title: siRNA_Cont_1

description: 100-bp read length


title: Yale Melanoma ITx1_2.5

status: Public on Oct 21 2022

type: RNA

city: New Haven

first: Ioannis

last: Vathiotis

address: 310 Cedar St

country: USA

institute: Yale

hyb_protocol: Probes and target transcripts were hybridized at 67°C for 16–24 hours per manufacturer’s recommendations.

scan_protocol: Hybridized samples were run on the NanoString nCounter preparation station using the high-sensitivity protocol, in which excess capture and reporter probes were removed and transcript-specific ternary complexes were immobilized on a streptavidin-coated cartridge. The cartridge was scanned at maximum scan resolution on the nCounter Digital Analyzer

data_processing: Raw data counts were normalized using the geomean of 10 housekeeping genes included in the nCounter PanCancer IO 360™ Panel and each gene was adjusted based on the average of 2 panel standards across all data. Then, the housekeeper- and panel standard-normalized data were log2 transformed.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Malignant melanoma

label_protocol: Per sample, 250 ng of total RNA in a final volume of 5 μl was mixed with a 3′ biotinylated capture probe and a 5′ reporter probe and tagged with a fluorescent barcode from the custom gene expression code set.

extract_protocol: Total RNA was isolated from 5 μm-thick pretreatment FFPE sections of tumors fixed on positively charged slides using the High Pure FFPET RNA Isolation Kit (Roche) following the manufacturer’s protocols. RNA was quantified using the NanoDrop ND1000 spectrophotometer (Thermo Fisher Scientific).

tag: age

tag: bor

value: PD

tag: long-term benefit

value: NO

tag: itx

value: IPI+NIVO

tag: prior checkpoint blockade


title: Yale Melanoma ITx1_1.11

value: SD

value: PEMBRO


title: Scram_Cont_0

type: SRA

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

description: 100-bp read length

library_source: transcriptomic

data_processing:
Read alignment and junction mapping to genome build GRCh37 were accomplished using STAR version 2.7.6a
Known splice junctions from the University of California Santa Cruz (UCSC) hg19 genome annotation were supplied to the aligner and de novo junction discovery was also permitted
Differential gene expression analysis and statistical testing were performed using Cuffdiff2 version 2.2.158, employing the hg19 genome annotation
Transcript expression was calculated as gene-level relative abundance in fragments per kilobase of exon model per million mapped fragments and employed correction for transcript abundance bias
Assembly: hg19
Supplementary files format and content: csv,FPKM of expression level

source_name: monocyte-derived macrophages

growth_protocol: CD14+ monocytes were cultured at 37°C and 5% CO2 in RPMI medium supplemented with 10% fetal calf serum (FCS) and 50 ng/mL macrophage colony-stimulating factor (M-CSF, Peprotech)

extract_protocol:
Total RNA was isolated from MDMs transfected with MBOAT7 siRNA or control with and without LPS using the RNA mini kit (Qiagen). RNA purity and integrity were confirmed using an Agilent Bioanalyzer. Sequencing libraries were prepared from 100–500 ng of total RNA using the TrueSeq RNA sample preparation kit v2 (Illumina). Briefly, mRNA was purified, fragmented, and used for first- and second-strand cDNA synthesis followed by adenylation of 3′-ends. Samples were ligated to unique adaptors and subjected to PCR amplification. Libraries were validated using the 2100 BioAnalyzer (Agilent), normalized and pooled for sequencing. RNA-seq libraries prepared from three biological replicates for each condition were sequenced on the Illumina HiSeq 2000 using barcoded multiplexing and a 100-bp read length.
Sequencing libraries were prepared from 100–500 ng of total RNA using the TrueSeq RNA sample preparation kit v2 (Illumina)

treatment_protocol: Small interfering RNA (siRNA)  transfection was performed with Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions using 50 nM of the specific siRNA or non-targeting control for 48 hours

tag: cell line

value: monocyte-derived macrophages

tag: cell type

value: primary cells

tag: treatment

tag: replicate


title: Zar -/- GV oocyte, biol rep 1

city: Göttingen

first: Shiya

last: Cheng

address: Am Fassberg 11

department: Meiosis

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

data_processing:
Basecalling with bcl2fastq v2.20.0.422
Adapter trimming with cutadapt v2.8 using the “-q 20 -m 35 -j 15” parameters
Read mapping with STAR v2.7.8a using the default settings
Read counting with HTSeq v0.13.5
Assembly: mm39
Supplementary files format and content: A table with counts for each feature

molecule: polyA RNA

organism: Mus musculus

source_name: GV oocyte

extract_protocol:
Libraries and polyA mRNA were extracted and prepared from 10 oocytes using the QIAseq FX Single Cell RNA Library Kit
Libraries and polyA mRNA were extracted and prepared from 10 oocytes using the QIAseq FX Single Cell RNA Library Kit

tag: tissue

value: GV oocyte

value: C57BL/6N strain background

tag: genotype

value: Zar1 knockout


title: Zar +/+ GV oocyte, biol rep 3

value: Wild type


title: ART (B45_B1) ATAC fragments

city: Philadelphia

first: Vincent

last: Wu

state: PA

address: 402 Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

library_source: genomic

data_processing:
ATAC libraries were demultiplexed using 10X Genomics cellranger-atac (v2.0) pipeline. NovaSeq-based sequences were filtered using 10X Genomics index-hopping-filter (v1.1).
ATAC libraries were processed (demultiplexing, alignment, and counting) using 10X Genomics cellranger-atac (v2.0) pipeline
ADT libraries were demultiplexed using bcl2fastq2 (v2.20.0.422)
ADT fastq files were mapped to the TotalSeaA cocktail catalog using kallisto (v0.46.2) and bustools (v0.40.0) as documented with the kite pipeline (https://github.com/pachterlab/kite)
Assembly: chimeric hg38 with viral genome (HXB2, SUMA, or autologous sequences)
Supplementary files format and content: fragment.tsv.gz output file from 10X Genomics cellranger-atac count for ATAC data
Supplementary files format and content: tar.gz folder of kallisto bus output for ADT data

molecule: genomic DNA

source_name: peripheral blood

growth_protocol: Cells were thawed and rested in complete RPMI supplemented with DNaseI.

extract_protocol:
Refer to Mimitou et al., Nature Biotechnology 2021 for ASAPseq protocol
OTHER: single cell ASAPseq

treatment_protocol: For in vitro sample, bulk CD4+ T-cells were negatively enriched and were activated for infection with HIV-1 (SUMA clone). For ex vivo samples, memory CD4+ T-cells were negatively enriched.

tag: component

value: ATAC


title: 15589X2_day14PLX

city: Salt Lake City

first: Amber

last: Syage

state: Utah

address: 2000 Circle of Hope

department: Pathology

institute: University of Utah

description: 10x Genomics, 5'

library_source: transcriptomic single cell

data_processing:
Fastq files were demultiplexed with cellranger mkfastq version 2.2.0 to create I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Reads were aligned to the refdata-cellranger-mm10-2.2.0 reference from 10X Genomics.
Barcodes and UMIs were counted using cellranger count with expected-cells=6,000
mm10
Assembly: Filtered feature-barcode matrices in TSV and MEX format from cellranger count.

source_name: Spinal cord

extract_protocol: Tissue was extracted from isofluorine euthanized mice after saline cardiac perfusion. Single cell suspensions were generated from tissue samples by grinding with frosted microscope slides. Immune cells were then enriched via a 2-step Percoll cushion (90% and 63%) and cells were collected at the interface of the two Percoll layers. These cells were then FACS sorted for CD45+DAPI- using CD45-APC conjugated Flow antibodies.

value: CD45+ cells

value: Spinal cord

tag: strain

value: 6-8 weeks old

tag: diet

tag: time

value: day 14


title: Scram_Cont_3

description: 100-bp read length


title: Zar +/+ GV oocyte, biol rep 2


title: CLL_103_D2

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Assembly: hg19
Supplementary files format and content: HTSeq counts from RNA-seq samples

source_name: PBMCs

growth_protocol: Blood samples were collected from the chronic lymphocytic leukemia (CLL) patients before and after vaccinations.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: gender

value: M

tag: cll-disease status

value: relapsed


title: Yale Melanoma ITx1_1.10

tag: age

value: CR

value: YES


title: Yale Melanoma ITx1_1.9

tag: bor

value: IPI+NIVO

value: NO


title: 15589X1_day14control

description: 10x Genomics, 5'

value: control


title: ART (B45_A2) ATAC fragments


title: Zar +/+ GV oocyte, biol rep 1


title: Zar -/- GV oocyte, biol rep 2


title: Yale Melanoma ITx1_1.8

tag: long-term benefit


title: ART (A01_3) ATAC fragments


title: ART (A01_4) ATAC fragments


title: Yale Melanoma ITx1_1.7

value: PD

tag: itx


title: ART (A01_2) ATAC fragments


title: Yale Melanoma ITx1_1.6

value: SD

value: PEMBRO

tag: prior checkpoint blockade


title: ATCC cell line CRL-3241 UPCI:SCC154

city: Manhasset

middle: R

last: Bonagura

state: New York

address: 350 Community Drive

department: Pediatric Immunology

institute: Northwell Health

data_processing:
Partek FLOW
Pre-alignment QA/QC was performed. Quality of reads was high across all samples.
Bases were trimmed from both ends. End minimum quality level was a Phred = 20.
Alignment was performed using STAR - 2.7.3a
Transcript data was normalized using the TMM method
Differential expression was assessed via DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file

growth_protocol: All 4 cell lines were maintained in E-media: DMEM:Ham's F12 at 3:1 ratio, supplemented with 10% Fetal Clone II (FBS), Penicillin/Streptomycin (100 U/mL), Epidermal Growth Factor (5 ng/mL), Transferrin (5 µg/mL), Insulin (5 µg/mL), and 3,3',5-Triiodo-L-thyronine (2nM). Cells were maintained in a humidified incubator in 5% CO2 at 37C

extract_protocol:
Cells were washed 3 times in 1x PBS, and trypsinized off their plates and resuspended in cold complete Emedia. Cells were pelleted by centrifugation, washed once with cold PBS and repelleted. RNA was harvested using Rneasy mini kit (Qiagen). Approximately 500 ng of total RNA was used for the construction of sequencing libraries.
Illumina - TruSeq Stranded mRNA Library Prep kit

treatment_protocol: At 70% confluency, low passage cell lines were given Emedia supplemented with 2% Fetal Clone II to condition for 48 hours. Cells were then harvested for total RNA.

