title: Donor 2 PB NK

city: West Allis

first: Ao

last: Mei

state: Wisconsin

address: 9442 West Maple Ct

institute: Medical College of Wisconsin

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol:
Natural killer cells are sorted from human PBMC as Lin-CD7+ population. Sorted cells are washed with ice-cold FACS buffer (PBS+10%FBS) and counted to be loaded into 10X Chromium machine.
scRNA libraries were prepared following the user guide of 10X Chromium Single Cell 3' Reagent Kits v3

value: Peripheral blood

tag: donor

value: healthy

value: Natural Killer cells

value: No treatment


title: 11H_M_2564

status: Public on Apr 26 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: 11H_M_2560


title: 11H_M_2559


title: 4sU-seq MCMV 1hpi new B

city: Wuerzburg

first: Florian

last: Erhard

address: Versbacher Straße 7

country: Germany

institute: Institute of Virology and Immunobiology, University of Wuerzburg

description:
Purified nascent RNA following 1h of 4sU labeling was subjected to strand-specific RNA sequencing using random priming without rRNA depletion.
MCMV_polya.tar.gz
MCMV_introns.tar.gz

library_source: transcriptomic

data_processing:
Bowtie2 2.3.0 was used to align all reads to ribosomal rRNA and Mycoplasma. Reads mapped to ribosomal rRNA and Mycoplasma were discarded.
STAR 2.5.3a was used to align the remaining reads to the mouse genome, Ensembl transcripts (v90), the MCMV genome (KY348373), and the MCMV transcripts (KY348373).
ContextMap 2.0 was used to identify poly(A) sites and introns as described in Whisnant A.W. et al, Nat. Commun (2020)
Assembly: GRCm38, KY348373
Supplementary files format and content: .bed files containing all poly(A) sites from each condition / time point. Tab separated files and Microsoft Excel files showing all introns.

molecule: total RNA

source_name: NIH-3T3 Murine embryonic fibroblasts

growth_protocol: NIH-3T3 cells were cultured in DMEM supplements with 10% NCS and Pen-Strep, 100 IU/mL and 100µg/mL, respectively. Cells at passage 6 after thawing were infected at 80% confluency 24h after the last split.

extract_protocol:
Cells were lyzed using Trizol and total cellular RNA was isolated. 4sU labelled RNA was biotinylated using Biotin-HPDP followed by separation of new and old RNA using streptavidin-coated magnetic beads. Bead bound RNA was recovered via DTT treatment followed by RNA purification using Qiagen RNeasy MinElute columns.
Sequencing libraries were prepared for both total and newly transcribed RNA (4sU-RNA) as described in Rutkowski, A.J. et al, Nat. Commun (2015).

treatment_protocol: Cells were infected for 30 min with Smith strain MCMV at an MOI of 10 with centrifugal enhancement at 800g/30mins. Cell culture media was replaced 30 min later (infection time point t=0). Metabolic RNA labelling was performed by adding 200µM 4sU to the cell culture medium one hour prior to cell lysis.

tag: cell type

value: Immortalized embryonic fibroblasts

tag: time post infection

value: MCMV, 1 h p.i.

tag: infection with

value: MCMV

tag: replicate

value: Replicate 2

tag: molecule subtype

value: Purified nascent RNA


title: Pbx1 ChIP-seq Replicate 1

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

data_processing:
Reads were aligned to the mm10 release of the mouse genome using Bowtie (PMID: 19261174) with parameters -v 2 -m 1.
Peak calling was performed using Model-Based Analysis for ChIP-seq (MACS) v1.4 (PMID: 18798982) with matched input DNA as control and parameters --gsize=mm --bw=150 --nomodel --shiftsize=100.
Genome_build: mm10
Supplementary_files_format_and_content: *_peaks.bed, list of peaks called with MACS

source_name: embryonic hindlimb bud, Pbx1 ChIP

growth_protocol: Mice were maintained in animal facilties under standard conditions.

extract_protocol:
Embryonic hindlimb buds were isolated from E10.5 mouse embryos, obtained from timed matings of wild-type Swiss Webster mice and immediately crosslinked for 10 min in 1% formaldehyde (Electron Microscopy Sciences, #15710). The crosslinked material was sonicated to 200-500 bp fragments with a Diagenode Bioruptor. Each ChIP-seq assay was performed from pooling 60-80 embryonic hindlimbs, by overnight incubation with specific antibodies (5 µg) at 4°C followed by 30 min incubation with Dynabeads protein A (Invitrogen). After washing, IP and input DNA were de-crosslinked and purified using the MicroChIP DiaPure kit (Diagenode, #C03040001).
Libraries were constructed using the MicroPlex Library Preparation Kit v2 (Diagenode, C05010012). Libraries were normalized to 10 nM, pooled, and sequenced in an Illumina HiSeq 4000 to generate 50 base pair single-end reads.

treatment_protocol: None.

value: Swiss Webster

tag: tissue

value: embryonic hindlimb bud

tag: developmental stage

value: gestational day e10.5

tag: antibody

value: Anti-PBX1; Cell Signaling, #4243S


title: 4sU-seq Mock2 new A

value: Mock

value: Replicate 1


title: H3K27ac ChIP-seq Replicate 2

source_name: embryonic hindlimb bud, H3K27ac ChIP

value: Anti-H3K27ac; Abcam, ab4729


title: Plasma, SECGRAD, rep3

city: Madrid

first: Celia

last: Perales

address: C. Darwin, 3

country: Spain

institute: Centro Nacional de Biotecnología

description:
SECGRAD3
raw_counts_extractionmethod_allmirna.tsv

data_processing:
Read trimming was performed with cutadapt (version 3.2) following the guidelines of each library preparation kit. Samples prepared with NEXTflex kit were trimmed by removing the 3' adapter 'TGGAATTCTCGGGTGCCAAGG', plus 4 bases from both sides of each read. TruSeq 3' adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCA' was trimmed from samples prepared with the NEBNext kit. Samples prepared with SMARTer were trimmed by removing the 3' PolyA adapter ('AAAAAAAAAA') plus 3 extra bases at the 5' end.
After adapter trimming, reads with lengths between 17 and 25 nucleotides were selected and mapped using Bowtie 2 (version 2.3.4.3) to the hg38 reference genome using default parameters.
Quantification was performed using HTSeq (version 0.13.5) with default parameters using mature miRNA coordinates provided by miRBase v22.1 (https://www.mirbase.org/ftp/22.1/genomes/hsa.gff3).
Low expressed miRNAs (those with less than 50 reads in total) were discarded
For spike-in analysis, selected reads between 17 and 25 nucleotides were mapped using Bowtie 2 (version 2.3.4.3) to the QIAseq™ miRNA Library QC Spike-In sequences. Mapping parameters were tuned for "perfect match" as recommended in QIAseq™ miRNA Library QC Spike-Ins protocol by setting the following parameters: "--end-to-end -N 0 --mp 10000 --np 10000 --rdg 10000 --rfg 10000".
Mapped reads were quantified by counting the number of reads mapped to each Spike-In sequence
Assembly: hg38 and QIAseq™ miRNA Library QC Spike-In sequences
Supplementary files format and content: “raw_counts_extractionmethod_allmirna.tsv”: Table (Tab-separated values) containing the raw couts of all mature miRNAs (in miRBase release 22.1). First column contains the miRNAs identifiers and the first row contains the sample names.
Supplementary files format and content: “raw_counts_librarykit_allmirna.tsv”: Table (Tab-separated values) containing the raw couts of all mature miRNAs (in miRBase release 22.1). First column contains the miRNAs identifiers and the first row contains the sample names.
Supplementary files format and content: “raw_counts_librarykit_spike-ins.tsv”: Table (Tab-separated values) containing the raw couts of all 52 QIAseq™ miRNA Library QC Spike-In. First column contains the miRNAs Spike-In identifiers and the first row contains the sample names.

organism: Homo sapiens

source_name: Blood

extract_protocol:
RNA was extracted from 250 µl of the plasma sample or from 250 µl EVs isolation samples using a miRNeasy Mini kit (QIAGEN) following the manufacturer’s instructions. Purified RNA was eluted in 20 μl of nuclease-free water. To monitor the purification and amplification of miRNAs, 52 spike-ins (synthetic miRNAs at different concentrations) (QIAseq miRNA Library QC PCR Assay Kit) were added to the initial sample before RNA extraction. Quantity and quality of the purified RNA were determined using NanoDrop and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). The RNA concentrations obtained ranged between 164 pg/µl and 349 pg/µl.
NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs, Ipswich, MA, USA), NEXTFlex Small RNA-Seq Kit v3 (PerkinElmer, Waltham, MA, USA), and SMARTer smRNA-seq kit (Clontech Laboratories, CA, USA)

value: Blood

tag: miRNA preparation kit

value: NEBNext

tag: extracellular vesicles isolation method

value: SECGRAD


title: H3K27ac ChIP-seq Replicate 1


title: Donor 1 PB NK

description: 10x Genomics

library_source: transcriptomic single cell

value: Peripheral blood

value: healthy

value: Natural Killer cells

tag: treatment


title: 4sU-seq Mock1 new A

value: Immortalized embryonic fibroblasts


title: 11H_M_2558


title: 11H_M_2557


title: 4sU-seq MCMV 6hpi new A

value: MCMV, 6 h p.i.

value: MCMV


title: Plasma, SECGRAD, rep2

description:
SECGRAD2
raw_counts_extractionmethod_allmirna.tsv


title: 11H_M_2556


title: ATAC-seq Hindlimb Replicate 2

data_processing:
Reads were aligned to the mm10 release of the mouse genome using Bowtie (PMID: 19261174) with parameters -v 2 -m 1.
Accessible regions were identified using Model-Based Analysis for ChIP-seq (MACS) v1.4 (PMID: 18798982) with no control and parameters --gsize=mm --bw=150 --nomodel --nolambda --shiftsize=75.
Genome_build: mm10
Supplementary_files_format_and_content: *_peaks.bed, list of peaks called with MACS

source_name: embryonic hindlimb bud, ATAC

growth_protocol: Swiss Webster mice were maintained in animal facilties under standard conditions.

extract_protocol:
Assay for Transposase Accessible Chromatin (ATAC-seq) was performed as originally described (PMID: 24097267) with minor modifications. Briefly, for each replicate, about 75.000 single cells from a pair of mouse hindlimb buds were processed.
Libraries were amplified according to Buenrostro et al., 2015 (PMID: 24097267), and paired-end sequenced on a HiSeq 4000.


