title: genomic DNA from three month whole blood 732

source_name: three month whole blood 732


title: genomic DNA from three month whole blood 713

status: Public on Aug 30 2023

type: genomic

city: Aurora

first: Sarah

middle: J.

last: Borengasser

state: Colorado

address: 12631 E. 17th Ave, Mailstop F-561

department: Pediatrics

country: USA

institute: University of Colorado - Anschutz Medical Campus

hyb_protocol: Per Illumina protocol

scan_protocol: Per Illumina protocol

data_processing: Array data were pre-processed and normalized using the SeSAMe R package. After removing cross-hybridizing probes, probes overlying SNPs with minor allele frequency >1% in the general population, and probes that failed across multiple samples with an average detection p-value > 0.05, a total of 739,397 cytosine-phosphate-guanine dinucleotide (CpG) probes remained for analysis.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: three month whole blood 713

label_protocol: Per Illumina protocol

extract_protocol: Genomic DNA was isolated from whole blood samples using the commercially-available PureLink Genomic DNA Kit (Invitrogen, Carlsbad, CA, USA). Quality was assessed via a NanoDrop 2000/2000c spectrophotometer (ThermoFisher Scientific, Grand Island, NY, USA) and concentrations measured by  Qubit Fluorometer 2.0 (Invitrogen, Carlsbad, CA, USA).

tag: sample id

tag: timepoint

tag: ChIP

tag: array

tag: age

tag: Sex

value: F

tag: race

value: Caucasian

tag: ethnicity

value: Non-hispanic

tag: tissue

value: whole blood collected at 3 months


title: genomic DNA from three month whole blood 684

source_name: three month whole blood 684


title: genomic DNA from three month whole blood 681 replicate

source_name: three month whole blood 681


title: genomic DNA from three month whole blood 726

source_name: three month whole blood 726

value: M

value: hispanic


title: genomic DNA from three month whole blood 681


title: genomic DNA from three month whole blood 625

source_name: three month whole blood 625


title: genomic DNA from three month whole blood 668

source_name: three month whole blood 668

value: Non-Caucasian


title: genomic DNA from three month whole blood 607

source_name: three month whole blood 607


title: genomic DNA from three month whole blood 712

source_name: three month whole blood 712


title: genomic DNA from three month whole blood 564

source_name: three month whole blood 564


title: genomic DNA from three month whole blood 559

source_name: three month whole blood 559


title: genomic DNA from three month whole blood 669

source_name: three month whole blood 669


title: genomic DNA from three month whole blood 548

source_name: three month whole blood 548


title: genomic DNA from three month whole blood 539

source_name: three month whole blood 539


title: genomic DNA from three month whole blood 602

source_name: three month whole blood 602


title: genomic DNA from three month whole blood 554

source_name: three month whole blood 554


title: genomic DNA from three month whole blood 509

source_name: three month whole blood 509


title: genomic DNA from three month whole blood 464

source_name: three month whole blood 464


title: genomic DNA from three month whole blood 436 replicate

source_name: three month whole blood 436


title: genomic DNA from three month whole blood 436


title: genomic DNA from three month whole blood 520

source_name: three month whole blood 520


title: genomic DNA from three month whole blood 432

source_name: three month whole blood 432


title: genomic DNA from three month whole blood 577

source_name: three month whole blood 577


title: genomic DNA from three month whole blood 356

source_name: three month whole blood 356


title: genomic DNA from three month whole blood 334

source_name: three month whole blood 334


title: mesenchymal stem cell 2

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

hyb_protocol: Converted gDNA was hybridized on Infinium®MethylationEPIC BeadChips (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

scan_protocol: Bead Array Slides were scanned using the Illumina Bead Array Reader according to the manufacturer's protocol.

data_processing: GenomeStudio (version 2011.1) with Methylation Module (version 1.9.0) was used to process the raw image data generated by the BeadArray Reader followed by import and preprocessing using the RnBeads R package. Beta values were normalized using the dasen method from the R watermelon package

source_name: mesenchymal stem cells

label_protocol: DNA methylation profiling was performed using Illumina Infinium MethylationEPIC 850 k arrays. Processing of DNA Methylation arrays was performed as follows: Bisulfite conversion of 500ng of DNA was done using the EZ DNA Methylation Kit (Zymo Research, Orange, CA, USA)  according to the manufacturer's protocol.

extract_protocol: Simultaneous DNA and RNA extraction using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Isolated DNA was quantified using the Qubit 2.0 fluorometer.

tag: cell type

value: mesenchymal stem cell


title: genomic DNA from three month whole blood 319

source_name: three month whole blood 319


title: genomic DNA from three month whole blood 454

source_name: three month whole blood 454


title: genomic DNA from three month whole blood 388

source_name: three month whole blood 388


title: genomic DNA from three month whole blood 422

source_name: three month whole blood 422


title: genomic DNA from three month whole blood 300

source_name: three month whole blood 300


title: genomic DNA from three month whole blood 298

source_name: three month whole blood 298


title: genomic DNA from three month whole blood 346

source_name: three month whole blood 346


title: fibroblasts 1

source_name: fibroblasts

value: fibroblast


title: genomic DNA from three month whole blood 289

source_name: three month whole blood 289


title: genomic DNA from three month whole blood 285

source_name: three month whole blood 285


title: genomic DNA from three month whole blood 254

source_name: three month whole blood 254


title: mesenchymal stem cell 1


title: genomic DNA from three month whole blood 244

source_name: three month whole blood 244


title: genomic DNA from three month whole blood 233

source_name: three month whole blood 233


title: genomic DNA from three month whole blood 189

source_name: three month whole blood 189


title: genomic DNA from three month whole blood 181

source_name: three month whole blood 181


title: genomic DNA from three month whole blood 178

source_name: three month whole blood 178


title: genomic DNA from three month whole blood 163

source_name: three month whole blood 163


title: genomic DNA from three month whole blood 139

source_name: three month whole blood 139


title: genomic DNA from three month whole blood 131

source_name: three month whole blood 131


title: genomic DNA from three month whole blood 126

source_name: three month whole blood 126


title: genomic DNA from three month whole blood 100

source_name: three month whole blood 100


title: genomic DNA from three month whole blood 122

source_name: three month whole blood 122


title: mesenchymal stem cell 3

source_name: mesenchymal stem cells


title: fibroblasts 3


title: mesenchymal stem cell 4


title: genomic DNA from three month whole blood 108

source_name: three month whole blood 108


title: genomic DNA from three month whole blood 123

source_name: three month whole blood 123


title: HZ_34

type: SRA

city: Boston

first: Huiping

last: Zhang

state: MA

address: 72 East Concord Street

institute: Boston University

description:
heterogeneous stock (HS) rat
miRNA transcriptome data

library_source: transcriptomic

data_processing:
The Comprehensive Analysis Pipeline for miRNA Sequencing Data (CAP-miRseq) workflow [BMC Genomics. 2014; 15:423] was used for raw reads (in fastq files) pre-processing, alignment, mature/precursor/novel miRNA qualification and prediction.
Assembly: mRatBN7.2/rn7
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Rattus norvegicus

source_name: snap-frozen rat brain

extract_protocol:
RNA was extracted with the Trizol reagent using the QIAGEN RNeasy mini kit and followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyzer System.
Small RNA-seq libraries were generated using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1) (NEB, Ipswich, MA, USA) with 250 ng of total RNAs.
RNA libraries were prepared for sequencing using the protocol for use with NEBNext Small RNA Library Prep Set for Illumina

tag: group

value: C

tag: cocaine withdrawal

value: Naïve

tag: brain region

value: Prelimbic Prefrontal Cortex

tag: rna integrity number


title: CTL-1

city: Hangzhou

first: Jianhong

last: Dong

state: 浙江

address: School of Pharmacy, Hangzhou Normal University

country: China

institute: Hangzhou Normal University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38.107
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: cell line

tag: treatment

value: Without special treatment


title: Th-1

value: 15 μM Thiotert for 24 h


title: CTL-2


title: Th-3


title: CTL-3


title: fibroblasts 2

source_name: fibroblasts


title: Th-2


title: HZ_36

value: Nucleus Accumbens


title: fibroblasts 4


title: fibroblasts 5


title: HZ_35

value: Infralimbic Prefrontal Cortex


title: HZ_29


title: HZ_26


title: HZ_33


title: HZ_27


title: HZ_30


title: HZ_32


title: HZ_31


title: HZ_28


title: HZ_25


title: HZ_24

value: B


title: HZ_23


title: HZ_18


title: HZ_17


title: HZ_19


title: HZ_20


title: HZ_22


title: HZ_16


title: HZ_15


title: HZ_14


title: HZ_13


title: HZ_12

value: A


title: HZ_6


title: HZ_10


title: HZ_4


title: HZ_11


title: HZ_9


title: HZ_7


title: HZ_21


title: HZ_1


title: C08.C.F

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description:
R08
Chicken_RNAseq.xlsx

data_processing:
Quality of sequenced CAGE reads was checked by using FastQC v0.11.5 and then trimmed with fastx_trimmer -Q33 -l 75 (FASTX Toolkit 0.0.14). Moirai removeN script was applied to remove reads with “N” nucleotides. CAGE reads matching to adapters or rRNA (Moirai defined rRNA for galGal3) were removed with Trimmomatic-0.38 and RNAdust 1.06, respectively.
Trimmed CAGE reads were aligned with BWA 0.7.10-r789 and unmapped reads realigned with Hisat2 v2.1.0
Alignments were processed into CTSS (CAGE transcription start sites) and CAGE peaks with PromoterPipeline (https://github.com/Population-Transcriptomics/C1-CAGE-preview) with default threshold of at least 10 TPM (tags per million) in one of the samples.
CAGE peaks were associated with nearby transcripts located on the same strand by using ChIPseeker v1.32.0 package for R.
Quality of sequenced RNAseq reads was checked by using FastQC v0.11.5 and then trimmed with Trimmomatic-0.38
Trimmed RNAseq reads were aligned to reference genome assemblies by using Hisat2 v2.1.0, counted with HTSeq v2.0.1, and normalized by library size and exon length in edgeR v3.42.2.
Assembly: galGal6 (GCF_000002315.6)
Assembly: Coturnix_japonica_2.1 (GCF_001577835.2)
Assembly: MGAL_WU_HG_1.0 (GCA_905368555.1)
Assembly: GT_SO_6221 (http://gigadb.org/dataset/100559)
Assembly: ZJU1.0 (GCF_015476345.1)
Assembly: bTaeGut2.pat.W.v2 (GCF_008822105.2)
Assembly: ZJU1.0 (GCA_016128335.1)
Supplementary files format and content: xlsx files with CAGE peaks coordinates, TSS position, associated genes, tag per million normalized counts
Supplementary files format and content: xlsx files with RNAseq raw and FPKM counts

organism: Gallus gallus

source_name: embryonic fibroblasts P5

growth_protocol: Embryonic fibroblast cells were isolated from eggs incubated for ~10 days at 38.5 °C to reach stage HH36. Embryos were then treated by resection of head and neck, limb, skin and fat deposit, and internal developing organs. The remained trunk portion was trypsinized at 37°C, followed by neutralization and centrifugation to obtain digested cell pellet. Cell pellet was resuspended with DMEM/10%FBS and seeded in DMEM/10%FBS or DMEM/F12/10%FBS for expansion.