tag: cell line

value: squamous mucosal epithelium

value: WT

value: 48 hour media conditioning


title: ATCC cell line CRL-3240 UPCI:SCC152

tag: cell type


title: ART (A01_1) ATAC fragments

value: ATAC


title: Yale Melanoma ITx1_1.5


title: 15590X2_day7control

description: 10x Genomics, 5'

source_name: Brain

value: CD45+ cells

value: Brain

value: day 7


title: ATCC cell line CRL-3212 2A3

tag: treatment


title: ART (B45_A3) ATAC fragments


title: Human NASH Liver 5 R5C5, snRNA-seq

city: South San Francisco

first: Ian

last: Driver

state: California

address: 486 Cabot Road

department: Bioinformatics

institute: Gordian Biotechnology

description:
10x Genomics
humanNASH_5_R5C5_20kNoFacsNuclei

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Liver

extract_protocol:
frozen human liver tissue (~60 mm3) was lysed by Dounce homogenization (Kimble 2mL: 20 times with Pestle A over ~60 seconds) in 2mL lysis buffer (10mM Tris pH 7.0, 10mM NaCl, 3mM MgCl2, 0.05% Triton X-100, 0.13% RNAse Inhibitor (Enzymatics Y9240L, MA, USA), 0.25% Superase RNAse Inhibitor (Thermo Fisher Scientific AM2694, MA, USA)) with 45mM Actinomycin D, then dripped through a 40mm cell strainer (Celltreat 229481, MA, USA) into a protein low-binding 15mL centrifuge tube and the filter was washed into the collection tube with another 2mL of lysis buffer. After 5 minutes total exposure time to lysis buffer, samples were spun for 2 minutes at 300xg at 4°C; the supernatant was aspirated from the top first to remove fat, then the nuclei-containing pellet was resuspended in 5mL of wash buffer (DPBS + 2% BSA + 0.13% Enzymatics RNAse Inhibitor + 0.25% Superase RNAse Inhibitor + 3mM Actinomycin D) and filtered again through a 35mm strainer into a 5mL FACS tube. Nuclei were sorted into a 1.7mL a protein low-binding microcentrifuge tube pre-coated with 900mL of wash buffer on a Biorad S3e FACS using FSC/SSC > FSC-H vs FSC-W > FL4 vs. SSC gating to eliminate debris. Nuclei were pelleted at 300xg for 3 minutes at 4°C in a swing-bucket centrifuge and resuspended in wash buffer for 10x capture using an LT200 pipettor.
Nuclei preparations were processed by the Chromium 3′ Gene Expression V3 Kit according to the manufacturer’s guidelines. Qubit 3 (Fisher Scientific) and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) were used for quality check of cDNA.

tag: disease state

value: NASH

value: Liver

tag: Sex

value: M

value: 50 years


title: 15590X1_day7PLX

description: 10x Genomics, 5'

tag: tissue

value: 6-8 weeks old


title: mbIL2_1

city: Chengdu

first: Qi

last: Xiong

address: Ke-yuan Road 4, No. 1, Gao-peng Street

department: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy

country: China

institute: Sichuan university

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data were processed by Fastp 0.19.5 and SeqPrep with the default parameters.
The raw data aligned to the reference genome GRCh38 (http://asia.ensembl.org/Homo_sapiens/Info/Index) in orientation mode using Bowtie2 version 2.4.1.
For bioinformatics analysis, fragments per transcript per million reads were used to calculate the expression levels, which were quantified using RSEM 1.3.3.
Assembly: GRCh38
Supplementary files format and content: Matrix table withTPM values for every gene and every sample.

source_name: human cell lines

extract_protocol:
Cultured NK-92 cells with consistently treatment were collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human NK cells

value: NK-92 cells transfected with mbIL2 expressed vectors and cultured 2 days without recombinant human IL2.


title: mbIL2_2


title: mbIL2_3


title: Mouse NASH 2, snRNA-seq

description:
10x Genomics
mouseNASH_2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol:
40-60mg of total liver tissue  was chopped on ice in 1mL of 0.03% TST buffer (146mM NaCl, 10mM Tris-HCl pH 7.5, 1mM CaCl2, 21mM MgCl2 with freshly added 0.03% Tween-20, 0.01%BSA, and 0.4U/mL Ribolock RNase Inhibitor (Thermo Fisher Scientific FEREO0382, MA, USA)) [30] with Tungsten Noyes Spring Scissors (FST 15514-12, CA, USA). The resulting nuclei suspension was then filtered through 40mm cell strainers (Thermo Fisher Scientific 352340, MA, USA) into a fresh 50mL conical tube on ice. 1 more mL of 0.03% TST was used to rinse the cell strainer and 3mL of ST buffer was added to the nuclei suspension followed by briefly mixing by gentle flicking. The nuclei suspensions were spun at 500xg for 5 minutes at 4°C in a swing-bucket centrifuge. The final nuclei pellet is suspended in 200mL of 0.4% BSA in PBS by pipetting 30 times with a regular p1000 tip. 20mg of liver from 3 FAT-NASH mice were pooled for each sample and processed together in an attempt to average out heterogeneity associated with the diseased liver.
Nuclei preparations were processed by the Chromium 3′ Gene Expression V2 Kit according to the manufacturer’s guidelines. Qubit 3 (Fisher Scientific) and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) were used for quality check of cDNA.

value: 30 weeks


title: ATCC cell line CRL-1628 SCC25

tag: genotype


title: VEC_3

value: NK-92 cells transfected with empty vectors and cultured 2 days with recombinant human IL2.


title: ESCs, DNMT3A, DNMT3B DKO,P4 2

city: Shanghai

first: zhen

last: Xu

state: Shanghai

address: Mid Huaxia road 393

institute: ShanghaiTech university

data_processing:
Raw sequencing reads were trimmed using Trim Galore (v0.4.1)  and aligned against  mouse genome using Bismark (v0.13.1).
Duplicate reads were removed using Picard tools.Methylation calls were made using bismark_methylation_extractor using default parameter and subsequently filtered for coverage (min 5 reads).
SNPsplit (v0.3.4)  was used to separate the allelic DNA methylation reads with default parameters.Methylation calls were made using bismark_methylation_extractor using default parameter.
Assembly: mm9
Supplementary files format and content: Bedgraph format(filtered for coverage over than 5 reads,alleic bedgraph are not filtered), columns: chr, start, end, methylation ratio (0 to 100)

growth_protocol: The ES cell growth medium contained DMEM with glutamine and high glucose and 15% heat inactivated fetal bovine serum (FBS), plus non-essential amino acids and b-mercaptoethanol. The cell culture plates were seeded with irradiated mouse embryonic fibroblast (MEF) or SNL feeder cells first before the resuspended ES cells were plated on top of the feeder cells. The medium was changed daily when there are enough ES cells growing to prevent spontaneous differentiation of ES cells.

extract_protocol:
DNA was extracted using the TIANamp Genomic DNA Kit following the manufacturer's instructions.
DNA was sonicated, bisulfite converted using the  EZ DNA Methylation-Gold Kit following the manufacturer's instructions.

value: ESCs

value: DNMT3A, DNMT3B DKO


title: ESCs, UHRF1 KO,P4 2

value: UHRF1 KO


title: ESCs, DNMT1 KO,P4 2

value: DNMT1 KO


title: ESCs, UHRF1 KO,P4 1


title: Human NASH Liver 4 R6C1, snRNA-seq

description:
10x Genomics
humanNASH_4_R6C1_20kNoFacsNuclei

value: 64 years


title: ESCs, DNMT1 KO,P4 1


title: ESCs, DNMT3A, DNMT3B DKO,P4 1


title: Mouse NASH 1, snRNA-seq

description:
10x Genomics
mouseNASH_1


title: ESCs, WT,P4 2

value: WT


title: VEC_2


title: ESCs, WT,P4 1


title: ESCs,DNMT1,DNMT3A, DNMT3B TKO,P4 1

value: DNMT1,DNMT3A, DNMT3B TKO


title: ESCs,DNMT1,DNMT3A, DNMT3B TKO,P4 2


title: Human NASH Liver 4 R4C1, snRNA-seq

description:
10x Genomics
humanNASH_4_R4C1_20kNoFacsNuclei


title: Yale Melanoma ITx1_1.1

value: CR

value: PEMBRO

value: NO


title: VEC_1


title: Yale Melanoma ITx1_1.3

value: PR

value: NIVO


title: Yale Melanoma ITx1_1.4

value: YES


title: Yale Melanoma ITx1_1.2

value: SD


title: Human NASH Liver 3 R6C1, snRNA-seq

description:
10x Genomics
humanNASH_3_R6C1_20kNoFacsNuclei

value: NASH

value: Liver

value: F

value: 53 years


title: Human NASH Liver 5 R3C8, snRNA-seq

description:
10x Genomics
humanNASH_5_R3C8_20kNoFacsNuclei

value: M

value: 50 years


title: Human NASH Liver 3 R5C2, snRNA-seq

description:
10x Genomics
humanNASH_3_R5C2_20kNoFacsNuclei


title: primary mouse oligodendroglia Klf13_ko, 6d diff, biological replicate 1

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

data_processing:
RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA)
Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).
The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
DESeq2 was used for differential gene expression analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delmited text files containing counts and DESeq results

source_name: primary mouse oligodendroglia derived from brain

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to QIAGEN protocol.

treatment_protocol: After Shake off, primary mouse OPC wer kept under differentiating conditions in SATO medium for six consecutive days.

value: primary mouse oligodendroglia

value: 6d differentation


title: Human NASH Liver 3 R4C1, snRNA-seq

description:
10x Genomics
humanNASH_3_R4C1_30kNuclei


title: primary mouse oligodendroglia Klf13_ctrl, 6d diff, biological replicate 4

value: primary mouse oligodendroglia derived from brain


title: Human NASH Liver 2 R2C1, snRNA-seq

description:
10x Genomics
humanNASH_2_R2C1_30kNuclei

value: 51 years


title: primary mouse oligodendroglia Klf13_ctrl, 6d diff, biological replicate 2


title: primary mouse oligodendroglia Klf13_ctrl, 6d diff, biological replicate 3


title: primary mouse oligodendroglia Klf13_ctrl, 6d diff, biological replicate 1


title: 129SvEv_WT_male_mouse_tail

data_processing:
Sequence reads were trimmed from 3' end until the final base had a quality score > 30, using Trim-galore.
Trimmed sequence reads were mapped to mm9 using bwa mem.
Duplicate reads were removed using Picard tools. SNP between 129 and DBA mouse strain were identified using GATK tools by default parameter.
Assembly: mm9
Supplementary files format and content: Variant call format file contain the SNV info between 129 and DBA mouse.(chr| position| REF(DBA starin)|ALT (129 strain)|QUAL|...)
Library strategy: WGS

source_name: Tail

extract_protocol:
DNA was extracted using the TIANamp Genomic DNA Kit following the manufacturer's instructions.
DNA was sonicated,  libraries were prepared using the TransNGS® DNA Library Prep Kit for Illumina®  following the manufacturer's instructions.

value: Tail

value: WT


title: Human NASH Liver 1 R1C1, snRNA-seq

description:
10x Genomics
humanNASH_1_40kNuclei_R1C1_DMSO

value: 34 years


title: Human Control Liver 3, snRNA-seq

description:
10x Genomics
humanCTRL_3

extract_protocol:
40-60mg of total liver tissue  was chopped on ice in 1mL of 0.03% TST buffer (146mM NaCl, 10mM Tris-HCl pH 7.5, 1mM CaCl2, 21mM MgCl2 with freshly added 0.03% Tween-20, 0.01%BSA, and 0.4U/mL Ribolock RNase Inhibitor (Thermo Fisher Scientific FEREO0382, MA, USA)) [30] with Tungsten Noyes Spring Scissors (FST 15514-12, CA, USA). The resulting nuclei suspension was then filtered through 40mm cell strainers (Thermo Fisher Scientific 352340, MA, USA) into a fresh 50mL conical tube on ice. 1 more mL of 0.03% TST was used to rinse the cell strainer and 3mL of ST buffer was added to the nuclei suspension followed by briefly mixing by gentle flicking. The nuclei suspensions were spun at 500xg for 5 minutes at 4°C in a swing-bucket centrifuge. The final nuclei pellet is suspended in 200mL of 0.4% BSA in PBS by pipetting 30 times with a regular p1000 tip.
Nuclei preparations were processed by the Chromium 3′ Gene Expression V3 Kit according to the manufacturer’s guidelines. Qubit 3 (Fisher Scientific) and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) were used for quality check of cDNA.