title: ATAC-seq Hindlimb Replicate 3


title: Plasma, SECGRAD, rep1

description:
SECGRAD1
raw_counts_extractionmethod_allmirna.tsv


title: H3K27me3 ChIP-seq Replicate 2

source_name: embryonic hindlimb bud, H3K27me3 ChIP

value: Anti-H3K27me3; Millipore, #07-449


title: 4sU-seq MCMV 48hpi new A

value: MCMV, 48 h p.i.

value: Purified nascent RNA


title: H3K27me3 ChIP-seq Replicate 1

value: Swiss Webster

value: embryonic hindlimb bud

value: gestational day e10.5


title: WT HAP1 cells, DMSO treated, 48hr, rep 1

first: Stefan

last: Kubicek

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTDM4801

data_processing:
RNA-seq: Read mapping was performed using STAR (Dobin et al., 2013) and the Ensembl transcript annotation from version e100 April2020 as reference transcriptome.
Assembly: hg38
Supplementary files format and content: Adenosine_counts_normalised.tsv: Tab-delimited text file includes raw read counts per gene per HAP1 cell line sample.
Supplementary files format and content: Patient_counts_normalised.tsv: Tab-delimited text file includes raw read counts per gene per fibroblast sample.

molecule: polyA RNA

growth_protocol: HAP1 (KBM7-derived) and HAP1 MTHFD1KO cell lines were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Sigma), supplemented with 10% Fetal Bovine Serum (FBS, Sigma) and 1% Penicillin/Streptomycin (P/S, Sigma). Patient-derived fibroblast and control fibroblast lines were cultured in Minimum Essential Medium alpha media (MEM-alpha, no nucleosides, Gibco), supplemented with 10% FBS and 1% P/S. For the experiments using dialyzed FBS, the dialyzed FBS was purchased from Gibco and added to IMDM at a final concentration of 10%. All the cell lines were incubated in 5% CO2 atmosphere at 37C.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts. Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-base-pair, single-end mode.

treatment_protocol: Cells were treated in various media conditions (standard media, dialyzed medium, or dialyzed media supplemented with adenosine) for the indicated time.

tag: cell line

value: chronic myelogenous leukemia

tag: genotype

value: wild-type

value: DMSO

tag: time point


title: ATAC-seq Hindlimb Replicate 1


title: 4sU-seq MCMV 4hpi new A

value: MCMV, 4 h p.i.

value: Replicate 1


title: Plasma, SEC, rep3

description:
SEC3
raw_counts_extractionmethod_allmirna.tsv

value: Blood

value: NEBNext

value: SEC


title: WT HAP1 cells, DMSO treated, 24hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTDM2403


title: 4sU-seq MCMV 24hpi new A

value: Immortalized embryonic fibroblasts

value: MCMV, 24 h p.i.


title: 4sU-seq MCMV 18hpi new A

value: MCMV, 18 h p.i.

value: MCMV


title: PTZ-4

city: Daegu

first: Sehyun

last: Chae

address: 61, Cheomdan-ro

department: Neurovascular Unit Research Group

country: South Korea

institute: Korea Brain Research Institute

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Illumina adapter sequences were removed using the Flexbar software (version 3.5.0), and the remaining reads sequences were aligned to the mouse genome (GRCm38) using Tophat2 software (version 2.1.1) with the default parameters.
After the alignment, the numbers of reads mapped to the gene features (GTF file of GRCm38.91) were counted using HTseq sofrware. The read counts for the samples in each condition were then normalized using the TMM (trimmed mean of M-values) normalization of the edgeR package.
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TMM-normalized read counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: brain endothelial cells

extract_protocol:
Total RNAs were obtained from BECs of the whole cortex tissues using Trizol reagent (Invitrogen Life Technologies, Grand Island, NY). NEBNext Single Cell/Low Input RNA Library Prep Kit for  Illumina kit was used for the construction of sequencing libraries, according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain endothelial cells (BECs)

value: cortex

value: tie2-Cre; ai9; rpl22HA/HA mice

tag: gender

value: male

value: 8-12 weeks old

value: pentylenetetrazol (PTZ)


title: PTZ-2

tag: age


title: 4sU-seq MCMV 2hpi new A

value: MCMV, 2 h p.i.

value: Purified nascent RNA


title: Plasma, SEC, rep1

description:
SEC1
raw_counts_extractionmethod_allmirna.tsv


title: Plasma, SEC, rep2

description:
SEC2
raw_counts_extractionmethod_allmirna.tsv


title: WT HAP1 cells, DMSO treated, 24hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTDM2402

value: chronic myelogenous leukemia

value: wild-type

value: DMSO


title: PTZ-1

tag: strain


title: PBS-4

tag: cell type

value: phosphate buffered saline (PBS)


title: Plasma, GRAD, rep3

description:
GRAD3
raw_counts_extractionmethod_allmirna.tsv

value: Blood

value: NEBNext

value: GRAD


title: WT HAP1 cells, DMSO treated, 6hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTDM0603


title: WT HAP1 cells, DMSO treated, 24hr, rep 1

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTDM2401


title: Plasma, GRAD, rep2

description:
GRAD2
raw_counts_extractionmethod_allmirna.tsv


title: 4sU-seq MCMV 12hpi new A

value: Immortalized embryonic fibroblasts

tag: time post infection

value: MCMV, 12 h p.i.

value: Replicate 1


title: Plasma, GRAD, rep1

description:
GRAD1
raw_counts_extractionmethod_allmirna.tsv


title: 4sU-seq MCMV 1hpi new A

value: MCMV, 1 h p.i.

tag: infection with

value: MCMV


title: PBS-1

value: brain endothelial cells (BECs)

value: cortex

value: tie2-Cre; ai9; rpl22HA/HA mice

value: male


title: WT HAP1 cells, DMSO treated, 6hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTDM0602


title: Plasma, SMARTer, rep2

description:
P2SMARTer
raw_counts_librarykit_allmirna.tsv
raw_counts_librarykit_spike-ins.tsv

value: SMARTer


title: E3 lung1

city: Valhalla

first: Sudhir

last: Jain

state: New York

address: 15 Dana Rd

department: Pathology, Microbiology and Immunology

institute: New York Medical Collage

data_processing:
Kallisto pseudo-alignment was used with Ensembl mouse transcriptome reference GRCm38
DESeq2 was used for differential gene expression
Genome_build: GRCm38
Supplementary_files_format_and_content: TPM for gene expression level in a csv file

source_name: lung tissue

extract_protocol:
RNA was extracted using Qiagen RNAeasy Kit
Illumina TruSeq Stranded Total RNA Library Preparation using the polyadenylated mRNA pull-down.

tag: group

value: Haplotype-I aged+LVS

value: lung


title: cRNA-seq MCMV 48hpi B

data_processing:
3' sequencing adapter sequence were removed from the 49 nt long reads using reaper 15.065
Barcode sequences (first 9 nt = 3 random bases followed by 4 bases of experiment specific barcodes followed by 2 random bases) were removed from all reads and stored for later use.
Bowtie 1.2 was used to align all reads to ribosomal rRNA and Mycoplasma. Reads mapped to ribosomal rRNA and Mycoplasma were discarded. The remaining reads were aligned to the mouse genome, Ensembl transcripts (v90), the MCMV genome (KY348373), and the MCMV transcripts (KY348373). Only reads with at most 3 mismatches were kept for further analyses.
The total number of unique sequences was taken as the conservative fragment count.
Mapped reads were further processed by iTiSS 1.3 to identify transcription start sites.
Assembly: GRCm38, KY348373
Supplementary files format and content: Tab separated file showing the read count of each transcription start sites. The processed file / iTiSS output is decribed in detasils here: https://github.com/erhard-lab/iTiSS#results

growth_protocol: NIH-3T3 cells were cultured in DMEM supplements with 10% NCS and Pen-Strep, 100 IU/mL and 100µg/mL, respectively. Cells at passage 6 were infected at 80% confluency 24h after the last split.

extract_protocol:
Cells were lyzed using Trizol and total cellular RNA was isolated.
Sequencing libraries were prepared using the cRNA-seq library preparation as described in Whisnant A.W. et al, Nat. Commun (2020)

treatment_protocol: Cells were infected for 30 min with Smith strain MCMV at an MOI with centrifugal enhancement at 800g/30mins, followed by PBS wash and media replacement.

value: MCMV, 48 h p.i.

tag: barcode

value: GGCA

tag: replicate

value: Replicate 2

tag: molecule subtype

value: 5' RNA ends enriched


title: WT HAP1 cells, Adenosine treated, 48hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTAD4803

value: chronic myelogenous leukemia

value: wild-type

value: Adenosine


title: cRNA-seq MCMV 24hpi B

value: Immortalized embryonic fibroblasts

value: MCMV, 24 h p.i.

value: TGGC


title: Plasma, NEXTFlex, rep2

description:
P2Nflex
raw_counts_librarykit_allmirna.tsv
raw_counts_librarykit_spike-ins.tsv

tag: tissue

value: Blood

value: NEXTFlex


title: WT HAP1 cells, Adenosine treated, 48hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTAD4802


title: E2 lung1


title: Plasma, NEBNext, rep2

description:
P2NEB
raw_counts_librarykit_allmirna.tsv
raw_counts_librarykit_spike-ins.tsv

tag: miRNA preparation kit

value: NEBNext


title: cRNA-seq MCMV 12hpi B

value: MCMV, 12 h p.i.

value: MCMV

value: GGCG


title: PBS-2

value: brain endothelial cells (BECs)

value: cortex

value: tie2-Cre; ai9; rpl22HA/HA mice

value: male

value: 8-12 weeks old

value: phosphate buffered saline (PBS)


title: WT HAP1 cells, Adenosine treated, 48hr, rep 1

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTAD4801

value: chronic myelogenous leukemia

value: wild-type


title: WT HAP1 cells, DMSO treated, 6hr, rep 1

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTDM0601

value: DMSO


title: E1 lung1

value: Haplotype-I aged+LVS

value: lung


title: cRNA-seq MCMV 6hpi B

value: Immortalized embryonic fibroblasts

value: MCMV, 6 h p.i.

value: CAAT

value: Replicate 2

value: 5' RNA ends enriched


title: Plasma, NEXTFlex, rep1

description:
P1Nflex
raw_counts_librarykit_allmirna.tsv
raw_counts_librarykit_spike-ins.tsv

value: Blood

value: NEXTFlex

tag: extracellular vesicles isolation method


title: cRNA-seq MCMV 2hpi B

value: MCMV, 2 h p.i.

