title: NPC Patient 14 rep2

city: Bangkok

first: Tavan

last: Janvilisri

address: 272 Rama 6 Road

department: Department of Biochemistry, Faculty of Science

country: Thailand

institute: Mahidol University

hyb_protocol: The OneArray were prehybridized for an hour at 42°C with pre-hybridization buffer according to manufacturer instruction. To reduce non-specific binding, microarray was blocked with sheared salmon sperm DNA (Agilent Technologies) and then hybridized with 3 μg of Cy3-labeled cDNA for 18 h at 42°C.

scan_protocol: After wash and dry according to Onearray’s instruction, The arrays were then scanned using the Agilent G2565CA Microarray Scanner System (Agilent Techonologies) The images of microarray slide were exported as a TIFF format. The Cy3-fluorescent intensities were quantified by the Genepix Pro software 6.3 (Molecular Devices).

data_processing: The Cy3 signal intensity of each spot was corrected by subtracting background signal intensities and the poor spots were flagged. Following the log2 transformation, the normalization was achieved using median with absolute deviation and RANK with RANKIT on SPSS, respectively.

source_name: Nasopharyngeal carcinoma

label_protocol: The amplified cDNA from each patient sample was used as template for Cy3 labeling of DNA. In brief, 3 μg of DNA were sonicated and then mixed with the random hexamers, Cy3-dCTP (GE Healthcare), and Klenow Fragment (exo-) (Fermentas) and incubated at 37°C for overnight. Cy-3 labeled DNA was purified with PCR purification Kit (Qiagen). The amount of purified Cy3-labeled cDNA was quantified by optical density reading using visible and UV/visible spectrophotometers (Thermo Scientific) and frequency of incorporation (FOI) was calculated.

extract_protocol: The FFPE tissues, with histopathologically-confirmed as NPC, were stained by cresyl violet. On average, 1.5x10 6 μm2 of 8 μm-thick FFPE sections were microdissected and prepared for the extraction of total RNA from NPC cells using RNeasy FFPE kit (Qaigen). Then each RNA sample was amplified by whole transcriptome amplification (WTA2, Sigma) and REPLI-g FFPE kit, respectively.

value: Nasopharyngeal carcinoma

tag: recurrence

value: Recurrence


title: NPC Patient 15 rep2

status: Public on Dec 30 2022

type: RNA

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: NPC Patient 13 rep2


title: T_I_24_R2

city: Lisbon

first: Vanessa

last: Azevedo

address: Campo Grande

department: Plant Biology Department

country: Portugal

institute: Biosystems & Integrative Sciences Institute

description: Gene Expression at 24hpi with P. viticola

hyb_protocol: Agilent Technologies, One-Color Microarray-based Gene expression Analyses, protocol version 6.9.1

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C), using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: Array images were analyzed using Agilent Feature Extraction software version 10.7.1.1 (Agilent Technologies, Santa Clara, CA). Default parameters (Protocol name_GE1_107_Sep09_grid name_028416_D_F_20100513) were used to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as non-uniform outliers were excluded. To improve the resolution of the analysis, for the outliers, R Sincell workpakage was applied to obtain gProcessed Signals. GeneSpring MultiOmics Analysis version 14.9 (Agilent Technologies, Santa Clara, CA) was used. Data was normalised through a percentile shift of 75%, baseline median of all samples and different types of filters (expression, flag, data file and error - coefficient of variance <20%).

organism: Vitis vinifera

source_name: Tolerant, Inoculates, 24hpi, Replicate 2

growth_protocol: Grapevine cuttings were harvested, cut in similar sizes (with 2 buds per cutting) and partially immersed in a 30°C water bath within a 4°C chamber for 2 months. The cuttings were transferred to square plastic pots with a mixture of seedling substrate and perlite (3:1 v/v). Afterwards, the cuttings were placed in a greenhouse for 2 months with natural light conditions at a temperature between 5°C and 30°C.

extract_protocol: Total RNA was extracted from 0.1 g of leaves with Total RNA Isolation Mini Kit (Agilent Technologies). RNA integrity was assessed by automated gel electrophoresis on 2100 Bioanalyzer (Agilent Technologies, Amstelveen, Netherlands).

treatment_protocol: On the adaxial side of the leaves of the different grapevine genotypes, P. viticola sporangia suspension (1.8x104 sporangia/ml) was sprayed on. As a control of the in vivo assay, plants were sprayed with water (mock inoculation).

tag: genotype

value: N23/018 from cross population Red Globe x  Regal Seedless

value: Leaf

tag: treatment

value: 24hpi with P. viticola


title: T_I_24_R1

source_name: Tolerant, Inoculates, 24hpi, Replicate 1

label_protocol: Agilent Technologies, One-Color Microarray-based Gene expression Analyses, protocol version 6.9.1


title: S_M_6_R3

description: Gene Expression at 6hpi with water

source_name: Susceptibe, Mock, 6hpi, Replicate3

value: N20/020 from cross population Red Globe x  Regal Seedless

value: 6hpi with water


title: NPC Patient 11 rep2

value: No Recurrence


title: Intestinal metaplasia 2 [IM2]

type: SRA

city: Jinan

first: Ai

last: Li

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼

country: China

institute: 山东大学

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Intestinal metaplasia

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stomach; gastric tissue

value: untreated

tag: tissue subtype

value: Intestinal metaplasia


title: Intestinal metaplasia 5 [IM5]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: NPC Patient 8 rep2


title: NPC Patient 9 rep2


title: NPC Patient 10 rep2


title: NPC Patient 12 rep2


title: S_M_6_R1

description: Gene Expression at 6hpi with water

source_name: Susceptibe, Mock, 6hpi, Replicate1


title: yZSJ025-1

city: Tianjin

first: Zhou

last: Sijie

address: No.135 Yaguan road

institute: Tianjin Unversity

data_processing:
Read count extraction and normalization were performed using CLC genomic benchwork
The significant differentially expressed genes   (DEGs) were identified by DEseq2 (v1.16.1)
Assembly: Saccharomyces cerevisiae S288c
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast strain yZSJ025 was grown from single colonies in liquid YPD culture until reaching  early-log phase (OD600 = 1)  at 30 °C with rotation

extract_protocol:
RNA was isolated using the TRIzol (Invitrogen)   method
The library preparation followed the standard procedure (BGI)

tag: strain

tag: cell type

value: yeast

value: synthetic yeast


title: yZSJ025-2


title: yZSJ025-3


title: S_M_24_R3

description: Gene Expression at 24hpi with water

source_name: Susceptibe, Mock, 24hpi, Replicate3

value: 24hpi with water


title: S_M_6_R2

description: Gene Expression at 6hpi with water

source_name: Susceptibe, Mock, 6hpi, Replicate2


title: Non-atrophic gastritis 9 [NAG9]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼

source_name: Non-atrophic gastritis

value: Non-atrophic gastritis


title: S_M_24_R2

description: Gene Expression at 24hpi with water

source_name: Susceptibe, Mock, 24hpi, Replicate2


title: S_I_6_R3

description: Gene Expression at 6hpi with P. viticola

source_name: Susceptibe, Inoculated, 6hpi, Replicate 3

value: 6hpi with P. viticola


title: NPC Patient 7 rep2


title: Non-atrophic gastritis 8 [NAG8]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: lin-53 RNAi input DNA-rep3 (ChIP-seq)