value: Control

value: 69 years


title: primary mouse oligodendroglia Klf13_ko, 6d diff, biological replicate 2


title: primary mouse oligodendroglia Klf13_ko, 6d diff, biological replicate 3


title: KS3

city: Nichinomiya

first: Kyosuke

last: Yamanishi

state: Hyogo

address: 1-1, Mukogawa

department: Neuropsychiatry

country: Japan

institute: Hyogo College of Medicine

description: PR1896_06_a = KS3

data_processing:
DRAGEN（Dynamic Read Analysis for GENomics）
Sequences were made with Nextera XT DNA Library Prep Kit (Illumina, Inc).
Sequence were read and mapped to mm39RC with DRAGEN（Dynamic Read Analysis for GENomics）
Read count extraction and normalization were performed using DRAGEN（Dynamic Read Analysis for GENomics）
Assembly: GENOCODE/GGRCm39 (mm39RC)
Supplementary files format and content: tab-delimited text files for each Sample

source_name: Il18-/- mice with restraint stress

extract_protocol:
We extracted total RNA using ISOGEN (cat. no. 311-02501, Wako Pure Chemical Industries, Ltd., Osaka, Japan), following the manufacturer’s protocol. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq was performed using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Illumina K.K., Tokyo, Japan) following the manufacture’s protocol.

treatment_protocol: Littermate Il18+/+ and Il18 -/- mice were exposed to a single restrain stress for 6 hours and all assessments were performed after 18 hours when the mice were released from the stress.

value: hippocampus

value: Il18-/- mice

value: restraint stress


title: PC9-OR-2

city: Hiroshima

first: Kentaro

last: Tokumo

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Molecular and Internal Medicine

institute: Hiroshima University

description: osimertinib-tolerant cells

hyb_protocol: 2.3 µg of single-strand DNA was incubated in GeneChip® Hybridization Oven 645 (Affymeterix) using the GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher). Hybridized with Clariom S Array, human (Termo Fisher).

scan_protocol: The arrays were then stained and washed in a GeneChip® Fluidics Station 450 (Affymetrix) and scanned in a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: A CEL file is automatically created after scanning. CEL files were analyzed with Transcriptome Analysis Console (TAC) ver. 4.0 to create a text file of expression levels.

source_name: EGFR mutation-positive lung adenocarcinoma cell line PC-9, after 1 week of osimertinib treatment

label_protocol: Using the GeneChip™ WT PLUS Reagent Kit (Thermo Fisher), 250 ng of total RNA to cRNA was processed into biotin-labeled single-stranded DNA.

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, penicillin, and streptomycin (100 U/mL and 100 µg/mL, respectively) in a humidified 5% CO2 atmosphere at 37°C in an incubator. Cells were seeded at a density of 1 × 10^5 cells/well in six-well plates

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: After 24 h of incubation, the medium of the plates was replaced with a medium containing 0.5 µM osimertinib. Starting from this time point as day 1, the medium was changed every 3 days (day 4, day 7), and the surviving cells on day 8 were determined to be EGFR-TKI-tolerant cells. Cells that were alive 48 hours after administration of 100 μM SK-216 to these EGFR-TKI tolerant cells were collected as PAI-1 inhibited cells.

value: OR


title: 20211208_Alexander_TE595_11 T

city: Regensburg

first: Alexander

last: Scheiter

address: Franz-Josef-Strauss Allee 11

department: Institute of Pathology

institute: University of Regensburg

hyb_protocol: Nanostring hybridization protocol by manufacturer

scan_protocol: nCounter digital analyzer

data_processing: nsolver advanced analysis

label: nanostring reporter and capture probes

source_name: NRAS injected mouse 3 T

growth_protocol: Mouse breeding

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Hydrodynamic tail vein injection of NRAS. Several months later sacrifice.

value: liver

tag: injected with

value: tumor


title: PC9-OR+SK100-2

description: PAI-1 inhibited osimertinib-tolerant cells

source_name: EGFR mutation-positive lung adenocarcinoma cell line PC-9, naive cells cultured for 1 week followed by a 48-hour exposure to SK-216, a PAI-1 inhibitor


title: 20211208_Alexander_TE612_12 T

source_name: NRAS injected mouse 4 T

label_protocol: Nanostring hybridization protocol by manufacturer


title: PC9-OR+SK100-3


title: 20211208_Alexander_TE582_10 T

source_name: NRAS injected mouse 2 T


title: PC9-OR-3

description: osimertinib-tolerant cells


title: Human NASH Liver 2 R1C2, snRNA-seq

description:
10x Genomics
humanNASH_2_R1C1_30kNuclei

value: NASH

value: Liver

value: F


title: PC9-OR+SK100-1


title: 20211208_Alexander_TE557_09 T

source_name: NRAS injected mouse 1 T


title: PC9-OR-1

description: osimertinib-tolerant cells


title: H1975-OR+SK100-3

source_name: EGFR mutation-positive lung adenocarcinoma cell line H1975, naive cells cultured for 1 week followed by a 48-hour exposure to SK-216, a PAI-1 inhibitor


title: H1975-OR+SK100-2


title: 20211208_Alexander_NTE557_05 NT

source_name: NRAS injected mouse 1 NT

value: nontumorous tissue with preneoplastic lesions


title: 20211208_Alexander_NTE582_06 NT

source_name: NRAS injected mouse 2 NT


title: Human NASH Liver 1 R1C2, snRNA-seq

description:
10x Genomics
humanNASH_1_40kNuclei_R1C2_Flash

value: M


title: Human Control Liver 1, snRNA-seq

description:
10x Genomics
humanCTRL_1

value: 63 years


title: 20211208_Alexander_NTE612_08 NT

source_name: NRAS injected mouse 4 NT


title: 20211208_Alexander_NTE595_07 NT

source_name: NRAS injected mouse 3 NT


title: 20211208_Alexander_EVE813_04 EV

source_name: EV injected mouse 4

value: emtpy vehicle


title: KS1

description: PR1896_04_a = KS1


title: H1975-OR+SK100-1


title: WS2

description: PR1896_02_a = WS2

source_name: Il18+/+ mice with restraint stress

value: Il18+/+ mice


title: WS3

description: PR1896_03_a = WS3


title: Human Control Liver 2, snRNA-seq

description:
10x Genomics
humanCTRL_2

source_name: Liver

value: 51 years


title: KS2

description: PR1896_05_a = KS2


title: WS1

description: PR1896_01_a = WS1


title: E14.5 UB Cells, HNF-1β deficient, biol rep 5

status: Public on Oct 20 2022

city: Minneapolis

first: Annie

last: Shao

state: Minnesota

address: 420 Washington Ave SE

department: Medicine

institute: University of Minnesota

description:
FACS sorted  HNF-1β deficient UB cells from E14.5 mice
m9072-7

data_processing:
RNA-sequencing reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control on raw sequence data for each sample was performed with FastQC
Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (GRCm38) as reference.
Gene quantification was done via Feature Counts for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts
Assembly: GRCm38/mm10
Supplementary files format and content: Raw Read Counts

source_name: kidney

growth_protocol: Mice were of mixed background (CFW and C57Bl/6) and maintained in conventional housing facilities.  Presence of a copulation plug in the morning was recorded as day E0.5. Experimental protocols and euthanasia protocols were approved by the University of Minnesota Animal Care and Use Committee.

extract_protocol:
E14.5 kidneys were harvested and made into single cell suspensions by incubating in collagenase solution followed by incubating in trypsin solution. Ureteric bud cells were isolated by fluorescence-actived cell sorting directly into Qiazol RNA lysis buffer. Total RNA was isolated using the Qiagen miRNAeasy kit.
Libraries were prepared using the New England Biolabs NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina following the manufacturer's protocol. cDNA was amplified for 12 PCR cycles and fragmented using the NEBNext Ultra II FS Enzyme Mix.

value: kidney

value: embryonic day 14.5

value: ureteric bud

value: HoxB7/Cre (Jackson 004692); Ai9-RCL-tdT (Jackson 007909); HNF-1beta Floxed/Floxed (PMID:11934849)

tag: strain

value: CFW and C57Bl/6 mixed


title: H1975-OR-3

description: osimertinib-tolerant cells

source_name: EGFR mutation-positive lung adenocarcinoma cell line H1975, after 1 week of osimertinib treatment

value: OR


title: 20211208_Alexander_EVE684_02 EV

source_name: EV injected mouse 2

value: liver


title: E14.5 UB Cells, HNF-1β deficient, biol rep 4

description:
FACS sorted  HNF-1β deficient UB cells from E14.5 mice
m9072-5


title: E14.5 UB Cells, HNF-1β deficient, biol rep 1

description:
FACS sorted  HNF-1β deficient UB cells from E14.5 mice
m7641-2


title: E14.5 UB Cells, HNF-1β deficient, biol rep 2

description:
FACS sorted  HNF-1β deficient UB cells from E14.5 mice
m7641-3


title: E14.5 UB Cells, wild-type, biol rep 5

description:
FACS sorted  UB cells from E14.5 mice
w9072-2

value: HoxB7/Cre (Jackson 004692); Ai9-RCL-tdT (Jackson 007909);HNF-1beta Floxed/wild-type (PMID:11934849)


title: 20211208_Alexander_EVE811_03 EV

source_name: EV injected mouse 3


title: H1975-OR-2

description: osimertinib-tolerant cells


title: E14.5 UB Cells, wild-type, biol rep 3

description:
FACS sorted  UB cells from E14.5 mice
w8867-5


title: 20211208_Alexander_EVE685_01 EV

source_name: EV injected mouse 1


title: E14.5 UB Cells, wild-type, biol rep 2

description:
FACS sorted  UB cells from E14.5 mice
w7641-5


title: E14.5 UB Cells, wild-type, biol rep 1

description:
FACS sorted  UB cells from E14.5 mice
w7641-1


title: E14.5 mouse kidney, IgG, biol rep 2

description:
Whole kidney from wild type E14.5 mice
IgG_E145_ChIPseq_MergedReplicates.bigWig

data_processing:
ChIP-sequencing reads were trimmed using Trimmomatic (v 0.32) using the TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25 parameters.
ChIP-seq read mapping was performed via BWA MEM (0.7.17) using the mouse genome (GRCm38) as reference.
ChIP peaks were identified using MACS  (2.1.1.20160309)  using the --call-summits -m 2 20 -g mm parameters.  Peak lists from each replicate were merged using R (4.1.2) to find high confidence peaks in present in both datasets.
Assembly: GRCm38/mm10

growth_protocol: Mice were of C57Bl/6 background and maintained in conventional housing facilities.  Presence of a copulation plug in the morning was recorded as day E0.5. Experimental protocols and euthanasia protocols were approved by the University of Minnesota Animal Care and Use Committee.

extract_protocol:
E14.5 kidneys were harvested and fixed with 2% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis by Dounce homogenizer, chromatin was sonicated using a Covaris S220 focused-ultrasonicator for 7.5 minutes at 7.5 Watts, peak power 75 and duty factor 10.
ChIP-seq libraries were prepared using the KAPA Hyperprep Kit using the xGen Stubby Adaptor and Illumina Index Primers. Libraries amplification cycle number was determined by performing a test amplification on 5% of the volume of each library for 40 cycles. The final amplification cycle number was the threshold cycle number +3 cycles (16 cycles for input samples, 20 cycles for IgG and HNF-1β IP samples). Post amplification libraries were size-selected at 200-400bp in length by gel electrophoresis.