extract_protocol:
Total RNA was prepared using commercial reagents (TRIzol, Invitrogen) from each sample of avian embryonic fibroblast cells at the fifth passage (P5).
5ug of RNA from each fibroblast sample was used for nAnTi-CAGE and polyA RNAseq libraries preparation and subsequent sequencing using the Illumina HiSeq2500 platform (K. K. DNAForm, Yokohama, Japan)

value: embryonic fibroblasts P5

value: female

tag: medium

value: DMEM/10percent FBS


title: HZ_5


title: CEF 2020-07 F12 P5 [C11]

description:
C11
Chicken_CAGE.xlsx

value: male

value: DMEM/F12/10percent FBS


title: HZ_3


title: C12.C.M

description:
R12
Chicken_RNAseq.xlsx


title: HZ_8


title: CEF 2020-06 High P5 [C10]

description:
C10
Chicken_CAGE.xlsx


title: HZ_2


title: CEF 2020-05 High P5 [C08]

description:
C08
Chicken_CAGE.xlsx


title: CEF 2020-05 F12 P5 [C07]

description:
C07
Chicken_CAGE.xlsx


city: London

first: Gabriella

last: Ficz

state: Rest of the World

address: Centre for Haemato-Oncology

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary University of London

description:
dCas9 3A3L+p15 gRNA_CD34+_cells_19_weeks_engraftment_5
Targeted_sequencing_data.txt

library_source: genomic

data_processing:
library strategy: Targeted bisulfite sequencing
The different genomic regions were pooled per sample and the mix was sequenced using MiSeq v2 Nano 300 (Illumina). Indexed samples were deconvoluted after sequencing and integrity of sequencing data was checked using FastQC (v 0.11.8). Bisulfite sequencing data was aligned and analysed using Bismark (v 0.22.1) to the human genome (hg38).
Assembly: hg38
Supplementary files format and content:
Targeted_sequencing_data.txt file contains methylation data from the p15 and p14 promoters as analysed using Bismark tool
Please note that all 113 samples were sequenced at the p15 gene promoter, but only 70 samples were sequenced at the p14 gene promoter because of the biological context. Therefore, in the file Targeted_sequencing_data.txt, the first 3 columns (A-C) show the chromosomal coordinates at the p15 promoter. Then columns D - DL show the data for all 113 samples at this region. Columns DM, DN and DO show the chromosomal coordinates at the p14 promoter, and the following 70 columns (DP - GG) show the samples where data for p14 was collected.

source_name: haematopoetic stem and progenitor cells

extract_protocol:
DNA was extracted using a PureLink Genomic DNA Mini Kit (ThermoFisher Scientific) and 250ng was used for bisulfite conversion (Zymo) and eluted in 10 ul. For single colony analysis, DNA was extracted by digesting cells using proteinase K (ThermoFisher Scientific) at 55°C for 30 min and RNAse A for 5 min at RT before purification using AmpureXP beads (Beckman Coulter) and eluting DNA in 15ul of PCR grade water. Half this volume was used for bisulfite conversion.
Regions to be sequenced in the p14, p15 and p16 promoters were amplified for 38 cycles using HotStarTaq (Qiagen) with bisulfite converted DNA added to a mastermix (1x reaction buffer, 2 mM MgCl2, 0.025 units/µl HotStarTaq, 200 µM of each deoxynucleoside tripho- sphate (dNTP), 0.20 μM forward and reverse primers).After the first PCR amplification PCR products were purified using AMPureXP beads before 1 µl was taken for a second round of amplification for 10 cycles to index the samples for pooling before sequencing

value: haematopoetic stem and progenitor cells

tag: genotype

value: p15 methylated

value: 19 weeks in vivo engraftment in mouse bone marrow

tag: molecule subtype

value: Bisulfite converted and PCR amplified genomic DNA


description:
dCas9 3A3L+p15 gRNA_CD34+_cells_19_weeks_engraftment_6
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_CD34+_cells_19_weeks_engraftment_4
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_CD34+_cells_19_weeks_engraftment_1
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_CD34+_cells_19_weeks_engraftment_2
Targeted_sequencing_data.txt


title: CEF 2020-07 High P5 [C12]

description:
C12
Chicken_CAGE.xlsx


description:
dCas9 3A3L+p15 gRNA_CD34+_cells_19_weeks_engraftment_3
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_G_cells_19_weeks_engraftment_2
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_G_cells_19_weeks_engraftment_5
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_G_cells_19_weeks_engraftment_6
Targeted_sequencing_data.txt


description:
dCas9 3A3L+non-targeting gRNA_G_cells_19_weeks_engraftment_3
Targeted_sequencing_data.txt

value: Control


title: CEF 2020-06 F12 P5 [C09]

description:
C09
Chicken_CAGE.xlsx


description:
dCas9 3A3L+p15 gRNA_G_cells_19_weeks_engraftment_4
Targeted_sequencing_data.txt


description:
dCas9 3A3L+non-targeting gRNA_G_cells_19_weeks_engraftment_1
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_G_cells_19_weeks_engraftment_1
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_M_cells_19_weeks_engraftment_3
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_M_cells_19_weeks_engraftment_4
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_M_cells_19_weeks_engraftment_5
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_M_cells_19_weeks_engraftment_2
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_B_cells_19_weeks_engraftment_6
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_B_cells_19_weeks_engraftment_5
Targeted_sequencing_data.txt


description:
dCas9 3A3L+non-targeting gRNA_M_cells_19_weeks_engraftment_3
Targeted_sequencing_data.txt


description:
dCas9 3A3L+non-targeting gRNA_M_cells_19_weeks_engraftment_2
Targeted_sequencing_data.txt


description:
dCas9 3A3L+non-targeting gRNA_M_cells_19_weeks_engraftment_1
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_M_cells_19_weeks_engraftment_6
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_B_cells_19_weeks_engraftment_4
Targeted_sequencing_data.txt


description:
dCas9 3A3L+non-targeting gRNA_B_cells_19_weeks_engraftment_5
Targeted_sequencing_data.txt


description:
dCas9 3A3L+non-targeting gRNA_B_cells_19_weeks_engraftment_6
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_B_cells_19_weeks_engraftment_1
Targeted_sequencing_data.txt


description:
dCas9 3A3L+non-targeting gRNA_B_cells_19_weeks_engraftment_3
Targeted_sequencing_data.txt


description:
dCas9 3A3L+non-targeting gRNA_B_cells_19_weeks_engraftment_2
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA and Cas9+TET2 gRNA Colony_10
Targeted_sequencing_data.txt

value: p14 and p15 methylation targeted, TET2 edited

value: CFU assay - individual colony picked


description:
dCas9 3A3L+p15 gRNA and Cas9+TET2 gRNA Colony_9
Targeted_sequencing_data.txt


description:
dCas9 3A3L+non-targeting gRNA_B_cells_19_weeks_engraftment_4
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA and Cas9+TET2 gRNA Colony_6
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA and Cas9+TET2 gRNA Colony_5
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA and Cas9+TET2 gRNA Colony_7
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA and Cas9+TET2 gRNA Colony_4
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA and Cas9+TET2 gRNA Colony_3
Targeted_sequencing_data.txt


title: dCas9 3A3L+p15+p14 gRNA CFU assay_1 [205800600189_R04C01]

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
Raw IDAT files were processed using the ChAMP package (v. 2.20.1) in R using BMIQ normalisation to generate methylation β-values and calculate significant DMRs. All downstream analysis was conducted using the hg38/GRCh38 human genome assembly.
betvalues_CFU_data.txt and detectionp_CFU_data.txt files contain data. Raw IDAT files were processed using the ChAMP package (v. 2.20.1) in R using BMIQ normalisation to generate average methylation β-values
Meth_intensity_CFU_data.txt and Unmeth_intensity_CFU_data.txt files contain unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: Haematopoetic stem and progenitor cells two weeks in the CFU assay

label_protocol: The Illumina Infinium HumanMethylationEPIC (EPIC) array was used to analyse global DNA methylation differences. DNA (400–500 ng) was bisulfite converted and DNA methylation was quantified using the EPIC BeadChIP (Illumina) run on an Illumina iScan System using the manufacturer’s standard protocol.

growth_protocol: HSPCs were nucleofected with dCas9 3A3L or 3A3L-mutant and gRNAs to p14 and p15 or non-targeting control. Cells were plated in a CFU assay and harvested after 14 days

extract_protocol: DNA was extracted from bulk colonies using a PureLink Genomic DNA Mini Kit (ThermoFisher Scientific)

value: Haematopoetic stem and progenitor cell


description:
dCas9 3A3L+p15 gRNA_G_cells_19_weeks_engraftment_3
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA and Cas9+TET2 gRNA Colony_2
Targeted_sequencing_data.txt


title: dCas9 3A3L+non-targeting gRNA CFU assay_2 [205800600189_R02C01]

description: Non


title: EPIC_patient_sample_G2_pre-AML8

description:
EPIC_patient_sample_G2_pre-AML8
Targeted_sequencing_data.txt

source_name: Peripheral blood

value: Peripheral blood


title: EPIC_patient_sample_G1_pre-AML7

description:
EPIC_patient_sample_G1_pre-AML7
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_A4_pre-AML6_2nd_timepoint
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_F1_pre-AML6_1st_timepoint
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA and Cas9+TET2 gRNA Colony_1
Targeted_sequencing_data.txt


description:
dCas9 3A3L+non-targeting gRNA_B_cells_19_weeks_engraftment_1
Targeted_sequencing_data.txt


title: dCas9 3A3L+p15+p14 gRNA CFU assay_3 [205800600189_R06C01]


title: EPIC_patient_sample_D1_pre-AML4

description:
EPIC_patient_sample_D1_pre-AML4
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_E1_pre-AML5_1st_timepoint
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_C1_pre-AML3_1st_timepoint
Targeted_sequencing_data.txt


title: dCas9 3A3L-mutant+p15+p14 gRNA CFU assay_3 [205800600177_R01C01]

description: mut


title: EPIC_patient_sample_B1_pre-AML2

description:
EPIC_patient_sample_B1_pre-AML2
Targeted_sequencing_data.txt


title: EPIC_patient_sample_A1_pre-AML1

description:
EPIC_patient_sample_A1_pre-AML1
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_C4_pre-AML5_2nd_timepoint
Targeted_sequencing_data.txt


title: EPIC_patient_sample_H3_Control16

description:
EPIC_patient_sample_H3_Control16
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_D3_pre-AML3_2nd_timepoint
Targeted_sequencing_data.txt


title: EPIC_patient_sample_H1_Control15

description:
EPIC_patient_sample_H1_Control15
Targeted_sequencing_data.txt


title: EPIC_patient_sample_F4_Control14

description:
EPIC_patient_sample_F4_Control14
Targeted_sequencing_data.txt


title: EPIC_patient_sample_F2_Control13

description:
EPIC_patient_sample_F2_Control13
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_D2_Control12_1st_timepoint
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_E4_Control12_2nd_timepoint
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_E3_Control11_2nd_timepoint
Targeted_sequencing_data.txt


title: dCas9 3A3L+non-targeting gRNA CFU assay_3 [205800600189_R03C01]

description: Non


description:
EPIC_patient_sample_C2_Control11_1st_timepoint
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_D4_Control10_2nd_timepoint
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_B_cells_19_weeks_engraftment_3
Targeted_sequencing_data.txt


title: dCas9 3A3L-mutant+p15+p14 gRNA CFU assay_1 [205800600189_R07C01]

description: mut


title: dCas9 3A3L+non-targeting gRNA CFU assay_1 [205800600189_R01C01]

description: Non


description:
dCas9 3A3L+non-targeting gRNA_G_cells_19_weeks_engraftment_2
Targeted_sequencing_data.txt