city: Beijing

first: Guangshuo

last: Ou

address: Tsinghua University Haidian District

department: School of Life Science

institute: Tsinghua university

library_source: genomic

data_processing:
Basic processing for all data: FastQC assessed the quality score, adaptor content, and duplication rates of sequencing read. And Trim_galore (v0.6.0) was used to remove the low-quality bases and adaptor sequences with default parameters.
For SPLiT-seq samples: For each paired-end sequencing read, a 10-bp UMI sequence and a 24-bp cell barcode were extracted from the Read 2 file by the tool “preprocess_splitseq.pl” of zUMIs (v0.0.6). The Read 1 was split by different cell barcodes in Read 2 and mapped to the modified C. elegans genome (WS263 with an artificial chromosome containing the C. elegans version of the GFP sequence) by zUMIs (v0.0.6) and STAR (v2.6.0c). The duplicated reads from the same transcript were excluded based on the UMI information in Read 2.
For RNA-seq samples:After trimming, paired-end reads with at least 20 nucleotides in length were aligned to C. elegans reference genome (WS263) using STAR (2.5.4b) with default parameters. Read counts representing gene expression levels were calculated with HTSeq (version 0.9.1) using default parameters. Uniquely mapped reads were included. Gene names were annotated in the Wormbase website (https://wormbase.org/tools/mine/simplemine.cgi). DESeq2 package in R programming language was used for differential expression analysis.
For ChIP-seq samples:Double-end reads were aligned to the C. elegans genome version WBcel235 using Bwa-mem2 version 2.1 with default parameters. Only uniquely mapped reads were kept. Samples were normalized by bins per million mapped reads (BPM) and averaged, and then treated samples were subtracted by input samples to calculate enrichment using deepTools2 (Ramirez et al., 2016).
Genome_build: For SPLiT-seq samples: modified WS263 with extra gene “gfp"
Genome_build: For RNA-seq samples:WS263
Genome_build: For ChIP-seq samples: WBcel235
Supplementary_files_format_and_content: For SPLiT-seq samples:The cell vs. gene counts expression matrix
Supplementary_files_format_and_content: For RNA-seq samples: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: For ChIP-seq samples: bw files were generated by deepTools2 (Ramirez et al., 2016) using averaged profiles normalized by bins per million mapped reads (BPM) and  subtracted by input samples.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: lin-53 RNAi input DNA

extract_protocol:
Mixture stage worms on RNAi NGM plates were harvested and washed three times with M9 buffer. 0.4 ml of packed worms were obtained and frozen into small balls by liquid nitrogen for each ChIP replicate. We quickly grounded the little worm balls into a frozen powder in liquid nitrogen. Worm powder was crosslinked in 4 ml crosslinking buffer (1.1% formaldehyde in PBS with protease and phosphatase inhibitors) with constant rotation for 15 min at room temperature. Fixed worm samples were quenched by incubation with 0.125 M glycine for 5 min and then washed in cold PBS-PIC (PBS buffer with protease inhibitor cocktail) three times. Tissue pellet resuspended in PBS-PIC was homogenized by 2-3 strokes in a Dounce homogenizer. The cell suspension was centrifuged at 2,000 g for 5 min at 4°C, and the supernatant was removed. We performed nuclei preparation, chromatin digestion, chromatin immunoprecipitation, and DNA Purification using SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signaling Technology, #9003). Samples were sonicated using a Qsonica sonicator (Qsonica Q800R) at 70% amplitude for 5 cycles of 30 sec on and 30 sec off with 4 repeats. The chromatin was digested using 6 μl of micrococcal nuclease (MNase) (CST catalog number 10011S) in 300 μl of buffer B (CST catalog number 7007) containing 0.5 mM DTT for 8 min at 37 °C. The quality of chromatin digestion was analyzed by Agilent 2100 bioanalyzer system. Before IP, the chromatin sample concentration was assessed by the BCA Protein Assay Kit (Tiangen, cat no. PA115-02). 1 μg H3K27ac antibody (Abcam ab4729) or 2 μg IgG was used per IP with 0.5-1 mg input chromatin protein.
According to the manufacturer, we used 200 ng purified DNA samples to construct the ChIP–seq library using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme ND607).

treatment_protocol: Synchronized young adult worms were cultured on lin-53 RNAi plates for 24 hours.

tag: developmental stage

value: all stage

value: lin-53 RNAi

tag: chip antibody


title: NPC Patient 6 rep2

value: Nasopharyngeal carcinoma

value: Recurrence


title: S_M_24_R1

description: Gene Expression at 24hpi with water

source_name: Susceptibe, Mock, 24hpi, Replicate1

value: Leaf


title: NPC Patient 4 rep2


title: lin-53 RNAi input DNA-rep2 (ChIP-seq)


title: Non-atrophic gastritis 7 [NAG7]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: NPC Patient 5 rep2


title: Intestinal metaplasia 1 [IM1]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: Non-atrophic gastritis 10 [NAG10]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: lin-53 RNAi input DNA-rep1 (ChIP-seq)


title: Non-atrophic gastritis 6 [NAG6]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: S_I_6_R1

source_name: Susceptibe, Inoculated, 6hpi, Replicate 1


title: S_I_24_R3

source_name: Susceptibe, Inoculated, 24hpi, Replicate 3

value: 24hpi with P. viticola


title: Non-atrophic gastritis 4 [NAG4]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: NPC Patient 2 rep2


title: Non-atrophic gastritis 5 [NAG5]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: Non-atrophic gastritis 3 [NAG3]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: hda-1 RNAi input DNA-rep2 (ChIP-seq)

source_name: hda-1 RNAi input DNA

treatment_protocol: Synchronized young adult worms were cultured on hda-1 RNAi plates for 24 hours.

value: hda-1 RNAi


title: hda-1 RNAi input DNA-rep1 (ChIP-seq)


title: hda-1 RNAi input DNA-rep3 (ChIP-seq)


title: Non-atrophic gastritis 1 [NAG1]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: WT input DNA-rep3 (ChIP-seq)

source_name: WT input DNA

treatment_protocol: Synchronized young adult worms were cultured on negative control RNAi plates for 24 hours.