value: embryonic kidney

value: Wild-type

tag: chip antibody

value: rabbit IgG (Cell Signaling Cat # 2729S, Lot # 7)


title: E14.5 mouse kidney, input, biol rep 2

description:
Whole kidney from wild type E14.5 mice
Input_E145_MergedReplicates.bigWig
HNF1B_E145_ChIP_Peaks.csv


title: E14.5 mouse kidney, HNF-1β, biol rep 2

description:
Whole kidney from wild type E14.5 mice
HNF1B_E145_ChIPseq_MergedReplicates.bigWig
HNF1B_E145_ChIP_Peaks.csv

value: HNF-1B ( Santa Cruz # 22840, Lot # I2013 )


title: E14.5 mouse kidney, HNF-1β, biol rep 1


title: E14.5 mouse kidney, IgG, biol rep 1


title: E14.5 UB Cells, HNF-1β deficient, biol rep 3

description:
FACS sorted  HNF-1β deficient UB cells from E14.5 mice
m8867-8


title: TH_864

city: Homburg

first: Masood

last: Abu-Halima

address: kirrberger st

department: Human genetics

institute: Saarland University

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing:
Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil-normalized and log2 transformed.
quantil normalized, log2 transformed intensity values for all samples in set

label: Cyanine 3-pcp

source_name: TGA-RV

label_protocol:
using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp
The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

extract_protocol: Total RNA including miRNAs was isolated using the Qiagen miRNeasy Kit according to manufacturers recommendations.

value: Blood

tag: gender

value: Female

tag: disease

value: TGA-RV


title: TH_634

hyb_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

tag: age


title: TH_876

value: Male


title: TH_866


title: TH_863


title: E14.5 UB Cells, wild-type, biol rep 4

description:
FACS sorted  UB cells from E14.5 mice
w9072-1


title: TH_413


title: TH_409


title: TH_488


title: TH_390


title: H1975-OR-1

description: osimertinib-tolerant cells


title: TH_457


title: E14.5 mouse kidney, input, biol rep 1


title: TH_508


title: TH_450


title: TH_779

source_name: TGA-LV

value: TGA-LV


title: TH_661


title: TH_502


title: TH_820


title: TH_501


title: TH_486


title: TH_444


title: TH_434


title: TH_474


title: TH_482


title: TH_673


title: TH_375


title: TH_397


title: TH_829


title: TH_645


title: TH_798


title: TH_831

source_name: Control

value: healthy control


title: TH_816


title: TH_824


title: TH_403


title: TH_833


title: TH_808


title: TH_809


title: TH_424


title: TH_391


title: TH_806


title: TH_810


title: TH_827


title: TH_811


title: TH_844


title: TH_823


title: TH_518


title: DRG, SCI, rep3

city: Monterrey

first: Raquel

last: Cuevas Diaz Duran

address: Av Morones Prieto No. 3000, Colonia Los Doctores

department: Escuela de Medicina y Ciencias de la Salud

country: Mexico

institute: Tecnologico de Monterrey

data_processing:
Read quality was assessed using FastQC. When necessary, adapters were trimmed with Trimmomatic.
Samples were mapped to reference genome rnor6 using TopHat2.
Gene expression was also quantified as read counts using HTSeq.
Differential gene expression was performed using DESeq2.
Assembly: Rnor6
Supplementary files format and content: Tab-delimited text files include raw count matrices for each sample

organism: Rattus norvegicus

source_name: DRG

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN)
Paired-end sequencing libraries were constructed using the TruSeq RNA Sample Prep Kit V2 (Illumina) according to manufacturer’s instructions

value: Sprague-Dawley

value: DRG

value: male

value: spinal cord injury (SCI)

tag: days post_injury

tag: drgs assayed


title: DRG, SCI, rep2


title: DRG, sham, rep1

value: sham


title: DRG, SCI, rep1


title: DRG, sham, rep3


title: TH_436


title: DRG, sham, rep2


title: DRG, naïve, rep3

value: naïve


title: DRG, naïve, rep2


title: DRG, naïve, rep1


title: TH_864

data_processing:
Raw expression values were extracted using the Feature Extraction Software. Data was quantil normalized and log transformed.
quantil normalized intensity values for all samples in set

label_protocol:
using Low Input Quick Amp Labeling Kit, one-color (Agilent Order ID 5190-2305), Cy3
The mRNA expression profile was determined using Agilent SurePrint G3 Human GE v3 8x60K Microarray according to the manufacturers recommendations

extract_protocol: Total RNA including miRNAs was isolated using theQiagen miRNeasy Kit according to manufacturers recommendations.  RNA concentration was measured using NanoDrop2000 (ThermoScientific). RNA integrity was measured using the NanoRNA kit (Agilent) on a Bioanalyzer2100.


title: TH_866

hyb_protocol: The mRNA expression profile was determined using Agilent SurePrint G3 Human GE v3 8x60K Microarray according to the manufacturers recommendations


title: TH_465


title: TH_863


title: TH_634


title: JHU_SZC_C10

city: Baltimore

first: Akira

last: Sawa

address: 600 North Wolfe St.

department: Psychiatry and Behavioral Sciences

institute: Johns Hopkins University School of Medicine

description: Gene expression data with olfacotry neuronal cells from a healthy control subject

hyb_protocol: The biotin-labeled cRNA was fragmented and hybridized on Affymetrix U133 Plus 2.0 chip at 45oC overnight. Post-hybridization washing was done as indicated in the Affymetrix instructions.

scan_protocol: The chips were stained with R-Phycoerythrin streptavidin (Invitrogen) and scanned for signal detection with the Affymetrix scanner.

data_processing: The Affymetrix Microarray Analysis Suite version 5 (MAS5) R package was used to process scanned chip images. Raw data were imported into a single AffyBatch object from CEL files. The array quality was assessed using the qc() function in the simpleaffy R package to check if any outlier chips exist. Expression values (signal intensities) and detection calls for each probe set were calculated. Each chip was globally scaled with a target value of 100 to make them comparable (MAS5-scaled). We eliminated unreliable signals by filtering out the probe sets whose detection calls were absent in all samples, and log2-transformed the cleaned data.

label: Biotin

source_name: Healthy control

label_protocol: Biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to the manufacturer’s protocol.

growth_protocol: Dissociated olfactory cells were prepared as follows. First, Olfactory epithelium tissue pieces were incubated with 2.4 U/mL Dispase II for 45 min at 37oC, and mechanically minced into small pieces. Then, the tissue pieces were further treated with 0.25 mg/mL collagenase A for 10 min at 37oC. Cells were gently suspended and centrifuged to obtain pellets. Cell pellets were resuspended in D- MEM/F12 supplemented with 10% FBS and antibiotics (D-MEM/F12 medium), and tissue debris was removed by transferring only the cell suspension into a new tube. Cells were then plated on 6-well plates in fresh D-MEM/F12 medium. Cells floating or loosely attached to the plate were collected on days 2 and 7, and further incubated on 6-well plates until they reached confluency. Finally, cells were collected by gentle trypsinization and stored in liquid nitrogen tank until further use. After recovery, cells were maintained in D-MEM/F12 medium and supplemented with fresh medium every 2-3 days.

extract_protocol: Total RNA was extracted from olfactory neuronal cells using RNeasy kit (Qiagen). The quality of RNA was 10 in RNA integrity number (RIN) score, which was assessed using a Bioanalyzer RNA 6000 Nano Chip (Agilent Technologies).

tag: diagnosis

value: Healthy control

value: Olfactory neuronal cells


title: JHU_SZC_SZ19

description: Gene expression data with olfacotry neuronal cells from a schizophrenia patient

source_name: Schizophrenia patient

value: Schizophrenia


title: JHU_SZC_SZ16


title: JHU_SZC_C4


title: JHU_SZC_SZ11


title: TH_521


title: JHU_SZC_C1


title: JHU_SZC_C11


title: TH_876


title: TH_488


title: JHU_SZC_SZ17


title: TH_413


title: JHU_SZC_C3


title: JHU_SZC_C2


title: TH_661


title: TH_390


title: TH_391


title: TH_502


title: TH_403


title: TH_508


title: TH_450


title: TH_820


title: TH_385


title: TH_457


title: TH_779


title: TH_798


title: TH_486


title: TH_501


title: TH_434


title: TH_444


title: TH_474


title: TH_482


title: TH_385


title: TH_673


title: TH_397


title: TH_645


title: TH_409


title: TH_833


title: TH_829


title: TH_831


title: TH_824


title: TH_809


title: TH_816


title: JHU_SZC_SZ20


title: TH_465


title: TH_806


title: TH_811


title: TH_810


title: TH_424


title: TH_808


title: TH_823


title: TH_844


title: TH_436


title: TH_375


title: Oocyte, 9C (Axolotl)

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

description:
Ambystoma_mexicanum_raw_counts.txt
Ambystoma_mexicanum_normalized_counts.txt

data_processing:
Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna (version 2) and the SILVA rRNA database (version 119). Reads were aligned against reference genome using STAR (v 2.5.3a).
Reads were counted using kallisto with the publicly available transcriptome model AmexT_v34
Transcripts that contained less than 30 reads in all samples were removed. Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT-qPCR method called NormQ (Naraine et al, 2020).
Genome_build: Transcriptome build Am_3.4 (Transcriptome available in database https://www.axolotl-omics.org/assemblies . Transcriptome version 3.4)
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized and normalized number of reads with name of the sample in first row of each column.

organism: Ambystoma mexicanum

source_name: Oocyte, 9C

extract_protocol:
Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using TriReagent.
80 ng of total RNA was used for rRNA depletion (Lexogen RiboCop rRNA Depletion Kit). Agilent SureSelect Strand-Specific RNA Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.

tag: segment

value: C

value: Oocyte

tag: oocyte id


title: Oocyte, 9D (Axolotl)

source_name: Oocyte, 9D

value: D

tag: cell type


title: Oocyte, 9B (Axolotl)

source_name: Oocyte, 9B

value: B


title: Oocyte, 5E (Axolotl)

source_name: Oocyte, 5E

value: E (last vegetal)


title: ICE36, AMF [AMF_207_4]

city: Taipei

first: Wei-Yi

last: Lin

state: Taipei City

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Agronomy

country: Taiwan

institute: National Taiwan University

data_processing:
R program
Sequence reads were trimmed for adaptor sequence/low-quality sequence and poor-quality bases elimination using Trimmomatic v0.38 with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Trimmed sequence reads were mapped to Setaria_italica_v2.0 using by the HISAT2 software (v2.1.0).
Read count extraction and normalization were performed using FeatureCounts (v2.0.0)  and DESeq2 (v1.26.0), respectively. The resulting p-values were adjusted using the Benjamini and Hochberg’s approach for controlling the FDR.
Assembly: Setaria_italica_v2.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Setaria italica

source_name: roots

growth_protocol: Surface-sterilized foxtail millet seeds germinated and grew  in a growth chamber with a 12 h light (28 °C)/ 12 h dark (22 °C) cycle.

extract_protocol:
RNA was harvested using using the method described by Wang and Vodkin (1994, Plant Mol Biol Report 12, 132-145). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit following manufacturer's protocols.

treatment_protocol:
Two weeks old seedings were transplanted to cones. Half of plants were inoculated with Claroideoglomus etunicatum and the rest were kept as mock.
At 6 weeks post inoculation, half of roots were harvested and stored at -80 °C for RNA isolation.