title: EPIC_patient_sample_B2_Control9

description:
EPIC_patient_sample_B2_Control9
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_G4_Control7_2nd_timepoint
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_A3_Control7_1st_timepoint
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_H4_Control6_1st_timepoint
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_A2_Control6_1st_timepoint
Targeted_sequencing_data.txt


title: EPIC_patient_sample_A5_Control8

description:
EPIC_patient_sample_A5_Control8
Targeted_sequencing_data.txt


title: dCas9 3A3L+p15+p14 gRNA CFU assay_2 [205800600189_R05C01]


title: EPIC_patient_sample_F3_Control4

description:
EPIC_patient_sample_F3_Control4
Targeted_sequencing_data.txt


title: EPIC_patient_sample_G3_Control5

description:
EPIC_patient_sample_G3_Control5
Targeted_sequencing_data.txt


title: dCas9 3A3L-mutant+p15+p14 gRNA CFU assay_2 [205800600189_R08C01]

description: mut


title: EPIC_patient_sample_C3_Control2

description:
EPIC_patient_sample_C3_Control2
Targeted_sequencing_data.txt


title: EPIC_patient_sample_B4_Control1

description:
EPIC_patient_sample_B4_Control1
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_M_cells_19_weeks_engraftment_1
Targeted_sequencing_data.txt


title: EPIC_patient_sample_E2_Control3

description:
EPIC_patient_sample_E2_Control3
Targeted_sequencing_data.txt


description:
dCas9-3A3L-mutant+p15+p16+p14 gRNA_single_colony_5
Targeted_sequencing_data.txt


description:
dCas9-3A3L-mutant+p15+p16+p14 gRNA_single_colony_6
Targeted_sequencing_data.txt


description:
EPIC_patient_sample_B3_Control10_1st_timepoint
Targeted_sequencing_data.txt


title: dCas9-3A3L+p15 gRNA_single_colony_6

description:
dCas9-3A3L+p15 gRNA_single_colony_6
Targeted_sequencing_data.txt

value: p15 hypermethylated


title: dCas9-3A3L+p15 gRNA_single_colony_5

description:
dCas9-3A3L+p15 gRNA_single_colony_5
Targeted_sequencing_data.txt


title: dCas9-3A3L+p16 gRNA_single_colony_4

description:
dCas9-3A3L+p16 gRNA_single_colony_4
Targeted_sequencing_data.txt

value: p16 targeted (unmethylated)


description:
dCas9-3A3L+p15+p16+p14 gRNA_single_colony_7
Targeted_sequencing_data.txt

value: p15 and p14 hypermethylated


description:
dCas9-3A3L+p15+p16+p14 gRNA_single_colony_6
Targeted_sequencing_data.txt


title: dCas9-3A3L+p16 gRNA_single_colony_2

description:
dCas9-3A3L+p16 gRNA_single_colony_2
Targeted_sequencing_data.txt


title: dCas9-3A3L+p16 gRNA_single_colony_3

description:
dCas9-3A3L+p16 gRNA_single_colony_3
Targeted_sequencing_data.txt


description:
dCas9-3A3L+p15+p16+p14 gRNA_single_colony_1
Targeted_sequencing_data.txt


description:
dCas9-3A3L+p15+p16+p14 gRNA_single_colony_5
Targeted_sequencing_data.txt


description:
dCas9-3A3L+p15+p16+p14 gRNA_single_colony_4
Targeted_sequencing_data.txt


description:
dCas9-3A3L+p15+p16+p14 gRNA_single_colony_2
Targeted_sequencing_data.txt


title: dCas9-3A3L+p15 gRNA_single_colony_4

description:
dCas9-3A3L+p15 gRNA_single_colony_4
Targeted_sequencing_data.txt


title: dCas9-3A3L+p15 gRNA_single_colony_2

description:
dCas9-3A3L+p15 gRNA_single_colony_2
Targeted_sequencing_data.txt


description:
dCas9-3A3L+p15+p16+p14 gRNA_single_colony_3
Targeted_sequencing_data.txt


description:
dCas9-3A3L-mutant+p15+p16+p14 gRNA_single_colony_3
Targeted_sequencing_data.txt


description:
dCas9-3A3L-mutant+p15+p16+p14 gRNA_single_colony_2
Targeted_sequencing_data.txt


title: dCas9-3A3L+p16 gRNA_single_colony_1

description:
dCas9-3A3L+p16 gRNA_single_colony_1
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA and Cas9+TET2 gRNA Colony_8
Targeted_sequencing_data.txt


description:
dCas9-3A3L-mutant+p15+p16+p14 gRNA_single_colony_4
Targeted_sequencing_data.txt


description:
dCas9 3A3L+p15 gRNA_B_cells_19_weeks_engraftment_2
Targeted_sequencing_data.txt


description:
dCas9-3A3L-mutant+p15+p16+p14 gRNA_single_colony_1
Targeted_sequencing_data.txt


title: dCas9-3A3L+p15 gRNA_single_colony_1

description:
dCas9-3A3L+p15 gRNA_single_colony_1
Targeted_sequencing_data.txt


description:
dCas9-3A3L+p15 gRNA1 and 2_bulk CFU_rep1
Targeted_sequencing_data.txt

value: CFU assay


title: EPIC_patient_sample_H2_pre-AML9

description:
EPIC_patient_sample_H2_pre-AML9
Targeted_sequencing_data.txt


title: dCas9-3A3L+p15 gRNA1_bulk CFU_rep2

description:
dCas9-3A3L+p15 gRNA1_bulk CFU_rep2
Targeted_sequencing_data.txt


title: dCas9-3A3L+p15 gRNA2_bulk CFU_rep2

description:
dCas9-3A3L+p15 gRNA2_bulk CFU_rep2
Targeted_sequencing_data.txt


title: dCas9-3A3L+p15 gRNA2_bulk CFU_rep1

description:
dCas9-3A3L+p15 gRNA2_bulk CFU_rep1
Targeted_sequencing_data.txt


description:
dCas9-3A3L+non-targeting gRNA_bulk CFU_rep2
Targeted_sequencing_data.txt


description:
dCas9-3A3L+non-targeting gRNA_bulk CFU_rep1
Targeted_sequencing_data.txt


title: dCas9-3A3L+p16 gRNA_bulk CFU

description:
dCas9-3A3L+p16 gRNA_bulk CFU
Targeted_sequencing_data.txt


title: dCas9-3A3L+p15 gRNA_bulk CFU

description:
dCas9-3A3L+p15 gRNA1_bulk CFU
Targeted_sequencing_data.txt


title: dCas9-3A3L+p15 gRNA_single_colony_3

description:
dCas9-3A3L+p15 gRNA_single_colony_3
Targeted_sequencing_data.txt


title: dCas9-3A3L-mutant+p15 gRNA_bulk CFU

description:
dCas9-3A3L-mutant+p15 gRNA1_bulk CFU
Targeted_sequencing_data.txt


title: Bald scalp, rep1

city: Tainan

first: Criselda Jean

last: Cruz

address: No. 1 University Rd.

department: Dermatology

country: Taiwan

institute: National Cheng Kung University

data_processing:
Mapping and whole transcriptome analysis were performed by LifeScope software package.
Gene expression analysis was performed using Partek software package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include reads, RPKM and normalized values for each Sample

source_name: scalp adipose

extract_protocol:
RNA was extracted using the Trizol RNA isolation protocol. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer Universal Low input RNA Kit (Clontech) following manufacturer's protocols.

value: scalp adipose

tag: disease

value: Androgenetic alopecia


title: Normal scalp, rep 1

value: male


title: C02.P.M

description:
R02
Peacock_RNAseq.xlsx

organism: Pavo cristatus

value: embryonic fibroblasts P5

value: DMEM/10percent FBS


title: Homo sapiens MNase digestion products

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

data_processing:
Adapter trimming with Cutadapt
Alignment to the reference Widom 601 145 bp DNA sequence using the Burrows-Wheeler Aligner
Filtering reads for length <= 145 bp
Assembly: reference sequence: ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACgTGTCAGATATATACATCGAT
Supplementary files format and content: "MNase_Sequencing_Processed.xlsx" - excel format; contains sequencing details and unfiltered/filtered read start and end positions

organism: synthetic construct

source_name: synthetic construct (Widom 601 145 bp DNA) amplified in Escherichia coli cells

growth_protocol: not applicable

extract_protocol:
Around 1μg of DNA was isolated from each MNase reaction using a Monarch PCR & DNA Cleanup Kit (elution volume of 15 μl, NEB). The DNA was treated with 5 U of Antarctic Phosphatase (NEB #M0289S) for 1h at 37°C in 20 μl reactions. The phosphatase was heat-inactivated for 2 min at 37°C.
Libraries were constructred using the Azenta Amplicon-EZ service

treatment_protocol: 3 μg of NCPs (A260 DNA-based quantification) and 18 U of MNase were incubated in 150 μl reactions for 30 min at 37°C (50 mM Tris pH 8.0, 2.5% glycerol, 25 mM NaCl, 5 mM CaCl2, 1.5 mM DTT). Reactions were quenched with 75 μl of stop solution (20 mM Tris pH 8.0, 80 mM EDTA, 80 mM EGTA, 0.25% SDS, 0.5 mg/ml Proteinase K).

value: not applicable


title: dCas9-3A3L+p15 gRNA1_bulk CFU_rep1

description:
dCas9-3A3L+p15 gRNA1_bulk CFU_rep1
Targeted_sequencing_data.txt

value: haematopoetic stem and progenitor cells


title: PEF 2020-01 F12 P5 [C01]

description:
C01
Peacock_CAGE.xlsx

value: DMEM/F12/10percent FBS


title: Proband99_VitD_deficient

type: RNA

city: Homburg/Saar

first: Konstantinos

last: Christofyllakis

state: Saarland

address: Kirrbergerstrasse 100

department: Hematology Oncology Rheumatology and clinical Immunology

institute: Department of Oncology, Hematology, Rheumatology and Clinical Immunology, Saarland University Hospital

description: total RNA isolated from NK cells isolated from peripheral blood before vitamin D supplementation

hyb_protocol: 3,8 µg of fragmented and labeled ss cDNA were hybridized to Affymetrix Human Gene 2.1 ST Array Plates.

scan_protocol: For hybridization, washing, staining and scanning an Affymetrix GeneTitan system, controlled by the Affymetrix GeneChip Command Console software v4.2, was used.

data_processing: Data processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de). Summarized probe set signals in log2 scale were calculated by using the RMA (1) algorithm with the Affymetrix GeneChip Expression Console v1.4 Software. [(1) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data, Biostatistics, April 2003; Vol. 4; Number 2: 249–264.]

label: biotin

label_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA).  In brief, 200 ng of total RNA were used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: none, the interventention occured in vivo.

extract_protocol: Peripheral blood mononuclear cells (PBMC) were first separated by density gradient centrifugation followed by NK cell enrichment by means of magnetically activated cell sorting (NK Cell Isolation Kit, human from Miltenyi Biotec GmbH). For RNA isolation, the miRNeasy Mini KitTM (Qiagen, Velno, Holland) was used, according to the included protocol.

treatment_protocol: Each individual received vitamin D supplementation a target 25(OH)D serum level of 65 ng/ml. For this a modified formula according the one proposed by van Groningen et al. was used. Cholecalciferol (I.U.) =Δ 25-OH-D3 (ng/ml) × body weight (kg) × 200 (with “Δ 25-OH-D3” meaning the difference between the current and the target 25-OH-D3 serum level). Applying this formula, the pre-defined serum level was achieved within a narrow margin in nearly all individuals. The cholecalciferol product Dekristol® 20.000 I. U. (mibe GmbH Arzneimittel, Brehna, Germany) was used.