value: wild type


title: S_I_24_R2

source_name: Susceptibe, Inoculated, 24hpi, Replicate 2

value: N20/020 from cross population Red Globe x  Regal Seedless


title: Non-atrophic gastritis 2 [NAG2]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼

value: stomach; gastric tissue


title: Rabbit SSP, uninjured, long term 9

city: Fayetteville

first: Jeffrey

last: Wolchok

address: 1 University of Arkansas

country: USA

institute: University of Arkansas

data_processing:
usegalaxy.eu pipeline
Use RNA-STAR for Gapped-read mapper for RNA-seq data ( input 2 pair-end raw files per sample for 2 week samples, single end files for 12 week samples)
Use feature to measure gene expression in RNA-Seq experiments from BAM files ( generated from RNA-Star)
Use edgeR to perform differential expression of count data
Assembly: OryCun2.0
Supplementary files format and content: tabular  files include normalized counted reads, per gene for each sample

organism: Oryctolagus cuniculus

source_name: supraspinatus muscle

extract_protocol:
RNA extarction was are performed by comercial lab BGI
RNA libraries were constructed by comercial lab BGI

value: supraspinatus muscle

value: uninjured


title: Rabbit SSP, uninjured, long term 10


title: Rabbit SSP, uninjured, long term 8


title: WT input DNA-rep2 (ChIP-seq)


title: Rabbit SSP, uninjured, long term 7


title: S_I_6_R2

source_name: Susceptibe, Inoculated, 6hpi, Replicate 2


title: lin-53 RNAi H3K27ac-rep3 (ChIP-seq)

source_name: lin-53 RNAi H3K27ac

value: H3K27ac antibody (Abcam ab4729)


title: NPC Patient 3 rep2

source_name: Nasopharyngeal carcinoma


title: NPC Patient 1 rep2


title: NPC Patient 14 rep1


title: NPC Patient 15 rep1


title: S_I_24_R1

source_name: Susceptibe, Inoculated, 24hpi, Replicate 1


title: NPC Patient 12 rep1

value: No Recurrence


title: NPC Patient 10 rep1


title: NPC Patient 11 rep1


title: lin-53 RNAi H3K27ac-rep2 (ChIP-seq)


title: WT input DNA-rep1 (ChIP-seq)


title: Rabbit SSP, uninjured, long term 6


title: NPC Patient 9 rep1


title: CA_45

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

data_processing:
first ten bases removed with fastx_trimmer (FASTX toolkit v0.0.14)
Truseq adapters and low-quality regions removed with trimmomatic (v0.36) ([adapter.fasta] :3 :30 :9 | SLIDINGWINDOW :4:15)
Poly-A tails at least 5bp long were removed with Prinseq (v.0.20.4). Reads smaller than 20bp were discarded.
Reads were aligned to human genome GRCh38 with Tophat (v.2.1.1). Paired-end reads that had lost their mate in processing were aligned separately
Htseq-count was used to quantify features extracted from ENSEMBL v77
Homo_sapiens.hg19.fa (reference genome).  The raw data is submitted as the BAMs received from our local sequencing centre. They aligned the data to a version of hg19. The exact genome is provided as a fasta (Homo_sapiens.hg19.fasta).  We reprocessed the data and aligned it to GRCh38 (hence this version of the genome being referenced in "genome build" despite the reference genome present in the submitted BAMs).
Genome_build: hg38
Supplementary_files_format_and_content: Tabulation delimited table containing the unnormalized amount of fragments mapping to features of interest for each sample.

source_name: Pyramidal Neurons

extract_protocol:
In the present study, we used LCM-seq to carry out a cell-type specific transcriptomic investigation of deep-layer pyramidal neurons in the PFC of individuals with a history of childhood abuse. RNA extraction was carried out via the PicoPure RNA Isolation Kit (ThermoFisher) according to the manufacturer’s protocol. Briefly, each LCM cap–microcentrifuge tube assembly was inverted such that the extraction buffer covered the Capsure HS LCM cap and dissected cells. Samples were then incubated at 42°C for 30 minutes followed by centrifugation to collect the total cellular extract at the bottom of each tube. The extract was then carried through the RNA isolation steps of the manufacturer’s protocol. RNA was eluted in a total volume of 11µl.   Full-length cDNA was synthesized, via the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), according to the manufacturer’s protocol. cDNA was amplified by LD PCR for 18 cycles and purified by immobilization on AMPure beads. The beads were then washed in 80% ethanol and cDNA was eluted in elution buffer. cDNA concentrations were measured using the Quant-iT™ PicoGreen® dsDNA Assay Kit (ThermoFisher).
cDNA libraries were normalized to 0.2ng/µl and carried through the Nextera XT DNA Library Prep Kit (Illumina). Libraries were amplified with Illumina i5 and i7 index adaptors for 18 cycles, purified with AMPure beads, and eluted in resuspension buffer. Libraries were quantified at the McGill University and Genome Quebec Innovation Center using a DNA High Sensitivity Chip (LabChip, PerkinElmer), quantitative PCR (KAPA Library Quantification, Kapa Biosystems), and PicoGreen (Life Technologies).
Seven to eight libraries were run per lane of an Illumina HiSeq 4000 (100bp paired-end), yielding ~42 million reads/library. Libraries were built and sequenced only for subjects with a history of childhood abuse and controls.

tag: status

value: Child Abuse

tag: Sex

value: Male

tag: age

tag: post-mortem interval

tag: ph

value: Pyramidal Neurons


title: NPC Patient 13 rep1


title: Rabbit SSP, uninjured, long term 5


title: C_43

value: Control

value: Female


title: C_42


title: C_44


title: Rabbit SSP, uninjured, long term 3


title: CA_41


title: lin-53 RNAi H3K27ac-rep1 (ChIP-seq)

value: all stage

value: lin-53 RNAi


title: CA_40


title: hda-1 RNAi H3K27ac-rep1 (ChIP-seq)

source_name: hda-1 RNAi H3K27ac


title: Rabbit SSP, uninjured, long term 1


title: Rabbit SSP, uninjured, long term 2


title: hda-1 RNAi H3K27ac-rep3 (ChIP-seq)


title: Rabbit SSP, uninjured, long term 4


title: Rabbit SSP, matrix gel treated, long term 5

value: matrix gel treated


title: hda-1 RNAi H3K27ac-rep2 (ChIP-seq)


title: Rabbit SSP, matrix gel treated, long term 3


title: Rabbit SSP, matrix gel treated, long term 4


title: CA_39


title: NPC Patient 8 rep1

value: Nasopharyngeal carcinoma

value: Recurrence


title: CA_37


title: WT H3K27ac-rep1 (ChIP-seq)

source_name: WT H3K27ac

value: wild type


title: WT H3K27ac-rep3 (ChIP-seq)


title: WT H3K27ac-rep2 (ChIP-seq)


title: Rabbit SSP, matrix gel treated, long term 2


title: CA_36


title: NPC Patient 6 rep1


title: NPC Patient 4 rep1


title: NPC Patient 7 rep1


title: NPC Patient 2 rep1


title: Rabbit SSP, matrix gel treated, long term 1


title: NPC Patient 5 rep1


title: NPC Patient 3 rep1


title: NPC Patient 1 rep1


title: Rabbit SSP, repair only treated, long term 5

value: repair only treated


title: CA_34


title: CA_38


title: CA_33


title: lin-53 RNAi embryo-rep1 (RNA-seq)

molecule: polyA RNA

source_name: lin-53 RNAi embryo

extract_protocol:
Eggs were harvested 5 hours post-laid and then lysed with TRIzol reagent (Invitrogen). We extracted the total RNA following the manufacturer’s protocol. The Qubit RNA High Sensitivity Assay Kit (Invitrogen) was used to quantify RNA concentration. The Agilent 2100 bioanalyzer system was used for the assessment of RNA quality. Samples with an RNA integrity number (RIN) above 6.0 were used for sequencing library construction.
We used the identical amounts of input total RNA (50 ng to 500 ng) between control and samples for library preparation using the KAPA RNA HyperPrep Kit (KAPA Biosystems, Wilmington, MA, USA). Libraries were analyzed by Agilent 2100 bioanalyzer system for quality control.