tag: landrace

value: roots

tag: treatment

value: Claroideoglomus etunicatum inoculation

tag: time

value: 6 weeks post inoculation


title: Oocyte, 5D (Axolotl)

source_name: Oocyte, 5D


title: Oocyte, 5C (Axolotl)

source_name: Oocyte, 5C


title: Oocyte, 9E (Axolotl)

source_name: Oocyte, 9E


title: Oocyte, 5B (Axolotl)

source_name: Oocyte, 5B


title: ICE36, AMF [AMF_207_3]


title: ICE36, AMF [AMF_207_1]


title: TH_518

tag: tissue

value: Blood

value: Female

value: healthy control


title: Oocyte, 9A (Axolotl)

source_name: Oocyte, 9A

value: A (first animal)


title: ICE36, mock [mock_207_4]

value: mock


title: TH_827


title: Oocyte, 5A (Axolotl)

source_name: Oocyte, 5A


title: Oocyte, 4B (Axolotl)

source_name: Oocyte, 4B


title: ICE36, mock [mock_207_1]


title: Oocyte, 4C (Axolotl)

source_name: Oocyte, 4C


title: Oocyte, 4D (Axolotl)

source_name: Oocyte, 4D


title: ICE36, mock [mock_207_2]


title: ICE36, mock [mock_207_3]


title: TT8, AMF [AMF_110_4]


title: Oocyte, 4E (Axolotl)

source_name: Oocyte, 4E


title: TT8, AMF [AMF_110_2]


title: Oocyte, 4A (Axolotl)

source_name: Oocyte, 4A


title: Oocyte, 10E (Axolotl)

source_name: Oocyte, 10E


title: TT8, AMF [AMF_110_1]


title: TT8, mock [mock_110_4]


title: Oocyte, 10D (Axolotl)

source_name: Oocyte, 10D


title: Oocyte, 10B (Axolotl)

source_name: Oocyte, 10B


title: Oocyte, 10C (Axolotl)

source_name: Oocyte, 10C


title: TT8, mock [mock_110_3]


title: Hanevalval, AMF [AMF_11Y_4]

value: Hanevalval


title: TT8, mock [mock_110_2]


title: Hanevalval, AMF [AMF_11Y_2]


title: Oocyte, 10A (Axolotl)

source_name: Oocyte, 10A


title: Hanevalval, AMF [AMF_11Y_1]

source_name: roots


title: TT8, mock [mock_110_1]


title: Hanevalval, mock [mock_11Y_2]


title: Hanevalval, mock [mock_11Y_3]


title: Hanevalval, mock [mock_11Y_4]


title: mouse prostate and urethra spatial expression sample 2 replicate 2

city: SEATTLE

first: Li

last: Xin

state: WA

address: 850 Republican Street Rm N326

department: Department of Urology

institute: University of Washington

description: 10x Genomics Visium

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Space Ranger software v1.3.0 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Downstream data processing, visualization, and statistics were completed using Scanpy (ver.1.8.1), Pandas (1.1.5), Scipy (1.4.1), Seaborn (0.11.2), and Matplotlib (3.2.2).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: prostate and urethra tissues

extract_protocol:
Frozen sections of urethra and connecting prostate tissues from C57BL/6 mice were fixed for H&E staining and imaging following the manufacturer’s instruction (CG000160, 10X Genomics, Pleasanton, CA). Tissue permeabilization was performed for 12 min and spatially barcoded full-length cDNA was generated using Visium Spatial Gene Expression Slide  & Reagent Kit (PN-1000187, 10X Genomics, Pleasanton, CA).
Library construction was performed according the the manufacturer protocol Visium Spatial Gene Expression Slide  & Reagent Kit (PN-1000187, 10X Genomics, Pleasanton, CA). CDNA amplification was conducted with 14 cycles of PCR reaction and 10 µl cDNA was used for the library preparation.

value: prostate and urethra tissues

tag: genotype

value: C57Bl/6 wild type mouse


title: TT8, AMF [AMF_110_3]


title: mouse prostate and urethra spatial expression sample 1 replicate 2

description: 10x Genomics Visium


title: TH_521

source_name: TGA-RV

value: Male

value: TGA-RV


title: T2_biorep1

city: Veszprém

first: László

last: Orbán

address: Egyetem u. 10

department: Department of Animal Sciences

country: Hungary

institute: University of Pannonia

description: sRNA

data_processing:
Obtain putative miRNA precursors: Map miRBase animal precursor sequence against the Asian Sea Bass genome using BLAST (E = 10e-6). Merge overlapping BLAST hits.
Validate putatitve miRNA precursor sequences: Align mature miRBase animal miRNAs against putative precursors using PatMaN allowing one mismatch only. Putatative miRNA precursors with a mature miRNA match were folded using RNAfold, and those forming a valid pre-miRNA hairpin structure were validated
Read trimming and filtering: HD adaptor sequences were trimmed by removing the first 4 bases of each read followed by the 3’ adaptor and preceding four bases. Sequences shorter than 18nt and comprised of two or fewer unique bases were removed from further analysis.
Novel miRNA prediction: Putative novel miRNA predictions were generated both miRCat and miRDeep2 algorithms using default parameters. Predictions were merged to obtain a non-redundant set of candidates and known miRNA families from miRBase identified previously were removed from the predicted novel miRNA set. Small RNA reads were aligned to predicted miRNAs and the read alignment pattern and secondary structure were checked manually to ensure that they are consistent with canonical miRNA biogenesis. Any predictions that did not meet these criteria were removed.
Determine raw read counts: Processed reads were aligned to annotated Asian seabass mature miRNAs using PatMan, generating a count for each miRNA isoform for a given annotated mature miRNA. PatMan output was further processed using a custom perl script in order to generate total counts for each annotate mature miRNA per sample.
Differential Expresson Analysis: DESeq2 (v 1.20.0) was used to identify differential expressed miRNAs between conditions from raw miRNA read count data. Default parameters were used, except for the ‘alpha’ parameter which was set at 0.05 when calling the DESeq2 'results' function.
Genome_build: ASM164080v1
Supplementary_files_format_and_content: Lates_calcarifer_gonads_sRNA-Seq_raw_counts.txt: A matrix of raw miRNA read counts for each sample, tab-separated values
Supplementary_files_format_and_content: Lates_calcarifer_mature_miRNAs.fa: Mature miRNA sequences in FASTA format

organism: Lates calcarifer

source_name: Transitional gonad stage 2

growth_protocol: Asian seabass were reared in seawater conditions at a temperature range of 28-31 ℃

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen)  and sRNA was purified using the mirVana miRNA isolation kit (Life Technologies). RNA concentration and integrity was measured on the NanoDrop 8000 spectrophotometer (Thermo Fisher Scientific) and was visually assessed by agarose gel electrophoresis with ethidium bromide staining. RNA was stored at -80 ℃
sRNA cDNA libraries were constructed by ligating sRNA to 3' and 5' HD adapters. Ligated RNA products were reverse transcribed to cDNA and amplified by PCR. The cDNA products expected to contain 19-33 base pair inserts were purified by 8% polyacrylamide gel electrophoresis and ethanol precipitation

value: Gonad

tag: developmental stage

value: Adult

tag: Sex

value: Intersex


title: T4_biorep2

description: sRNA

source_name: Transitional gonad stage 4


title: T1_biorep7

description: sRNA

source_name: Transitional gonad stage 1


title: T4_biorep1

description: sRNA


title: T1_biorep6

description: sRNA


title: mouse prostate and urethra spatial expression sample 2 replicate 1

description: 10x Genomics Visium


title: mouse prostate and urethra spatial expression sample 1 replicate 1

description: 10x Genomics Visium


title: T3_biorep1

description: sRNA

source_name: Transitional gonad stage 3


title: Col1a2-Foxf2-TRAMP prostate immune cells

description:
processed data file:
immune_barcodes.tsv.gz
immune_features.tsv.gz
immune_matrix.mtx.gz

data_processing:
BCLConvert v3.8.4 -  Fastq generation
Cell Ranger v6.1.1 count - Demultiplex and generate count matrix
Cell Ranger v6.1.1 aggr - Aggregate immune sample data and aggregate stroma sample data
Seurat v4.0.5 - Further analysis of Cell Ranger Count matrices
Genome_build: mm10
Supplementary_files_format_and_content: Counts matrix (matrix marker file -.mtx), features list (tab separated values -.tsv), barcodes list (tab separated values -.tsv)

source_name: Prostate

extract_protocol:
Prostate tissues were incubated in DMEM/Collagenase/Hyaluronidase/FBS for 3 hours at 37Â°C, followed by one hour-incubation in 0.25% Trypsin-EDTA on ice. Thereafter, mouse prostate tissues were pelleted, resuspended in Dispase and DNase I, and pipetted vigorously to dissociate cell clumps. Dissociated cells were then passed through 70 Î¼m cell strainers to obtain single cells. Stromal: Lin(CD45CD31CD235a)-Trop2-,  and immune: CD45+, fractions were purified by FACS
10X Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1

value: CD45+ cells isolated by flow cytometry

tag: strain


title: Hanevalval, AMF [AMF_11Y_3]

value: roots


title: T1_biorep3

description: sRNA


title: Mouse lung (male), 24-months old 3

city: Obu

first: Masataka

last: Sugimoto

state: Aichi

address: 7-430 Morioka-cho

department: Cellular Pathology

institute: National Center for Geriatrics and Gerontology

data_processing:
Analysis was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene scripts
Alignments were parsed using Tophat program.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. y. Indexes of the reference genome was built using STAR   and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file (matrix table) including raw counts and FPKM values for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted using RNeasy Kit (Qiagen), and integrity was validated on an Agilent 2100 (Agilent Technologies) prior to library construction.
Poly A-tailed mRNA was isolated from the total RNA, and library was constructed using NEBNext® Ultra Library Prep kit.

treatment_protocol: Mice were euthanized by cervical dislocation, and lung tissues were resected. Tissues were minced and soaked in RNA later™ solution (invitrogen), incubated for overnight at room temperature and stored at -80 ℃ until use.