tag: gender

value: female

tag: vitamin d status

value: deficient


title: Proband74_VitD_supplemented

description: total RNA isolated from NK cells isolated from peripheral blood after vitamin D supplementation

value: supplemented


title: Proband92_VitD_deficient


title: Proband74_VitD_deficient


title: Proband92_VitD_supplemented


title: Proband71_VitD_deficient


title: Proband73_VitD_deficient


title: Proband70_VitD_deficient


title: Trypanosoma brucei MNase digestion products

value: synthetic construct (Widom 601 145 bp DNA) amplified in Escherichia coli cells


title: Proband72_VitD_supplemented


title: Proband75_VitD_deficient


title: Proband99_VitD_supplemented


title: Proband75_VitD_supplemented


title: Proband72_VitD_deficient


title: Proband73_VitD_supplemented


title: PEF 2020-01 F12 P5 [C05]

description:
C05
Peacock_CAGE.xlsx

tag: Sex


title: E.coli K-12, intracellular RNAs, Dps, M9 medium

city: Pushchino

first: Konstantin

middle: S.

last: Shavkunov

address: Institutskaya street, 3

country: Russia

institute: Institute of Cell Biophysics RAS

data_processing:
Sequencing data sets were processed as follows. Poor-quality reads were discarded using the Filter by Quality tool on the usegalaxy.org server, requiring at least 90% presence of nucleotides with a quality threshold of Q20 in the reads. Reads were sorted by size (12–50 nt) and fragments of each size were separately mapped to the genome of E. coli K-12 MG1655 downloaded from the NCBI RefSeq database (accession number NC_000913.3). Matcher software (http://www.mathcell.ru/DnaRnaTools/Matcher.zip) was used for 5’-end mapping, and only precise coincidence with the genome was required. Reads with sequences matching several loci in the genome were assigned to all of them in equal proportion. Reads with different lengths in each position were summarized, providing the profile of their distribution over the entire genome. For correlation analysis, the genome was dissected into non-overlapping 10 bp bins, starting from the first position, and the total number of 5’-ends in each bin was calculated. The resulting whole-genome profiles were used for further analysis.
NCBI RefSeq NC_000913.3
Processed data are presented as Excel tables containing the per strand mapping of 5’-ends of sequence reads over the entire E. coli K-12 MG1655 genome (RefSeq accession number NC_000913.3) and the sums of these reads per nucleotide. Some reads falling into genes present in the genome in ≥2 copies were divided be the number of identical sequences and ascribed to each of them. As a result the distribution profile contains nonintegral values.

organism: Escherichia coli str. K-12 substr. MG1655

extract_protocol:
Total intracellular RNAs were isolated from E. coli K-12 MG1655 cells grown in M9 medium. They were applied to Dps immobilized on PierceTM Protein A/G UltraLinkTM Resin (Thermo Fisher Scientific) beads. For immobilization, antibodies were precipitated with 60% (NH4)2SO4, collected by centrifugation for 10 minutes at 12,000 rpm and dissolved on ice in IP buffer (50 mM Tris-HCl pH 8.1, 100 mM NaCl, 5 mM EDTA, 0.2% NaN3, 0.4% SDS, 1.2% Triton X100). Dps protein solution was mixed with IP buffer, and anti-Dps antibodies were added to the sample. Both samples were incubated at 4 ○C for 14 hours with rotation. To immobilize Dps-antibody complexes, beads were added to each sample, followed by 2-hour rotation at 4 ○C. After incubation, the beads were washed twice with TB buffer (50 mM Tris-HCl pH 8.0, 100 mM EDTA, 50 mM NaCl, 10 mM MgCl2) and collected by centrifugation (2.5 min at 2,500 rpm). Beads in TB buffer were mixed with RNA sample, and RNA-Dps complexes were formed at 37 ○C for 2 hours. Before eluting the Dps-bound RNAs with 200 mM NaCl, the beads were washed twice with 50 mM NaCl. RNA fractions were purified using a PCR Purification Kit (Evrogen, Russia) and precipitated with isopropanol overnight at -20 ○C. Then RNA samples were washed twice with 70% ethanol and resuspended in nuclease free water.
Libraries for sequencing were prepared using the obtained RNA samples according to the standard protocol of Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, USA) with minor modifications. Samples were reverse transcribed and purified using Nucleic Acid Binding Beads (Thermo Fisher Scientific, USA) according to the protocol of the manufacturer. After amplification with 0.7 μl of each v2 primers, the samples were again purified using Monarch PCR & DNA Cleanup Kit (New England Biolabs, USA) and fractionated on a 6% polyacrylamide gel, using Quick-Load pBR322 DNA-MspI Digest DNA ladder (New England Biolabs, USA). Gel pieces with cDNA amplicons in the range of 90-123 bp in length were excised and minced. Target products were eluted overnight with subsequent ethanol sedimentation. After dilution to 100 pM, the samples were used for emulsion PCR on Ion OneTouchTM 2 System with Ion PGM Hi-Q View OT2 Kit (Thermo Fisher Scientific, USA). Sequence libraries were obtained using an Ion Torrent PGM analyzer (Thermo Fisher Scientific).

value: bacterial cells

value: WT

value: Dps immobilization


title: C06.P.F

description:
R06
Peacock_RNAseq.xlsx


title: E.coli K-12 delta-dps, extracellular RNAs, rep. 2

extract_protocol:
Bacteria were grown aerobically in M9 medium and harvested at OD600 0.4-0.6. Extracellular RNAs were obtained from culture medium after bacteria removal (20 min centrifugation at 2,000 rpm, followed by double supernatant filtration through 0.22 μm sterile syringe filters). exoRNAs were purified using miRNeasy Serum/Plasma Kit (Qiagen, Germany)
Libraries for sequencing were prepared using the obtained RNA samples according to the standard protocol of Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, USA) with minor modifications. Samples were reverse transcribed and purified using Nucleic Acid Binding Beads (Thermo Fisher Scientific, USA) according to the protocol of the manufacturer. After amplification with 0.7 μl of each v2 primers, the samples were again purified using Monarch PCR & DNA Cleanup Kit (New England Biolabs, USA) and fractionated on a 6% polyacrylamide gel, using Quick-Load pBR322 DNA-MspI Digest DNA ladder (New England Biolabs, USA). Gel pieces with cDNA amplicons in the range of 90-123 bp in length were excised and minced. Target products were eluted overnight with subsequent ethanol sedimentation. After dilution to 100 pM, the samples were used for emulsion PCR on Ion OneTouchTM 2 System with Ion PGM Hi-Q View OT2 Kit (Thermo Fisher Scientific, USA). Sequence libraries were obtained using an Ion Torrent PGM analyzer (Thermo Fisher Scientific).

value: Dps-knockout


title: PEF 2020-01 High P5 [C06]

description:
C06
Peacock_CAGE.xlsx


title: dCas9-3A3L+p15+p16+p14 gRNA_bulk CFU

description:
dCas9-3A3L+p15+p16+p14 gRNA_bulk CFU
Targeted_sequencing_data.txt

value: p15 and p14 hypermethylated

value: CFU assay

value: Bisulfite converted and PCR amplified genomic DNA


title: E.coli K-12 delta-dps, extracellular RNAs, rep. 1


title: PEF 2020-01 High P5 [C02]

description:
C02
Peacock_CAGE.xlsx

value: male


title: E.coli K-12, intracellular RNAs, Dps, LB medium


title: PEF 2020-02 F12 P5 [C03]

description:
C03
Peacock_CAGE.xlsx

value: embryonic fibroblasts P5


title: E.coli K-12 delta-dps, intracellular RNAs, rep. 1

extract_protocol:
Bacteria were grown aerobically in M9 medium and harvested at OD600 0.4-0.6. Intracellular RNAs were isolated from pelleted cells using TRIzol (Invitrogen, USA). The sample was then enriched with short RNAs using mirVana miRNA Isolation Kit (Ambion, USA).
Libraries for sequencing were prepared using the obtained RNA samples according to the standard protocol of Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, USA) with minor modifications. Samples were reverse transcribed and purified using Nucleic Acid Binding Beads (Thermo Fisher Scientific, USA) according to the protocol of the manufacturer. After amplification with 0.7 μl of each v2 primers, the samples were again purified using Monarch PCR & DNA Cleanup Kit (New England Biolabs, USA) and fractionated on a 6% polyacrylamide gel, using Quick-Load pBR322 DNA-MspI Digest DNA ladder (New England Biolabs, USA). Gel pieces with cDNA amplicons in the range of 90-123 bp in length were excised and minced. Target products were eluted overnight with subsequent ethanol sedimentation. After dilution to 100 pM, the samples were used for emulsion PCR on Ion OneTouchTM 2 System with Ion PGM Hi-Q View OT2 Kit (Thermo Fisher Scientific, USA). Sequence libraries were obtained using an Ion Torrent PGM analyzer (Thermo Fisher Scientific).


title: Proband71_VitD_supplemented


title: E.coli K-12, intracellular RNAs, rep. 2


title: PEF 2020-02 High P5 [C04]

description:
C04
Peacock_CAGE.xlsx

value: DMEM/10percent FBS


title: H24, sRNA, replicate 1

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
Sequenced reads were aligned to M. smegmatis genome using bowtie2 v2.3.4.3 with parameters --local --dovetail
For full-transcriptome samples, counts were calculated. Fragments counting was performed using FeatureCounts software (Annotation of the genome was retrieved from Mycobrowser). For every annotated gene, the number of fragments overlapping the gene at least by one nucleotide was calculated. Only unambiguously mapped, non-chimeric fragments were used. The processed data files represent these raw counts for each sample. File "counts_ALL.csv" contains values for all full-transcriptome samples.
Sequenced samples of the short RNA fraction were used to annotate new transcripts. Processed files represent sequencing coverage tracks in bigWig format.
Assembly: NC_008596.1
Supplementary files format and content: csv table, raw counts - the numbers of overlapping reads for every annotated gene
Supplementary files format and content: bigWig, sequencing coverage tracks

organism: Mycolicibacterium smegmatis

source_name: bacterial culture

growth_protocol: M. smegmatis mc2 155 cells from the bacterial collection of the Bach Institute of Biochemistry (Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia) were pre-cultured from frozen stock in Nutrient Broth rich medium (Himedia, India) supplemented with 0.05% (v/v) Tween 80 for 30 h at 37 °C on an orbital shaker (200 rpm). For cold stress experiments cells were regrown using the growth same medium up to the mid-logarithmic phase (OD600 = 0.7) in Nutrient Broth rich medium supplemented with 0.05% Tween 80.

extract_protocol:
Total RNA was isolated by phenol-chloroform extraction and cell disruption using Bead Beater (BioSpec Products, Bartlesville, OK, USA) as described previously (Rustad et al., 2009) and treated with Turbo DNase (Life Technologies, Carlsbad, CA, USA) to remove traces of genomic DNA.
To isolate the short RNA fraction the extracted total RNA was subjected to denaturing electrophoresis to separate the size-specific RNA fraction (~ 50-500 nucleotides).The eluted RNA was purified using phenol-chloroform extraction.
Total RNA samples were depleted of rRNA using The NEBNext® rRNA Depletion Kit (Bacteria) (NEB, USA) and used to generate sequencing libraries with the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, USA) according to the manufacturers’ protocol.
The short RNA fraction was sequenced as one replicate per each time point, with no RNA depletion step performed, and the fragmentation step was skipped in order to preserve the integrity of the transcripts.