value: embryo 5 hours post laid


title: lin-53 RNAi embryo-rep2 (RNA-seq)


title: Rabbit SSP, repair only treated, long term 4

value: supraspinatus muscle


title: hda-1 RNAi embryo-rep3 (RNA-seq)

source_name: hda-1 RNAi embryo

value: hda-1 RNAi


title: IYB4

city: Houston

first: exRNA

last: BRL

state: TX

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

institute: Baylor College of Medicine

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: *.tar: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Bile

extract_protocol:
RNA Isolation kit was miRNeasy (Qiagen), miRcury biofluids (Exiqon), or SeraMir (System Biosciences).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were multiplexed. Type of Starting Material was total RNA.

tag: disease state

value: cancer

value: Bile

tag: anatomical location

value: Entire bile duct

tag: rna source

value: extracellular vesicle

tag: rna isolation kit

value: miRNeasy (Qiagen)

tag: patient


title: IYB5

tag: tissue

value: SeraMir Kit (System Biosciences)


title: IYB2

value: miRcury biofluids (Exiqon)


title: IYB3

value: normal


title: Rabbit SSP, repair only treated, long term 3

tag: treatment


title: C_31

value: Control

value: Male

value: Pyramidal Neurons


title: CA_32

value: Child Abuse


title: hda-1 RNAi embryo-rep2 (RNA-seq)

tag: genotype


title: Rabbit SSP, repair only treated, long term 2


title: IYB1


title: lin-53 RNAi embryo-rep3 (RNA-seq)

tag: strain

value: lin-53 RNAi


title: CA_35

tag: cell type


title: CA_30

value: Female


title: hda-1 RNAi embryo-rep1 (RNA-seq)

tag: developmental stage

value: embryo 5 hours post laid


title: WT embryo-rep3 (RNA-seq)

source_name: WT embryo

value: wild type


title: Rabbit SSP, repair only treated, long term 1

value: supraspinatus muscle

value: repair only treated


title: Rabbit SSP, injury only, short term 4

value: injury


title: C_29


title: C_27


title: WT embryo-rep2 (RNA-seq)


title: Rabbit SSP, injury only, short term 3


title: C_28


title: Rabbit SSP, injury only, short term 2


title: Rabbit SSP, injury only, short term 1


title: WT embryo-rep1 (RNA-seq)


title: 38EM (Treatment 3) Replicate 3

city: San Francisco

first: Liliana

last: Soroceanu

state: CA

address: 475 Brannan Street

institute: California Pacific Medical Center Research Institute

description: Gene expression of glioblastoma sample treated with Erlotinib+MLN0128

hyb_protocol: Phalanx OneArray Plus Protocol

scan_protocol: Agilent 0.1 XDR Protocol

data_processing: Human OneArray(®) Annotation HOA v7 release 1.0, 2015-09-23

source_name: Brain

label_protocol: Cyanine-5 (Cy5) labeled aRNA was prepared from 5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and aRNA yield were checked with the NanoDrop ND-1000 Spectrophotomete

growth_protocol: Not applicable, PDX samples from in vivo experiment were used

extract_protocol: RNA was extracted using the RNA Easy Qiagen kit and associated protocol

treatment_protocol: Mice were treated 5 days a week for the duration of  the experiment (6 weeks) either with vehicle (DMSO), Erlotinib (30mg/kg), MLN0128 (1mg/kg), or the combination of both Erlotinib and MLN0128. Drugs were administered via i.p. injections.

value: Tumor


title: Control PHx 24 h-input

city: Shanghai

first: Yanhao

last: Chen

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were mapped to the mm10 genome assembly using bowtie2 version 2.2.9
Sam files were converted to Bam format using Samtools version 1.8
Peak calling was done using MACS2 version 2.1.0
big wig files was done using deeptools version 3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: big wig files include read count data

organism: Mus musculus

source_name: Liver

extract_protocol:
Minced liver tissue were washed in PBS then cross-linked with 1% formaldehyde for 10min at room temperature.Cross-linked cells were washed with ice-cold PBS.For each sample,20 million fixed cells were lysed to prepare nuclear extracts.After chromatin shearing by sonication,lysates were incubated overnight at 4℃ with proteinA/G Dynabeads coupled with 5ug of antibody.After immunoprecipitation, beads were recovered using a magnet and washed.DNA was eluted and cross-links reverted at 65℃ for 4 hours then purified with QIAGEN Kit.DNA was quantitated using the Qubit® dsDNA HS assay and a Qubit® 2.0 Fluorimeter (Invitrogen).
A total amount of 50 ng DNA per sample was used as input material for the ChIP sample preparations.The purified  DNA was end prepared.After end preparation, the Adaptor were ligated to prepare for hybridization.Then the Adaptor liagted DNA was puried by DNA clean beads.The PCR was performed with PCR primers and Index Primers for library amplification.At last,PCR products were purified and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Liver

value: AAV-Cre

value: PHx 24 h

tag: chip antibody


title: Mier1 KO PHx 24 h-H3K27ac

value: AAV-Mier1 sgRNA

value: H3K27ac antibody (Active Motif, 38133)


title: Mier1 KO PHx 24 h-input


title: Control PHx 24 h-H3K27ac


title: 17EM (Treatment 3) Replicate 1


title: 33EM (Treatment 3) Replicate 2


title: Rabbit SSP, matrix gel treated, short term 3

value: matrix gel treated


title: Mier1 KO PHx 0 h-input

value: PHx 0 h


title: 36M (Treatment 2=MLN0128) Replicate 2

description: Gene expression of MLN0128 treated glioblastoma sample


title: CV (Vehicle)- Replicate 2

description: Gene expression of Sham treated glioblastoma sample

value: sham


title: C_25

tag: status

value: Control

value: Pyramidal Neurons


title: C_26

tag: Sex

value: Male


title: CA_24

value: Child Abuse

tag: age


title: C_22

value: Female

tag: post-mortem interval


title: Rabbit SSP, matrix gel treated, short term 5

value: supraspinatus muscle


title: Rabbit SSP, matrix gel treated, short term 2


title: A2102

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

data_processing:
Illumina Casava software
Sequencing adaptors, low-complexity reads, and reads containing low  quality bases were removed in an initial data-filtering step. Reads with a PhredScore lower than 30 were filtered out. After QC, clean reads (38 samples) were mapped to the Bos taurus reference genome (ARS-UCD 1.2) using the STAR aligner v. 2.7.3a. The –quantMode GeneCounts flag from STAR and the annotation information (release 100, Ensembl) were used to determine the number of raw counts per gene in each sample.  The gene expression normalization procedure was performed through the DESeq2 v.1.28.1 using the VST function. The DESeq2 design model included the dam’s age, offspring sex, and treatment group. Differentially expressed genes (DEGs) were identified between the treatments considering the t-test method proposed by Reverter et al. and implemented in the R-package CeTF v.1.0.7
Genome_build: Bos taurus ARS-UCD 1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: Longissimus dorsi muscle

extract_protocol:
Total RNA was isolated using the RNeasy Fibrous Tissue Mini Kit (Qiagenâ, Germantown, MA), following the manufacturer's protocol.
Strand-specific libraries (poly-A enrichment) were prepared using the NEBNextâ Ultraä II Directional RNA Library Prep Kit for Illumina (New England BioLabsâ, Ipswich, MA).

