLEC


title: 5-FU_10_days-3 RNA-Seq


title: 5-FU_10_days-6 RNA-Seq


title: 5-FU_6_days-3 RNA-Seq


title: 5-FU_10_days-4 RNA-Seq


title: Uncultured-2 RNA-Seq


title: 5-FU_10_days-5 RNA-Seq


title: Uncultured-3 RNA-Seq


title: DMSO_mLEC_1


title: 5-FU_6_days-2 RNA-Seq


title: Untreated-4 (5-FU control RNA-Seq)


title: Untreated-1 (5-FU control RNA-Seq)


title: Untreated-2 (5-FU control RNA-Seq)


title: 5-FU_10_days-2

data_processing:
Deep sequencing was performed by Illumina Next-Seq 500
Trimming, alignment, peak calling, and Quantification were performed by FASTX-toolkit, Bowtie2, MACS2, and HOMER, respectively.
Genome_build: mm9
Supplementary_files_format_and_content: peak files

extract_protocol:
Sorted HSCs were lysed with ATAC-resuspension buffer containing detergents, which are listed in a previous study(Corces et al., 2017 Nat Methods 14, 959-962.).
After optical amplification by PCR using ATAC-Primers (Buenrostro et al., 2015 Curr Protoc Mol Biol 109, 21 29 21-21 29 29.), these DNA fragments were purified libraries were sequenced by Next-seq.


title: +PBS (Control/Reference) Replicate 3


title: 5-FU_6_days-2


title: +PBS (Control/Reference) Replicate 1


title: Untreated-2 (5-FU control)


title: 5-FU_6_days-1


title: Uncultured-4 RNA-Seq


title: E18.5 (Bmx-CreER Wls): HSPC+microenvironmental cells;

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v1.0.1) used for cell barcode and UMI counting
STAR (v2.7.1a) used for mouse reference genome (mm10) alignment
Subread featureCounts (v1.6.4) used for UMI quantification
Genome_build: mm10
Supplementary_files_format_and_content: tsv files include UMI counts for each cell barcode and genes

source_name: bone marrow

extract_protocol:
Bone marrow from corresponding time point is crushed by pestle and collected for lysis by collagenase type 4. The cell lysate is filtered to obtain single cell suspension solution. Lineage committed hematopoietic cells are magnetically depleted by MACS separation protocol.  The remaining Lin- cells, which contain HSPC and microenvironemental cells, are used for scRNA-seq library preparation and sequencing
Single cell whole transcriptome analysis libraries were prepared according to the manufacturer’s instructions using BD Rhapsody WTA Reagent kit (BD)

value: Bmx-CreER Wls

tag: developmental stage

value: lineage commitment hematopoietic cell depletion


title: E18.5 (WT): HSPC+microenvironmental cells;

value: WT


title: 5-FU_10_days-1


title: HepG2_polyA_FTO-_rep1

city: Chicago

first: Yong

last: Peng

state: IL

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

description:
HepG2 without FTO treatment
HepG2_polyA.bed

data_processing:
Basecalls performed using CASAVA version 1.4
Adapters of all raw m6A-sac-seq data sets from two FTO+/- replicates of HeLa, HEK293, HepG2, and four time points of HSPC differentiation into monocytes were clipped away by Cutadapt v1.15, repectively. Then adapter-free reads plus 5’ and 3’ barcodes were collapsed in order to remove PCR duplicates by fastx_collapser or BBMap. After PCR deduplication, the leftmost five and rightmost eleven bases of reads were trimmed to discard 5’ and 3’ barcodes.
All reads from pre-processed m6A-sac-seq data sets were mapped to the human genome (hg38) and the GENCODE v27 gene annotation using STAR v2.5.3a with parameters according to ENCODE long RNA-Seq processing pipeline, except that the criteria to allow mismatches depending on read length was slightly less stringent in order to capture more potential base mutations (--outFilterMismatchNoverReadLmax 0.06).
Mutation calling was performed by the VarScan v2.3 subcommand somatic with the parameters (--min-var-freq 0.05 --min-coverage 10 --validation 1) in three pair-wise comparison: 1) FTO- vs input; 2) FTO+ vs input; and 3) FTO- vs FTO+.
For each comparison, mutation sites were kept if: (1) Reference position is adenine (A). (2) p-value < 0.1 (3) Mutation frequency: experiment - control > 5% (4) Coverage is more than 5 reads. (5) The 5-mer context is DRACH. Remaining sites were further filtered, only the intersection of two or three biological replicates were kept. Finally, only the intersection of the two comparisons, FTO- vs Input, and FTO- vs FTO+, were kept for further analysis.
Genome_build: Human hg38
Supplementary_files_format_and_content: bed

source_name: HepG2 Cell line

growth_protocol: Hela, HEK293 and HepG2 cells were cultered on uncoated plastic in DMEM, high glucose, pyruvate medium (Thermal Fisher Scientific, Catalog number: 11995123 ) supplemented with 10% FBS(Gibco) and 1 x Penicillin-Streptomycin (Gibco). Human CD34+ hematopoietic stem/progenitor cells (HSPCs) were isolated from umbilical cord blood (UBC) samples.

extract_protocol:
m6A-sac-seq experiments require parallel construction of three libraries: 1) Input library: the RNA is subjected to standard library construction without any treatment by MjDim1 or I2 and is used as a reference to call mutations; 2) Experimental library: RNA is treated with the MjDim1 enzyme with cofactor allylic-SAM to convert m6A sites into allylic-m6A by MjDim1; 3) Background noise group: m6A sites were erased by FTO first, then followed by allylic labeling. Both experimental groups and background noise group were treated with I2 for the cyclization reaction, followed by reverse transcription with HIV reverse transcriptase (Worthington Biochemical Corp).
For expermental and negative control groups: RNA samples were ligated to self-designed 5' and 3' adapter and libraries were amplified with NEBNext Ultra™ II Q5 Master Mix.For  input group: libraries were made with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: The RNA is treated with recombinant MjDim1 enzyme with allylic-SAM cofactor under optimized conditions to selectively convert m6A residues to a6m6A, followed by adding I2 to convert am6A to EA. Reverse transcription induces mutations at EA sites, enabling identification of the sites labeled with a6m6A.

value: FTO-

tag: ip antibody

tag: agent


title: HepG2_polyA_Input

description:
Input for call mutation
HepG2_polyA.bed

value: Input


title: HepG2_polyA_FTO-_rep2


title: HepG2_polyA_FTO+_rep1

description:
HepG2 with FTO treatment
HepG2_polyA.bed

value: FTO+

value: FTO


title: HepG2_polyA_FTO+_rep2


title: HeLa_RIP_polyA_FTO-_rep2

description:
HeLa without FTO treatment
HeLa-RIP_polyA.bed

source_name: HeLa Cell line

value: HeLa


title: HeLa_RIP_polyA_Input_rep1

description:
Input for call mutation
HeLa-RIP_polyA.bed


title: HeLa_RIP_polyA_FTO-_rep3


title: HeLa_RIP_polyA_Input_rep2


title: HeLa_RIP_polyA_FTO-_rep1


title: HeLa_polyA_Input

description:
Input for call mutation
HeLa_polyA.bed


title: 5-FU_6_days-1 RNA-Seq

value: Bone marrow


title: HeLa_RIP_polyA_FTO+_rep2

description:
HeLa with FTO treatment
HeLa-RIP_polyA.bed


title: Untreated-3 (5-FU control RNA-Seq)

value: 8-10 weeks


title: HeLa_polyA_FTO+_rep1

description:
HeLa with FTO treatment
HeLa_polyA.bed


title: HeLa_polyA_FTO-_rep1

description:
HeLa without FTO treatment
HeLa_polyA.bed


title: HeLa_polyA_FTO+_rep2

description:
HeLa with FTO treatment
HeLa_polyA.bed


title: HeLa_polyA_FTO-_rep2


title: HEK293_polyA_FTO-_rep2

description:
HEK293 without FTO treatment
HEK293_polyA.bed

source_name: HEK293 Cell line


title: HEK293_polyA_Input

description:
Input for call mutation
HEK293_polyA.bed


title: HEK293_polyA_FTO+_rep2

description:
HEK293 with FTO treatment
HEK293_polyA.bed


title: HEK293_polyA_FTO-_rep1


title: HEK293_polyA_FTO+_rep1


title: Untreated-1 (5-FU control)