treatment_protocol: To simulate cold stress, the flasks were moved into orbital shaking water bath with a temperature 15 °C (200 rpm). At time points 0 (before stress), 2, 5 and 24 hours, 10 ml of culture were taken and centrifuged (4 °C, 4000 rpm, 15 min). The pellets were washed twice with fresh medium, rapidly cooled on ice, and centrifuged again.

value: bacterial culture

tag: strain

tag: stress

value: cold stress

tag: time point

value: 24 hours

tag: fraction

value: size-selected RNA fraction


title: E.coli K-12 delta-dps, intracellular RNAs, rep. 2

tag: tissue

tag: cell type


title: H2, sRNA, replicate 1

value: 2 hours


title: E.coli K-12, intracellular RNAs, rep. 1


title: E.coli K-12, extracellular RNAs, rep. 2


title: H5, sRNA, replicate 1

value: 5 hours


title: H24, replicate 3

value: total RNA


title: H0, sRNA, replicate 1

value: control

value: 0 hours


title: H5, replicate 3


title: H5, replicate 2


title: H24, replicate 1


title: H24, replicate 2


title: H2, replicate 3


title: H5, replicate 1


title: H0, replicate 2


title: E.coli K-12, extracellular RNAs, rep. 1

value: bacterial cells

value: WT


title: H2, replicate 1


title: H2, replicate 2


title: H0, replicate 1


title: CON5 human and mouse

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

description: control PDX

data_processing:
Illumina’s Real Time Analysis software (RTA)
Illumina’s CASAVA 1.8.2 software was used to perform image capture, base calling and demultiplexing.
contaminant scan was done with fastQscreen and sequences were filtered with fastp (default settings)
Samples were deconvoluted to split the human and mouse reads with a pipeline that consists of STAR (v2.6.1a) alignment followed by XenofilteR (v0.99 under R3.5.1) combined with samtools (v1.7)
Transcript level quantification was performed with Salmon (v1.3.0) (parameters= --p4, --numBootstraps 100 --validateMappings --libtype A –gcBias)
Gene-level count matrices were created using tximport
Assembly: hg38, mm10
Supplementary files format and content: Salmon directories include transcript-level quantification files for each sample (quant.sf)

organism:
Homo sapiens
Mus musculus

source_name: DLBCL PDX

extract_protocol:
Tumors were harvested at day 11 and RNA isolated by using RNAeasy Plus micro kit (Qiagen) according to manufacturer' s protocol.
RNA-Seq library preparations were done using established Illumina methods for mRNA-Seq (Part #RS-122-2001)

treatment_protocol: Xenografted mice were randomized to receive  vehicle, CHOP (day1 q7), selinexor (day3,5 q7) or their combination.

value: DLBCL PDX

value: vehicle


title: Proband70_VitD_supplemented

value: supplemented


title: KPT1 human and mouse

description: PDX treated with selinexor

value: selinexor


title: KPT3 human and mouse

description: PDX treated with selinexor


title: KPT5 human and mouse

description: PDX treated with selinexor


title: CON3 human and mouse

description: control PDX


title: CON1 human and mouse

description: control PDX


title: COMBO5 human and mouse

description: PDX treated with CHOP + selinexor

value: CHOP+selinexor


title: COMBO2 human and mouse

description: PDX treated with CHOP + selinexor


title: COMBO8 human and mouse

description: PDX treated with CHOP + selinexor


title: CHOP5 human and mouse

description: PDX treated with CHOP

value: CHOP


title: CHOP3 human and mouse

description: PDX treated with CHOP


title: H0, replicate 3

value: bacterial culture


title: CHOP1 human and mouse

description: PDX treated with CHOP


title: MEF_CTNS-KD-rescue_rep2

city: Ithaca

first: Saori

last: Uematsu

address: 526 Campus Road, Cornell University

institute: Cornell University

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters: -g “^GGG” -a “A{10}” -n 2 -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Read count extraction and normalization were performed using the custom Python script.
Assembly: GRCm39.106
Supplementary files format and content: tab-delimited text files including raw count values for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: MEF cells

extract_protocol:
Total RNA was extracted using TRIzol reagent from cell lysates. Messanger RNA (mRNA) was isolated by oligo (dT) magnetic beads (NEB) and separated on a 15% polyacrylamide TBE-urea gel (Invitrogen). The mRNA at 50-100 nt was excised.
The RNA was dephosphorylated by T4 PNK (NEB) followed by poly(A) tailing by PAP1 (NEB). After adapter ligation by T4 RNA ligase 2 truncated KQ (NEB), cDNA synthesis was performed by m-MLV-mut5. The synthesized cDNA was amplified by PCR using barcoded sequencing primers. The PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). Expected DNA was excised and recovered from DNA gel elution.

value: MEF cells

value: transfected with sh-CTNS and CTNS plasmid


title: MEF_Cysteamine_rep2

value: cysteamina treatment


title: MEF_AA_rep2

value: full amino acid starvation


title: MEF_Cys_rep2

value: cysteine starvation


title: MEF_NT2_rep2

value: no treatment


title: MEF_CTNS-KD_rep2

value: transfected with sh-CTNS


title: MEF_Cysteamine_rep1


title: MEF_NT2_rep1


title: MEF_AA_rep1


title: MEF_NT_rep1


title: MEF_NT_rep2


title: MEF_Cys_rep1


title: AAA patient 3 (techn. Rep. 1)

city: München

first: Francesca

last: Fasolo

address: biedersteinerstr. 29

institute: TUM

library_source: transcriptomic single cell

data_processing:
The demultiplexing, alignment and gene counting were made using the Cell Ranger software v3.1.0 (for sample AAA1), v5.0.0 (for sample AAA2 and AAA3) and  v6.0.1 (for sample AAA4) (10x Genomics), using GRCh 38 and Gencode annotation v33
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Abdominal Aorta

extract_protocol:
After enzymatic digestion, tissue dissociation was performed by using the GentleMACS Dissociator according to the manufacturer's instructions. The cell suspension was strained (70 µm, 40 µm) and Dead Cell Removal (Miltenyi Biotech, 130-090-101) using MS Columns (Miltenyi Biotech, 130-042-201) was performed. Cells were resuspended in PBS + 0,04% BSA.
Cells were loaded into a 10x Genomics microfluidics Chip G and encapsulated with barcoded oligo-dT-containing gel beads by utilizing the 10x Genomics Chromium Controller. Gel Beads-in-emulsion (GEM) clean-up, cDNA Amplification and 3'Gene Expression Dual Index Library Construction was performed according to the manufacturer's instructions (CG000315 Rev C). Sequencing was performed by taking advantage of an Illumina NovaSeq 6000 Sequencing system.

value: Abdominal Aorta

value: primary cells

value: all cells from tissue

tag: subject status/id

value: AAA patient 3


title: AAA patient 3 (techn. Rep. 2)


title: AAA patient 2 (techn. Rep. 2)

value: AAA patient 2


title: AAA patient 2 (techn. Rep. 1)


title: MEF_CTNS-KD_rep1

value: WT


title: MEF_CTNS-KD-rescue_rep1


title: RD cells, shSCR

city: Rome

first: Matteo

last: Cassandri

address: Viale di San Paolo 15

department: Department of Oncohematology

country: Italy

institute: Bambino Gesù Children's Hospital

data_processing:
Sequence reads were aligned to the GRCh38 reference genome usign STAR v2.7.9a.
Gene expression was calculated as Trasnscript Per Million (TPM) reads using RSEM V1.3.2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: RD

growth_protocol: RD, JR1 cells were cultured in DMEM high-glucose (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% penicillin-streptomycin. All the cell lines were cultured at 37°C in a humidified atmosphere of 5% CO2/ 95% air and regularly checked for mycoplasma contamination.

extract_protocol:
RNA was extracted from JR1 and RD FN-RMS cell lines, using the RNeasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit following manifacturer's instruction.

value: RD

value: Fusion-Negative Rhabdomyosarcoma


title: JR1 cells, shSCR


title: JR1 cells, shSKP2

value: SKP2 knockdown


title: RD cells, shSKP2


title: AAA patient 1 (techn. Rep. 1)

value: AAA patient 1


title: AAA patient 4 (techn. Rep. 1)

value: AAA patient 4


title: AAA patient 4 (techn. Rep. 2)


title: RD_shSCR, MYOD, ChIP

data_processing:
ChIP-seq reads were aligned to the GRCh38 reference genome using BWA version 0.7.17.
ChIP-seq reads were normalized to reads per million mapped Drosophila spike-in reads, previously aligned on dm3 reference genome.
Peak calling was performed using MACS3 with the significant cut-off p-value<4. Mapping artifacts were removed by excluding regions listed in ENCODE exclusion list (ENCFF356LFX).
Heatmaps and average density profiles were generated using deepTools by plotting H3K27ac and MYOD ChIP-seq read coverages over MYOD-bound genomic regions.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes (BED files) including coordinates of peaks after the exclusion of regions listed in ENCODE blacklist (ENCFF356LFX)

growth_protocol: RD cells were cultured in DMEM high-glucose (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% penicillin-streptomycin. Cells were cultured at 37°C in a humidified atmosphere of 5% CO2/ 95% air and regularly checked for mycoplasma contamination.

extract_protocol:
Cells were fixes with 1% formaldehyde for 10 min. After quenching, cells were digested to achieve chromatin fragmented to a range of 150–900 bp using Micrococcal Nuclease. Chromatin samples were immunoprecipitated overnight at 4 °C.
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep kit, following manifacturer's instruction.

tag: chip-antibody


title: RD_shSKP2, MYOD, ChIP

tag: cell line


title: RD_shSKP2, H3K27ac, ChIP

value: H3K27ac (Active Motif, #39133)


title: AoSMCs Control 20 (techn rep 2)

description:
AoSMC_C_20_2
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt

data_processing:
Raw FASTQ files were analysed using FastQC to assess sequencing quality, GC content, sequence length distribution and adapter content.
Sequencing reads were aligned to the human genome (GRCh38) using the STAR aligner. Two samples, AAASMC_86_1 and AoSMC_C_20_1 failed two out of four automated outlier detection tests and were subsequently excluded from the data set. After manual evaluation of the remaining sample data, all were considered to be of sufficient quality for further analysis. In detail: for raw data quality check (QC), a total of 42,513 features with low read counts were identified by filterbyExpr from the edgeR package and removed.
A total of 24 samples were assessed for quality by automatically identifying outliers in each of the following statistical summaries:
Sum of Euclidean distance to other samples
Kolmogorov-Smirnov test statistic
Mean Pearson correlation with other samples
Hoeffding’s D statistic
A sample was classified as an outlier if it failed 2 or more of the 4 objective statistical summaries. For normalized data QC, the count data for the samples were normalised using trimmed mean of M-values normalisation and transformed with voom, resulting in log2-counts per million with associated precision weights.
A total of 23 samples were assessed for quality by automatically identifying outliers in each of the following statistical summaries:
Sum of Euclidean distance to other samples
Kolmogorov-Smirnov test statistic
Mean Pearson correlation with other samples
Hoeffding’s D statistic
A sample was classified as an outlier if it failed 2 or more of the 4 objective statistical summaries.
The count data for the samples were normalised using trimmed mean of M-values normalisation and transformed with voom, resulting in log2-counts per million with associated precision weights.
Assembly: GRCh38
Supplementary files format and content: raw counts (tab-delimited text file)
Supplementary files format and content: normalised log-2 counts per million (tab-delimited text file)
Supplementary files format and content: precision weights (tab-delimited text file)
Supplementary files format and content: differentially expressed genes (tab-delimited text file)

growth_protocol: hAoSMCs  were maintained in Smooth Muscle Cell Basal Medium  supplemented with 10% fetal calf serum (FCS), glutamin, EGF, insulin, FGF and gentamici in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq stranded total RNA kit (Illumina), following manufacturer's protocols.