treatment_protocol: Except in the CTR group, cows received Se-supplementation during their corresponding pregnancy trimester in the form of three Se-yeast (Phibro Selenium Yeast 2000, Prince Agri Products, Inc., Quincy IL) boluses per week for 13 weeks, equaling 105 mg Se/wk throughout their treatment trimester. Thus, cows received Se-yeast during the first (TR1), second (TR2), or third (TR3) trimester of gestation. In addition, cows had access to a mineral supplement containing 120 mg/kg Se (US FDA regulations) from Na selenite.

value: Muscle

value: M

tag: dam age

tag: treatment group


title: 32M (Treatment 2=MLN0128) Replicate 1

value: Tumor


title: 28E (Treatment 1=Erlotinib) Replicate 2

description: Gene expression of Erlotinib treated glioblastoma sample

value: Erlotinib


title: 38E (Treatment 1=Erlotinib) Replicate 1


title: Mier1 KO PHx 0 h-H3K27ac

value: Liver


title: CA_21

tag: ph


title: Control PHx 0 h-input

value: AAV-Cre


title: 15V (Vehicle)- Replicate 1


title: C_20


title: Rabbit SSP, repair only treated, short term 5

value: repair only


title: Rabbit SSP, matrix gel treated, short term 4


title: A2085

value: F


title: Control PHx 0 h-H3K27ac

value: H3K27ac antibody (Active Motif, 38133)


title: CA_19


title: Rabbit SSP, repair only treated, short term 4


title: CA_23


title: C_18


title: Rabbit SSP, repair only treated, short term 3


title: A2073


title: CA_17


title: Rbbp5KO_epi_Brif_1

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

data_processing:
Library strategy: Brif-seq
For RNA-seq data, adapter sequences were trimmed off using Trimgalore (version 0.6.4), clean data were mapped to the mouse reference genome (mm10) using STAR (version 2.7.3) with --quantMode GeneCounts option to output read count tables.
For ChIP-seq, reads  were aligned to mm10 by bowtie2 (version 2.3.5) with the parameters: --t --q --N 1 --L 25. PCR duplicates and multiple mapped reads were removed. Peaks calling was performed with MACS2 (version 2.2.6) and enriched transcription factor (TF) motifs were analyzed by Homer (version 4.10.4, findMotifsGenome).
For ATAC-seq, paired-end raw reads were processed using TrimGalore to trim adaptor and low-quality reads. Adaptor-trimmed paired-end reads from ATAC-seq were mapped to mm10 by bowtie2 (version 2.3.5). PCR duplicates and mutiple mapped reads were removed. Calling peakswas performed with MACS2 (version 2.2.6).
For Brif-seq, clean reads were mapped back to the C-T converted mm10 genome by Bismark. PCR duplicates, unmapped reads, and non-uniquely mapped reads were diminished by 'deduplicate' function of Bismark. Methylation sites were identified by 'methylation extractor' function of Bismark.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of gene names and FPKM values for each RNA-seq sample. Bigwig for each ChIP-seq and ATAC-seq sample. Text files of CpG islands values for each Brif-seq sample.

source_name: single cell

growth_protocol: WT and Rbbp5 KO preimplantation embryos were collected and cultured in KSOM at 37.5℃. E3.5 ICM, E4.5 epiblast, E4.5 primitive endoderm, E4.5 trophectoderm were isolated by immune surgery. To collect epiblast from E5.5 embryos, WT and Rbbp5 KO postimplantation embryos were dissected from the uterus at E5.5,  and epiblast part was manually dissected.

extract_protocol:
Freshly isolatedE.3.5 ICM, E4.5 epiblast, E4.5 primitive endoderm, E4.5 trophectoderm and E5.5 ICM and epiblast were lysed and used for RNA-seq, STAR ChIP-seq, miniATAC-seq and Brif-seq.
For RNA-seq, cDNA was generated using the SMART-seq2 protocol. cDNA libraries were conduced using the Tn5 library construction protocol (Picelli et al. Nature protocols. 2014). Finally, the acquired cDNA libraries were sequenced on HiSeq X Ten platform. For STAR ChIP-seq (Zhang et al. Nature. 2016), target DNA fragments were followed by TELP library construction protocol (Peng et al. Nucleic Acids Research, 2015). Open chromatin analysis was done according to miniATAC-seq protocol (Wu et at al, Nature, 2018). Single cell methylome analysis was conducted by Brif-seq protocol (Li et at al, Molecular Plant, 2019).

treatment_protocol: For Rbbp5 knockout, wild-type zygotes were injected with sgRNA targetting Rbbp5 plus Cas9 mRNA, Rbbp5 flox/flox zygotes were injected with Cre mRNA. Injected zygotes were cultured in KSOM in 37℃ incubator to blastocyst stage, or cultured to 2-cell stage and transfered to pseudo-pregnant mice.

value: E4.5 epiblast

value: single cell


title: Rbbp5KO_epi_Brif_2


title: Rabbit SSP, repair only treated, short term 2


title: C_16

value: Control


title: Rabbit SSP, repair only treated, short term 1


title: A2065


title: WT_epi_Brif_2

value: WT


title: Rabbit SSP, matrix gel treated, short term 1

value: matrix gel treated


title: A2087


title: A2033


title: WT_epi_Brif_1


title: A2024


title: CD73+ cells, biol rep 3

city: Tokyo

first: Daisuke

last: Hisamatsu

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

country: Japan

institute: Juntendo University Graduate School of Medicine

data_processing:
To generate a sequence alignment, quality control and preprocessing of FASTQ data were performed using fastp v.0.20.1 (https://github.com/OpenGene/fastp).
Transcript was quantified using Salmon (https://combine-lab.github.io/salmon/).
Read count normalization were performed using edgeR.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: subcutaneous white adipose tissue

growth_protocol: CD73+ cells and cMSCs were maintained in DMEM supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from these cells using an RNeasy Mini kit (Qiagen, Hilden, Germany).
Sequencing library was prepared using the SMART-Seq v4 Ultra Low Input RNA kit (Takara, Kusatsu, Japan).

value: subcutaneous white adipose tissue

value: mesenchymal stem/stromal cells

tag: cell subtype

value: female

value: untreated

tag: disease state

value: healthy


title: A2020

value: Muscle

value: M


title: Rbbp5KO_ICM_ATAC_1

data_processing:
For RNA-seq data, adapter sequences were trimmed off using Trimgalore (version 0.6.4), clean data were mapped to the mouse reference genome (mm10) using STAR (version 2.7.3) with --quantMode GeneCounts option to output read count tables.
For ChIP-seq, reads  were aligned to mm10 by bowtie2 (version 2.3.5) with the parameters: --t --q --N 1 --L 25. PCR duplicates and multiple mapped reads were removed. Peaks calling was performed with MACS2 (version 2.2.6) and enriched transcription factor (TF) motifs were analyzed by Homer (version 4.10.4, findMotifsGenome).
For ATAC-seq, paired-end raw reads were processed using TrimGalore to trim adaptor and low-quality reads. Adaptor-trimmed paired-end reads from ATAC-seq were mapped to mm10 by bowtie2 (version 2.3.5). PCR duplicates and mutiple mapped reads were removed. Calling peakswas performed with MACS2 (version 2.2.6).
For Brif-seq, clean reads were mapped back to the C-T converted mm10 genome by Bismark. PCR duplicates, unmapped reads, and non-uniquely mapped reads were diminished by 'deduplicate' function of Bismark. Methylation sites were identified by 'methylation extractor' function of Bismark.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of gene names and FPKM values for each RNA-seq sample. Bigwig for each ChIP-seq and ATAC-seq sample. Text files of CpG islands values for each Brif-seq sample.