title: HSC-day9_Ribo-_FTO+_rep2

description:
Ribo minus RNA
HPSC_day9 with FTO treatment
HSC-day9_Ribo-.bed

source_name: human CD34+ hematopoietic stem/progenitor cells

value: HPSC

tag: time point


title: HSC-day9_Ribo-_Input_rep1

description:
Ribo minus RNA
Input for call mutation
HSC-day9_Ribo-.bed


title: HSC-day9_Ribo-_FTO-_rep2

description:
Ribo minus RNA
HPSC_day9 without FTO treatment
HSC-day9_Ribo-.bed


title: HSC-day9_Ribo-_Input_rep2


title: HSC-day9_Ribo-_FTO-_rep1


title: HSC-day6_Ribo-_Input_rep1

description:
Ribo minus RNA
Input for call mutation
HSC-day6_Ribo-.bed


title: HSC-day9_Ribo-_FTO+_rep1


title: HeLa_RIP_polyA_FTO+_rep1


title: HSC-day6_Ribo-_FTO+_rep1

description:
Ribo minus RNA
HPSC_day6 with FTO treatment
HSC-day6_Ribo-.bed


title: HSC-day6_Ribo-_FTO-_rep2

description:
Ribo minus RNA
HPSC_day6 without FTO treatment
HSC-day6_Ribo-.bed


title: HSC-day6_Ribo-_FTO+_rep2


title: HSC-day3_Ribo-_Input_rep1

description:
Ribo minus RNA
Input for call mutation
HSC-day3_Ribo-.bed


title: HSC-day3_Ribo-_FTO-_rep2

description:
Ribo minus RNA
HPSC_day3 without FTO treatment
HSC-day3_Ribo-.bed


title: HSC-day3_Ribo-_Input_rep2


title: HSC-day6_Ribo-_FTO-_rep1


title: HSC-day3_Ribo-_FTO+_rep2

description:
Ribo minus RNA
HPSC_day3 with FTO treatment
HSC-day3_Ribo-.bed


title: HSC-day0_Ribo-_Input_rep2

description:
Ribo minus RNA
Input for call mutation
HSC-day0_Ribo-.bed


title: HSC-day3_Ribo-_FTO+_rep1


title: HSC-day0_Ribo-_FTO-_rep1

description:
Ribo minus RNA
HPSC_day0 without FTO treatment
HSC-day0_Ribo-.bed


title: HSC-day0_Ribo-_FTO+_rep2

description:
Ribo minus RNA
HPSC_day0 with FTO treatment
HSC-day0_Ribo-.bed


title: HSC-day0_Ribo-_FTO-_rep2


title: HSC-day3_Ribo-_FTO-_rep1


title: HSC-day0_Ribo-_Input_rep1


title: HEK293_Ribo-_FTO-_rep2.bam

description:
Ribo minus RNA
HEK293 without FTO treatment
HEK293_Ribo-.bed

value: HEK293 Cell line


title: HEK293_Ribo-_Input

description:
Ribo minus RNA
Input for call mutation
HEK293_Ribo-.bed


title: HSC-day0_Ribo-_FTO+_rep1


title: HEK293_Ribo-_FTO-_rep1.bam


title: HEK293_Ribo-_FTO+_rep2.bam

description:
Ribo minus RNA
HEK293 with FTO treatment
HEK293_Ribo-.bed


title: RNA-Seq H9 (primed) 7d+EZH2i rep3

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Processing pipeline: Paired-end reads were processed in a single run by nf-core/rnaseq pipeline v2.0 (https://nf-co.re/rnaseq/2.0), a pipeline implemented in Nextflow. Below there is a brief description of the main steps. nf-core documentation provides detail of all the individual steps in the pipeline.
Parameters: --aligner star_rsem
Pipeline manager: nextflow 20.10.0
Adapter and quality trimming: Reads are trimmed using trimgalore 0.6.6
Mapping: Reads mapped to reference using STAR aligner
Deduplication: BAM files generated by STAR are deduplicated using picard (2.23.8) markDuplicates
Scaling: Gene counts and TPM estimated with RSEM 1.3.1
Genome_build: hg38 (Homo_sapiens_UCSC_hg38.tar.gz - Illumina iGenomes: http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg38/Homo_sapiens_UCSC_hg38.tar.gz )
BigWig file generation: BigWig files were generated from mapped BAM files using deepTools (v3.3.2) bamCoverage --normalizeUsing BPM --filterRNAStrand reverse and forward, respectively
Supplementary_files_format_and_content: BigWig files with read profiles.

source_name: Embryonic Stem Cell

growth_protocol: Primed H9 (Wicell; WA09) p28(11) were cultured in Nutristem hESC XF medium and passaged when they reached 70-80% confluency. Naive H9 p28(8) naive p7 were grown on high-density mouse embryonic fibroblast (MEF) plates using NaïveCult expansion media supplemented with 10µM ROCKi. Cells were passaged every four to five days. Both hESCs were cultured at 37°C, 5% O2 and 5% CO2.

extract_protocol:
Flash frozen hESCs were thawed and spiked in with 5e4 Drosophila cells per sample and then total RNA was purified using the RNeasy Plus Mini Kit ( Qiagen; 74136) according to the manufacturer's protocol. Purified RNA quantities were estimated using the Qubit RNA HS assay kit (Life technologies; Q32852) and the samples were subsequently flash frozen.
RNA-seq libraries were generated and sequence through BGI service for strand specific RNA-seq with PolyA selection (DNBseq Eukaryotic Transcriptome De novo Sequencing).

treatment_protocol: Naïve and primed H9 cells where treated with 10 uM EZH2 inhibitor (EPZ-6438; BIOV2428-5) for 7 days. During harvesting, mouse feeder removal microbeads (Milteny Biotech; 130-095-531) were used to reduce the amount of MEFs in the naive cell samples, according to the manufacturer's protocol. Primed cells were dissociated and centrifuged directly.Three replicates of 1e6 cells per condition were collected and pellets were resuspended in RNA extraction buffer (Qiagen; 74106) and flash frozen.

tag: background

value: H9 (female)

tag: condition

value: primed

value: 10 uM EZH2 for 7 days


title: HEK293_Ribo-_FTO+_rep1.bam


title: Brain, AD_TilingArray_M01

type: RNA

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

hyb_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

data_processing:
We used the TileShuffle algorithm (Otto C, Reiche K, Hackermuller J. Detection of differentially expressed segments in tiling array data. Bioinformatics 2012; 28: 1471–1479) to determine expressed and differentially expressed genomic intervals. Affymetrix Human Whole Genome Tiling Array 1.0 Set raw signal intensities were mapped to human genome version NCBI36 using Affymetrix BPMAP files. Expressed segments were detected with the TileShuffle parameter settings: window size = 200, the window score was defined as the arithmetic mean trimmed by the maximal and minimal values over signal intensities of all probes in a window, number of permutations = 10 000 and number of GC classes = 4. All windows with an adjusted p < 0.05 according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995) were defined to be significantly expressed. DE-TARs are differentially expressed TileShuffle intervals with adjusted p < 0.05 (window size = 200, the window score was defined as the logfold-change discarding all probes with converse behavior as observed for the relevant significantly expressed windows, number of permutations = 100 000 and number of GC classes = 1). Finally, the genome coordinates of all significantly expressed and all significantly differentially expressed segments were lifted over to GRCh37 (hg19) using liftOver (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver).
[additional results files] Ueberham_AD_K_highdiff3.bed:  significantly differentially expressed segments (adjusted p<0.05)

label: biotin

source_name: human brain tissue

label_protocol: The Affymetrix Human Whole Genome Tiling Array 1.0 Set consisting of 14 arrays was used according to the manufacturer’s instructions, except that separate labeling reactions were used for each array starting from 10 μg pooled total RNA.