value: MCMV

value: TTGT


title: Plasma, SMARTer, rep1

description:
P1SMARTer
raw_counts_librarykit_allmirna.tsv
raw_counts_librarykit_spike-ins.tsv

value: SMARTer


title: C1 lung1

value: Haplotype-I aged


title: WT HAP1 cells, Adenosine treated, 24hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTAD2402

value: chronic myelogenous leukemia

tag: treatment

value: Adenosine


title: cRNA-seq Mock B

value: Mock

value: GGTT


title: cRNA-seq MCMV 48hpi A

value: MCMV, 48 h p.i.

value: Replicate 1


title: Plasma, NEBNext, rep1

description:
P1NEB
raw_counts_librarykit_allmirna.tsv
raw_counts_librarykit_spike-ins.tsv

value: NEBNext


title: WT HAP1 cells, Adenosine treated, 24hr, rep 1

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTAD2401

tag: cell line

value: wild-type


title: C2 lung1

value: lung


title: WT HAP1 cells, Adenosine treated, 6hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTAD0603

tag: genotype


title: Human ESC CLIP-seq IgG control

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

institute: Sejong University

description: Sequences from IgG CLIP libraries were combined to obtain sequence coverage.

data_processing:
Reads were demuliplexed by using codes in the id of each reads by using the ShortRead package in BioConductor. Identical sequences were collapsed using the occurrenceFilter function in the ShortRead package.
3' adapter sequences were trimmed using the trimLRPatterns function in the ShortRead package. The 3' adapter sequences trimmed were sequences containing CCTGTGGTCGTAGCATCAGCTA.
The trimmed sequences were collapsed and converted to reverse complementary sequences. After conversion to complementary sequences, the last 5 nucleotides at the 3' ends are randomized nucleotides followed by the TC dinucleotide. The 5' ends frequently contain nontemplated nucleotides introduced by Taq DNA polymerase.
CLIP-seq reads were sequentially mapped to rRNA, snRNA, snoRNA, tRNA and microRNA precursors sequences using Bowtie verions 1.0.1  with the following configurations -q –m 70 -n 2 -l 44 -5 1 -3 5 -a --best --strata -p 11 --sam --norc for noncoding RNAs. The remaining reads were aligned with the hg19 human genome with the configuration -q –m 1 -n 0 -l 70 -5 1 -3 5 -a --best --strata -p 11 --sam  unique genomic sequences to generate bedGraph files.

source_name: Human embryonic stem cell H1

growth_protocol: The H1 hESC cells were maintained on a mitotically inactivated mouse feeder (MEF) layer as follows. As a culture medium, DMEM/F12 supplemented with 20% Knockout Serum Replacement, 1% MEM non-essential amino acids, 1mM L-glutamine, 0.1mM β-mercaptoethanol and 4ng/ml basic FGF (Invitrogen) was used. Before analyses, hESCs were passaged three times without the feeder cells. For feeder-free culture, hESCs were dissociated with collagenase IV and plated on a Geltrex-coated plate with MEF-conditioned media supplemented with 50ng/ml basic FGF.

extract_protocol:
Two million cells were resuspended in 250 μl lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1 mM MgCl2, 0.1 mM CaCl2, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) containing EDTA-free protease inhibitor cocktail (Roche) and RNase inhibitor (Ambion) and briefly sonicated by using the Bioruptor.
The lysates were treated with 5 μl of Turbo DNase (Ambion) and 10 μl of 1 U/μl RNase I (Ambion) at 37°C for 3 min. Cellular debris was removed by centrifugation at 13,000 rpm for 15 min. Protein-RNA complexes were immunopurified with 1ug of anti-SF3B1 (Bethyl, A300-996A) or IgG antibody (Bethyl laboratories) bound to Protein A/G Dynabeads. Beads were washed twice with high-salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, and 0.1% SDS) followed by two washes with PNK buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, and 0.2% Tween-20). For dephosphorylation of 3’ ends, 1U of FastAP alkaline phosphatase (Fermentas) was added to the beads and incubated at 37°C for 20 min. After washing the beads twice with PNK buffer, protein-bound RNAs were ligated to a pre-adenylylated 3’ adaptor overnight at 16°C (5' AppNNNTCCGTCGTGTAGGGAAAGAGTGTAGATC/3Bio/). Beads were washed twice with PNK buffer again. The ligated RNAs were separated by 4-12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane, and excised from the membrane. The protein was degraded by proteinase K treatment, and RNA was recovered by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. The RNA-adapter hybrids were converted into cDNAs with RT primer (5' /Phos/CCTGTGGTCGTAGCATCAGCTAGATCTACACTCTTTCCCTACACGA) and SuperScript III reverse transcriptase (Invitrogen). The cDNAs were size-fractionated by electrophoresis on a 12% denaturing polyacrylamide gel and circularized by single-stranded DNA ligase (Epicentre). Circularized cDNAs were amplified with PCR primers, (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACG,  CAAGCAGAAGACGGCATACGAGA[code]TAGCTGATGCTACGACCACAGG) in which one of them contained a 5-nt primer code for de-multiplexing. PCR products were purified by agarose gel elution and subjected to next-generation sequencing.
CLIP-seq. Since the oligonucleotides for library constructruction were different from commercial kits, the sequencing primer for enriched RNA has the sequence of AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACG and 76 nucleotides were read. For de-multiplexing, a special primer (CCTGTGGTCGTAGCATCAGCTA) was used to obtain 6-nt codes.

treatment_protocol: For CLIP experiments H1 cells were irradiated with 300 mJ/cm2 of UVC light (254 nm) by using the CL-1000 ultraviolet crosslinker (UVP).

value: Human embryonic stem cell H1

tag: antibody

value: IgG

value: Wild type


title: WT HAP1 cells, Adenosine treated, 6hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTAD0602

tag: time point


title: Human ESC SF3B1 CLIP-seq biological replicate2

description:
Sequences from indepentent SF3B1 CLIP libraries were combined to obtain sequence coverage.
SF3B1_coverage_neg.bedGraph.gz
SF3B1_coverage_pos.bedGraph.gz


title: B2 lung1

value: Haplotype-II aged


title: cRNA-seq MCMV 12hpi A

value: Immortalized embryonic fibroblasts

value: MCMV, 12 h p.i.

value: MCMV

value: TGGC

value: 5' RNA ends enriched


title: B3 lung1


title: WT HAP1 cells, Adenosine treated, 6hr, rep 1

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTAD0601

value: chronic myelogenous leukemia

value: Adenosine


title: MTHFD1 KO HAP1 cells, DMSO treated, 48hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5DM4803

value: MTHFD1 Knockout

value: DMSO


title: cRNA-seq MCMV 24hpi A

value: MCMV, 24 h p.i.

value: GGCG

value: Replicate 1


title: peripheral blood allergic Sample 22

city: Taipei

first: Jyh-Hong

last: Lee

address: 8 Chung-Shan South Road

country: Taiwan

institute: National Taiwan University Hospital

description: peripheral blood

data_processing:
Unaligned data were written to a FASTQ file, and then clean reads were annotated with miRBase to identify known miRNAs using Bowtie 1 (v1.3.1)[25]. MiRNA expression levels are expressed as reads per million (RPM). We used DESeq2 (version 1.26.0) for normalization and differential expression analysis.
Supplementary files format and content: EXCEL files include RPM values for each Sample

source_name: blood

extract_protocol:
Total RNA was extracted from peripheral blood white blood cells using the miRNeasy Extraction Kit (Qiagen) according to the manufacturer’s protocol.
Sequencing libraries were generated using the TruSeq Small RNA Library Prep Kit (Illumina) following the manufacturer’s recommendations and index codes were added to attribute sequences to the samples.

value: blood

value: tissue


title: cRNA-seq MCMV 6hpi A

value: MCMV, 6 h p.i.

value: TTGT


title: Human ESC SF3B1 CLIP-seq biological replicate1

value: Human embryonic stem cell H1

value: Wild type


title: peripheral blood allergic Sample 21

description: peripheral blood


title: cRNA-seq Mock A

value: Immortalized embryonic fibroblasts

value: Mock

value: GGTC


title: peripheral blood allergic Sample 20

description: peripheral blood


title: C3 lung1

value: Haplotype-I aged

value: lung


title: A2 lung1

value: Haplotype-I adult


title: WT HAP1 cells, Adenosine treated, 24hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTAD2403

value: chronic myelogenous leukemia

value: wild-type

value: Adenosine


title: peripheral blood allergic Sample 19

description: peripheral blood


city: Portland

first: June

last: Treerat

state: Oregon

address: 3181 SW Sam Jackson Park Rd, MRB 433

department: Restorative Dentistry

institute: Oregon Health & Science University

data_processing:
Sequence reads were trimmed to remove any possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the S. sanguinis SK36 reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6. As a result, BAM files were generated.
Unique gene hit counts (yield .counts files) were calculated by using featureCounts from the Subread package v.1.5.2.
DESeq2 was used to compare gene expression between Group A (JT1, JT2, and JT3) and Group D (JT8, JT9, and JT10) samples.
The Wald test was used to generate p-values and Log2 fold changes. The Log2 fold change of the normalized hit counts was calculated by: Log2(Group D mean normalized counts/Group A mean normalized counts). padj was the result of the Benjamini-Hochberg algorithm adjusted p-value.
Genes with an adjusted p-value < 0.05 and absolute Log2 fold change > 1 were called as differentially expressed genes for each comparison.
Supplementary files format and content: DEseq2-normalized counts for S.sanguinis SK36 cultured in ASS medium replicate 1 "JT1.counts.txt"
Supplementary files format and content: DEseq2-normalized counts for S.sanguinis SK36 cultured in ASS medium replicate 2 "JT2.counts.txt"
Supplementary files format and content: DEseq2-normalized counts for S.sanguinis SK36 cultured in ASS medium replicate 3 "JT3.counts.txt"
Supplementary files format and content: DEseq2-normalized counts for S.sanguinis SK36 cultured in C. durum ATCC33822 supernatant replicate 1 "JT8.counts.txt"
Supplementary files format and content: DEseq2-normalized counts for S.sanguinis SK36 cultured in C. durum ATCC33822 supernatant replicate 2 "JT9.counts.txt"
Supplementary files format and content: DEseq2-normalized counts for S.sanguinis SK36 cultured in C. durum ATCC33822 supernatant replicate 3 "JT10.counts.txt"

organism: Streptococcus sanguinis

source_name: Prokaryotes

growth_protocol: S. sanguinis SK36 was grown  in chemically defined artificial saliva solution (ASS) medium until the optical density at 600 nm (OD600) was approximately 0.4.