source_name: bulk embryos

value: E3.5 ICM

value: bulk embryos


title: A2074


title: CD73+ cells, biol rep 1


title: WT_ICM_ATAC_1


title: CD73+ cells, biol rep 2


title: C_14

value: Female

value: Pyramidal Neurons


title: C_13

value: Male


title: C_12


title: cMSCs, biol rep 3

value: cMSC


title: Rbbp5KO_E5.5epiblast_H3K4me3_1

value: E5.5 Epiblast


title: A2100


title: A2090


title: cMSCs, biol rep 2


title: CA_11

value: Child Abuse


title: WT_E5.5epiblast_H3K4me3_2

value: WT


title: C_10

value: Control


title: WT_E5.5epiblast_H3K4me3_1


title: A2084

value: F


title: Rbbp5KO_ICM_H3K4me3_2


title: A2083


title: CA_15


title: C_9


title: Rbbp5KO_ICM_H3K4me3_1


title: MDA-MB-231 cells-DSF_Cu treated -3

city: ChangChun

first: Chu

last: Meiran

address: 5333 XI an road

department: Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Human breast

growth_protocol: MDA-MB-231 cells were seeded in plated on 6-well cell plates with 2 × 105 cells, and were grown in RPMI 1640 medium (Gibco, USA) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin solution (Gibco, USA)

treatment_protocol: MDA-MB-231 cells were treated with DSF/Cu (0.2 µM) for 24 h.

value: Human breast

tag: cell line

value: MDA-MB-231 cells

value: Disulfiram/Cu


title: MDA-MB-231 cells-DSF_Cu treated -2

tag: tissue


title: WT_ICM_H3K4me3_2


title: cMSCs, biol rep 1

value: subcutaneous white adipose tissue

value: mesenchymal stem/stromal cells

value: female

tag: treatment

value: untreated

value: healthy


title: CA_7


title: MDA-MB-231 cells-DSF_Cu treated -1


title: WT_ICM_H3K4me3_1

value: E3.5 ICM

value: bulk embryos

tag: genotype


title: MDA-MB-231 cells-DMSO treated -3

value: DMSO


title: A2079

value: Muscle


title: A2066

value: M


title: A2068


title: C_6

value: Male

value: Pyramidal Neurons


title: CA_5

value: Child Abuse

value: Female


title: A2099


title: Rbbp5KO_E5.5epiblast_RNA-2

source_name: single embryo

value: E5.5 Epiblast

value: single embryo


title: Rbbp5KO_E5.5epiblast_RNA-3


title: CA_4


title: MDA-MB-231 cells-DMSO treated -1

value: Human breast

value: MDA-MB-231 cells


title: A2023


title: Rbbp5KO_E5.5epiblast_RNA-1


title: CA_3


title: A2092


title: healthy children donor 3

city: Chongqing

first: Qilin

address: No. 1 Yixueyuan Road, Yuzhong District, Chongqing

institute: Chongqing Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
the raw sequencing reads were processed using Cell Ranger (version 6.0.0).
Assembly: GRCh38
Supplementary files format and content: matrix files

source_name: blood

extract_protocol:
2 ml of venous blood was collected in EDTA anticoagulant tubes and transferred to the laboratory on ice. PBMCs were isolated from whole blood by density gradient centrifugation using Ficoll medium (TBD, Tianjing, China). PBMCs were frozen until analyzed according to the 10X genomics recommended protocol (CG00039).
BMCs from healthy children donors were thawed according to the 10X genomics recommended protocol (CG00039), and the cell viability of each sample was >80%. The PBMCs from each sample were diluted to a final concentration of 700~1200 cells/µl, and approximately 16000 cells per reaction were loaded on a Chromium Single Cell Controller (10X Genomics, Pleasanton, CA). The libraries for scRNA-seq were constructed using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121) following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq6000. Each sample was processed independently.

value: blood

value: PBMCs


title: C_8

value: Control


title: WT_E5.5epiblast_RNA-3

value: WT


title: CA_2


title: healthy children donor 2

description: 10x Genomics


title: A2067


title: C_1


title: WT_E5.5epiblast_RNA-2


title: A2058


title: TURB35-NK

city: Paris

first: Nicolas

last: Dulphy

address: 1, avenue Claude Vellefaux

department: Institut de Recherche Saint-Louis

country: France

institute: UNIV PARIS

data_processing:
Sequenced reads were trimmed for adaptor sequence using TrimGalore 0.6.6
Trimmed reads were aligned to GRCh38 whole genome using Bismark 0.22.3
Methylation extraction was performed using Bismark 0.22.3
Differential methylation analysis was performed using RnBeads2 with a minimum coverage of 10x
Genome_build: GRCh38
Supplementary_files_format_and_content: Bed files with methylation percentage and number of methylated and unmethylated reads

source_name: NK Cell

growth_protocol: Not applicable

extract_protocol:
Total DNA has been extracted from sorted NK and T-cells with the DNeasy KIT provided by Qiagen according to manufacturer's instructions
100 ng of purified genomic DNA were used for RRBS
Sequencing was performed in paired-end mode 50bp (PE50), quality control of sequencing reads was performed using FastQC, and reads alignment against human reference genome hg38/GRCh38 using bismark v0.20.0 according to Diagenode protocol

treatment_protocol: Not applicable

value: NK Cell

value: TET2 mut


title: A2057


title: MDA-MB-231 cells-DMSO treated -2

value: DMSO


title: WT_3

city: Yangling

first: Xingjie

last: Lan

state: Shaanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

data_processing:
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis
Approximately 10 ug of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA).
Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature.
And then we performed the paired-end sequencing on an illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Plants were grown in a growth chamber under normal conditions (13 h light/11 h dark cycle and 23±2 ℃ temperature).