extract_protocol: RNA was isolated by Trizol™ method (Invitrogen, Karlsruhe, Germany). 100mg deeply frozen human brain tissue (temporal cortex) was homogenized in the presence of 1ml Trizol in a glass-Teflon™ homogenizer. The homogenate was transferred to a microtube and after adding chloroform, samples were centrifuged at 15 000 g (4 °C) for 15min and the supernatant transferred to a fresh tube. Samples were mixed with equal amounts of isopropanol and centrifuged at 12 000 g (4 °C) for 15min to precipitate the RNA. After washing, the pellet was air-dried and dissolved in water. RNA quality was assessed by denaturing formaldehyde agarose gel electrophoresis, by spectrophotometry (scanning at 220−320 nm) and by analysis using Agilent 2100 bioanalyzer. Only samples with RIN > 5 were further processed. The RNA concentration was estimated spectrophotometrically by absorbance at 260 nm, concentration was adjusted to 1mg/ml and RNA was stored at −80 °C until use.

tag: disease state

value: Alzheimer's disease (AD)

value: brain


title: HSC-day6_Ribo-_Input_rep2


title: RNA-Seq H9 (primed) 7d+EZH2i rep1


title: RNA-Seq H9 (primed) rep3


title: Brain, Control_TilingArray_M01

scan_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

value: Control

tag: tissue


title: RNA-Seq H9 (primed) 7d+EZH2i rep2


title: Brain, Control_TilingArray_M02


title: RNA-Seq H9 (primed) rep1


title: Brain, Control_TilingArray_M03


title: Brain, AD_TilingArray_M02


title: RNA-Seq H9 (naïve) 7d+EZH2i rep2

value: naive (t2iGoY)


title: Brain, AD_TilingArray_M03


title: AAV-Nd3-9577-(1)-mtDNA [mouse_32_F12]

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to ChrM (GRCm38) or the NUMT sequence on Chr 1 or Chr14 with Bowtie2
Samtools mpileup and Cutadapt to count nucleotides surrounding the editing site
Genome_build: GRChm38
Supplementary_files_format_and_content: Supp Dataset 1 = excel file showing the % of base editing at individual Cs within the editing window for each sample; Supp Dataset 2=excel file showing the % of off targets on ChrM and a NUMT region of Chr1 and Chr14 for each sample

growth_protocol: The animals were maintained in a temperature- and humidity-controlled animal care facility with a 12-h light/12-h dark cycle and free access to water and food, and they were sacrificed by cervical dislocation.

extract_protocol:
NIH/3T3 mouse cells were collected by trypsinization, washed once in PBS and re-suspended in lysis buffer (1mM EDTA, 1 % Tween20, 50 mM Tris (pH = 8)) with 200 µg/ml of proteinase K. Lysates were incubated at 56 ºC with agitation (300 RPM) for 1 h, and then incubated 95 ºC for 10 min before use in downstream applications. Genomic DNA from mouse heart samples (~50 mg) was extracted with a Maxwell® 16 Tissue DNA Purification Kit in a Maxwell® 16 Instrument (Promega), according to manufacturer´s instructions.
Illumina NexteraXT

treatment_protocol: In adult experiments, 8-week-old mice were administered systemically by tail vein injection with 1 x 10*12 AAV particles of each monomer [AAV- DdCBE (L) - Nd3-9577 - G1333-C and AAV- DdCBE (H) - Nd3-9577- G1333-N]. An equal dose was applied in newborn pups (Postnatal day 1) via the temporal vein

value: heart

tag: ddcbe halves

value: L-strand:1333C ; H-strand:1333N

tag: weeks after intervention

tag: injected as

value: Neonate

tag: target

value: mtDNA


title: RNA-Seq H9 (naïve) 7d+EZH2i rep1

tag: treatment


title: RNA-Seq H9 (naïve) rep3


title: AAV-Nd3-9577-(1)-mtDNA [mouse_26_F11]


title: Vehicle-mtDNA [mouse_23_F10]

source_name: Vehicle-mtDNA

value: Vehicle


title: RNA-Seq H9 (naïve) rep1


title: RNA-Seq H9 (naïve) rep2


title: AAV-Inactive-mtDNA [mouse_21_F8]

source_name: AAV-Inactive-mtDNA


title: AAV-Inactive-mtDNA [mouse_22_F9]


title: Vehicle-mtDNA [mouse_20_F7]


title: Col-0 8 hours high light replicate 2

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

description: T8H rep 2

data_processing:
Raw read quality was first diagnosed using FastQC (v0.11.7).
Trim Galore! (v0.4.4) was used for adapter and low-quality read trimming with PHRED score < 20 (-q 20).
Paired-end alignments were performed using trimmed reads using Subread (v1.5.0) with flags -t 0 and -u to report uniquely mapping reads, prior to sorting, indexing and compressing using Samtools (v1.3.1).
Transcript quantification was performed at the gene-level using featureCounts. This output was utilized in differential gene expression testing with edgeR (quasi-likelihood pipeline).
Genome_build: Araport11; https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Athaliana_er
Supplementary_files_format_and_content: .counts: raw counts per gene-level feature for each sample.
Supplementary_files_format_and_content: .csv: matrix of normalized log2 RPKM per gene-level feature across all samples and differentially expressed genes between samples using glmTreat [logFC > log2(1.5) and FDR < 0.05]

organism: Arabidopsis thaliana

source_name: Col-0 3-week old whole rosette shoot tissue; dark - high light, 8 hours

growth_protocol: Plants were soil-grown for three weeks prior to light transitions under standard growth conditions (22 °C, 50% RH, 100 uE, 16/8 -h day/night).

extract_protocol:
Total RNA was extracted with an adapted protocol using TRI reagent (Crisp et al 2017 Plant Cell).
Total RNA-sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, CA, USA) as per manufacterers instructions but with reaction volumes adjusted 1/3x.

value: leaf/shoot tissue

tag: ecotype

value: 3 weeks old

value: high light

tag: time


title: Col-0 8 hours high light replicate 3

description: T8H rep 3


title: Col-0 8 hours high light replicate 1

description: T8H rep 1


title: AAV-Inactive-mtDNA [mouse_19_F6]


title: Col-0 5 hours high light replicate 3

description: T5H rep 3

source_name: Col-0 3-week old whole rosette shoot tissue; dark - high light, 5 hours


title: Col-0 5 hours high light replicate 2

description: T5H rep 2


title: AAV-Nd3-9577-(1)-mtDNA [mouse_17_F4]


title: Vehicle-mtDNA [mouse_18_F5]


title: Col-0 5 hours high light replicate 1

description: T5H rep 1


title: AAV-Nd3-9577-(1)-mtDNA [mouse_15_F2]


title: Col-0 2 hours high light replicate 3

description: T2H rep 3

source_name: Col-0 3-week old whole rosette shoot tissue; dark - high light, 2 hours


title: Col-0 2 hours high light replicate 2

description: T2H rep 2


title: RNA-Seq H9 (primed) rep2


title: RNA-Seq H9 (naïve) 7d+EZH2i rep3


title: AAV-Inactive-mtDNA [mouse_11_E11]

value: Adult


title: AAV-Nd3-9577-(1)-mtDNA [mouse_14_F1]


title: Col-0 8 hours standard light replicate 1

description: T8L rep 1

source_name: Col-0 3-week old whole rosette shoot tissue; dark - standard light, 8 hours

value: standard light


title: Vehicle-mtDNA [mouse_10_E10]


title: Col-0 8 hours standard light replicate 2

description: T8L rep 2


title: AAV-Nd3-9577-(1)-mtDNA [mouse_8_E8]


title: Vehicle-mtDNA [mouse_9_E9]


title: Col-0 5 hours standard light replicate 1

description: T5L rep 1

source_name: Col-0 3-week old whole rosette shoot tissue; dark - standard light, 5 hours