value: Lung

value: wild-type

value: 24-months old


title: Mouse lung (male), 24-months old 2


title: T1_biorep2

description: sRNA


title: T1_biorep4

description: sRNA


title: T1_biorep1

description: sRNA


title: Mouse lung (male), 24-months old 1


title: Col1a2-Foxf2-TRAMP prostate stroma

description:
processed data file:
stroma_barcodes.tsv.gz
stroma_features.tsv.gz
stroma_matrix.mtx.gz

value: Lin(CD45CD31CD235a)-Trop2- stromal cells isolated by flow cytometery


title: T3_biorep2

description: sRNA


title: Testis_biorep4

description: sRNA

source_name: Testis


title: Mouse lung (male), 12-months old 3

value: 12-months old


title: Testis_biorep5

description: sRNA


title: ICE36, AMF [AMF_207_2]

value: Claroideoglomus etunicatum inoculation

value: 6 weeks post inoculation


title: Control - Col1a2-TRAMP prostate stroma


title: T1_biorep5

description: sRNA


title: Hanevalval, mock [mock_11Y_1]

value: Hanevalval

value: mock


title: Testis_biorep1

description: sRNA


title: Mouse lung (male), 12-months old 1


title: Testis_biorep2

description: sRNA


title: Mouse lung (male), 12-months old 2


title: Ovary_biorep4

description: sRNA

source_name: Ovary

value: Female


title: Control - Col1a2-TRAMP prostate immune cells


title: Mouse lung (male), 6-months old 3

value: 6-months old


title: Ovary_biorep2

description: sRNA


title: Ovary_biorep3

description: sRNA


title: Control MSC 2

city: New

first: Sean

last: Houghton

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

description: Control

data_processing:
All processing was done through Illumina Basespace Workflow
Alignment with STAR (v  2.5.2.b)
Cell and gene quantification plus filtering with SureCell RNAseq Single-cell app ( v 1.1.0)
Assembly: UCSC hg19
Supplementary files format and content: UMI Counts

source_name: MSCs

growth_protocol: Cells were enriched from human bone marrow aspirations, grown, sorted, and cultured in MSC growth mediaaaa

extract_protocol:
Cultured MSCs were harvested using accutase, sorted for live cells, and processed for single cell RNAseq analysis.
Illumina Bio-Rad SureCell WTA 3′ Library Prep Kit using the Bio-Rad ddSEQ Single-Cell Isolator system

treatment_protocol: MSCs were transfected with either empty control or ERG and FLI1 lentivectors in MSC transfection media and later cultured in EC media

tag: time points

value: Donor MSC Control

tag: source

value: Cultured MSCs


title: Mouse lung (male), 6-months old 1


title: Mouse lung (male), 6-months old 2


title: ZA19

city: Wuhan

first: Qiang

last: Li

state: Saskatchewan

address: #1 Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Trimming using Trimmomatics
Read mapping using STAR
Alignment using Cufflinks
featureCounts was then employed to count the reads spread across the exonic regions of each gene model.
Differentially expression analysis using DESeq2
Genome_build: IWGSC RefSeq 1.1
Supplementary_files_format_and_content: featureCounts was then employed to count the reads of each gene model.

organism: Triticum aestivum

growth_protocol: Wheat plants were grown in growth chambers under long-day conditions of 16 h of light, 22°C and 8 h of dark, 20°C, with light intensity of 100 to 120 μmol m−2 s−1 (Philips high-output F54T5/835-841 bulbs) for the whole life cycle.

extract_protocol:
Total RNA from crowns were extracted using a Plant RNA Isolation Mini Kit (Agilent Technologies, Mississauga, ON).
144 cDNA libraries were constructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina) with two replicates for each sample at each stage.

treatment_protocol: Spikelets were emasculated and pollinated at the heading stage to ensure sufficient and developmentally coordinated F1 seed production for embryo and endosperm isolation.

value: endorsperm

value: late endosperm

tag: maternal ploidy

value: hexploid

tag: paternal ploidy

tag: line

value: Z×A


title: Ovary_biorep1

description: sRNA

value: Gonad

value: Adult


title: Control MSC 1

description: Control


title: Mouse lung (male), 3-months old 3

value: Lung

value: wild-type

value: 3-months old


title: ZA17

value: embryo

value: mature


title: ZA16

value: leaf late


title: Testis_biorep3

description: sRNA

value: Male


title: ZA15

value: leaf middle


title: ZA18

value: early endosperm


title: Mouse lung (male), 3-months old 2


title: FE Overexpression MSC 2

description: ERG and FLI1

value: Donor MSC ERG and FLI1


title: ZA14

value: leaf early


title: Ovary_biorep5

description: sRNA

value: Female


title: FE Overexpression MSC 1

description: ERG and FLI1

value: Cultured MSCs


title: ZA13

value: transition

value: hexploid


title: skeletal muscle CON rep5

first: Xiangyi

last: Chen

address: No. 1239, Siping Road, Shanghai, China

institute: Weida Li

data_processing:
Quality Control:pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data.
Mapping:Hisat2 (v2.0.1) was used to index reference genome sequence
Expression analysis:HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Genome_build: 89.38 GRCm38.89
Supplementary_files_format_and_content: xls files include FPKM values for each Sample

source_name: skeletal muscle

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 7 was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skeletal muscle

tag: age

value: 12 month

tag: group

value: sedentary


title: Mouse lung (male), 3-months old 1

value: Lung

value: wild-type


title: skeletal muscle CON rep6


title: ZA11

value: embryo

value: 2 cell

value: Z×A


title: ACH-2 with fentanyl replicate 2

city: Cincinnati

first: Janani

last: Madhuravasal Krishnan

state: Ohio

address: 3230 Eden Ave

department: Internal Medicine

institute: University of Cincinnati

description: ACH-2 + 10ug Fentanyl - replicate 2

data_processing:
Raw reads were processed using Kallisto, which employs pseudoalignment to quickly and accurately determine if reads are compatible with genomic targets.
Raw data were log2-tranformed and baselined to the median of all samples.  Transcripts were filtered further to include only those with TPM > 3 in 50% of samples (N = 10,703 transcripts).  The level of differential expression was determined using moderated t-tests with a significance cutoff of p<0.05.
Significant transcripts were assessed for ontological significance using ToppGene and ToppCluster, with figures generated in Cytoscape, focusing on biological processes and pathways.
To construct comprehensive gene sets for candidate biological functions, Gataca (https://gataca.cchmc.org/gataca/) and ToppGene were used (https://toppgene.cchmc.org)
Candidate gene sets were then used to generate principal components through principal component analysis (PCA), which were plotted to determine each candidate gene set’s ability to segregate samples according to drug exposure.
Assembly: mm10
Supplementary files format and content: text file containing gene symbol and transcipts per million

source_name: ACH-2 + 10ug Fentanyl - replicate 2

growth_protocol: Cells were maintained in RPMI 1640 medium supplemented with 10% heat inactivated FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37°C and 5% CO2.

extract_protocol:
Total RNA of fentanyl-treated and untreated ACH-2 cells was isolated using the commercially available miRNA Isolation Kit (miVana; Applied Biosystems; Carlsbad, CA) according to the manufacturer's protocol.  A NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific; Waltham, MA) was used to determine total RNA concentration and purity.  A 2100 Bioanalyzer (Agilent; Santa Clara, CA) and agarose electrophoresis were used to assess RNA integrity.
Bioanalyzer was used to test the quality of total RNA (Agilent; Santa Clara, CA).  The Poly(A) mRNA Magnetic Isolation Module (NEBNext; Ipswich, MA) was used to isolate polyA RNA for library preparation with 1 µg of high-quality total RNA as input.  SMARTer Apollo automated NGS library prep system (Takara Bio USA; Mountain View, CA) was used for enrichment of polyA RNA.  For library preparation, the New England BioLabs NEBNext Ultra II Directional RNA Library Prep kit (PCR cycle number 8) was used.  The individual indexed libraries were proportionally pooled, and sequenced on the NextSeq 550 sequencer (Illumina; San Diego, CA) under the sequencing setting of single read 1x85 bp after QC and quantification via real-time qPCR (NEBNext Library Quant Kit; New England BioLabs; Ipswich, MA).

treatment_protocol: Cells were treated with 10ug of fentanyl for 24 hours

tag: cell line

value: T lymphocyte cell line

value: 10ug Fentanyl


title: skeletal muscle CON rep3

city: Shanghai


title: ZA9

value: endorsperm

value: late endosperm


title: skeletal muscle CON rep4


title: ZA6

value: leaf late


title: ZA8

value: early endosperm


title: ZA7

value: mature


title: ZA4

value: leaf early


title: ACH-2 no fentanyl replicate 2

description: ACH-2  No drug control - replicate 1

source_name: ACH-2  No drug control - replicate 1

tag: cell type

value: No drug control


title: skeletal muscle CON rep1

value: skeletal muscle


title: colonic epithelial cells from control mice 144

city: Beijing

first: Junxiu

last: Shi

address: Xueyuan Road No. 38

department: Immunology

institute: Peking University Health Science Center

description: Gene expression data from colonic epithelial cells of control mice

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: All mice, according to weight, were randomly divided into 2 groups: ground control (Ctrl) and HU. The mice in HU groups were hindlimb unloaded for 28 days, while the Ctrl groups were kept in the same room without treatment.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: After washing off fecal contents and mucus, mouse colons were cut into 1.5 cm-long pieces and incubated twice in CMF (Ca2+/Mg2+-free)-HBSS containing 1 mM DTT and 5 mM EDTA in an orbital shaker at 250 rpm for 20 min at 37°C. After passing through a 150 μm cell strainer, the epithelial cells in the supernatant were enriched by centrifugation at 1600 rpm for 5 min at 4°C.

tag: gender

value: female

value: colon

value: 12 weeks old


title: colonic epithelial cells from control mice 141


title: colonic epithelial cells from hindlimb unloading mice 148

description: Gene expression data from colonic epithelial cells of hindlimb unloading mice


title: colonic epithelial cells from control mice 143


title: colonic epithelial cells from hindlimb unloading mice 145


title: colonic epithelial cells from hindlimb unloading mice 146


title: Thyroid, control, ID 246TA

city: Palmerston North

first: Andrea

last: Grana

address: Tennent Drive

country: New Zealand

institute: Massey University

data_processing:
Quality of the raw 150-base paired-end sequence files was examined using FastQC (version 0.11.9).
Then the paired-end reads were trimmed to remove low quality bases and adapter sequences with Trimmomatic (version 0.39), using the options: SLIDINGWINDOW:4:20, MINLEN:50, ILLUMINACLIP:TruSeq3-PE.fa:2:30:10.
Reads were mapped to a reference genome (Oar_rambouillet_v1.0) from the RefSeq database (https://www.ncbi.nlm.nih.gov/assembly/GCF_002742125.1/) using STAR (version 2.7.7a).
After mapping, featureCounts (Subread package, version 2.0.0) was used to quantify the aligned reads, allowing multi-mapping reads to be counted as well with the option -M.
Assembly: Oar_rambouillet_v1.0, from the RefSeq database (https://www.ncbi.nlm.nih.gov/assembly/GCF_002742125.1/)
Supplementary files format and content: Tab-delimited text file includes count values for each sample.

organism: Ovis aries

source_name: thyroid tissue

extract_protocol:
RNA was extracted using the TRIzol method (Invitrogen, Carlsbad, CA, USA) in a TissueLyser II (Qiagen, Hilden, Germany). Quality checks were done through RIN scores and the mRNA was purified from total RNA using oligo(dT)-attached magnetic beads. The resulting mRNA molecules were fragmented, and reverse transcribed into double-stranded cDNA by using random hexamer-primers. The synthesized cDNA was subjected to an end-repair and then was 3’ adenylated, where adapters were ligated to the ends of these fragments. The cDNA fragments were amplified by PCR and its product was purified with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). Afterwards, a quality check was done on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The PCR product was then heat denatured and the single strand DNA was circularized by splint oligo and DNA ligase.
All cDNA libraries were sequenced using paired-end strategy of 150 bp read length, through the BGISEQ-500 platform folloiwing BGI Genomics protocols.

treatment_protocol: Brown adipose tissue from around the kidneys and the thiroyd glands were stored at -80°C after collection.