extract_protocol:
RNA was extracted from whole cells using a Trizol-based protocol, genomic DNA was digested using TURBO DNaseI according to manufacters protocol and samples were cleaned using Qiagen RNeasy kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA samples were submitted to GENEWIZ Inc (South Plainfield, NJ). After that, rRNA was eliminated and performed cDNA library construction following GENEWIZ's protocols.

treatment_protocol: C. durum ATCC33822 supernatant collected from the overnight culture in ASS medium was used to grow S. sanguinis SK36 until the OD600 was approximately 0.4.

value: Prokaryotes

value: WT

value: C. durum ATCC33822 supernatant

tag: time


title: Astrocytes, DIZE-2

city: Nanjing

first: Rui

last: Duan

address: No.68 Changle road

country: China

institute: Nanjing first hospital

data_processing:
Reads obtained from the sequencing machines included dirty reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get clean tags,raw reads were further filtered according to the following rules:
1) Removing low quality reads containing more than one low quality (Q-value≤20) base or
containing unknown nucleotides(N);
2) Removing reads without 3’adapters;
3) Removing reads containing 5’adapters;
4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them;
5) Removing reads containing ployA in small RNA fragment;
6) Removing reads shorter than 18nt (not include adapters).
Subsequent RNA-seq reads were mapped to GenBank, Rfam, Genome and miRBase databases.
miRNAs differential expression analysis was performed by edgeR software between two different groups or samples.We identified miRNAs with a fold change ≥2 and P value <0.05 in a comparison as significant DE miRNAs
Assembly: mm9
Supplementary files format and content: miRNA expression, differential expression

source_name: brain

extract_protocol:
Trizol total RNA isolation Kit was used to extract total RNA following the manufacturer’s instructions. The concentration and integrity of RNA were determined by Nanodrop  and Agilent 2100 Bioanalyzer.
RNAs were first ligated with a 3′ adapter followed by size fraction and ligation to 5′ adapter. Then, the small RNA libraries were constructed and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: Injected intraperitoneally with 15 mg/kg DIZE once a day for 30 consecutive days

value: astrocytes

value: brain

tag: strain

value: diminazene aceturate (DIZE)


title: MTHFD1 KO HAP1 cells, DMSO treated, 48hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5DM4802

tag: cell type

value: MTHFD1 Knockout

value: DMSO


title: MTHFD1 KO HAP1 cells, DMSO treated, 48hr, rep 1

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5DM4801


title: cRNA-seq MCMV 2hpi A

value: Immortalized embryonic fibroblasts

tag: time post infection

value: MCMV, 2 h p.i.

value: MCMV

value: CCAC

value: Replicate 1

value: 5' RNA ends enriched


title: A1 lung1

value: Haplotype-I adult

value: lung


title: A3 lung1


title: MTHFD1 KO HAP1 cells, DMSO treated, 24hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5DM2403

value: chronic myelogenous leukemia


title: peripheral blood allergic Sample 18

description: peripheral blood

value: blood

value: tissue


title: MTHFD1 KO HAP1 cells, DMSO treated, 24hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5DM2402


title: SK36 cultured in C. durum ATCC33822 supernatant replicate 1

value: Prokaryotes

value: WT

value: C. durum ATCC33822 supernatant


title: Astrocytes, APP-2

treatment_protocol: Injected intraperitoneally with vehicle (0.9% sterile saline) once a day for 30 consecutive days

value: astrocytes

value: brain

value: control


title: MTHFD1 KO HAP1 cells, DMSO treated, 6hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5DM0603

value: MTHFD1 Knockout

value: DMSO


title: MTHFD1 KO HAP1 cells, DMSO treated, 24hr, rep 1

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5DM2401


title: Astrocytes, APP-3


title: peripheral blood allergic Sample 15

description: peripheral blood


title: SK36 cultured in ASS defined medium replicate 3

value: Chemically defined artificial saliva solution (ASS) medium


title: Astrocytes, DIZE-3

value: diminazene aceturate (DIZE)


title: SK36 cultured in C. durum ATCC33822 supernatant replicate 2


title: SK36 cultured in ASS defined medium replicate 1


title: HepG2_caffeine_24h 1000 μM_rep3

city: Beijing

first: Yuan

last: Li

address: 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing

department: Post-translational modification

institute: Beijing Proteome Research Center

data_processing:
Cleaned reads were aligned to the genome reference of Ensembl GRCh38 with Hisat2 using strand specific parameters.
For RNAseq data, a stringent pre-filtering criterion of median counts over all samples < 5 was carried out. The normalization and analysis of differentially expressed genes (DEGs) were conducted by using DESeq2
Assembly: genome reference of Ensembl GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HepG2 cells

growth_protocol: About 5×107 HepG2 cells were treated in triplicates using 6 concentrations of caffeine and a control for 24 h.

extract_protocol:
After the culture medium with caffeine was removed, the cells were harvested by digestion of trypsin-EDTA solution and washed with ice-cold PBS twice and then centrifuged at 12,000 g for 15 min at 4 °C. RNAs were then purified by Trizol reagent. RNAs were quantified by a NanoPhotometer.
The RNA samples were purified by poly (dT) beads, converted to cDNA using SmartScribe Rtase kit according to manufacturer’s protocol.

treatment_protocol: Caffeine was dissolved in DMEM (100 mM stock solutions). Further dilutions were made with serum-free DMEM. At the time of caffeine exposure, after the FBS-DMEM culture medium was removed, HepG2 cells were washed with PBS once and were finally treated in the fresh serum-free DMEM culture medium containing different concentrations of caffeine (0-1000 μM) for 24 h.

value: HepG2 cells

value: treated with 1000 microM caffeine for 24 h


title: Astrocytes, APP-1


title: Astrocytes, DIZE-1


title: SK36 cultured in ASS defined medium replicate 2


title: MTHFD1 KO HAP1 cells, DMSO treated, 6hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5DM0602


title: HepG2_caffeine_24h 1000 μM_rep2


title: peripheral blood allergic Sample 14

description: peripheral blood


title: peripheral blood allergic Sample 12

description: peripheral blood


title: peripheral blood allergic Sample 17

description: peripheral blood


title: B1 lung1

value: Haplotype-II aged


title: MTHFD1 KO HAP1 cells, Adenosine treated, 48hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5AD4803

value: Adenosine


title: Male_AL_biol rep 6

city: Edinburgh

first: William

middle: P

last: Cawthorn

address: 47 Little France Crescent

department: University/BHF Centre for Cardiovascular Science

country: United Kingdom

institute: The University of Edinburgh

description: A

data_processing:
After the trimming by TrimGalore and quality control by FastQC, sequences were aligned to the mouse genome (mm10) with the annotation data from the website of University of California Santa Cruz (https://hgdownload.soe.ucsc.edu) using STAR (v2.7.10a)
Mapped reads were counted using featureCounts in Subread package (v1.5.2).
Assembly: GRCm38/mm10
Supplementary files format and content: Count data were normalised using DESeq2 (v1.36.0) and saved in .txt format, which includes normalised values for each sample.

source_name: Liver

growth_protocol: C57BL/6NCrl mice were fed ad libitum (AL) or underwent caloric restriction (CR) (70% of AL intake) from 9-13 weeks of age.

extract_protocol:
At necropsy, livers were harvested and stored on dry ice. RNA was isolated from tissues using RibozolTM solution (Amresco, cat. No. N580) according to the manufacturer’s protocol.
Library preparation and sequencing was performed by BGI (Shenzhen, Guangdong, China)

value: Liver

tag: Sex

value: Male

value: AL


title: peripheral blood allergic Sample 13

description: peripheral blood

value: blood

value: tissue


title: MTHFD1 KO HAP1 cells, DMSO treated, 6hr, rep 1

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5DM0601

value: chronic myelogenous leukemia


title: MTHFD1 KO HAP1 cells, Adenosine treated, 48hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5AD4802


title: HepG2_caffeine_24h 1000 μM_rep1


title: peripheral blood allergic Sample 16

description: peripheral blood


title: Female_CR_biol rep 6

value: Female

tag: group

value: CR

value: WT


title: MTHFD1 KO HAP1 cells, Adenosine treated, 48hr, rep 1

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5AD4801

value: MTHFD1 Knockout


title: peripheral blood non-allergic Sample 11

description: peripheral blood


title: HepG2_caffeine_24h 100 μM_rep3

value: treated with 100 microM caffeine for 24 h


title: MTHFD1 KO HAP1 cells, Adenosine treated, 24hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5AD2403


title: peripheral blood non-allergic Sample 10

description: peripheral blood


title: HepG2_caffeine_24h 100 μM_rep2


title: MTHFD1 KO HAP1 cells, Adenosine treated, 24hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5AD2402


title: Female_AL_biol rep 4


title: HepG2_caffeine_24h 100 μM_rep1


title: peripheral blood non-allergic Sample 8

description: peripheral blood


title: MTHFD1 KO HAP1 cells, Adenosine treated, 24hr, rep 1

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5AD2401


title: Male_CR_biol rep 5

description: B


title: Female_CR_biol rep 5


title: peripheral blood non-allergic Sample 7

description: peripheral blood


title: MTHFD1 KO HAP1 cells, Adenosine treated, 6hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5AD0602


title: HepG2_caffeine_24h 10 μM_rep3

value: treated with 10 microM caffeine for 24 h


title: MTHFD1 KO HAP1 cells, Adenosine treated, 6hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5AD0603


title: peripheral blood non-allergic Sample 6

description: peripheral blood


title: HepG2_caffeine_24h 10 μM_rep2


title: HepG2_caffeine_24h 10 μM_rep1


title: Male_CR_biol rep 4


title: Male_AL_biol rep 5


title: MTHFD1 KO HAP1 cells, Adenosine treated, 6hr, rep 1

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
F5AD0601


title: Female_AL_biol rep 3


title: peripheral blood non-allergic Sample 4

description: peripheral blood


title: peripheral blood non-allergic Sample 5

description: peripheral blood


title: HepG2_caffeine_24h 1 μM_rep3

value: treated with 1 microM caffeine for 24 h


title: Neural Stem Cell exosome miRNA

city: wuhan

first: Meng

last: Cai

state: hubei

address: Building 5, Precision Medicine Industrial Base, East Lake New Technology Development Zone

institute: iregene

data_processing:
Raw data (raw reads) of fastq 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.
The clean reads were de-redundant using miRDeep2 software, and the collasped reads were compared with the reference genome.
The collasped reads were compared with the Rfam database using cmscan to identify small RNA species.
The known miRNA sequences of species were obtained in miRBase. The information of known miRNA expression levels in samples and the prediction of novel miRNAs were obtained using miRDeep2.
Assembly: Homo sapiens GRCh38.94
Supplementary files format and content: tab-delimited text files include read count for each miRNA

source_name: Neural Stem Cell exosome

extract_protocol:
Small RNA (< 200 nt) was isolated using the miRNeasy micro kit (Qiagen) according to manufacturer's instructions.
The Illumina® Truseq small RNA Sample Prep Kit was used to process the samples according to the kit-specific guidelines.