value: Smooth Muscle Cells

tag: subject id

value: Control 20

tag: subject status

value: non-AAA donor


title: AoSMCs Control 18 (techn rep 3)

description:
AoSMC_C_18_3
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt

value: Control 18


title: AoSMCs Control 20 (techn rep 1)

description:
AoSMC_C_20_1
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: AoSMCs Control 21 (techn rep 3)

description:
AoSMC_C_21_3
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt

value: Control 21


title: AoSMCs Control 21 (techn rep 1)

description:
AoSMC_C_21_1
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt

value: Abdominal Aorta


title: AoSMCs Control 21 (techn rep 2)

description:
AoSMC_C_21_2
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt

value: primary cells


title: AoSMCs Control 20 (techn rep 3)

description:
AoSMC_C_20_3
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: AAA SMCs Patient V1 (techn rep 2)

description:
AAASMC_V1_2
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt

value: Patient V1

value: AAA patient


title: AAA SMCs Patient V1 (techn rep 3)

description:
AAASMC_V1_3
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: AAA SMCs Patient V1 (techn rep 1)

description:
AAASMC_V1_1
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: RD_shSCR, H3K27ac, ChIP

tag: genotype


title: AAA SMCs Patient 234 (techn rep 3)

description:
AAASMC_234_3
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt

value: Patient 234


title: AAA SMCs Patient 234 (techn rep 2)

description:
AAASMC_234_2
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: AAA patient 1 (techn. Rep. 2)

value: all cells from tissue


title: AAA SMCs Patient 179 (techn rep 2)

description:
AAASMC_179_2
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt

value: Patient 179


title: AAA SMCs Patient 234 (techn rep 1)

description:
AAASMC_234_1
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: AAA SMCs Patient 179 (techn rep 1)

description:
AAASMC_179_1
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: AAA SMCs Patient 179 (techn rep 3)

description:
AAASMC_179_3
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: AAA SMCs Patient 86 (techn rep 3)

description:
AAASMC_86_3
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt

value: Patient 86


title: AAA SMCs Patient 86 (techn rep 2)

description:
AAASMC_86_2
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: AAA SMCs Patient 21 (techn rep 3)

description:
AAASMC_21_3
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt

value: Patient 21


title: AAA SMCs Patient 21 (techn rep 2)

description:
AAASMC_21_2
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: AoSMCs Control 18 (techn rep 2)

description:
AoSMC_C_18_2
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: AAA SMCs Patient 86 (techn rep 1)


title: AAA SMCs Patient 21 (techn rep 1)

description:
AAASMC_21_1
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: AoSMCs Control 18 (techn rep 1)

description:
AoSMC_C_18_1
AoSMCs_Seq_DEGs.txt
AoSMCs_Seq_normalised_weights.txt
AoSMCs_Seq_normalised_data.txt
AoSMCs_Seq_raw_data.txt


title: OFP+ Untreated replicate 1

city: Milano

last: Barcella

address: Via Olgettina 60

institute: SR-TIGET

data_processing:
FastQC + Trimming (trimagalore v0.5.0)
reads alignment with STAR (v2.7.0d)
featurecounts v1.6.3 (min overlap 10 + nochimera + uniquely mapping)
Assembly: GRCh38 gencodegenes primary assembly
Supplementary files format and content: tab-delimited file

source_name: BALL blasts

extract_protocol:
BM derived 126-OE-OFP+ cells Exposed or not to chemotherapy were sorted and processed to perform RNAseq
Sequencing libraries were produced with TruSeq Total RNA kit, as per manufacturer’s instructions

treatment_protocol: PDXs were exposed to doxycycline for 17 days and to Vincristine and Dexamethasone (or to PBS) for 2 weeks

tag: cell population

value: BALL blasts

tag: treatment

value: PBS


title: OFP+ Treated replicate 4

value: Vincristine + Dexamethasone


title: OFP+ Untreated replicate 3


title: OFP- Untreated replicate 1


title: OFP- Treated replicate 2


title: OFP+ Treated replicate 3


title: OFP- Untreated replicate 2


title: OFP- Treated replicate 4


title: OFP+ Untreated replicate 2


title: PT13_37 GFP_L_2

source_name: Xenograft BALL blasts

extract_protocol:
PDX`s bm derived GFPhigh(miR-126low) and GFPlow(miR-126high) cells were freshly sorted andprocessed for transcriptomic analysis by RNAseq
Sequencing libraries were produced with SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Mountain View, CA, USA), as per manufacturer’s instructions

value: Xenograft BALL blasts

tag: donor


title: OFP- Untreated replicate 3


title: OFP- Treated replicate 1


title: OFP- Treated replicate 3


title: OFP+ Treated replicate 1


title: PT13_37 GFP_L_1


title: PT13_37 GFP_H_1


title: PZ5114 scRNAseq Diagnosis

description: 10X Genomics

data_processing:
Cellranger 10X pipeline (v5.0.1) for demultiplexing and quantification (count)
Seurat data analysis workflow according to methods described in manuscript
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: .rds files with list of counts matrices and metadata in dataframe structure

source_name: BALL blasts at Diagnosis

extract_protocol:
Freshly thawed BM or PB cells were washed and counted prior to chip loading. Cells were loaded according to the manufacturer's instructions.
Chromium(TM) Single Cell 3' v2 and 5' Library & Gel Bead Kit and ChromiumTM Single Cell V(D)J Enrichment Kit (10xGENOMICS) according to manufacturer’s instructions.

value: BALL blasts at Diagnosis


title: PZ170160 scRNAseq Diagnosis

description: 10X Genomics


title: PZ1227 scRNAseq Diagnosis

description: 10X Genomics


title: PZ114966 scRNAseq Diagnosis

description: 10X Genomics


title: LNCaP-N-Myc, SP2509, H3K4me2, replicate 2

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

data_processing:
*library strategy: CUT&RUN
Read QC, alignment and peak-calling was performed using thenf-core/cutandrunpipeline v3.0.0(Ewelset al., 2020).
MACS2 was used to call peaks
DiffBind v3.6.5was used for the differential analysis
Assembly: hg38 reference genome
Supplementary files format and content: bigWig files

source_name: LNcaP-N-Myc

growth_protocol: LNcaP-NMyc cells were grown in RPMI with 10% FBS.

extract_protocol:
Samples were processed using CUT & RUN protocol from epicypher version 1.8.
Libraries were prepared using NEBNext® Ultra™ II Library Prep Kit for Illumina.

treatment_protocol: LNCaP-N-Myc cells were treated with 600 nM SP2509 for 48hours.

value: LNcaP-N-Myc

value: Prostate cancer cell line

tag: chip antibody

value: H3K4me2 (Epicypher #13-0027)


title: OFP+ Treated replicate 2


title: LNCaP-N-Myc, SP2509, IgG, replicate 2

value: IgG (Epicypher #13-0042)


title: LNCaP-N-Myc, DMSO, H3K4me2, replicate 1


title: LNCaP-N-Myc, SP2509, H3K4me2, replicate 1


title: LNCaP-N-Myc, SP2509, IgG, replicate 1


title: LNCaP-N-Myc, DMSO, IgG, replicate 2


title: LNCaP-N-Myc, DMSO, H3K4me2, replicate 2


title: LNCaP-N-Myc, DMSO, IgG, replicate 1


title: plasma exosomes, FOS, rep9 (miRNA)

city: Taiyuan City

first: Xinzhe

last: Du

state: Shanxi Province

address: Jiefang Road

institute: Shanxi Medical University

data_processing: tab-delimited text files include RPKM values for each Sample ...

source_name: Peripheral Blood

extract_protocol:
About 5 ml of plasma was isolated from 10 ml of peripheral blood. The plasma exosome was extracted from 5 ml plasma of participants. The exosomes were isolated using the exoEasy Maxi Kit (Qiagen) following the manufacturer’s protocol.Total RNA was used for removing the rRNAs with NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral Blood

tag: disease state

value: schizophrenia


title: plasma exosomes, FOS, rep3 (miRNA)


title: plasma exosomes, HC, rep8 (miRNA)

value: healthy control


title: plasma exosomes, FOS, rep7 (miRNA)


title: plasma exosomes, FOS, rep8 (miRNA)


title: plasma exosomes, HC, rep9 (miRNA)


title: plasma exosomes, FOS, rep10 (miRNA)


title: plasma exosomes, FOS, rep2 (miRNA)


title: PT13_37 GFP_H_2


title: plasma exosomes, FOS, rep4 (miRNA)


title: plasma exosomes, FOS, rep5 (miRNA)


title: plasma exosomes, FOS, rep6 (miRNA)


title: plasma exosomes, FOS, rep1 (miRNA)


title: PZ13000037 scRNAseq Diagnosis

description: 10X Genomics


title: plasma exosomes, HC, rep6 (miRNA)


title: plasma exosomes, HC, rep4 (miRNA)


title: plasma exosomes, HC, rep5 (miRNA)


title: plasma exosomes, HC, rep7 (miRNA)


title: plasma exosomes, HC, rep2 (miRNA)


title: plasma exosomes, HC, rep1 (miRNA)


title: MMP006

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

data_processing:
Raw data were aligned using STAR and counts were extracted using HTSeq
Assembly: hg38
Supplementary files format and content: read count data in .csv format

source_name: peripheral nerve

extract_protocol: TruSeq stranded library kit

value: peripheral nerve

value: Controls


title: MMP007


title: plasma exosomes, HC, rep10 (miRNA)


title: MMP005


title: MMP002

value: CIPN


title: MMP001


title: MMP003


title: M4

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: 10x Genomics

data_processing:
Chromium single cell data was analyzed with the Cell Ranger v2.1 pipeline (10x Genomics). The pipeline performed demultiplexing of Illumina raw base call (BCL) files into FASTQ files, read alignment with STAR to the GRCh38/hg38 human reference genome and human herpesvirus 8 strain JSC-1 clone BAC16, complete genome (GQ994935.1), quantification of transcript counts (e.g., UMI counting, cell-barcode association), generation of generate feature-barcode matrices, and multi-library aggregation.
Processed data is feature-barcode matrix consisting of the number of UMIs associated with a feature (row) and a barcode (column).
Assembly: GRCh38/hg38 + Human herpesvirus 8 strain JSC-1 clone BAC16, complete genome (GQ994935.1)
Supplementary files format and content: Tab-separated values files and matrix cloupe.cloupe files

source_name: peripheral blood mononuclear cells

growth_protocol: Peripheral blood mononuclear cells (PBMC; Vitlant) were purified by a standard Ficoll gradient method and were cultured in RPMI 1640 medium containing 10% FBS plus antibiotics.