value: thyroid tissue

tag: treatment

value: control


title: ZA5

value: embryo

value: leaf middle

value: hexploid


title: ZA3

value: transition

value: Z×A


title: ACH-2 with fentanyl replicate 1

description: ACH-2 + 10ug Fentanyl - replicate 1

source_name: ACH-2 + 10ug Fentanyl - replicate 1

value: T lymphocyte cell line

value: 10ug Fentanyl


title: ZA2

value: octant


title: ACH-2 no fentanyl replicate 1

description: ACH-2  No drug control - replicate 1


title: skeletal muscle CON rep2

value: 12 month

value: sedentary


title: ZA1

value: 2 cell


title: skeletal muscle EX rep5

value: skeletal muscle

value: exercise


title: ZA12


title: SA17

value: mature

value: tetraploid

value: S×A


title: skeletal muscle EX rep6


title: syn_D120_2

city: Vienna

first: Jaydeep

last: Sidhaye

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

data_processing:
Reads were trimmed using trim-galore v0.5.0
Genome alignment was performed using BWA MEM v0.7.17
Duplicate reads were marked with Picard MarkDuplicates v2.19.0.
Alignment were filtered using samtools v1.9 to remove multimapping and duplicated reads.
Peaks were called from the filtered and sorted BAM using macs2 v2.1.2 with parameters --broad --BAMPE --keep-dup all --nomodel
Assembly: hg38
Supplementary files format and content: broadPeak

source_name: brain organoids

extract_protocol: To generate ATAC-seq libraries, Tn5 treatment was done on isolated nuclei for 30 mins and the library was prepared using Nextera unquie dual index primers.

value: brain organoids

value: WT


title: syn_D120_1


title: Thyroid, cold, ID 244TA

value: thyroid tissue

value: cold conditions (4°C)


title: SA19

value: endorsperm

value: late endosperm

value: hexploid


title: BAT, ambient, ID 245FA

source_name: brown adipose tissue

value: brown adipose tissue

value: ambient conditions (20-22°C)


title: syn_D90_2


title: skeletal muscle EX rep3

value: 12 month


title: skeletal muscle EX rep2


title: syn_D90_1


title: BAT, control, ID 246FA

value: control


title: SA18

value: early endosperm


title: BAT, cold, ID 244FA


title: skeletal muscle EX rep4

value: skeletal muscle


title: SA14

value: embryo

value: leaf early


title: Thyroid, ambient, ID 245TA


title: syn_D40_2


title: SA12

value: octant

value: tetraploid


title: syn_D60_2

value: brain organoids


title: skeletal muscle EX rep1

value: exercise


title: Thyroid, ambient, ID 243TA

value: thyroid tissue


title: SA13

value: transition

value: S×A


title: Thyroid, cold, ID 242TA

value: cold conditions (4°C)


title: skeletal muscle CD47-KO rep3


title: SA16

value: leaf late

value: hexploid


title: SA9

value: endorsperm

value: late endosperm


title: SA15

value: leaf middle


title: sox2_D120_2

value: WT


title: syn_D60_1


title: BAT, cold, ID 242FA

value: brown adipose tissue


title: syn_D40_1


title: skeletal muscle CD47-KO rep2

value: skeletal muscle

value: 12 month


title: sox2_D90_2


title: SA11

value: embryo

value: 2 cell


title: sox2_D120_1

value: brain organoids


title: sox2_D90_1


title: skeletal muscle CD47-KO rep1


title: BAT, ambient, ID 241FA

value: ambient conditions (20-22°C)


title: SA7

value: mature

value: tetraploid


title: BAT, ambient, ID 243FA


title: CCA_Serum_1

city: Jinan

first: Shu

middle: Li

last: zhuang

state: China/Shandong

address: Department of General Surgery, Qilu Hospital, Shandong University, 107, Jinan Culture Road, Jinan, 250012, China.

department: Qilu Hospital

institute: Shandong University

data_processing:
The raw sequencing data are called raw tags. We obtained clean tags using the SOAPnuke. The filtering rules were as follows: removed low quality tags; removed tags with 5’ primer contaminants; remove tags without 3’ primer; removed tags without insertion; removed tags with poly A; removed tags shorter than 15nt.
After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2. Particularly, cmsearch was performed for Rfam  mapping. In the annotation information of different RNAs, to ensure that each small RNA was mapped to a unique category, we set the following rules: MiRbase(v22) > pirnabank(v1.0) > snoRNA(v1.2 human/plant ) > Rfam (v12.1)> other sRNA. The miRDeep-P2 [4] or miRDeep2[5] package was used to identify potentially novel miRNAs. The potentially novel miRNAs and were named novel_mirXXX, in which XXX is a unique number specified for each novel miRNA candidate.
RNAhybrid, miRanda and TargetScan were used to predict target genes of miRNAs (Only for animal; TargetFinder and TAPIR were used for plant).
The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. The expression formula is: C is the number of UMIs of reads that were mapped to the small RNA, T is the UMI number of total clean reads of the sample.
Differential expression analysis was performed using the DEGseq (or DESeq2 or PoissonDis) on Dr. Tom Multi-omics Data Mining System. Q value≤ 0.05 (or FDR value≤0.001) was used to judge the significance of expression difference.
Supplementary files format and content: excel,expression profiles

source_name: serum

extract_protocol:
Add 700 μL QIAzol Lysis Reagent to the exosome’s suspension. Mix by vortexing 10 s. Centrifuge for a short time and leave at room temperature for 5min.  Add 140 μL of chloroform/isoamyl alcohol (24:1), invert vigorously up and down for 15 s, and incubate for 2~3 min at room temperature.Centrifuge in 12,000×g for 8min in 4℃. Transfer the supernatant to a new tube. Add ethanol absolute two times of an equal volume to the supernatant, mix thoroughly. Pipet up to all sample into a spin column in a 2 mL collection tube and discard the flow-through.  Wash the column with 500 µL Buffer RPE.  Wash the column with 500 µL Buffer RPE.  Place the RNeasy MinElute spin column into a new 2 mL collection tube. Centrifuge at 12,000×g for 2 min to dry the membrane. Discard the collection tube with the flow-through. Place the RNeasy MinElute spin column in a new 1.5 mL collection tube. Add 20 µL RNase-free water directly to the center of the spin column membrane. Incubate for 1min at room temperature and centrifuge for 1 min at full speed to elute the RNA.
Select the corresponding testing methods for quality inspection according to the requirements of samples and products. Take a certain amount of RNA sample, purified 18-30nt small RNA with PAGE gel. The purified RNA is combined with 3’ Adapter, and incubated. Then combine 5’ Adapter, and incubate. Prepare the Reverse Transcription Reaction Mixture, into the thermocycler and run the program. Prepare the PCR Reaction Mixture, into the thermocycler and run the program.Then the PCR products are purified with PAGE gel, dissolve the recylced products in EB solution.The corresponding library quality control protocol will be selected depending upon product requirements.Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: serum


title: CCA_Serum_2


title: Thyroid, ambient, ID 240TA

value: thyroid tissue


title: SA6

value: leaf late

value: S×A


title: BAT, ambient, ID 240FA


title: CBDS_Serum_3


title: CCA_Serum_3


title: Thyroid, cold, ID 239TA

value: cold conditions (4°C)


title: CBDS_Serum_2


title: SA8

value: endorsperm

value: early endosperm

value: hexploid


title: sox2_D60_2

value: WT


title: sox2_D60_1


title: SA5

value: leaf middle


title: SA3

value: transition


title: SA4

value: embryo

value: leaf early


title: sox2_D40_2

value: brain organoids


title: BAT, cold, ID 239FA

value: brown adipose tissue


title: SA2

value: octant


title: CBDS_Serum_1


title: sox2_D40_1


title: ssCAGE, Heart, (Sample 108)

city: Tokyo

first: Ruslan

last: Deviatiiarov

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

department: Intractable Disease Research Center

institute: Juntendo University

data_processing:
Illumina Casava1.8 software used for basecalling.
CAGE sequences were trimmed with fastx_trimmer ( -Q33 -l 50), adapters were removed with trimmomatic, rRNAdust program was used to remove ribosomal sequences matched to ribosomal DNA repeating unit U13369.1
Reads were mapped with BWA, unmapped reads remapped by HISAT2.
CAGE transcription start sites (CTSS) files produced by CAGEr Bioconductor package with the following parameters: sequencingQualityThreshold = 10, mappingQualityThreshold = 20, removeFirstG = TRUE, correctSystematicG = TRUE
Signal clustering done through DPI (https://github.com/hkawaji/dpi1/) and bidir_enhancers (https://github.com/anderssonrobin/enhancers) algoritms
Genome_build: hg38 UCSC
Supplementary_files_format_and_content: CTSS files were created from BAM files using python script and shell commands; BED files for robust (TPM>1), permissive (>3 tags) DPI clusters, and bidirectional enhancers were produced with DPI and bidir_enhancers algorithms.

source_name: Heart

extract_protocol:
Explanted hearts were arrested with the cardioplegic solution and cooled down to +4 °C for transportation. 0.5 cm3 pieces were collected from the left and right atrial free wall, right and left ventricular base, and inferior and superior sinoatrial node. The tissue was flash frozen or stored in RNAlater (Invitrogen) overnight at +4 °C and stored at -80 °C. Total mRNA was extracted from 40 mg of tissue with RNeasy Fibrous Tissue Mini Kit (Qiagen). RNA purity and yield were quality checked with Agilent Bioanalyzer to satisfy RIN >7 and total RNA amount 3-5 μg.
Total RNA was submitted for no-amplification non-tagging CAGE (nAnT-iCAGE) library preparation for the first 13 samples; the rest of the samples were processed through recent single strand (ss) CAGE protocol (Morioka et al., Methods in Molecular Biology, 2020).

value: M

tag: chamber

value: left atrium

tag: state


title: SA1

tag: tissue

value: 2 cell

value: tetraploid


title: BAT, control, ID 238FA

value: control


title: Thyroid, control, ID 238TA

value: thyroid tissue


title: ssCAGE, Heart, (Sample 107)

value: F

value: right atrium


title: aorta_ko_5

city: Paris

first: Hafid

last: Ait-Oufella

address: 56, Rue Leblanc

country: France

institute: Inserm

data_processing:
Raw fastq files were mapped to mouse genome GRCm38 release 96 with STAR 2.7.1a
STAR --genomeDir [/path/to/STAR/ref] --sjdbGTFfile [path/to/gtf --runThreadN 20 --readFilesIn $fastq1 $fastq2 --outFileNamePrefix [id] --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
The count of the reads was carried out with RSEM
rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output $alignedToTransciptomFile $reference_name $sample_name
Assembly: GRCm38
Supplementary files format and content: raw counts per gene

source_name: aorta

extract_protocol:
Total RNA was extracted from thoracic aorta samples with Qiagen columns (RNeasy MiniSpin Columns) using a polytron (T25 basic, IKA, Labortechnik)
The libraries were prepared following the NEBNext Ultra II RNA Library Prep Kit protocol from New England BioLabs, starting from 100 ng of high quality total RNA

value: aorta

tag: genotype

value: KO


title: CA19

value: endorsperm

tag: developmental stage

value: late endosperm

value: hexploid

value: C×A


title: Thyroid, control, ID 237TA


title: BAT, control, ID 237FA


title: aorta_ko_4


title: aorta_ko_3


title: Thyroid, ambient, ID 241TA

value: ambient conditions (20-22°C)


title: ssCAGE, Heart, (Sample 106)


title: Thyroid, ambient, ID 236TA


title: ssCAGE, Heart, (Sample 105)

value: right ventricle


title: aorta_ko_2


title: ssCAGE, Heart, (Sample 109)


title: CA16

value: embryo

value: leaf late


title: CA17

value: mature


title: BAT, ambient, ID 236FA

value: brown adipose tissue


title: Thyroid, cold, ID 235TA

value: cold conditions (4°C)


title: ssCAGE, Heart, (Sample 104)


title: CA15

value: leaf middle

value: tetraploid


title: aorta_wt_5

value: WT


title: ssCAGE, Heart, (Sample 103)