title: AAV-Nd3-9577-(1)-mtDNA [mouse_7_E7]


title: Col-0 5 hours standard light replicate 2

description: T5L rep 2


title: AAV-Inactive-mtDNA [mouse_6_E6]


title: Col-0 2 hours standard light replicate 3

description: T2L rep 3

source_name: Col-0 3-week old whole rosette shoot tissue; dark - standard light, 2 hours


title: AAV-Inactive-mtDNA [mouse_5_E5]


title: Col-0 2 hours standard light replicate 2

description: T2L rep 2


title: AAV-Nd3-9577-(1)-mtDNA [mouse_4_E4]


title: Col-0 2 hours standard light replicate 1

description: T2L rep 1


title: Vehicle-mtDNA [mouse_2_E2]


title: Vehicle-mtDNA [mouse_1_E1]


title: AAV-Nd3-9577-(1)-mtDNA [mouse_3_E3]


title: Col-0 dark replicate 3

description: T0D rep 3

source_name: Col-0 3-week old whole rosette shoot tissue; end of night (dark harvested)

value: end of night (dark control)


title: Col-0 dark replicate 1

description: T0D rep 1


title: AAV-Nd3-9577-(1)-NUMT-Ch14 [mouse_32_D12]


title: Brain, Control_TilingArray_M05


title: Col-0 dark replicate 2

description: T0D rep 2


title: AAV-Nd3-9577-(1)-mtDNA [mouse_16_F3]


title: Col-0 2 hours high light replicate 1

description: T2H rep 1


title: AAV-Inactive-mtDNA [mouse_12_E12]


title: Col-0 8 hours standard light replicate 3

description: T8L rep 3


title: Col-0 5 hours standard light replicate 3

description: T5L rep 3


title: Vehicle-NUMT-Ch14 [mouse_23_D10]


title: T1_Horse16

city: Edinburgh

first: Anna Eleonora

last: Karagianni

address: Easter Bush Campus

department: Veterinary Clinical Sciences

institute: The Roslin Institute and the Royal Dick School of Veterinary Studies

data_processing:
Raw sequencing reads were processed to remove adaptors and poor-quality sequences (Q25 and below) using the Cutadapt program
Quality control of trimmed data was assessed using FASTQC and Multiqc
Kallisto (0.46.0.1) was ran on all samples, using as its index the complete set of 59,087 predicted transcripts for the EquCab3.0 genome
Genome_build: EquCab3.0 genome
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

organism: Equus caballus

source_name: Tracheal wash

extract_protocol:
Fresh tracheal wash cells were isolated, and total RNA was harvested using Trizol-Qiagen reagents. Total RNA was processed using NEBNext Ultra Directional RNA Library Prep Kit by Novogene (Novogene Europe) to generate cDNA libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Thoroughbred

tag: cell type

value: Tracheal wash derived cells

value: intense traininng

tag: group

value: ~ 2.5 months in training


title: Brain, AD_TilingArray_M05

value: Alzheimer's disease (AD)

value: brain


title: Brain, AD_TilingArray_M07


title: Brain, Control_TilingArray_M14

value: Control


title: AAV-Nd3-9577-(1)-NUMT-Ch14 [mouse_26_D11]

value: heart

value: L-strand:1333C ; H-strand:1333N


title: T1_Horse15


title: Brain, Control_TilingArray_M07


title: T1_Horse13


title: T1_Horse14


title: Brain, AD_TilingArray_M14


title: Brain, AD_TilingArray_M12


title: AAV-Inactive-NUMT-Ch14 [mouse_21_D8]

value: Neonate


title: AAV-Inactive-NUMT-Ch14 [mouse_22_D9]


title: AAV-Inactive-NUMT-Ch14 [mouse_19_D6]


title: Vehicle-NUMT-Ch14 [mouse_20_D7]

value: Vehicle


title: T1_Horse11


title: T1_Horse10


title: T1_Horse9


title: Vehicle-NUMT-Ch14 [mouse_18_D5]


title: Brain, Control_TilingArray_M12


title: AAV-Nd3-9577-(1)-NUMT-Ch14 [mouse_16_D3]


title: T1_Horse8


title: T1_Horse6


title: Peripheral blood monocytes from COPD Smokers replicate 1

city: New delhi

first: Anjana

last: Talwar

state: Delhi

address: Ansari Nagar

department: Physiology

country: India

institute: All India Institute of Medical Sciences

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55  µl containing 1X Agilent fragmentation buffer and 2X Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µl of 2X Agilent hybridization buffer was added to the fragmentation mixture and hybridized to 4 X 44k Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one colour scan setting for 4 X 44k array slides (Scan Area 61X21.6 mm, Scan resolution 5 µm, Dye channel was set to Green, and Green PMT was set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1 and Design Id: 014850) to obtain background subtracted and  spatially detrended Processed Signal Intensities. Features were flagged in Feature Extraction and Non-uniforn Features and outliers were excluded.

source_name: Peripheral blood monocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the One-Color Low Input quickAmp Labeling kit (Agilent) according to manufacturer's instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Peripheral blood from Control Smokers, Control Never smokers, COPD Smokers and COPD Ex-smokers was isolated followed by isolation of Peripheral Blood mononuclear cells (PBMC's). CD14+ monocytes were isolated from PBMC's using CD14 microbeads following manufacturer's instructions. RNA was isolated from peripheral blood CD14+ monocytes using DirectZol RNA extraction kit following manufacturer's recommendations.This protocol includes RNA isolation and an on-column DNase digestion. RNA was quantified using a Nanodrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: gender

value: MALE

tag: cells

value: peripheral blood monocytes

tag: age

tag: phenotype

value: COPD Smokers


title: AAV-Nd3-9577-(1)-NUMT-Ch14 [mouse_14_D1]


title: T1_Horse7


title: T1_Horse12


title: Peripheral blood monocytes from Control Never Smokers replicate 4

value: COPD EX Smokers


title: AAV-Inactive-NUMT-Ch14 [mouse_12_C12]

value: Adult


title: HSC-4

data_processing:
mRNA profile generated by deep sequencing using Illumina Hi-Seq 2000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using CLC genomic workbench v.11.0.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by CLC genomic workbench v.12.0.4
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM, RPKM, and Read number for each Sample.

source_name: hematopoietic stem cells

extract_protocol:
After 5000 HSCs were sorted, total RNA was extracted using ISOGEN reagent. First strand cDNA were synthesized using a SMARTer Pico cDNA amplification kit. Double-stranded cDNA was then amplified by 18 cycles of PCR.
Using Nextera XT DNA sample Prep Kit (Illumina Inc., San Diego, CA), libraries were prepared.

tag: strain

value: Bone marrow

value: HSC

tag: cell markers

value: CD150+ CD34- Sca1+ c-Kit+ Lineage-

value: 8-10 weeks


title: Peripheral blood monocytes from COPD Smokers replicate 2


title: T1_Horse5

value: Thoroughbred

value: Tracheal wash derived cells

value: intense traininng

value: ~ 2.5 months in training


title: T1_Horse4


title: HSC-3

tag: tissue


title: Peripheral blood monocytes from COPD ExSmokers replicate 3


title: Peripheral blood monocytes from COPD Smokers replicate 4


title: Peripheral blood monocytes from Control Never Smokers replicate 3

value: Control Never Smokers


title: Peripheral blood monocytes from COPD ExSmokers replicate 4


title: Peripheral blood monocytes from COPD ExSmokers replicate 2


title: Peripheral blood monocytes from Control Smokers replicate 4

value: Control Smokers


title: AAV-Nd3-9577-(1)-NUMT-Ch14 [mouse_17_D4]

value: heart

tag: ddcbe halves

value: L-strand:1333C ; H-strand:1333N

value: Neonate


title: Peripheral blood monocytes from Control Smokers replicate 2

value: MALE

value: peripheral blood monocytes


title: AAV-Inactive-NUMT-Ch14 [mouse_11_C11]