extract_protocol:
PBMCs were purified by a standard Ficoll gradient method and cultured in RPMI 1640 medium containing 10% FBS plus antibiotics. Subsequently, PBMCs (2 x 10^6 cells/culture) were suspended in RPMI 1640 medium containing 10% FBS supplemented with 8 ug/ml polybrene, and infected with rKSHV.291 at MOI=1. At various time points (day 0, 1, 2, and 4) after infection, the cells for each group were washed and fixed with paraformaldehyde according to the 10x Genomics Cell Preparation Guide (CG000053).
Single-cell suspensions (1x10^4 cells) were processed on the Chromium Controller (10x Genomics) for cell partitioning into individual Gel Bead-In-EMulsions (GEMs), generation of barcoded cDNAs containing containing an Illumina R1 primer sequence and unique molecular identifiers (UMIs), cDNA amplification, and construction of barcoded sequencing libraries using the Chromium Single Cell 3’ Reagent Kit v2 (10x Genomics). Prior to library construction, cDNA amplicon size was optimized by enzymatic fragmentation and size selection. Subsequently, Illumina P5 and P7 adaptors, a sample index, and Illumina R1 primer sequence are incorporated during library construction via end repair, A-tailing, adaptor ligation, and PCR.

treatment_protocol: PBMCs (2 x 10^6 cells) were suspended in RPMI 1640 medium containing 10% FBS supplemented with 8 ug/ml polybrene, and infected with rKSHV.291 at MOI=1. At various time points (day 0, 1, 2, and 4) after infection, the cells for each group were washed and fixed with paraformaldehyde according to the 10x Genomics Cell Preparation Guide (CG000053).

value: peripheral blood mononuclear cells

value: PBMC

value: KSHV infection

tag: time post-infection

value: 4 days


title: M3

description: 10x Genomics

value: 2 days


title: plasma exosomes, HC, rep3 (miRNA)


title: M1

description: 10x Genomics

value: Pre-infection

value: 0 days


title: K2_Pos_1

data_processing:
RNA-Seq data was analyzed using a STAR-HTSeq pipeline. Raw sequence reads (FASTQ format) were mapped with STAR to the reference human genome assembly (GRCh38/hg38, GENCODE release 36) and gene-level read counts were quantified with HTSeq (htseq-count).
Processed data is a matrix of gene-level read counts generated from the output of STAR alignment and quantified with HTSeq (htseq-count).
Assembly: GRCh38/hg38
Supplementary files format and content: Data matrix in tab-delimited text format. The file contains Ensembl ID, gene name, and gene-level counts for each sample.

growth_protocol: Monocytes were isolated from PBMCs (Vitalant) with the EasySepTM Human monocyte isolation kit (STEMCELL) according to the manufacturer’s protocol. PBMCs and CD14+ monocytes were cultured in RPMI 1640 medium containing 10% FBS plus antibiotics. KSHV infection was conducted at multiplicity of infection (MOI)=1.

extract_protocol:
Total RNA was isolated using the RNeasy Miniprep Kit (Qiagen)
Indexed, stranded mRNA-seq libraries were prepared from total RNA (100 ng) using the KAPA Stranded mRNA-Seq (Roche) according to the manufacturer’s standard protocol.

treatment_protocol: PBMCs or monocytes (1-5 x 10^6 cells) were suspended in RPMI 1640 medium containing 10% FBS supplemented with 8 ug/ml polybrene, and infected with the appropriate amount of KSHV vIL6REV, KSHV vIL6STOP, or PBS alone (i.e., as mock infection). Cells were harvested 7 days post-infection for RNA isolation.

value: infection with vIL6-sufficient KSHV (vIL6REV)

value: 7 days


title: K2_Neg_1

value: infection with vIL6-deficient KSHV (vIL6STOP)


title: oocytes before DHP, biol rep 3

city: Leiden

first: Ron

middle: P

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

description:
FG2112_3_7_11_vs_1_5_9_Oocyte_before_DHP_vs_Oocyte_before_P.xlsx
FG2112_4_8_12_vs_3_7_11_Stripped_after_DHP_vs_Oocyte_before_DHP.xlsx

data_processing:
Image analysis and base calling were done by the Illumina pipeline (Illumina Inc., San Diego, CA, USA)
Reads were aligned against the Anguilla anguilla reference genome using TopHat (version 2.0.13) (Trapnell et al., 2009)
The resulting files were filtered and secondary alignments were removed using SAMtools (version 1.2 using htslib 1.2.1) (Li et al., 2009)
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.6.1p1) (Anders and Huber, 2014)
Differentially expressed genes were identified using DESeq (Anders and Huber, 2010) and data were further processed using Microsoft Excel
Assembly: Genome assembly fAngAng1.pri (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_013347855.1/)
Supplementary files format and content: Microsoft Office Excel file (.xlsx) with the following columns: Gene_Name; Gene_ID; Gene_Product; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj; sample #; sample #; sample #; sample #; sample #; sample #;

organism: Anguilla anguilla

source_name: oocyte

extract_protocol:
RNA was extracted using miRNeasy Mini kit (Qiagen). 0.5 ug of total RNA was used for the construction of sequencing libraries.
TruSeq Stranded mRNA Library Prep kit (Illumina)

value: oocyte

value: WT

value: control


title: PBS_2

value: mock infection (PBS)


title: M2

description: 10x Genomics

value: 1 day


title: oocytes before progesterone, biol rep 3

description:
FG2112_2_6_10_vs_1_5_9_Stripped_after_P_vs_Oocyte_before_P.xlsx
FG2112_3_7_11_vs_1_5_9_Oocyte_before_DHP_vs_Oocyte_before_P.xlsx


title: PBS_1


title: eggs after DHP, biol rep 2

description:
FG2112_2_6_10_vs__4_8_12_Stripped_after_P_vs_Stripped_after_DHP.xlsx
FG2112_4_8_12_vs_3_7_11_Stripped_after_DHP_vs_Oocyte_before_DHP.xlsx

source_name: egg

value: egg

value: DHP


title: eggs after progesterone, biol rep 3

description:
FG2112_2_6_10_vs_1_5_9_Stripped_after_P_vs_Oocyte_before_P.xlsx
FG2112_2_6_10_vs__4_8_12_Stripped_after_P_vs_Stripped_after_DHP.xlsx

value: progesterone


title: K2_Pos_2

value: peripheral blood mononuclear cells

value: PBMC


title: oocytes before progesterone, biol rep 2


title: eggs after progesterone, biol rep 2


title: eggs after DHP, biol rep 1


title: eggs after progesterone, biol rep 1


title: WT_2

city: stockholm

first: mengzhen

last: Li

address: Drottning Kristinas Väg 36A

country: Sweden

institute: KTH Royal Institute of Technology

data_processing:
The FASTQ files were assessed by FastQC (v0.11.9) software to ensure the quality of every sequenced sample.
Raw sequences from FASTQ files were aligned to the Ensembl reference mouse cDNA (GRCh38 v108 for Homo sapiens) using kallisto (v0.48.0).
Based on the Ensembl GTF annotation file, the transcript read counts were assembled to gene level using the R package tximport (v1.24.0), with only protein-coding transcripts and genes included.
Genes have an average count below 5 were considered underexpressed and were filtered out, resulting in a total of 13961 genes for the downstream analysis.
Assembly: GRCh38 v108
Supplementary files format and content: exp_counts.tsv
Supplementary files format and content: Tab-delimited text files include read count values for all protein-coding genes of each sample.

source_name: Liver

growth_protocol: 10%FBS, 1%P/S supplimented RPMI (R2405)

extract_protocol:
RNeasy Plus Mini Kit (74134,QIAGEN).
The Ilumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit was used for the construction of NGS libraries from the samples with acceptable quality parameters.

treatment_protocol: 6well plate 1 million cells seeding, 10%FBS, 1%P/S supplimented DMEM (D0819) +  10µg/ml insulin, and 10µM T0901317 for one week

value: Liver

value: hepatocellular carcinoma cell

value: 10%FBS, 1%P/S supplimented RPMI (R2405)


title: oocytes before DHP, biol rep 1


title: WT_1


title: oocytes before progesterone, biol rep 1


title: OA_2

value: 10%FBS, 1%P/S supplimented DMEM (D0819) +  25uM Oleic acid that dissolved in 11%BSA in PBS for 6hr


title: K2_Neg_2


title: C18.T.F

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

institute: Juntendo University

description:
R18
Turkey_RNAseq.xlsx

data_processing:
Quality of sequenced CAGE reads was checked by using FastQC v0.11.5 and then trimmed with fastx_trimmer -Q33 -l 75 (FASTX Toolkit 0.0.14). Moirai removeN script was applied to remove reads with “N” nucleotides. CAGE reads matching to adapters or rRNA (Moirai defined rRNA for galGal3) were removed with Trimmomatic-0.38 and RNAdust 1.06, respectively.
Trimmed CAGE reads were aligned with BWA 0.7.10-r789 and unmapped reads realigned with Hisat2 v2.1.0
Alignments were processed into CTSS (CAGE transcription start sites) and CAGE peaks with PromoterPipeline (https://github.com/Population-Transcriptomics/C1-CAGE-preview) with default threshold of at least 10 TPM (tags per million) in one of the samples.
CAGE peaks were associated with nearby transcripts located on the same strand by using ChIPseeker v1.32.0 package for R.
Quality of sequenced RNAseq reads was checked by using FastQC v0.11.5 and then trimmed with Trimmomatic-0.38
Trimmed RNAseq reads were aligned to reference genome assemblies by using Hisat2 v2.1.0, counted with HTSeq v2.0.1, and normalized by library size and exon length in edgeR v3.42.2.
Assembly: galGal6 (GCF_000002315.6)
Assembly: Coturnix_japonica_2.1 (GCF_001577835.2)
Assembly: MGAL_WU_HG_1.0 (GCA_905368555.1)
Assembly: GT_SO_6221 (http://gigadb.org/dataset/100559)
Assembly: ZJU1.0 (GCF_015476345.1)
Assembly: bTaeGut2.pat.W.v2 (GCF_008822105.2)
Assembly: ZJU1.0 (GCA_016128335.1)
Supplementary files format and content: xlsx files with CAGE peaks coordinates, TSS position, associated genes, tag per million normalized counts
Supplementary files format and content: xlsx files with RNAseq raw and FPKM counts

organism: Meleagris gallopavo

source_name: embryonic fibroblasts P5

extract_protocol:
Total RNA was prepared using commercial reagents (TRIzol, Invitrogen) from each sample of avian embryonic fibroblast cells at the fifth passage (P5).
5ug of RNA from each fibroblast sample was used for nAnTi-CAGE and polyA RNAseq libraries preparation and subsequent sequencing using the Illumina HiSeq2500 platform (K. K. DNAForm, Yokohama, Japan)

value: embryonic fibroblasts P5

tag: Sex

value: female

tag: medium

value: DMEM/10percent FBS


title: C14.T.M

description:
R14
Turkey_RNAseq.xlsx

value: male


title: eggs after DHP, biol rep 3

value: WT


title: oocytes before DHP, biol rep 2

value: oocyte

value: control


title: OA_1


title: DNL_3

value: 10%FBS, 1%P/S supplimented DMEM (D0819) +  10ug/ml insulin, and 10uM T0901317 for one week


title: T-EF 2020-04 High P5 [C18]

description:
C18
Turkey_CAGE.xlsx


title: WT_3


title: DNL_1


title: T-EF 2020-03 F12 P5 [C15]

description:
C15
Turkey_CAGE.xlsx

value: DMEM/F12/10percent FBS


title: DNL_2


title: T-EF 2020-02 High P5 [C14]

description:
C14
Turkey_CAGE.xlsx


title: Day-4_LACT_3

city: Utrecht

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

institute: Utrecht University

data_processing:
The read qualities for each fastq file were accessed with FastQC (V 0.11.9), and low-quality bases and adapters were removed with Trimmomatic.
The sequenced reads were mapped to the bovine reference genome (bosTau 9) with the STAR aligner (V 2.7.0b)
Read counts were estimated at the gene level, and the counting was done with featureCounts, part of the Subread software (V 2.0.3).
Assembly: bosTau 9
Supplementary files format and content: tab delimited text file containing raw read counts for each sample.