value: F

value: left atrium


title: BAT, cold, ID 235FA


title: CA14

value: leaf early


title: ssCAGE, Heart, (Sample 102)

value: right atrium


title: Thyroid, cold, ID 234TA

value: thyroid tissue


title: ssCAGE, Heart, (Sample 101)

value: left ventricle


title: aorta_wt_4

value: aorta


title: CA13

value: transition

value: hexploid

value: C×A


title: aorta_wt_3


title: aorta_wt_2


title: Thyroid, ambient, ID 233TA

value: ambient conditions (20-22°C)


title: CA12

value: embryo

value: octant


title: BAT, cold, ID 234FA

value: brown adipose tissue

value: cold conditions (4°C)


title: CA11

value: 2 cell

value: tetraploid


title: ssCAGE, Heart, (Sample 100)

value: M

value: right ventricle


title: aorta_wt_1

value: WT


title: Thyroid, cold, ID 232TA


title: ssCAGE, Heart, (Sample 98)

value: F


title: aorta_ko_1

value: KO


title: BAT, ambient, ID 233FA


title: ssCAGE, Heart, (Sample 97)

value: left atrium


title: CA8

value: endorsperm

value: early endosperm


title: CIH groupn replicate3 [ST3]

city: 泉州

first: 清石

last: 陈

state: 福建省

address: 福建省泉州市鲤城区中山北路34号

institute: 医科大学附属第二医院

data_processing:
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads were normalized by calculated CPM value
Assembly: miRBase Release 22
Supplementary files format and content: The xlsx format file contains the cpm value of gene in every sample

source_name: kidney tissues

growth_protocol: Briefly, mice assigned to CIH group were placed in a specially designed chamber. The chamber was connected to a gas control delivery system which allows the flow of pure nitrogen to reduce O2 to 6% within 60 seconds, after which the control system also allows a quick replacement of oxygen resulting in a rapid reoxygenation to 21% O2 within 60 seconds. This 2-minute IH cycle was repeated 30 times per hour for 8 hours per day, for a total duration of 8 weeks. For the Control group, room air was forced into the chamber during the entire experiment. After exposure to CIH for 8 weeks, all mice were sacrificed, and the kidney tissues were isolated.

extract_protocol:
Total RNA was extracted from tissue using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).  Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135-155 bp PCR amplified fragments (corresponding to 15-35 nt small RNAs).

treatment_protocol: Tissues from kidney tissues and promptly cooled at -80℃ refrigerator.

value: kidney tissues

value: CIH


title: CIH group replicate2 [ST2]

address: 福建省泉州市鲤城区中山北路34号


title: ssCAGE, Heart, (Sample 96)

value: right atrium


title: CA7

value: embryo

value: mature

value: hexploid

value: C×A


title: ssCAGE, Heart, (Sample 95)

value: left ventricle


title: CA6

value: leaf late

value: tetraploid


title: Control group replicate2 [SC2]

address: 福建省泉州市鲤城区中山北路34号

value: Control


title: CA5

value: leaf middle


title: Control group replicate3 [SC3]

address: 福建省泉州市鲤城区中山北路34号


title: ssCAGE, Heart, (Sample 93)

value: F

value: right ventricle


title: ssCAGE, Heart, (Sample 94)

value: left atrium


title: ssCAGE, Heart, (Sample 99)

value: M


title: CA9

value: endorsperm

value: late endosperm


title: CA4

value: leaf early


title: ssCAGE, Heart, (Sample 92)


title: BAT, cold, ID 232FA

value: brown adipose tissue

value: cold conditions (4°C)


title: CA3

value: embryo

value: transition


title: MLL-AF4 sPTRS leukemic cells, 2nd transplantation

city: Yokohama

first: Hiroshi

last: Okuda

state: Kanagawa

address: 3-9 Fukuura, kanazawa-ku

institute: Yokohama city university school of medicine

data_processing:
Trimmed sequence reads were mapped to GrCM38 using star (default parameters)
Read count extraction were performed using rsem
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Bone marrow

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) with RNase-Free DNase Set (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Sure Select Strand Specific RNA Library Prep Kit (Agilent Technologies) following manufacturer's protocols.

value: Bone marrow

tag: strain

value: Bone marrow cells

value: WT

tag: disease state

value: leukemia

tag: transduction

value: pMSCV retroviral transduction carrying synonymous murant of MLL-AF4 gene

tag: transplantation

value: 2nd transplantation


title: CIH group replicate1 [ST1]

address: 福建省泉州市鲤城区中山北路34号

value: kidney tissues

value: CIH


title: CA2

value: octant

tag: maternal ploidy

value: tetraploid

tag: paternal ploidy

value: hexploid

value: C×A


title: MLL-AF4 sPTRS leukemic cells, 1st transplantation

value: 1st transplantation


title: MLL-mAf4 leukemic cells, biol rep 2

value: pMSCV retroviral transduction carrying MLL-ｍAf4 gene


title: ssCAGE, Heart, (Sample 91)

value: M

value: right atrium

tag: age


title: CA1

value: embryo

value: 2 cell

tag: line


title: ssCAGE, Heart, (Sample 89)

value: right ventricle


title: MLL-mAf4 leukemic cells, biol rep 3

value: Bone marrow

value: Bone marrow cells

value: WT


title: AZ19

value: endorsperm

value: late endosperm

value: A×Z


title: ssCAGE, Heart, (Sample 88)

value: left ventricle


title: MLL-mAf4 leukemic cells, biol rep 1

value: leukemia


title: AZ18

value: early endosperm

value: hexploid


title: Control group replicate1 [SC1]

address: 福建省泉州市鲤城区中山北路34号

value: kidney tissues

value: Control


title: ssCAGE, Heart, (Sample 87)

value: M


title: AZ17

value: mature


title: MLL-ENL leukemic cells

value: pMSCV retroviral transduction carrying MLL-ENL gene


title: AZ16

value: embryo

value: leaf late


title: ssCAGE, Heart, (Sample 86)


title: ssCAGE, Heart, (Sample 85)

value: left atrium


title: Sample_R21024781-XZ-33

first: yan

middle: ling

last: jie

address: No. 100 Haike Road, Pudong, Shanghai

institute: Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences

data_processing:
Sequencing reads were mapped to the reference genome mm10 (GRCm38) from Gencode with hisat2 by default parameter. The read counts for each gene were calculated by featureCounts58. The count files were used as input to R package DESeq2 (v1.26.0)59 for normalization and the differential expression genes
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each Sample

source_name: liver

extract_protocol: RNA libraries were prepared according to instructions of Vazyme VAHTS mRNA-seq V3 Library Prep kit for Illumina(NR611-01)

value: liver

value: 4 months


title: AZ15

value: leaf middle


title: ssCAGE, Heart, (Sample 90)


title: Sample_R21024781-XZ-32


title: AZ14

value: leaf early


title: CA18

value: endorsperm

value: tetraploid

value: C×A


title: ssCAGE, Heart, (Sample 83)

value: right atrium


title: ssCAGE, Heart, (Sample 84)

value: left ventricle


title: Sample_R21024781-XZ-30


title: AZ13

value: transition

value: hexploid

value: A×Z


title: Sample_R21024781-XZ-31


title: Sample_R21024781-XZ-29


title: AZ12

value: octant


title: ssCAGE, Heart, (Sample 82)

value: M


title: ssCAGE, Heart, (Sample 81)

value: right ventricle


title: Sample_R21024781-XZ-28


title: AZ9

value: late endosperm


title: ssCAGE, Heart, (Sample 80)


title: Sample_R21024781-XZ-27


title: AZ11

value: embryo

value: 2 cell


title: Sample_R21024781-XZ-26

value: liver


title: ssCAGE, Heart, (Sample 79)

value: left atrium


title: AZ7

value: mature


title: AZ8

value: endorsperm

value: early endosperm


title: Sample_R21024781-XZ-25


title: ssCAGE, Heart, (Sample 77)


title: AZ6

value: leaf late


title: ssCAGE, Heart, (Sample 76)

value: F

value: healthy


title: GC264T_HME-U

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

label: Cy5 and Cy3

source_name: low methylation gastric cancer case

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell lines or clinical samples using QIAquick DNA mini kit according to standard instructions

tag: sample type

value: clinical sample

value: gastric cancer


title: ssCAGE, Heart, (Sample 78)


title: Sample_R21024781-XZ-24


title: Sample_R21024781-XZ-23


title: AZ5

value: leaf middle

value: hexploid

value: A×Z


title: ssCAGE, Heart, (Sample 75)

value: right atrium


title: GC064T

source_name: high methylation gastric cancer case


title: GC270T_HME-U_EGJ-II


title: GC136T1_HME-U

source_name: normal fundic gland mucosa


title: GC075T

label: Cy5 and Cy4


title: GC159T_EME


title: AZ4

value: leaf early


title: GC219T

label: Cy5 and Cy6


title: GC151T_HME-U


title: GC209T

label: Cy5 and Cy5


title: Sample_R21024781-XZ-22


title: AZ2

value: embryo

value: octant


title: ssCAGE, Heart, (Sample 73)


title: ssCAGE, Heart, (Sample 74)

value: left ventricle


title: AZ3

value: transition


title: ssCAGE, Heart, (Sample 72)

value: iSAN


title: Sample_R21024781-XZ-21

value: liver


title: GC131T_HME-U

source_name: low methylation gastric cancer cell


title: AZ1

value: 2 cell


title: GC087T_LME


title: ssCAGE, Heart, (Sample 71)

value: sSAN


title: AS19

value: endorsperm

value: late endosperm

value: tetraploid

value: A×S


title: GC256T_EBV

source_name: immortalised normal gastric epithelial cell

value: clinical sample

value: gastric cancer


title: Sample_R21024781-XZ-19


title: AS18

value: early endosperm

value: hexploid


title: AS16

value: leaf late


title: AS17

value: embryo

value: mature


title: ssCAGE, Heart, (Sample 68)

value: M

value: right atrium

value: healthy


title: AS15

value: leaf middle


title: ssCAGE, Heart, (Sample 69)

value: right ventricle


title: GC287T_EBV


title: GC39T_LME


title: GC277T_EBV


title: GC24T_LME


title: GC250T_EBV


title: AS14

value: leaf early


title: AS13

value: transition


title: ssCAGE, Heart, (Sample 66)

value: left atrium


title: GC192T_HME


title: ssCAGE, Heart, (Sample 64)


title: ssCAGE, Heart, (Sample 65)


title: GC280T_EBV


title: AS12

value: octant

value: tetraploid


title: AS11

value: 2 cell

value: A×S


title: ssCAGE, Heart, (Sample 63)

value: left ventricle


title: AS9

value: endorsperm

value: late endosperm

value: hexploid


title: GC153T_HME

value: clinical sample

value: gastric cancer


title: GC216T_HME


title: ssCAGE, Heart, (Sample 62)

value: M


title: AS8

value: early endosperm


title: ssCAGE, Heart, (Sample 61)

value: healthy


title: ssCAGE, Heart, (Sample 60)

value: right atrium


title: ssCAGE, Heart, (Sample 70)


title: AS7

value: embryo

value: mature


title: EGJ522N

value: non-neoplastic gastric mucosa


title: ssCAGE, Heart, (Sample 59)


title: AS6

value: leaf late


title: GC3T_OUT


title: EGJ202N


title: GC_014T1_1


title: ssCAGE, Heart, (Sample 58)

value: left atrium


title: Sample_R21024781-XZ-20

value: liver


title: AS5

value: leaf middle

value: tetraploid

value: A×S