value: Neural Stem Cell exosome


title: Male_CR_biol rep 3


title: HepG2_caffeine_24h 1 μM_rep2

value: HepG2 cells


title: peripheral blood non-allergic Sample 3

description: peripheral blood


title: HepG2_caffeine_24h 1 μM_rep1


title: peripheral blood non-allergic Sample 9

description: peripheral blood


title: peripheral blood non-allergic Sample 2

description: peripheral blood


title: Male_AL_biol rep 4


title: Female_AL_biol rep 5


title: HepG2_caffeine_24h 0.1 μM_rep3

value: treated with 0.1 microM caffeine for 24 h


title: Male_AL_biol rep 3


title: HepG2_caffeine_24h 0.1 μM_rep2


title: AGS cells 1

city: Changzhi

first: Jia

last: Wang

state: Shanxi

address: Jiefang East Street

department: Immunology

institute: Changzhi Medical College

data_processing:
Clean Data was obtained by filtering Raw Data, removing joint sequences and low-quality reads
Then, effective reads were obtained by comparing with ribosomal RNA sequences in RNAcentral database and removing ribosomal RNA sequences.
Effective reads were compared with the reference genome using BWA-MEM
CIRI2 software was used to predict the circrnas before and after formation, and further identify candidate circRNA.
Based on predicted junction reads of circrnas, THE JUNCTION reads were calibrated by RPM and normalized
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

source_name: stomach

growth_protocol: AGS cells were grown in DMEM medium containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml).All cells were incubated at 37°C in 5% CO2.

extract_protocol:
By Ribo zero rRNA removal kit and RNase R-treated RNA sequencing (circRNA-seq)
After rRNA was removed by probe and linear RNA was removed by RNase R, circrnas library was constructed.

treatment_protocol: Transfectd AGS cell with FLAG-DDX5 or FLAG-tagged empty vector (negative control, NC)

value: stomach

value: AGS

value: adenocarcinoma cells

value: DDX5 Control

value: transfected AGS with FLAG-tagged empyt vector


title: peripheral blood non-allergic Sample 1

description: peripheral blood

value: blood

value: tissue


title: Male_CR_biol rep 2

value: Liver

value: Male


title: Female_CR_biol rep 4

value: Female

value: CR

value: WT


title: AGS cellls,transfected AGS 2

value: DDX5 OE

value: transfected AGS with FLAG-DDX5


title: AGS cells,transfected AGS 1


title: HepG2_caffeine_24h 0.1 μM_rep1


title: Female_CR_biol rep 3


title: Patient 3, Standard Media Treated, Replicate 3

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P3FUR3

source_name: Patient-derived

value: Patient-derived

value: Fibroblast

value: Standard FBS Media


title: HepG2_caffeine_24h 0.01 μM_rep3

value: HepG2 cells

value: treated with 0.01 microM caffeine for 24 h


title: Male_AL_biol rep 2

value: AL


title: AGS cells 2

value: stomach

value: AGS

value: adenocarcinoma cells

value: DDX5 Control


title: Patient 3, Standard Media Treated, Replicate 1

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P3FUR1


title: Female_AL_biol rep 2

value: Liver


title: Female_CR_biol rep 2


title: HepG2_caffeine_24h 0 μM_rep3

value: untreated


title: Patient 3, Dialyzed Media Treated, Replicate 2

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P3DIR2

value: Dialyzed Media


title: Female_AL_biol rep 1

value: Female


title: HepG2_caffeine_24h 0 μM_rep2


title: ctrl_dLN_CD40Lneg - replicate 2

type: RNA

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.

data_processing: In DRFZ with GeneChip Operating System (GCOS, Affymetrix) generated CHP and CEL files were analyzed at INRAE, France (Luc Jouneau). Only chips, which fulfilled all chip and hybridization quality criteria, were selected for analysis. Normalization has been performed using R package GCRMA. To detect which probe sets were expressed in a given sample and to get Present/Marginal/Absent calls mas5calls function of affy R package was used. Differential expression was detected using limma R package.

label: biotin

source_name: CD4+CD40L- from dLN of control EAE mice

growth_protocol: For EAE induction, each mouse received 100 μg of MOG(35–55) peptide emulsified in CFA containing 50 μg of heat-killed Mycobacterium tuberculosis H37Ra (Sigma-Aldrich) at a final volume of 100 μl injected s.c. into the hind legs. In addition, 200 ng of pertussis toxin (European Cell and Culture Collection, Dorset, U.K.) was given in 0.5 ml of PBS i.p. on the same day and 2 days later. Draining lymph nodes (a pair of popliteal LN, paraaortic LN, and inguinal LN) and spleens were processed to obtain single cell suspensions, followed by red blood cells lysis. Single cell suspensions were then treated as indicated in the summary.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

tag: gender

value: female

value: dLN (popliteal, paraaortic, inguinal)


title: Male_CR_biol rep 1

value: Male

value: CR

value: WT


title: HepG2_caffeine_24h 0 μM_rep1


title: Patient 3, Adenosine Treated, Replicate 3

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P3ADR3

value: Patient-derived

value: Fibroblast

value: Adenosine


title: Male_AL_biol rep 1

value: AL


title: HepG2_caffeine_24h 0.01 μM_rep2

value: HepG2 cells

value: treated with 0.01 microM caffeine for 24 h


title: Patient 3, Adenosine Treated, Replicate 2

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P3ADR2


title: Female_CR_biol rep 1


title: ctrl_dLN_CD40Lneg - replicate 3

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.


title: CpG_spleen_CD40Lpos - replicate 3

source_name: CD4+CD40L+ from the spleen of CpG-treated EAE mice

value: spleen


title: CpG_spleen_CD40Lpos - replicate 1


title: CpG_spleen_CD40Lpos - replicate 2


title: ctrl_spleen_CD40Lpos - replicate 3

source_name: CD4+CD40L+ from the spleen of control EAE mice


title: Patient 3, Standard Media Treated, Replicate 2

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P3FUR2

value: Standard FBS Media


title: ctrl_spleen_CD40Lpos - replicate 2


title: Patient 3, Adenosine Treated, Replicate 1

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P3ADR1


title: HepG2_caffeine 1000 μM_rep2

growth_protocol: About 5×10^7 HepG2 cells were treated in triplicates using 6 concentrations of caffeine and a control for 6 h.

treatment_protocol: Caffeine was dissolved in DMEM (100 mM stock solutions). Further dilutions were made with serum-free DMEM. At the time of caffeine exposure, after the FBS-DMEM culture medium was removed, HepG2 cells were washed with PBS once and were finally treated in the fresh serum-free DMEM culture medium containing different concentrations of caffeine (0-1000 μM) for 6 h.

value: treated with 1000 microM caffeine for 6 h


title: HepG2_caffeine_24h 0.01 μM_rep1


title: HepG2_caffeine 1000 μM_rep3


title: HepG2_caffeine 100 μM_rep3

value: treated with 100 microM caffeine for 6 h


title: ctrl_dLN_CD40Lneg - replicate 1


title: Patient 3, Dialyzed Media Treated, Replicate 1

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P3DIR1

value: Dialyzed Media


title: HepG2_caffeine 100 μM_rep2


title: HepG2_caffeine 100 μM_rep1


title: HepG2_caffeine 1000 μM_rep1


title: Patient 3, Dialyzed Media Treated, Replicate 3

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P3DIR3


title: Patient 2, Standard Media Treated, Replicate 2

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P2FUR2


title: Patient 2, Standard Media Treated, Replicate 1

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P2FUR1


title: Patient 2, Dialyzed Media Treated, Replicate 2

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P2DIR2


title: Patient 2, Adenosine Treated, Replicate 2

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P2ADR2


title: Patient 2, Adenosine Treated, Replicate 1

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P2ADR1


title: Control Fibroblast, Standard Media Treated, Replicate 3

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
CTFUR3

source_name: BJ

value: BJ

value: wild-type


title: CpG_dln_CD40Lpos - replicate 3

source_name: CD4+CD40L+ from dLN of CpG-treated EAE mice

value: female

value: dLN (popliteal, paraaortic, inguinal)


title: Control Fibroblast, Standard Media Treated, Replicate 2

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
CTFUR2


title: HepG2_caffeine 10 μM_rep1

value: treated with 10 microM caffeine for 6 h


title: CpG_dln_CD40Lpos - replicate 1


title: ctrl_spleen_CD40Lpos - replicate 1


title: ctrl_dln_CD40Lpos - replicate 1

source_name: CD4+CD40L+ from dLN of control EAE mice


title: HepG2_caffeine 1 μM_rep2

value: treated with 1 microM caffeine for 6 h


title: CpG_dln_CD40Lpos - replicate 2


title: Patient 2, Dialyzed Media Treated, Replicate 1

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
P2DIR1

value: Patient-derived


title: ctrl_dln_CD40Lpos - replicate 3


title: HepG2_caffeine 10 μM_rep3


title: Control Fibroblast, Standard Media Treated, Replicate 1

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
CTFUR1

value: Fibroblast


title: HepG2_caffeine 1 μM_rep1


title: HepG2_caffeine 10 μM_rep2


title: HepG2_caffeine 1 μM_rep3


title: HepG2_caffeine 0.1 μM_rep2

value: treated with 0.1 microM caffeine for 6 h


title: HepG2_caffeine 0.1 μM_rep1


title: HepG2_caffeine 0.1 μM_rep3


title: d3_ctr_dln - replicate 3

source_name: dLN cells taken on day 3 from mice immunized with classical EAE protocol

growth_protocol: For EAE induction, each mouse received 50 μg of MOG(35–55) peptide emulsified in CFA containing 400 μg of heat-killed Mycobacterium tuberculosis H37Ra (Sigma-Aldrich) at a final volume of 100 μl injected s.c. into the hind legs. In addition, 200 ng of pertussis toxin (European Cell and Culture Collection, Dorset, U.K.) was given in 0.2 ml of PBS i.v. on the same day and 2 days later. Draining lymph nodes (a pair of popliteal LN, paraaortic LN, and inguinal LN) were processed to obtain single cell suspensions, followed by red blood cells lysis. Single cell suspensions were then treated as indicated in the summary.