tag: weeks after intervention


title: Peripheral blood monocytes from Control Smokers replicate 3


title: Peripheral blood monocytes from Control Never Smokers replicate 1


title: Peripheral blood monocytes from Control Smokers replicate 1


title: Peripheral blood monocytes from COPD ExSmokers replicate 1


title: HSC-2


title: Peripheral blood monocytes from COPD Smokers replicate 3

value: COPD EX Smokers


title: Peripheral blood monocytes from Control Never Smokers replicate 2


title: HPC-4

value: HPC

value: CD150+ CD34+ Sca1+ c-Kit+ Lineage-


title: HPC-3

value: Bone marrow


title: AAV-Nd3-9577-(1)-NUMT-Ch14 [mouse_15_D2]

tag: injected as


title: Vehicle-NUMT-Ch14 [mouse_10_C10]

value: Vehicle

value: Adult

tag: target


title: Vehicle-NUMT-Ch14 [mouse_9_C9]


title: T1_Horse1

value: Thoroughbred

tag: treatment


title: AAV-Nd3-9577-(1)-NUMT-Ch14 [mouse_7_C7]


title: AAV-Inactive-NUMT-Ch14 [mouse_6_C6]


title: T0_Horse16

value: Tracheal wash derived cells

value: rest

value: ~2 months at rest


title: HPC-2

value: 8-10 weeks


title: NP_KO_TRAP_R5

city: New York

first: Caryn

last: Hale

state: New York

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Illumina's bcl2fastq2 Conversion Software v2.19 was used for basecalling.
Salmon quantifications were derived using Salmon (version 0.8.2) from raw FastQ against the mm10 transcriptome sequences retrieved in the Bioconductor TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.10.0)
Differential expression analysis was performed directly from Salmon quantifications using Tximport (version 1.8.0 ) and DESeq2 (version 1.20.0)
Genome_build: mm10 - (From Bioconductor package - BSgenome.Mmusculus.UCSC.mm10 version 1.4.0)
Supplementary_files_format_and_content: Salmon transcript quantifications against the mm10 transcriptome sequences.

source_name: Microdissected hippocampus CA1

extract_protocol:
Microdissected CA1 from mouse brain hippocampal slices were sectioned into HBSS containing 0.1 mg/mL cycloheximide and resuspended in 0.5 mL ice-cold polysome buffer supplemented with 40 U/ml RNasin Plus (Promega) and cOmplete Mini EDTA-free Protease Inhibitor (Roche) and homogenized by mechanical homogenization with 10 strokes at 900 rpm. NP-40 was added to 1% final concentration, incubated on ice for 10 minutes and centrifuged at 2000 x g for 10 minutes. Supernatant was centrifuged at 20,000g for 10 minutes. 10% of the resulting lysate was used for bulk RNA-seq, and the remaining lysate was pre-cleared with 1.5 mg Protein G Dynabeads for 45 min. HA-tagged ribosomes were collected by indirect IP by adding 40 ug of anti-HA antibody (Abcam ab9110) to CB lysate pools and 5 ug to NP lysate pools. Immunoprecipitation proceeded overnight with rotation at 4°C, followed by addition of 7.2 mg (CB pools) or 4.44 mg (NP pools) Protein G Dynabeads and further incubated with rotation at 4°C for 1 hour.  Beads were washed with 1 mL polysome buffer containing 1% NP-40 once for 5 minutes and twice for 20 minutes, followed by 4 x 10 minute washes in 50 mM Tris pH 7.5, 500 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 0.1 mg/mL cycloheximide. RNA was extracted from beads by incubating in 500 uL Trizol at room temperature for 5 minutes. RNA was quantified with RiboGreen Quant-IT assays (Invitrogen). Bulk RNA-seq samples were treated with RQ1 RNase-free DNase (Promega) prior to library preparation.
Polyadenylated mRNA was collected by Dynabeads mRNA Purification Kit (Ambion). The libraries were prepared by TruSeq RNA Sample Preparation Kit v2 (Illumina) following manufacturer’s instructions. High-throughput sequencing was performed on HiSeq (Illumina) to obtain 100 nucleotide paired-end reads.
polyA selection, TruSeq library prep (unstranded)

tag: genotype

value: Camk2a x RiboTag x Fmr1-/y

tag: region

value: CA1 neuropil

tag: trap antibody

value: anti-HA (Abcam ab9110)

tag: sample type

value: TRAP


title: NP_WT_TRAP_R5

value: Camk2a x RiboTag x Fmr1+/y


title: T0_Horse14

tag: breed

tag: cell type

tag: group


title: T0_Horse15


title: T1_Horse3

value: intense traininng

value: ~ 2.5 months in training


title: HSC-1

value: HSC

value: CD150+ CD34- Sca1+ c-Kit+ Lineage-

tag: age


title: AAV-Nd3-9577-(1)-NUMT-Ch14 [mouse_8_C8]

value: heart

value: L-strand:1333C ; H-strand:1333N


title: NP_CreNeg_TRAP_R5

value: RiboTag x Fmr1+/y


title: CB_KO_TRAP_R5

value: CA1 cell bodies layer


title: CB_WT_TRAP_R5


title: AAV-Inactive-NUMT-Ch14 [mouse_5_C5]

value: Adult


title: Production _phase

city: Suita

first: Kazuya

last: Yamanaka

state: Osaka

address: 3-3-35 Yamate-cho

institute: Kansai University

data_processing:
RTA (Real Time Analysis. v1.18) was used for basecalling.
Sequence reads cleaned using the Trimmomatic (Ver. 0.39) were mapped and aligned to the S. albulus NBRC14147 genome (GenBank accession number ASM385166v1) using the BWA (Ver. 0.7.17).
The expression levels of each transcript was quantified using the StringTie (Ver. 2.1.3b) followed by calculation of read counts in Python script prepDE.py.
Gene-level read counts were normalized with the trimmed mean of M-values (TMM) option in edgeR (Ver. 3.16.5).
Genome_build: S. albulus NBRC14147 genome (GenBank accession number ASM385166v1)
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with expression differences growth phase vs production phase

organism: Streptomyces noursei

source_name: whole cells

growth_protocol: The strain NBRC14147 was grown in M3G medium at 30°C for 20 h. The culture broth was then inoculated to 1 l of M3G medium in the jar-fermentor (model MDL-8C; B.E. Marubishi). Fermentation production of poly-L-Lys was carried at 30°C with agitation stirring at 500 rpm, and the aeration was kept at 3.5 VVM (liters air/liters medium/min) throughout the fermentation. After the growth-to-production phase transition, 10% aqueous ammonia was continuously fed to have kept poly-L-Lys being produced at around pH 4.2.

extract_protocol:
rRNA was depleted from the total RNA using the Ribo-Zero Magnetic kit (Illumina).
RNA libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina) and assessed using the Agilent 2100 BioAnalyzer DNA 1000 chip.