organism: Bos taurus

source_name: embryo

extract_protocol:
A minimum of 100 ng of total RNA was used and samples were enriched for non- rRNA during cDNA synthesis. No ribosomal depletion or polyA-RNA enrichment steps were carried out while all non-rRNA were captured
Libraries were constructed using the Encore Complete RNA- Seq library system of NuGEN and sequenced on the Illumina HiSeq 1500 as 100 bp single end reads. Sequencing of the multiplexed libraries generated 30 millions reads for each library. After demultiplexing, adaptor sequences and poly A tails were removed and an additional number of sequencing runs was performed to ensure sufficient coverage.

value: embryo

tag: developmental stage

value: 16-cell embryos

tag: enviromental condition

value: lactating dairy cow oviduct


title: Day-4_LACT_2

tag: tissue


title: OA_3

tag: cell type


title: SiMENA rep 2

first: Lorenzo

last: D'Ambrosio

address: Via Elio Chianesi 53

department: Dept. Of Research, Advanced Diagnostic, and Technological Innovation

institute: Regina Elena National Cancer Institute, IRCCS

data_processing:
Read quantification was performed with the function “quant” of the Kallisto tool (parameters: -b 100)
Assembly: GRCh37
Supplementary files format and content: TPM normalized expression values

growth_protocol: Human lung H2030 cells were maintained in RPMI 1640 Medium (Euroclone), supplemented with 10% fetal bovine serum (Euroclone), 1% Glutamine, 1% Penicillin/Streptomycin (Euroclone), and incubated at 37°C in a 5% CO2 air-humidified atmosphere.

extract_protocol:
Total RNA was harvested using Qiazol (Qiagen), purified from DNA contamination through DNase I (Qiagen) and enriched by  RNeasy (Qiagen) columns for gene expression profiling. Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and by Agilent 2100 Bioanalyzer (Agilent Technologies, CA), respectively.
RNA libraries for sequencing were generated  using 500ng of RNA for each sample according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, CA). Libraries were quantified by qPCR and sequenced in paired-end mode (2x75 bp) with NextSeq 500 (Illumina, CA).

treatment_protocol: 3 × 105 cells/well in exponential growth phase were plated in 6-well plates. The next day, cells were transfected with 20 nmol/L of hMENA(t)-specific pooled siRNA duplexes (siGENOME SMARTpool Human ENAH), or 20 nmol/L of mix of three siRNAs each matching 21 nucleotides within the 11a exon sequences (51) or 20nmol/l of ON-TARGETplus Nontargeting Control Pool (GEHealthcare, Dharmacon, Lafayette, CO, USA) using Lipofectamine® RNAiMAX Transfection Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.

value: Human Non-Small Cell Lung Cancer

value: transfection with hMENA(t) siRNA pool


title: SiMENA rep 3


title: T-EF 2020-02 F12 P5 [C13]

description:
C13
Turkey_CAGE.xlsx


title: Day-4_DRY_3

value: dry dairy cow oviduct


title: Day-4_LACT_1


title: T-EF 2020-03 High P5 (2nd) [C16]

description:
C16
Turkey_CAGE.xlsx


title: SiMENA11a rep 3

value: transfection with hMENA11a siRNA pool


title: Day-4_DRY_2


title: Day-4_DRY_1


title: T-EF 2020-04 F12 P5 [C17]

description:
C17
Turkey_CAGE.xlsx


title: Day-4_IVP_2

value: in vitro culture


title: SiMENA rep 1


title: SiMENA11a rep 2


title: Day-4_IVP_3


title: Day-4_IVP_1


title: Day-2_IVP_5

value: 4-cells embryos


title: elective_AAA_E15

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array v2 (8x15K, Arraystar). 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering.

source_name: vascular tissue

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: On average,50-100mg of AAA or CTRL vascular tissue were used for RNA extraction according to Qiazol´s standard protocol.

value: vascular tissue

tag: disease

value: AAA

tag: gender

tag: age


title: elective_AAA_E14

value: male


title: elective_AAA_E16


title: elective_AAA_E13


title: elective_AAA_E17


title: Day-2_IVP_4


title: Control rep 3

tag: cell line

value: Control:transfection with non-targeting RNA pool


title: Day-2_IVP_2


title: Day-2_IVP_1


title: Control rep 2


title: T6-1

city: Guangzhou

first: Qianjun

email: qqjun8@yeah.net, qqjun8@163.com

state: Guangdong

address: No. 1838, North Guangzhou Avenue

department: Sleep Medicine Center

institute: Nanfang Hospital, Southern Medical University

data_processing:
Sequencing data were filtered to remove low-quality sequences.Sequence splicing was performed using FLASH (Fast Length Adjustment of Short reads, V1.2.11)
Remove the primer sequence from the Tags sequence using the software CUTADAPT (version 1.16).
Using UCHIME method in VSEARCH(V2.3.4) software and combined with Gold Database (V20110519) chimera database to remove chimera sequences to get high-quality Tags sequence.
The software VSEARCH (V2.3.4) was used to cluster high-quality Tags sequence into OTU, and the REPRESENTATIVE sequence of OTU was obtained.
Using RDP Classifer (V2.2) software combined with Silva (V128) database, species annotation was performed for OTU representative sequences.
Based on 16S data, Alpha(α) diversity index (Observed OTU richness and Shannon Diversity) and Beta(β) diversity index based on Principal Coordinate Analysis (PCoA) (unweighted-Unifrac distance, Adonis) was used to assess the differences between groups. Linear discriminant analysis (LDA) and LDA Effective Size (LEfSe) was used to assess the taxonomic differences among groups.The network was then utilized to present the relationship between intestinal microbiome, intestinal barrier biomarkers, and AHI (Cytoscape v3.7.2). Statistical analysis of data was conducted in SPSS (version 21.0) and R software (v3.5.1).
Genome_build: 16S rDNA Sequences were aggregated into operational taxonomic units (OTUs) using 97% identity of the Silva v128 database
Supplementary_files_format_and_content: ConnectTags_stat.txt
Supplementary_files_format_and_content: OTU_table_for_biom.txt
Supplementary_files_format_and_content: Genus.absolute_abundance.txt
Supplementary_files_format_and_content: Alpha_diversity_detail.txt
Supplementary_files_format_and_content: unweighted_unifrac_Beta_diversity.txt

organism: human feces metagenome

source_name: Human feces

extract_protocol:
Bead beading isolation was done to extract genomic DNA using the QIAamp DNA Kit (QIAGEN, Hilden, Germany), following the manufacturer's protocol. The extracted DNA concentration was measured by Qubit 2.0 Fluorometer (Life Technology, Carlsbad, CA). DNA quality was detected by 1.0% agarose gel electrophoresis. Then, the 16S rDNA gene regions (V3 and V4) were amplified by PCR.
The 16S rDNA libraries were sequenced on the Illumina MiSeq platform PE300 mode (Illumina, USA)

treatment_protocol: One gram of fresh fecal samples was collected in a sterile fecal tube on the first day after admission and were immediately stored in the -20℃ refrigerator of the department, then sent to the -80℃ refrigerator of the central laboratory of Nanfang Hospital for cold storage within 4 hours by the researchers.

value: Fecal

tag: diagnosis

value: Mild-OSA

value: CPAP therapy for 6 months


title: T12-2

value: Severe-OSA

value: CPAP therapy for 12 months


title: Control rep 1


title: B13

value: No-OSA

value: No


title: SiMENA11a rep 1

value: Human Non-Small Cell Lung Cancer


title: B24


title: B12


title: T12-1


title: B11


title: DMSO_182

city: Chicago

first: Atieh

last: Hajirahimkhan

state: Illinois

address: 303 E Superior, 4-220

institute: Northwestern University

data_processing:
quality control of the raw sequence data was assessed using FASTQC
Sequence reads were mapped to the reference genome hg38 using STAR.
To evaluate the quality of the RNA-seq data, the number of reads falling into different annotated regions of the reference genes was determined with bamUtil
To analyze the data, low quality mapped reads were excluded and feature counts were used to quantify the gene level expression. Differential gene expression analysis was performed with edgeR
Assembly: hg 38
Supplementary files format and content: excell speadsheet containing raw counts

source_name: breast microstructure, control, 24 h

extract_protocol:
RNA was harvested using Direct-Zol RNA prep kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Roche KAPA Hyperprep kit and QIAseq Fast Select rRNA removal kit following manufacturers' protocols.

value: tissue

value: high-risk human breast microstructures

tag: genotype

value: postmenopausal

value: DMSO

tag: time


title: DMSO_187

tag: treatment


title: DMSO_173


title: control_C3

value: CTRL


title: control_C7

value: vascular tissue


title: B10


title: elective_AAA_E12

value: AAA


title: Day-2_IVP_3

value: embryo

value: 4-cells embryos

value: in vitro culture


title: B9

value: Fecal


title: control_D36

value: male


title: DMSO_183


title: control_D32


title: B6


title: DMSO_181


title: elective_AAA_E504


title: B5


title: elective_AAA_E503


title: B3


title: elective_AAA_E552


title: B2


title: control_AA25C


title: LigF_182

source_name: breast microstructure, liquritigenin, 24 h

value: liquiritigenin


title: A56

value: Moderate-OSA


title: B8

value: No-OSA


title: A53

value: Severe-OSA

value: No


title: LigF_173

value: tissue


title: control_AA02C


title: A54


title: elective_AAA_E22

value: female


title: LigF_187

value: high-risk human breast microstructures

value: postmenopausal


title: A48


title: A52


title: A45

value: Mild-OSA


title: A42


title: dna2-md spo11Y135F-7h-ChIP

city: Jinan

first: liangran

last: zhang

state: Shandong

address: Jingshi Street

department: State Key Laboratory of Microbial Technology

institute: Shandong University

data_processing:
Adaptors and bases with a quality rating of less than 25 were trimmed by Trim-galore.
ChIP-Seq reads were mapped to the reference genome (SacCer3) by Bowtie2.
Peaks were called by MACS2 with default settings,and the folds enrichment ≥ 2.
Assembly: SacCer3
Supplementary files format and content: bigWig

organism: Saccharomyces cerevisiae SK1

source_name: Budding yeast

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 90 min. The reaction was quenched with glycine. The cells were broken with glass beads in lysis buffer and the chromatin was sheared by sonication.
The library was prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, Cat# ND607-01) according to the manufacturer’s manual.

value: Budding yeast

value: dna2-md spo11Y135F (pCLB2-DNA2 spo11Y135F)

tag: antibody

tag: time point


title: A43


title: A51


title: dna2-md spo11Y135F-4h-Input


title: LigF_183


title: dna2-md spo11Y135F-7h-Input


title: elective_AAA_E19

value: vascular tissue

value: AAA


title: A38


title: A37


title: A36


title: dna2-md spo11Y135F-4h-ChIP


title: dna2-md-7h-Input-repeat2

value: dna2-md (pCLB2-DNA2)


title: A35

value: Fecal


title: DMSO_178

value: DMSO


title: A34


title: dna2-md-7h-Input-repeat1


title: LigF_181

value: liquiritigenin