value: classical EAE protocol

value: day 3


title: Control Fibroblast, Dialyzed Media Treated, Replicate 2

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
CTDIR2


title: d3_CpG_dln - replicate 1

source_name: dLN cells taken on day 3 from mice immunized with CpG-B-supplemented EAE protocol

value: CpG-B-supplemented EAE protocol


title: ctrl_dln_CD40Lpos - replicate 2


title: d3_CpG_dln - replicate 3


title: d3_CpG_dln - replicate 2


title: Control Fibroblast, Dialyzed Media Treated, Replicate 3

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
CTDIR3


title: Control Fibroblast, Dialyzed Media Treated, Replicate 1

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
CTDIR1


title: HepG2_caffeine 0.01 μM_rep3

value: treated with 0.01 microM caffeine for 6 h


title: d3_ctr_dln - replicate 2


title: Control Fibroblast, Adenosine Treated, Replicate 3

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
CTADR3

value: Adenosine


title: Control Fibroblast, Adenosine Treated, Replicate 1

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
CTADR1


title: WT HAP1 cells, DMSO treated, 48hr, rep 2

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTDM4802

value: chronic myelogenous leukemia

value: DMSO


title: HepG2_caffeine 0 μM_rep2

value: untreated


title: HepG2_caffeine 0.01 μM_rep2


title: Control Fibroblast, Adenosine Treated, Replicate 2

description:
poly-A enriched RNA
Patient_counts_normalised.tsv
CTADR2

value: BJ


title: d3_ctr_dln - replicate 1


title: d1_CpG_dln - replicate 2

source_name: dLN cells taken on day 1 from mice immunized with CpG-B-supplemented EAE protocol

value: day 1


title: d1_CpG_dln - replicate 3

value: female


title: HepG2_caffeine 0 μM_rep1


title: HepG2_caffeine 0.01 μM_rep1


title: HepG2_caffeine 0 μM_rep3


title: WT HAP1 cells, DMSO treated, 48hr, rep 3

description:
poly-A enriched RNA
Adenosine_counts_normalised.tsv
WTDM4803

value: wild-type


title: d1_ctr_dln - replicate 3

source_name: dLN cells taken on day 1 from mice immunized with classical EAE protocol

value: dLN (popliteal, paraaortic, inguinal)


title: d1_ctr_dln - replicate 2


title: ZNF593-AS_rep3

city: Wuhan

first: rong

last: xie

state: Hubei

address: Jiefang Ave.

institute: Huazhong university of science and technology

data_processing:
Illumina Casava software was used for basecalling.
Cutadapt (Version 1.2.1) (Martin M, 2011) was used to remove 3' end joints, at least 10 bp Overlap (AGATCGGAAG), and 20% base error rate was allowed.
QCofsequencedreadsweredonebyFASTQC.
Reads were than aligned to the GRCm38 genome assembly using Bowtie2 and Tophat2.
Assembly: GRCm38
Supplementary files format and content: xlsx files include reads counts for each Sample

source_name: HL-1 cell

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen Life Technologies).
Sequencing libraries were prepared according to Illumina’s protocols.

value: HL-1 cell

value: palmitic acid stimulation and ZNF595-AS overexpression


title: ZNF593-AS_rep2

value: palmitic acid stimulation and ZNF594-AS overexpression


title: vector_rep3

value: palmitic acid stimulation


title: ZNF593-AS_rep1

value: palmitic acid stimulation and ZNF593-AS overexpression


title: vector_rep2


title: MV3, day2, core, replicate2

city: Nijmegen

first: Peter

last: Friedl

address: Geert Groteplein 28

department: Cell Biology

country: Netherlands

institute: RIMLS, Radboudumc

data_processing:
Raw FASTQ data was cleaned from ribosomal RNA using Bowtie and the sequencing reads with quality score higher than 15 were chosen for subsequent analysis. Processed reads were aligned to human genome (hg38) using STAR aligner with default parameters. Human uniquely mapped reads were annotated and counted against human genome using HTSeq-count. The data table was constructed based on the empirical counted reads.
To obtain the differentially expressed genes between conditions, size factor normalization and pair-wise negative binomial test were used within the DESeq2 package. Genes with expression difference of 2-fold change and p-value < 0.05 were considered to be differentially expressed. Heatmaps of variable genes were created with ComplexHeatmap package. The enrichR package for R were used for the database query and visualization of the enrichment results.
Assembly: hg38
Supplementary files format and content: comma separated count table

extract_protocol:
MV3 H2B-GFP spheroids with a diameter of 1 mm (50,000 cells) were cultured for two days. Higher number of cells was required to obtain enough material for RNA sequencing. After replacing the medium by PBS, samples were transferred to a sterile fluorescence stereomicroscope for image guided dissection (Leica MZFLII, 0.125 NA., EL6000external light source, GFP Plus filter sets). PBS was removed and the core was punched out with a 1 mm biopsy puncher (Miltex, Sterile Biopsy punch with plunger, #3331AAP/25) by pressing the punch down around the spheroid core and sucking it out using the punch plunger. The core was released into a sterile 1.5 ml Eppendorf tube and placed on dry ice for snap-freezing. The corresponding invasion zone was controlled on any left-over core region, recognizable by much brighter fluorescence and removed from the collagen gel with a 3 mm biopsy puncher (Miltex, Sterile Biopsy punch with plunger, #3332P/25). Exclusion criteria were ellipsoid shaped spheroids and unsuccessfully punched spheroids with ruptured gels. Samples were stored at -80°C until RNA extraction.
RNA was isolated using an RNA isolation kit (Qiagen, RNeasy Micro Kit) according to the manufacturer’s protocol. RNA concentration was measured using a NanoDrop 2000 (ThermoFisher) and stored at -80°C. The integrity and quality of RNA was evaluated using the Experion RNA HighSens AnalysisKit (Biorad, 7007105) on a 2100 Bioanalyzer platform (Agilent). For CDNA synthesis starting from 1-10 ng total RNA, SMARTer Ultra low Input RNA kit (Clontech, 634936) was used and processed according to the manufacturer’s protocol. The transcribed DNA was sheared into fragments of 200-600 bp using Bioruptor Pico sonication device (Diagenode). Subsequently the library preparation for Next Generation Sequencing has been carried out according to the Illumina standard protocol using the KAPA Hyper prep kit (KAPA Biosystems).

value: core

value: Highly metastatic melanoma

value: Day 2


title: MV3, day2, invasion, replicate2

value: 3D invasion


title: MV3, day2, invasion, replicate1


title: d1_ctr_dln - replicate 1

value: classical EAE protocol


title: vector_rep1


title: MV3, day2, core, replicate1


title: d0_dln - replicate 1

source_name: dLN cells from naive mice

value: naïve


title: GOT1_A1M_7dpi_rep1

status: Public on Apr 25 2023

city: Gothenburg

first: Nishte

last: Rassol

address: Gula stråket 2b

country: Sweden

institute: University of Gothenburg

description: SAMPLE 20

data_processing:
Sham-treated samples were used as a control. We compared the relative expression in GOT1 tumor tissue between the controls and three treatment groups (177Lu-octreotate, 177Lu-octreotate+A1M, A1M) at one and seven days after administration. For data analysis, we used Microsoft Excel to calculate fold-expression of the target genes based upon the the 2-ΔΔCt method (Livak and Schmittgen 2001). The relative expression compared to controls were analyzed by Welch T-test, and p<0.05 was considered significant. For differentially expressed genes in at least one group, one-way ANOVA followed by Welch T-test was used to determine significant differences between the 177Lu-octreotate, 177Lu-octreotate+A1M and A1M group. Target gene signals in all samples (test and controls) are normalized to geometric average of housekeeping genes provided in the same array, resulting in ΔCt values, where ΔCt=(Ct_Target-Ct_HKG). ΔCt values for all test replicates (at 1dpi and 7 dpi) were normalized against the average of corresponding control replicates, resulting in ΔΔCt, where ΔΔCt= ΔCt_test replicate– average ΔΔCt_control. 2^-ΔΔCT values for each condition were considered as fold change expression of test samples compared to controls (untreated). Fold change is determined for target genes in all replicates of test samples as 2^-ΔΔCt where -ΔΔCt= ΔCt_test replicate– average ΔΔCt_control
Non-normalized raw data matrix reports Ct values for target and housekeeping genes in all control and test replicates. Normalized Ct and fold change worksheet reports ΔCt and 2^-ΔΔCt, respectivly, calculates as indicated in the data processing

label: SYBR Green

source_name: GOT1, A1M, 7 dpi, replicate 1

label_protocol: For each reaction, a final volume of 25 µl was used which contained 12.5 µl of RT2 SYBR Green Mastermix (QIAGEN, Valencia, USA), 11.5 µl of nuclease free water and 1 µl of cDNA (1.7 µg of total RNA). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with thermal profile starting by activation of HotStart DNA Taq polymerase at 95°C for 10 min followed by 45 cycles of 95°C for 15 sec and 65°C for 1min. Analysis of RT-qPCR raw data (cycle numbers) was performed with the LightCycler 480 Soft Ware 1.5.1.

extract_protocol: According to the manufacturer's protocol, total RNA was extracted from frozen tumor tissue samples using the RNeasy Lipid Tissue Mini Kit (QIAGEN, Valencia, USA). The purity, integrity and concentration of isolated RNA were assessed with Nanodrop 1000 Spectrometer (Thermo Scientific), RNA 6000 Nano LabChip Kit and Agilent 2100 Bioanalyzer (both from Agilent Technologies) and Qubit 3.0 Fluorometer (Thermo Fisher Scientific), respectively. Reverse transcription was performed from 200 ng total RNA using the RT2 First Strand Kit (QIAGEN, Valencia, USA).

treatment_protocol: At study start (t=0), animals were divided into four groups. Six groups of three animals received a tail vein injection of either Lu-177-octreotate (30 MBq), Lu-177-octreotate + A1M (30 MBq, 5mg/kg) or A1M (5 mg/kg) and terminated one or seven days after injection. In addition, two control groups of two animals were sham treated with saline solution and terminated after one or seven days after injection. At termination, tumors were dissected and snap frozen in liquid nitrogen and kept at -80°C.