tag: Stage

value: production phase

value: 35 hours


title: T1_Horse2

value: Thoroughbred

value: Tracheal wash derived cells


title: T0_Horse12

value: rest

value: ~2 months at rest


title: Growth_phase

tag: strain

value: growth phase

value: 8 hours


title: CB_CreNeg_TRAP_R5

value: anti-HA (Abcam ab9110)

value: TRAP


title: AAV-Nd3-9577-(1)-NUMT-Ch14 [mouse_3_C3]


title: T0_Horse13


title: NP_KO_RNAseq_R5

value: Camk2a x RiboTag x Fmr1-/y

value: CA1 neuropil

value: bulk RNA-seq


title: AAV-Nd3-9577-(1)-NUMT-Ch14 [mouse_4_C4]

value: heart

value: L-strand:1333C ; H-strand:1333N


title: T0_Horse11


title: HPC-1

value: Bone marrow

value: HPC

tag: cell markers

value: CD150+ CD34+ Sca1+ c-Kit+ Lineage-

value: 8-10 weeks


title: NP_WT_RNAseq_R5

value: Camk2a x RiboTag x Fmr1+/y


title: Vehicle-NUMT-Ch14 [mouse_2_C2]

tag: tissue

value: Vehicle

value: Adult


title: NP_CreNeg_RNAseq_R5

value: RiboTag x Fmr1+/y


title: Vehicle-NUMT-Ch14 [mouse_1_C1]

tag: ddcbe halves


title: T0_Horse10

value: Thoroughbred

value: Tracheal wash derived cells

value: rest

value: ~2 months at rest


title: T0_Horse9


title: AAV-Nd3-9577-(1)-NUMT-Ch1 [mouse_32_B12]

tag: weeks after intervention

value: Neonate


title: T0_Horse8


title: CB_KO_RNAseq_R5

value: Camk2a x RiboTag x Fmr1-/y

value: CA1 cell bodies layer


title: CB_WT_RNAseq_R5

value: bulk RNA-seq


title: T0_Horse7


title: CB_CreNeg_RNAseq_R5


title: Vehicle-NUMT-Ch1 [mouse_23_B10]

value: heart

tag: injected as


title: T0_Horse6


title: NP_KO_TRAP_R4

value: CA1 neuropil

value: anti-HA (Abcam ab9110)

value: TRAP


title: AAV-Inactive-NUMT-Ch1 [mouse_22_B9]

value: L-strand:1333C ; H-strand:1333N

tag: target


title: NP_WT_TRAP_R4

value: Camk2a x RiboTag x Fmr1+/y


title: T0_Horse5

tag: treatment


title: AAV-Inactive-NUMT-Ch1 [mouse_21_B8]


title: NP_CreNeg_TRAP_R4

tag: genotype


title: T0_Horse4


title: Vehicle-NUMT-Ch1 [mouse_20_B7]

value: Vehicle


title: T0_Horse3


title: AAV-Inactive-NUMT-Ch1 [mouse_19_B6]


title: CB_KO_TRAP_R4

tag: region


title: CB_WT_TRAP_R4

tag: trap antibody


title: T0_Horse2


title: AAV-Nd3-9577-(1)-NUMT-Ch1 [mouse_26_B11]


title: Vehicle-NUMT-Ch1 [mouse_18_B5]


title: CB_CreNeg_TRAP_R4

tag: sample type


title: T0_Horse1

tag: breed


title: NP_WT_RNAseq_R4


title: AAV-Nd3-9577-(1)-NUMT-Ch1 [mouse_16_B3]


title: NP_KO_RNAseq_R4


title: P_J3: Plasmid_replicate_Jurk_amp_3

first: Terence

middle: D

last: Capellini

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard Univserity

data_processing:
Library strategy: MPRA
Barcodes were extracted from sequence files and matched to oligos using the attached barcode_oligo_tab.gz file. The barcode is the first column and the oligos attached to it are in the last column. Any barcodes matched to duplicate oligos were excluded. Oligo sequences that match the oligo ids can be found in the attached oligo_name_seq_tab.txt (column 1 is the oligo sequence, column 2 is the oligo id).
Counts per oligo per replicate were determined by summing all barcode matches together for each replicate and a reported unnormalized in the included count file.
Supplementary_files_format_and_content: Counts per oligo per replicate were determined by summing all barcode matches together for each replicate and a reported unnormalized in the included count file.

molecule: other

organism: synthetic construct

source_name: Plasmid DNA amplified as many times as the Jurkat replicates

growth_protocol: K562 cells were grown with RPMI 1640 Complete Medium is supplemented with 2mM L-Glutamine + 10% FBS + 1% Penicillin-Streptomycin to a density of ~6*10^5 cells/ML

extract_protocol:
Twenty-four hours after transfection, cells were collected and snap frozen in liquid N2. Total RNA was extracted and GFP mRNA was isolatedand converted to cDNA Tewhey and colleagues 2016.
Following Tewhey et al. 2016, cDNA libraries were quanitified using qPCR including the plasmid pool used to transfect the cells. They were then diluted to be of equal concentration with the lowest library per cell type (15 cycles for K562 cells and 21.5 for Jurkat cells) and amplified using one fewer cycle than the lowest cycle threshold. An addition PCR was performed to add P7 indexing primers.
Libraries were than molar pooled and sequenced  with 1x50bp chemistry on a Illumina HiSeq 2500

treatment_protocol: For K562 cells 60 million cells per replicate were transfected with 60ug the MPRA library using electroporation with the Neon transfection system following the manufacturers protocol. For Jurkat cells, for each of 2 replicates 60 million cells per replicate were transfected 120ug of the MPRA library the Lonza Nucleofection system.

value: Plasmid DNA


title: P_J2: Plasmid_replicate_Jurk_amp_2


title: P_J1: Plasmid_replicate_Jurk_amp_1


title: AAV-Nd3-9577-(1)-NUMT-Ch1 [mouse_14_B1]


title: P_K4: Plasmid_replicate_K562_amp_4

source_name: Plasmid DNA amplified as many times as the k562 replicates


title: AAV-Inactive-NUMT-Ch1 [mouse_12_A12]

value: Adult


title: AAV-Nd3-9577-(1)-NUMT-Ch1 [mouse_17_B4]


title: NP_CreNeg_RNAseq_R4

value: RiboTag x Fmr1+/y


title: CB_WT_RNAseq_R4


title: CB_KO_RNAseq_R4


title: CB_CreNeg_RNAseq_R4


title: AAV-Nd3-9577-(1)-NUMT-Ch1 [mouse_15_B2]


title: AAV-Inactive-NUMT-Ch1 [mouse_11_A11]


title: P_K2: Plasmid_replicate_K562_amp_2


title: Vehicle-NUMT-Ch1 [mouse_10_A10]


title: NP_WT_TRAP_R3


title: AAV-Nd3-9577-(1)-NUMT-Ch1 [mouse_8_A8]


title: P_K1: Plasmid_replicate_K562_amp_1


title: P_K3: Plasmid_replicate_K562_amp_3


title: NP_KO_TRAP_R3


title: G_164_GSP_215_no_tumor_16_M.txt

city: Genova

first: Roberta

last: Resaz

address: via Gerolamo Gaslini 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

data_processing:
Data processing, categorization, normalization, filtering, imputation and differential expression was carried out by PIPE-T galaxy tool.  Ct values falling within the range 14-32 were categorized as reliable values as recommended by the manufacturer guidelines. Global mean normalization was used to reduce any technical variability introduced in the data by the RT-qPCR experiments.    Only Exo-miR with at most 20% of missing values were retained for the analysis to reduce the bias introduced by imputation.  Mestdagh method was employed to assign a numeric expression value to missing values. The rank product method implemented by RankProd R package was used to identify significant differentially expressed microRNA.
non-normalized file reports raw Ct values. Ct value of 40 indicates a missing value. normalized data file reports delta Ct values (Ct – sample mean expression ). NA value indicates a missing value.

label: Applied Biosystems Human TaqMan Low Density Array (TLDA, v2.0) (Card A)

source_name: Plasma exosomes

label_protocol: Exo-miR were analyzed by the TaqMan Array Card Technology. Exo-miR were reverse transcribed with the TaqMan microRNA Reverse Transcription Kit, using the MegaplexTM RT primers Human Pool A (Thermo Fisher Scientific, Monza, MB, Italy). Pre-amplification of cDNA was performed with TaqMan PreAmp Master Mix and MegaplexTM  Pre-Amp primers Human Pool A. The pre-amplification product was diluted according to the manufacturer’s instructions and used to perform microRNA profiling on the ViiATM 7 Real-Time PCR System.

extract_protocol: Exosomes isolation and RNA extraction from plasma was performed with the exoRNeasy Serum/Plasma Midi kit (Qiagen Italia, Milano, Italy).