extract_protocol:
The 30-day-old detached Arabidopsis rosette leaves of wild type Col-0, knock-out line VQ28KO12 and overexpression line VQ28OE9 were collected to isolate total RNA without infection. Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: rosette leaves


title: Rbbp5KO_PE_RNA-2

value: E4.5 primitive endoderm

value: single cell


title: A2054

value: Muscle

value: F


title: WT_1


title: WT_E5.5epiblast_RNA-1


title: A2047


title: Rbbp5KO_PE_RNA-1


title: WT_2


title: OULN45-NK


title: A2052


title: JAVE60-NK


title: A2040

value: M


title: VQ28OE9_3


title: GREAM52-NK

value: TET2 wt


title: VQ28OE9_2


title: A2032


title: Rbbp5KO_epi_RNA-3

value: E4.5 Epiblast


title: Rbbp5KO_epi_RNA-2


title: VQ28OE9_1


title: A2029


title: TURB35-T

source_name: T Cell

value: T Cell

value: wild type


title: healthy children donor 1

description: 10x Genomics

value: blood


title: Rbbp5KO_epi_RNA-1


title: VQ28KO12_3


title: OULN45-T


title: VQ28KO12_2


title: JAVE60-T


title: A2098

value: CON


title: WT_PE_RNA-1


title: WT_epi_RNA-6


title: A2096


title: WT_epi_RNA-7


title: A2091


title: VQ28KO12_1


title: GREAM52-T


title: WT_epi_RNA-5


title: smIs89 embryo (SPLiT-seq)

source_name: smIs89 embryo

growth_protocol: Worms were cultivated at 20 °C on nematode growth medium (NGM) agar plates seeded with the Escherichia coli OP50

extract_protocol:
The RNA extraction follows SPLiT-seq protocol
The RNA-seq libraries were generated as previously described (Rosenberg et al., 2018) with minor modifications. After cell fixation, all the centrifugations were performed at 3220 g for 3 min according to the C. elegans cell size. The RT-primers are poly-dT and random hexamer mixture with UMIs (Unique Molecular Identifiers). All the barcodes used in this study were described the published protocol (Rosenberg et al., 2018). The first 24 barcodes were used in the first round of barcoding, named “Round1_01” to “Round1_24”, and 48 barcodes were used in the third round of barcoding, named “Round3_49” to “Round3_96”. Each cell barcode came from three rounds of barcoding. TruePrep DNA Library Prep Kit V2 constructed the sequencing library for Illumina (Vazyme Biotech #TD502) according to the manufacturer’s instructions.

tag: strain

value: embryo 3-4 hours post laid


title: DEAM41-NK

tag: cell type


title: WT_epi_RNA-4

value: WT


title: HEK293_E2 (NovaSeq 6000)

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

description: HEK293 cell line is a permanent line established from primary embryonic human kidney

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference human genome using Tophat.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq functions estimate Size Factors and nbinomTest. P value < 0.05 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: human genome GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each samples

source_name: HEK293 cells transfected with GFP-EBV EBNA2 vector for 48 hours

growth_protocol: The human HEK293 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
For RNA-seq, mRNA was enriched by polyA selection.
RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurate quantification using StepOnePlus™ Real-Time PCR System (Library valid concentration＞10 nM).
Then the cell RNA was sequenced by the Illumina NovaSeq 6000 sequencing service.

treatment_protocol: HEK293 cells were transfected with either GFP-EBV EBNA2 vector or empty vector (NC)  for 48 hours.

value: embryonic human kidney

tag: genotype/variation

value: transfected with GFP-EBV EBNA2 vector


title: A2075


title: A2042


title: WT_epi_RNA-2


title: Lien14V

city: Fuzhou

first: Jia

middle: pei

last: zhi

address: Shangjie Town, Minhou County, Fuzhou City, Fujian Province

institute: Fujian University of Chinese Medicine

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: vascular tissue

extract_protocol:
The hearts were dissected and cardiac tissues were stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: vascular tissue

value: Hypertension+Lien


title: Lien13V


title: D3207

city: Pittsburgh

first: Samantha

last: Fontaine

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is U. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).

data_processing:
Raw RNA-seq reads were trimmed to remove indexes and for quality using Trim Galore. Reads were mapped to an available reference draft genome of the green frog’s congeneric, the American bullfrog (L. catesbeiana, GenBank accession number GCA_002284835.2) using BWA. We used StringTie to generate a matrix of read counts across samples for each transcript.
Assembly: L. catesbeiana, GenBank accession number GCA_002284835.2
Supplementary files format and content: comma separated value file containing a matrix of gene counts for each gene (row) across all samples (columns)

organism: Lithobates clamitans

source_name: Gut

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit from QIAGEN. At step 3 of the protocol, we used 350µL of buffer RLT and a TissueLyser II (QIAGEN) set to 30 Hz for one minute for disruption and homogenization. RNA was stored at -20 Celsius before processing.
mRNA was isolated, cDNA libraries constructed, and unique sample indexes added using the TruSeq RNA Library Prep Kit (Illumina) following the manufacturer’s protocol.

treatment_protocol: Guts were dissected from tadpoles and placed in RNAlater for 24 hours. The RNAlater was then removed and guts were kept frozen at -80 Celsius before extraction.

value: Gut

tag: developmental stage

value: tadpole

tag: temperature

value: Warm (32C)

tag: microbial colonization_treatment

value: Depleted


title: A2041

value: Muscle

tag: Sex

value: F


title: WT_epi_RNA-1

value: E4.5 Epiblast

value: single cell


title: Lien12V


title: D3206

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is T. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).


title: A2038

value: M


title: Rbbp5KO_ICM_RNA-7

value: E3.5 ICM

value: single embryo


title: A2035

value: CON


title: D3205

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is S. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).


title: DEAM41-T

value: T Cell

value: wild type


title: A2088


title: AngII 10 V

value: Hypertension


title: Lien15V

value: vascular tissue


title: D3203

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is R. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).


title: A2034


title: Rbbp5KO_ICM_RNA-5


title: WT_epi_RNA-3

value: WT


title: D3202

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is Q. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).

value: Gut


title: AngII 9 V


title: Combined3

city: Daejeon

first: Sang-Min

last: Park

address: Youseong-Daero

department: College of Pharmacy

country: South Korea

institute: Chungnam National University

data_processing:
NOT PROVIDED; REQUESTED
Assembly: NOT PROVIDED; REQUESTED
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: tumor cells

growth_protocol: MC38 cells were grown in DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/ml streptomycin at 37°C in a humidified atmosphere containing 5% CO2. MC38 tumor-bearing mice were established by injecting MC38 cells into the right flank subcutaneously of specific pathogen-free 6-week-old female C57BL/6 mice. Mice were housed under controlled environmental conditions of temperature (23°C), humidity (50%), and a 12-h light/dark cycle. The animals were fed a standard chow diet and provided free access to drinking water.

extract_protocol:
Total RNA was isolated from tumor tissues using TRIzol (Invitrogen) following the manufacturer’s protocol. The RNA quality was assessed using a Bioanalyzer 2100 System (Agilent Technologies, Santa Clara, CA, USA). RNA concentration was measured using a NanoDrop ND-2000 (Thermo Fisher Scientific).
The cDNA libraries were constructed using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen, Inc., Vienna, Austria) and sequenced on a NextSeq 500 (Illumina Inc., San Diego, CA, USA) to generate single-end 75 bp reads according to the manufacturer’s instructions.

treatment_protocol: The mice were intraperitoneally injected with 50 mg/kg SFIH daily and/or 200 μg PD-1 antibody two times a week. Control mice were injected with the same volume of saline and IgG2a antibody.

value: tumor cells

value: combined treatment

tag: time

value: Day 19


title: HEK293_NC (NovaSeq 6000)

source_name: HEK293 cells transfected with empty vector (NC) for 48 hours

value: embryonic human kidney

value: transfected with empty vector (NC)


title: Rbbp5KO_ICM_RNA-4


title: Combined2


title: D2209

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is P. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).