value: 7 dpi

tag: treatment group

value: A1M (5 mg/kg)

tag: tissue type

value: GOT1 xenograft

tag: host mouse strain

value: Balb/c NM

tag: sample group

value: Test


title: GOT1_A1M_7dpi_rep2

description: SAMPLE 21

source_name: GOT1, A1M, 7 dpi, replicate 2


title: GOT1_30MBq_A1M_7dpi_rep1

description: SAMPLE 17

source_name: GOT1, 30MBq Lu-177-octreotate + A1M, 7 dpi, replicate 1

value: Lu-177-octreotate (30 MBq)+A1M (5mg/kg)


title: GOT1_30MBq_7dpi_rep3

description: SAMPLE 16

source_name: GOT1, 30MBq Lu-177-octreotate, 7 dpi, replicate 3

value: Lu-177-octreotate (30 MBq)


title: GOT1_A1M_1dpi_rep2

description: SAMPLE 12

source_name: GOT1, A1M, 1 dpi, replicate 2

value: 1 dpi


title: GOT1_A1M_1dpi_rep3

description: SAMPLE 13

source_name: GOT1, A1M, 1 dpi, replicate 3


title: d0_dln - replicate 3

value: female

tag: tissue

value: dLN (popliteal, paraaortic, inguinal)


title: GOT1_30MBq_7dpi_rep1

description: SAMPLE 14

source_name: GOT1, 30MBq Lu-177-octreotate, 7 dpi, replicate 1


title: GOT1_A1M_1dpi_rep1

description: SAMPLE 11

source_name: GOT1, A1M, 1 dpi, replicate 1


title: DTA1M-sol-Sam/DTA1M-sol-Ct

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: All mice were housed specific pathogen-free conditions and kept at 20-26 ℃ under 12h:12h light-dark cycle and provide regular chow ad libitum and tap water during the experiment.

extract_protocol: After euthanasia by cardiac puncture under isoflurane anesthesia, fresh soleus muscles were removed and  quickly frozened in nitrogen.  Samples were homogenized with TRIzol prior to isolation of total RNA using the QIAGEN RNEasy Mini kit.

treatment_protocol: Mice(12-16 week-old) were treated with 100mg/kg tamoxifen to induce Cre-recombinase for 5days, and the soleus muscle was corrected at 1months after tamoxifen treatment.

value: male

value: soleus muscle

tag: ct-gene

value: NG2CreERT(-/-)/ STOP-floxed DTA(+/+)

tag: gene

value: NG2CreERT(+/-)/ STOP-floxed DTA(+/+)


title: GOT1_30MBq_A1M_1dpi_rep3

description: SAMPLE 10

source_name: GOT1, 30MBq Lu-177-octreotate + A1M, 1 dpi, replicate 3


title: GOT1_30MBq_A1M_1dpi_rep2

description: SAMPLE 9

source_name: GOT1, 30MBq Lu-177-octreotate + A1M, 1 dpi, replicate 2


title: GOT1_30MBq_1dpi_rep2

description: SAMPLE 6

source_name: GOT1, 30MBq Lu-177-octreotate, 1 dpi, replicate 2


title: GOT1_30MBq_A1M_1dpi_rep1

description: SAMPLE 8

source_name: GOT1, 30MBq Lu-177-octreotate + A1M, 1 dpi, replicate 1


title: GOT1_A1M_7dpi_rep3

description: SAMPLE 22

source_name: GOT1, A1M, 7 dpi, replicate 3


title: GOT1_30MBq_7dpi_rep2

description: SAMPLE 15

source_name: GOT1, 30MBq Lu-177-octreotate, 7 dpi, replicate 2


title: GOT1_30MBq_A1M_7dpi_rep2

description: SAMPLE 18

source_name: GOT1, 30MBq Lu-177-octreotate + A1M, 7 dpi, replicate 2


title: GOT1_30MBq_1dpi_rep1

description: SAMPLE 5

source_name: GOT1, 30MBq Lu-177-octreotate, 1 dpi, replicate 1


title: GOT1_Control_7dpi_rep2

description: SAMPLE 4

source_name: GOT1, saline, 7 dpi, replicate 2

value: 0.9% NaCl

value: Control


title: GOT1_Control_1dpi_rep2

description: SAMPLE 2

source_name: GOT1, saline, 1 dpi, replicate 2


title: GOT1_Control_7dpi_rep1

description: SAMPLE 3

source_name: GOT1, saline, 7 dpi, replicate 1


title: GOT1_30MBq_A1M_7dpi_rep3

description: SAMPLE 19

source_name: GOT1, 30MBq Lu-177-octreotate + A1M, 7 dpi, replicate 3


title: GOT1_Control_1dpi_rep1

description: SAMPLE 1

source_name: GOT1, saline, 1 dpi, replicate 1


title: d1_CpG_dln - replicate 1

source_name: dLN cells taken on day 1 from mice immunized with CpG-B-supplemented EAE protocol

tag: treatment

value: CpG-B-supplemented EAE protocol

value: day 1


title: 160796D_R-G-7-1

first: Yan

last: Zheng

address: 22 Zhongguancun South Avenue, Haidian District

institute: School and Hospital of Stomatology, Peking University

description: Gene expression data from human bone marrow-human mesenchymal stem cells on the 7 days of osteogenic induction

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner (G2565CA).

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: Cells were cultured in osteogenic media comprised DMEM with 10% FBS, 1% antibiotics, 100nM dexamethasone, 10mM β-glycerophosphate and 0.2 mM L-ascorbic acid.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: hMSCs cultured in the forth passage were inducing osteogenesis for different time period(0,7days).

value: human bone marrow

value: 7 days of osteogenic induction


title: 160796D_R-G-7-2

source_name: human mesenchymal stem cells on the 7 days of osteogenic induction


title: 160796E_2R-G-0-1

description: Gene expression data from human bone marrow-human mesenchymal stem cells before osteogenic induction

value: before osteogenic induction


title: 160796E_2R-G-0-2

source_name: human mesenchymal stem cells before osteogenic induction


title: emm87 - 1057-S2 - biol rep2

city: Houston

middle: Charles

last: Shropshire

state: TX

address: 1901 East Road

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Untrimmed, paired-end 75-bp reads were QC'd with fastqc-v0.11.8
Untrimmed reads were aligned using STAR-v2.7.9a with default parameters to each respective emm-type reference
HTSeq-v0.11.0 was used to enumerate read counts
DESeq2 package-v1.30.1was used to perform differential gene expression analysis on normalized read counts using the DESeq2 median of ratios read normalization method
Supplementary files format and content: comma separated value files with normalized read counts and fold change results

organism: Streptococcus pyogenes

source_name: bacteria

extract_protocol:
RNA was extract with QIAGEN Rneasy mini kit. 500 ng of total RNA was used as input for downstream libraries
RNA-Seq libraries were completed by the University of Texas MD Anderson Cancer Center Core Genomic Center (ATGC)

value: bacteria

tag: genotype

value: CovS knockout


title: emm87 - 1057-S1 - biol rep1


title: emm89 - M1-4 - biol rep2

value: WT


title: emm87 - 1057-1 - biol rep1


title: emm89 - M1-2 - biol rep1


title: emm89 - M1-S2 - biol rep1


title: emm28 - 902-S3 - biol rep2


title: emm89 - M1-S4 - biol rep2


title: DRG-LAS rep3

city: Hangzhou

first: Chengyu

last: Yin

state: Zhejiang

address: 548 Binwen Road, Binjiang District, Hangzhou

department: The Third Clinical Medical College

institute: Zhejiang Chinese Medical University

description: DRG-LAS rep3

data_processing:
The fragments were enriched by PCR amplification to construct a library ready for sequencing using BGISEQ-500 by BGI Group (Shenzhen, China).
Primary sequencing data produced by RNA-Seq (raw reads) were subjected to quality control (QC).
Raw reads were filtered into clean reads by internal software SOAPnuke (version 1.5.2), followed by: Remove reads in which unknown bases (N) are more than 10%; Remove reads with adaptors; Remove low quality reads (we define the low quality read as the percentage of base which quality is less than 15 and greater than 50% in a read).
QC of alignment was performed to determine if re-sequencing was needed. If the alignment result passed QC, downstream analysis including gene expression, differentially expressed genes, cluster analysis, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, etc. was proceeded with
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Mice were randomly allocated, and 5 rats were housed per cage(12 hour light–dark cycles and 24 ± 2 ℃). Food and water were provided ad libitum.

extract_protocol:
Briefly, the L3-5 DRG segments ipsilateral to the side of the ankle sprain injury were harvested and used for generating libraries for RNA-Seq. On day 14, mice were anesthetized with sodium pentobarbital and were perfused with saline. After perfusion, the L3-5 DRG segments were immediately preserved in RNAlater solution (Thermo Fisher Scientific, USA). Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific, USA) according to the manufacturer's instructions with DNaseI to degrade contaminating DNA. The purity and concentration of the samples were assessed by the Nanodrop Spectrophotometer (NanoDrop Products, CA, USA), and the RNA integrity was assessed by the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Briefly, for LAS group, a small incision in the ankle was made, and the ATFL and CFL were both transected, and the skin was then closed with a 6-0 surgical suture. For sham group, a small incision was retracted in the same place as the LAS group, but no ligament was cut.

value: Dorsal root ganglia

value: Day 14

value: a small incision in the ankle was made, and the ATFL and CFL were both transected, and the skin was then closed with a 6-2 surgical suture


title: emm28 - 902-S1 - biol rep1


title: emm28 - 902-3 - biol rep2


title: DRG-sham rep3

description: DRG-sham rep3

value: a small incision was retracted in the same place as the LAS group, but no ligament was cut


title: DRG-sham rep2

description: DRG-sham rep2


title: DRG-sham rep1

description: DRG-sham rep1


title: emm87 - 1057-2 - biol rep2


title: DRG-LAS rep1

description: DRG-LAS rep1

value: a small incision in the ankle was made, and the ATFL and CFL were both transected, and the skin was then closed with a 6-0 surgical suture


title: DRG-LAS rep2

description: DRG-LAS rep2

value: a small incision in the ankle was made, and the ATFL and CFL were both transected, and the skin was then closed with a 6-1 surgical suture


title: emm28 - 902-1 - biol rep1


title: KP4_DMSO_sample3

city: Chiba

first: Jason

last: Lin

state: Chiba

address: 666-2 Nitona-cho, Chuo-ku

institute: Chiba Cancer Center Research Institute

description: RNA from KP4 cells treated with DMSO (negative control, biological replicate 3)

hyb_protocol: Sample preparations were performed on SurePrint G3 Human GE 8x60K V2 microarrays per Agilent Technologies’ recommendations.

scan_protocol: Data acquisition was performed on an Agilent SureScan microarray scanner.