value: Plasma exosomes

tag: patient diagnosis

tag: molecule subtype

value: microRNA


title: G_162_GSP_213_no_tumor_7_F.txt


title: AAV-Nd3-9577-(1)-NUMT-Ch1 [mouse_7_A7]


title: Vehicle-NUMT-Ch1 [mouse_9_A9]


title: NP_CreNeg_RNAseq_R3


title: NP_WT_RNAseq_R3


title: G_165_GSP_216_no_tumor_6_M.txt


title: NP_KO_RNAseq_R3


title: AAV-Inactive-NUMT-Ch1 [mouse_6_A6]


title: G_152_GSP_203_no_tumor_10_F.txt


title: G_133_GSP_183_no_tumor_14_F.txt


title: NP_CreNeg_TRAP_R3


title: AAV-Inactive-NUMT-Ch1 [mouse_5_A5]


title: AAV-Nd3-9577-(1)-NUMT-Ch1 [mouse_4_A4]


title: CB_WT_TRAP_R3


title: G_132_GSP_182_no_info_12_F.txt


title: Brain_control_sample11

hyb_protocol: 1.65 μg of labeled cRNA was used for hybridization following manufacturer’s instructions.

scan_protocol: After hybridization the arrays were washed according to the manual and scanned using the Agilent G2565CA Microarray Scanner System with Agilent Scan Control Software (Version A851) following settings for scanning: Profile: AgilentG3 GX 1Color; Channels Green; Scan Region: Agilent HD (61 × 21.6mm); Resolution 3 μm double pass; Tiff: 20 bit; Green PMT Gain: 100%. Result tables were extracted after grid placement using Agilent Feature Extraction Software (Version 11.5.1.1)

data_processing: Differential expression analysis was performed using R and the Bioconductor package Limma. Quality control of arrays was performed by checking distribution of “bright corner”, “dark corner” probes, and relative spike-in concentration versus normalized signal. The controls confirmed high quality of the results and consequently all microarray data were included in the downstream analysis. Initially, independent filtering was performed, removing probes (i) with signal intensity above the background in less than one third of all arrays and (ii) exhibiting an interquartile range of log2 signal intensity across all samples of less than 1. Background expression was defined by the mean intensity plus three times the standard deviation of negative control spots (Agilent’s 3xSLv spots). 113 047 out of 931 898 probes were retained after filtering. Signal intensities were quantile normalized but not background corrected, due to the low background intensities of Agilent arrays. Differential expression between AD and control samples was determined using a linear model that includes age because on average, individuals from the AD group were older than controls. The linear model was fitted using the R package limma and reliable variance estimates were obtained by Empirical Bayes moderated t-statistics. False discovery rate was controlled by a modified Benjamini-Hochberg procedure that incorporates an estimated proportion of the null p-values 23 to compute q-values using the fdrtool R package.

source_name: brain tissue

label_protocol: 1 μg of total RNA was labeled using the Quick Amp Labeling Kit (Agilent, Waldbronn, Germany), according to the manufacturer’s instructions with the adaptation of using 120 pmol of a random N6 − T7 primer (Metabion, Planegg, Germany) instead of a polyT-T7 primer. cRNA quantity was checked using a NanoDrop ND-1000 UV-VIS Spectrophotometer, as enlisted in the manufacturer’s instructions.

extract_protocol: RNA was isolated by Trizol™ method (Invitrogen, Karlsruhe, Germany). 100mg deeply frozen human brain tissue (temporal cortex) was homogenized in the presence of 1ml Trizol in a glass-Teflon™ homogenizer. The homogenate was transferred to a microtube and after adding chloroform, samples were centrifuged at 15 000 g (4 °C) for 15min and the supernatant transferred to a fresh tube. Samples were mixed with equal amounts of isopropanol and centrifuged at 12 000 g (4 °C) for 15min to precipitate the RNA. After washing, the pellet was air-dried and dissolved in water. RNA quality was assessed by denaturing formaldehyde agarose gel electrophoresis, by spectrophotometry (scanning at 220−320 nm) and by analysis using Agilent 2100 bioanalyzer. Only samples with RIN > 5 were further processed. The RNA concentration was estimated spectrophotometrically by absorbance at 260 nm, concentration was adjusted to 1mg/ml and RNA was stored at −80 °C until use.

tag: disease state

value: Control

tag: age

tag: gender

value: w

value: brain


title: Brain_control_sample16

value: m


title: Brain_control_sample13


title: Brain_control_sample19


title: Brain_control_sample18


title: Brain_control_sample12


title: G_124_GSP_174_no_tumor_16_F.txt


title: AAV-Nd3-9577-(1)-NUMT-Ch1 [mouse_3_A3]


title: Brain_control_sample20


title: G_122_GSP_172_no_info_8_M.txt


title: G_103_GSP_156_no_tumor_7_F.txt


title: Vehicle-NUMT-Ch1 [mouse_1_A1]


title: Brain_control_sample7


title: Brain_control_sample2


title: Brain_control_sample10


title: Vehicle-NUMT-Ch1 [mouse_2_A2]


title: Brain_control_sample5


title: CB_KO_TRAP_R3

value: Camk2a x RiboTag x Fmr1-/y

value: CA1 cell bodies layer

tag: strain


title: CB_CreNeg_TRAP_R3


title: AAV-Nd3-9577-(1), mouse_32

description:
mouse_32
32_S32

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to ChrM (GRCm38) with Bowtie2
Samtools mpileup and Cutadapt to count nucleotides surrounding the editing site
Genome_build: GRChm38
Supplementary_files_format_and_content: Supp Dataset 1 = excel file showing the % of base editing at individual Cs within the editing window for each sample; counts_ddCBE = xls file with Adaptor counts generated by Cutadapt

source_name: heart

extract_protocol:
NIH/3T3 mouse cells were collected by trypsinization, washed once in PBS and re-suspended in lysis buffer (1mM EDTA, 1 % Tween20, 50 mM Tris (pH = 8)) with 200 µg/ml of proteinase K. Lysates were incubated at 56 ºC with agitation (300 RPM) for 1 h, and then incubated 95 ºC for 10 min before use in downstream applications. Genomic DNA from mouse heart samples (~50 mg) was extracted with a Maxwell® 16 Tissue DNA Purification Kit in a Maxwell® 16 Instrument (Promega), according to manufacturer´s instructions.
Illumina NexteraXT
DNA resequencing

tag: tissue

value: heart

tag: time

value: 3 week(s) after intervention

value: Neonate


title: CB_WT_RNAseq_R3

value: bulk RNA-seq


title: Brain_control_sample17


title: Brain_control_sample8


title: Brain_control_sample4


title: G_115_GSP_165_tumor_63_F.txt


title: Brain_control_sample15


title: CB_KO_RNAseq_R3


title: AAV-Nd3-9577-(1), mouse_31

description:
mouse_31
31_S31

tag: ddcbe halves

value: L-strand:1333C ; H-strand:1333N


title: G_183_GSP_235_tumor_53.txt


title: CB_CreNeg_RNAseq_R3


title: Brain_AD_sample16

value: AD


title: Vehicle, mouse_30

description:
mouse_30
30_S30

value: Vehicle

tag: injected as


title: NP_WT_TRAP_R2

value: Camk2a x RiboTag x Fmr1+/y

value: CA1 neuropil

value: anti-HA (Abcam ab9110)

value: TRAP


title: G_13_GSP_17_tumor_49_F.txt

value: Plasma exosomes

value: microRNA


title: Brain_control_sample6

value: Control

value: w

value: brain


title: NP_WT_RNAseq_R2


title: Vehicle, mouse_29

description:
mouse_29
29_S29


title: Brain_control_sample9


title: Brain_AD_sample18


title: Vehicle, mouse_28

description:
mouse_28
28_S28


title: Brain_control_sample3


title: AAV-Inactive, mouse_27

description:
mouse_27
27_S27


title: NP_KO_TRAP_R2

value: Camk2a x RiboTag x Fmr1-/y


title: Brain_control_sample1

value: m


title: NP_KO_RNAseq_R2


title: G_35_GSP_58_tumor_39_M.txt


title: G_137_GSP_187_tumor_40_F.txt


title: G_92_GSP_129_tumor_37_F.txt


title: Brain_AD_sample17


title: G_82_GSP_152_no_tumor_11_M.txt


title: NP_CreNeg_RNAseq_R2

value: RiboTag x Fmr1+/y


title: AAV-Inactive, mouse_24

description:
mouse_24
24_S24

value: heart

value: 3 week(s) after intervention

value: Neonate


title: Vehicle, mouse_25

description:
mouse_25
25_S25


title: Vehicle, mouse_23

description:
mouse_23
23_S23


title: AAV-Nd3-9577-(1), mouse_26

description:
mouse_26
26_S26

value: L-strand:1333C ; H-strand:1333N


title: G_48_GSP_76_tumor_34_F.txt


title: EPCR+++(1) ATAC-seq

data_processing:
Deep sequencing was performed by Illumina Next-Seq 500
Trimming, alignment, peak calling, and Quantification were performed by FASTX-toolkit, Bowtie2, MACS2, and HOMER, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: peak files