data_processing: Differential expression analyses were performed with our previously developed custom R workflow (Lin et al PLoS ONE 14:e0215247, 2019). Replicates underwent background correction by the “normexp” method with an offset of 9, and scale-normalized for replicate spots between arrays. Differential downregulation was initially determined for the bottom 20-percentile downregulated candidates (log2FC < 0) with p-values below the predefined significance level (p < 0.0001).

label_protocol: Cy3via RNA Spike-In kit

growth_protocol: Human PDAC KP-4 cells were maintained in DMEM/F12 and supplemented with 10% FBS and penicillin/streptomycin in a humidified atmosphere at 37°C with 5% carbon dioxide.

extract_protocol: Qiagen RNeasy Plus Mini Kit

treatment_protocol: KP-4 cells were plated overnight prior to the administration of polyamide (100 nM) for 12 h. DMSO (0.01%) was used as control.

value: pancreatic ductal cell carcinoma

tag: cell line

value: DMSO


title: P42Mwt3

city: Hong Kong

first: Andrew

middle: M.

last: Chan

address: Room 407, 4/F, Lo Kwee-Seong Integrated Biomedical Sciences Building,, Area 39, The Chinese University of Hong Kong

department: School of Biomedical Science

country: Hong Kong

institute: The Chinese University of Hong Kong

description: SSC.csv  SSC.F.csv  SSC.M.csv  SSC.P30.csv  SSC.P42.csv

data_processing:
Mapped by HISAT2
Quantified by featureCounts
Differential analysis by DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: csv, matrix of all samples in the comparison with normalized counts, p-value and adjusted p-value

source_name: Somatosensory cortex

extract_protocol:
TRIzol
NEB

value: Somatosensory cortex

tag: age

value: wild type

value: Male


title: P42Mwt2

tag: strain


title: P42Mwt1


title: KP4_CCC-002_sample3

description: RNA from KP4 cells treated with CCC-002 (biological replicate 3)

tag: cell type


title: KP4_KR12_sample3

description: RNA from KP4 cells treated with KR12 (biological replicate 3)


title: KP4_CCC-002_sample2-rep2

description: RNA from KP4 cells treated with CCC-002 (biological replicate 2B)


title: KP4_DMSO_sample1

description: RNA from KP4 cells treated with DMSO (negative control, biological replicate 1)


title: P42Fwt2

value: Female


title: KP4_KR12_sample2-rep1

description: RNA from KP4 cells treated with KR12 (biological replicate 2A)


title: P42Fwt3


title: P42Fwt1


title: P42Mht2

value: Pten+/-


title: P42Mht1


title: P42Fht3


title: KP4_DMSO_sample2

description: RNA from KP4 cells treated with DMSO (negative control, biological replicate 2)


title: KP4_KR12_sample2-rep2

description: RNA from KP4 cells treated with KR12 (biological replicate 2B)


title: KP4_CCC-003_sample3-rep2

description: RNA from KP4 cells treated with CCC-003 (biological replicate 3B)


title: KP4_KR12_sample1-rep2

description: RNA from KP4 cells treated with KR12 (biological replicate 1B)


title: KP4_CCC-002_sample2-rep1

description: RNA from KP4 cells treated with CCC-002 (biological replicate 2A)


title: P42Fht1


title: P42Fht2


title: KP4_CCC-003_sample1

description: RNA from KP4 cells treated with CCC-003 (biological replicate 1)


title: KP4_CCC-003_sample2

description: RNA from KP4 cells treated with CCC-003 (biological replicate 2)


title: d0_dln - replicate 2

source_name: dLN cells from naive mice

value: female

value: naïve

tag: time

value: dLN (popliteal, paraaortic, inguinal)


title: KP4_KR12_sample1-rep1

description: RNA from KP4 cells treated with KR12 (biological replicate 1A)


title: P42Mht3


title: P30Mwt3


title: P30Mwt2


title: P30Fwt2


title: P30Mht1


title: P30Fht1


title: P30Mwt1


title: P30Fwt1


title: P30Mht2


title: P30Fht3


title: 22-S-1 SSB

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

description: SSB profiling from the same DNA used for AP profiling in the sample 22-S-1

data_processing:
The genomic site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the two additional filtering steps. One, PCR duplicates were removed. Two, a read-pair was used only if the first base of the read 2 aligned to the reference sequence. The coordinate of  the first aligning base of the read 2 was assigned as the position of the SSB site.
Assembly: Mm10 (GRCm38) for the mouse reads mapping
Supplementary files format and content: All BED files contain coordinates of SSB sites mapped to mouse genomes. The 4th columns show the number of reads representing the SSB site.

source_name: Sperm

extract_protocol:
12 male mice of C57BL/6J strain from 4 age groups (3-, 12-, 19- and 22-month-old) were used to extract brains, hearts, livers, bone marrow, PBMCs and sperms. Red cells in bone marrow were removed by Red Blood Cell Lysis Buffer (Beyotime). PBMCs were isolated from blood using Ficoll-Paque PLUS (GE Healthcare). The motile spermatozoa were isolated from the mouse epididymal tail by collecting cells floating in the upper layer of RPMI 1640 (Thermo Fisher Scientific). The isolated tissues were immediately put into liquid nitrogen for quick freezing. The whole organs were cut into small pieces and ground into powder by tissue homogenizer in presence of liquid nitrogen to avoid heating. All ground tissue samples were stored at -80℃ prior to DNA isolation. Genomic DNA from the mouse brain, bone marrow, heart, liver and PBMCs was isolated using TIANamp Genomic DNA kit (Tiangen, DP304) with RNaseA treatment according to the manufacturer’s protocols. Genomic DNA from sperm cells was extracted using Sperm DNA Purification Kit (Simgen, 4202050) following the manufacturer’s instructions. All DNA samples were eluted in UltraPure™ DNase/RNase-Free Distilled Water (Invitrogen), measured the concentration using SMA6000 (Merinton) and stored at -20℃.
SSiNGLe method

value: Sperm

value: 22 months


title: 22-S-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-S-2


title: 22-S-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-S-3


title: 19-S-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-S-2

value: 19 months


title: 19-S-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-S-3


title: P30Fwt3

description: SSC.csv  SSC.F.csv  SSC.M.csv  SSC.P30.csv  SSC.P42.csv


title: KP4_CCC-003_sample3-rep1

description: RNA from KP4 cells treated with CCC-003 (biological replicate 3A)


title: 19-S-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-S-1


title: P30Fht2


title: 12-S-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-S-3

value: 12 months


title: 12-S-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-S-1


title: 3-S-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-S-3

value: 3 months


title: 3-S-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-S-2


title: 22-P-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-P-3

source_name: PBMC

value: PBMC


title: 22-P-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-P-1


title: 22-P-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-P-2


title: 3-S-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-S-1


title: KP4_CCC-002_sample1

description: RNA from KP4 cells treated with CCC-002 (biological replicate 1)


title: 19-P-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-P-3


title: 19-P-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-P-2


title: 19-P-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-P-1


title: 12-P-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-P-3


title: 12-P-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-P-2


title: 3-P-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-P-3


title: 3-P-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-P-2


title: 12-P-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-P-1


title: 12-S-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-S-2


title: 3-P-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-P-1


title: 19-L-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-L-2

source_name: Liver

value: Liver


title: 22-L-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-L-3


title: 22-L-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-L-1


title: 19-L-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-L-1


title: 3-L-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-L-2


title: 3-L-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-L-3


title: 22-H-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-H-3

source_name: Heart

value: Heart


title: 22-H-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-H-2


title: 12-L-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-L-2


title: 22-L-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-L-2


title: 19-L-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-L-3


title: 3-L-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-L-1


title: 19-H-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-H-1


title: 12-L-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-L-1


title: 12-L-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-L-3


title: 19-H-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-H-3


title: 19-H-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-H-2


title: 12-H-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-H-3


title: 12-H-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-H-2


title: GOT1_30MBq_1dpi_rep3

description: SAMPLE 7

source_name: GOT1, 30MBq Lu-177-octreotate, 1 dpi, replicate 3

tag: time point

value: 1 dpi

value: Lu-177-octreotate (30 MBq)

value: GOT1 xenograft

value: Balb/c NM

value: Test


title: 3-H-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-H-3


title: 12-H-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-H-1


title: 3-H-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-H-2


title: 3-H-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-H-1


title: 22-B-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-B-2

source_name: Brain

value: Brain


title: 19-B-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-B-3


title: 19-B-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-B-2


title: 22-H-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-H-1


title: 19-B-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-B-1


title: 22-M-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-M-2

source_name: Bone marrow

value: Bone marrow


title: 3-B-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-B-3


title: 12-B-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-B-3


title: 12-B-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-B-2


title: 19-M-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-M-1


title: 3-B-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-B-2


title: 12-M-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-M-2


title: 3-B-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-B-1


title: 19-M-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-M-3


title: 19-M-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 19-M-2


title: 12-M-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-M-3


title: 22-M-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-M-3


title: 12-M-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-M-1


title: 3-M-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-M-3


title: 3-M-2 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-M-2


title: 22-B-3 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-B-3


title: 11G_M_3063

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 11G_M_3068


title: 11G_M_3067


title: 11G_M_3065


title: 11G_M_3060


title: 11G_M_3061


title: 11G_M_3062


title: 12-B-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 12-B-1


title: 22-M-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 22-M-1


title: 11G_M_3059


title: 11G_M_3057


title: 11G_M_3058


title: 11G_M_3055


title: 11G_M_3056


title: 11G_M_3054


title: 11G_M_3052


title: 11G_M_3050


title: 11G_M_3049


title: 11G_M_3051


title: 11G_M_3053


title: 11G_M_3046


title: 11G_M_3043


title: 3-M-1 SSB

description: SSB profiling from the same DNA used for AP profiling in the sample 3-M-1


title: 11G_M_3045


title: 11G_M_3042


title: 11G_M_3048


title: 11G_M_3064


title: 11G_M_3066


title: 11G_M_3038


title: 11G_M_3037


title: 11G_M_3040


title: 11G_M_3039


title: 11G_M_3036


title: 11G_M_3041


title: 11G_M_3034


title: 11G_M_3035


title: 11G_M_3029


title: 11G_M_3031


title: 11G_M_3030


title: 11G_M_3032


title: 11G_M_3028


title: 11G_M_3033


title: 11G_M_3027


title: 11G_M_3022


title: 11G_M_3021


title: 11G_M_3023


title: 11G_M_3020


title: 11G_M_3044


title: 11G_M_3017


title: 11G_M_3018


title: 11G_M_3019


title: 11G_M_3016