extract_protocol:
Sorted HSCs were lysed with ATAC-resuspension buffer containing detergents, which are listed in a previous study(Corces et al., 2017 Nat Methods 14, 959-962.).
After optical amplification by PCR using ATAC-Primers (Buenrostro et al., 2015 Curr Protoc Mol Biol 109, 21 29 21-21 29 29.), these DNA fragments were purified libraries were sequenced by Hi-seq.

value: Bone marrow

value: 8-10 weeks


title: CB_WT_RNAseq_R2

value: Camk2a x RiboTag x Fmr1+/y

value: CA1 cell bodies layer

value: bulk RNA-seq


title: CB_WT_TRAP_R2

value: anti-HA (Abcam ab9110)

value: TRAP


title: Brain_AD_sample14

value: AD


title: NP_CreNeg_TRAP_R2

value: CA1 neuropil


title: AAV-Inactive, mouse_22

description:
mouse_22
22_S22


title: G_96_GSP_133_tumor_32_M_BIS.txt

value: Plasma exosomes

value: microRNA


title: CB_KO_TRAP_R2

value: Camk2a x RiboTag x Fmr1-/y


title: G_12_GSP_16_tumor_36_F.txt


title: EPCR+++(2) ATAC-seq


title: AAV-Inactive, mouse_21

description:
mouse_21
21_S21


title: CB_KO_RNAseq_R2


title: G_77_GSP_114_tumor_45_M.txt


title: G_129_GSP_179_tumor_31_M.txt


title: EPCR+(1) ATAC-seq


title: Vehicle, mouse_20

description:
mouse_20
20_S20

value: Vehicle


title: G_1_GSP_02_tumor_31_M.txt


title: CB_CreNeg_TRAP_R2

value: RiboTag x Fmr1+/y


title: AAV-Inactive, mouse_19

description:
mouse_19
19_S19

value: heart

value: 3 week(s) after intervention


title: G_17_GSP_25_tumor_31_F.txt


title: CB_CreNeg_RNAseq_R2


title: L929 derived exosome replicate 2

city: Guangzhou

first: Tian

last: Zhou

state: Guangdong

address: NO.7 Jinsui Road

department: State Key Laboratory of Ophthalmology

country: China

institute: Zhongshan Ophthalmic Center

data_processing:
illumina instrument for small RNA sequencing
Clean reads were trimmed by removing the sequences smaller than 15 nt or longer than 35 nt.
Reads were alligned to mm10 by Bowtie v0.12.2 and compared with databases including Silva,GtRNAdb,Rfam and Repbase databases. The following RNAs were filtered including ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and novel miRNA predicted by comparing with Genome and known miRNAs from miRBase.
Differential expression analysis was performed using the DESeq2 R package (1.10.1)
Genome_build: mm10
Supplementary_files_format_and_content: All-counts.csv

source_name: Exosome of L929 cells

growth_protocol: Primary murine bone marrow MSCs and L9292 cells were cultured in medium containing 10% exosome-free FBS for 48 hours before the supernatants were collected

extract_protocol:
Exosomes were derived by ultracentrifuge from the supernant of primary murine bone marrow MSCs and L929 cells
Library preparation and miRNA sequencing were performed by Biomarker Technologies Corporation (Beijing, China). Standard PAGE gel electrophoresis was used to examine RNA integrity. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and single-end reads and paired-end reads were generated.

tag: cell type

value: Fibroblasts


title: Expert_rep6

first: Chloe

last: Delepine

state: Massachusetts

address: 43 vassar st

institute: MIT

data_processing:
Reads were aligned to the mouse mm9 genome using the TopHat sliced read mapper (Trapnell et al., 2012).
Fragment counts were obtained using the Cufflinks pipeline (Trapnell et al., 2012)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

source_name: Motor cortex astrocytes

extract_protocol:
RNA was purified and concentrated with proteinase K cell digestion, ethanol precipitation and washing on a silica column (Zymo, Quick-RNA FFPE)
Indexed cDNA libraries were generated using the SMARTer Stranded Total RNA-Seq Kit v2 (Illumina, #634411)
Multiplexed sequencing (RNAseq) was performed on Illumina HiSeq 2000

value: 13 wks

tag: Sex

value: M

tag: learning

value: Expert

value: Motor cortex astrocytes


title: L929 derived exosome replicate 3


title: G_5_GSP_7_tumor_30_M.txt


title: L929 derived exosome replicate 1


title: AAV-Nd3-9577-(1), mouse_17

description:
mouse_17
17_S17

value: L-strand:1333C ; H-strand:1333N

value: Neonate


title: Expert_rep5

value: 15 wks


title: Brain, Control_TilingArray_M08

source_name: human brain tissue

value: Control

value: brain


title: AAV-Nd3-9577-(1), mouse_16

description:
mouse_16
16_S16


title: G_10_GSP_14_tumor_26_F.txt

value: Plasma exosomes


title: Brain_AD_sample15

value: AD

value: w


title: G_40_GSP_66_tumor_28_F.txt

value: microRNA


title: Expert_rep3

value: F


title: Brain, AD_TilingArray_M08

value: Alzheimer's disease (AD)


title: G_44_GSP_71_tumor_24_F.txt


title: Brain, Control_TilingArray_M09


title: Expert_rep2

value: 14 wks


title: G_67_GSP_148_tumor_22_M.txt


title: AAV-Nd3-9577-(1), mouse_14

description:
mouse_14
14_S14

value: heart

value: 3 week(s) after intervention


title: EPCR+(2) ATAC-seq

value: Bone marrow

value: 8-10 weeks


title: AAV-Inactive, mouse_13

description:
mouse_13
13_S13


title: G_49_GSP_78_tumor_22_M.txt


title: Expert_rep1

value: 13 wks

value: Expert

value: Motor cortex astrocytes


title: Vehicle, mouse_18

description:
mouse_18
18_S18

value: Vehicle

value: Neonate


title: Expert_rep4

value: 15 wks

value: M


title: Brain, Control_TilingArray_M10

value: Control

value: brain


title: Brain, AD_TilingArray_M10


title: Novice_rep6

value: 11 wks

value: Novice


title: AAV-Inactive, mouse_12

description:
mouse_12
12_S12

value: L-strand:1333C ; H-strand:1333N

value: 24 week(s) after intervention

value: Adult


title: Brain, AD_TilingArray_M09

value: Alzheimer's disease (AD)


title: Novice_rep5

value: F


title: Vehicle, mouse_10

description:
mouse_10
10_S10

value: heart


title: G_52_GSP_85_no_tumor_37_M.txt

value: Plasma exosomes

value: microRNA


title: G_18_GSP_26_no_info_36_M.txt


title: G_160_GSP_211_tumor_20_F.txt


title: Vehicle, mouse_9

description:
mouse_9
9_S9


title: Novice_rep3

value: 13 wks

value: Motor cortex astrocytes


title: G_118_GSP_168_no_tumor_35_F.txt


title: AAV-Inactive, mouse_11

description:
mouse_11
11_S11


title: AAV-Nd3-9577-(1), mouse_8

description:
mouse_8
8_S8