value: tadpole

value: Warm (32C)

value: Colonized


title: AngII 8 V


title: Rbbp5KO_ICM_RNA-3

value: E3.5 ICM


title: Combined1


title: Rbbp5KO_ICM_RNA-2

value: single embryo


title: D2203

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is N. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).


title: AngII 7 V


title: Lien11V

value: Hypertension+Lien


title: PD3

value: anti-PD-1 antibody monotherapy


title: AngII 6 V


title: NS 5 V

value: Normal


title: D2202

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is M. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).


title: D2201

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is L. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).


title: NS 4 V


title: Rbbp5KO_ICM_RNA-1


title: PD1


title: PD2


title: D2206

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is O. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).


title: WT_ICM_RNA-7


title: Rbbp5KO_ICM_RNA-6


title: WT_ICM_RNA-6


title: NS 3 V


title: SFIH3

value: SFIH monotherapy


title: C3210

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is K. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).

value: Cool (22C)

value: Depleted


title: C3208

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is J. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).

value: Gut


title: WT_ICM_RNA-4

value: WT


title: NS 2 V

value: vascular tissue


title: WT_ICM_RNA-5


title: SFIH2

value: tumor cells

value: Day 19


title: NS 1 V


title: SFIH1


title: C3205

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is H. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).


title: IgG

city: Chandigarh

first: Pawan

last: Gupta

state: Chandigarh

address: Department of Cell Biology and Molecular Immunology, CSIR-Institute of Microbial Technology, Sector-39A

country: India

institute: CSIR-Institute of Microbial Technology

data_processing:
The obtained libraries were pooled and diluted to final optimal loading concentration before cluster amplification on Illumina flow cell. Once the cluster generation is completed, the cluster was loaded on Illumina HiSeq X instrument to generate 60M, 150bp paired end reads. The paired end reads were aligned to the reference Mus musculuc release (mm10) downloaded from Sanger institute database. Alignment was performed using BWA MEM (ver-0.7.12).
The alignment files after filteration from previous step were considered for peak detection. The Seqpeak function of CisGenome (Ver-v2.0) was used for peak calling analysis. The peak were considered to be significant if their p-value was less than or equal to 0.05 and peak length greater than 200. The significant peaks were annotated using Homer tool (Ver-v4.10) and annotations were filtered for Promoter-TSS region. GO enrichment and pathway analysis for the final filtered peaks (Promoter-TSS region) were performed using David and Panther database. Further, filtered peaks sequences were subjected to motif prediction using MEME software. The sequence of 30 bp around each peak call was extracted from the mouse reference genome and this was then provided as an input for the meme-chip module of MEME.
Genome_build: mm10

source_name: Type1 helper (Th1) cells

growth_protocol: Naive T-cell isolation was performed from the secondary lymphoid organ of 4-6 weeks old mice by employing the IMagTM Mouse CD4 T lymphocyte enrichment set along with a biotin-tagged anti-mouse CD44 antibody. In-vitro differentiation was carried out with plate bound anti-CD3 and soluble anti-CD28 antibodies. For differentiating into Th1 cells, cytokines IL-12 and IFNγ were added in addition to anti-IL4 antibody. The cells were harvested after 3-4 days for ChIP experiment.

extract_protocol:
To obtain DNA fragments, cells were sonicated in SDS-lysis buffer. The remaining debris were cleared by centrifugation at 4oC and the supernatant was proceeded for immunoprecipitaion with Nr1d1 antibody. High speed centrifugation collected the immune complexes as a pellet, which were washed in order with low-salt buffer, high-salt buffer, LiCl wash buffer and then twice with 1X TE buffer. The immunoprecipitated DNA was eluted using the elution buffer.
The ChIP samples passed the QC and were proceeded for the library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L).

treatment_protocol: In order to isolate chromatin, fixation of cells were performed using 1% (wt/vol) formaldehyde for 30 minutes. To quench the cross-linking,100mM glycine solution was added and cell pellet was subsequently washed with ice-cold PBS solution.

value: programmed Th1 cells

tag: strain and genotype

value: C57BL/6, wild-type

tag: chip antibody

value: Nr1d1 antibody (sc-47626 X, Santa Cruz Biotechnology)


title: miRNA isolated from non-treated sample

city: ISTANBUL

first: Wissem

last: Mhiri

address: DAVUTPASA MAH. DAVUTPASA CADDESI ESENLER

department: chemistry

country: Turkey

institute: Yildiz technial university

data_processing:
Solexa/Illumina FASTQ variants for base-calling
Reads were filtered in order to obtain clean tags, which were then stored in FASTQ format.
Clean tags were mapped using Bowtie2 (Version 2.3.5; http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and annotated using Rfam database.
Filtered tags were aligned against the sRNA database miRbase (http://www.mirbase.org/) to identify based on the utterly matched sequences known and conserved miRNAs. After identifying target genes using TargetFinder software, differentially expressed miRNAs and genes were identified using DEGSeq software.
Selected DE target genes were compared to KEGG pathway database and Gene Ontology for pathway mapping and GO-term enrichment, respectively.
Genome_build: TAIR10.1, miRBase v20
Supplementary_files_format_and_content: text file with TPM

source_name: callus from root explants

growth_protocol: Calli were developed using root explants which were cut and placed into fresh MS medium containing 0.5 mL of 2,4-dichlorophenoxyacetic acid (2,4-D). The obtained callus cultures were continuously sub-cultured for 9 months.

extract_protocol:
Total RNA was isolated from the frozen calli of A. thaliana using TRIzol reagent
Libraries were constructed following the High-Throughput illumina sequencing library protocol. After being checked for integrity, 40µg of total RNA was used to purify the poly-A-containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Small RNA are selected by PAGE gel (separate 18-30nt RNA segment). The cleaved RNA fragments are used to synthesize cDNA strands and to amplify them using using a high-ping polymerase and enriched with both 3’ and 5’ adapter.  Library fragments (PCR products of 100~120 bp) were selected by PAGE to eliminate primer, dimer and other byproducts. Separation of the obtained fragments and the cyclization of single-strand DNA have occurred under high temperature. ssDNA circle was used to develop DNA nanoballs (DNBs).

treatment_protocol: Calli were then divided into two groups based on the supplemented CAG concentration: control group and 1 µM CAG. Three biological repetitions were set for each concentration. Calli were developed in a plant growth cabin at 25°C ±1°C under 16h light/8h dark light conditions for 21 days

value: callus

tag: ecotype

tag: rna-seq profile

value: Sample 1A


title: WT_ICM_RNA-1

city: Beijing

value: E3.5 ICM

value: single embryo


title: WT_ICM_RNA-2


title: Control1

value: vehicle


title: C2207

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is E. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).

value: tadpole

value: Colonized


title: C2208

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is F. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).

value: Cool (22C)


title: Control2


title: WT_ICM_RNA-3


title: Reverb_c


title: C2204

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is C. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).


title: Control3


title: miRNA isolated from 1µM CAG treated sample

value: Sample 1B


title: C2201

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is B. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).

value: Gut


title: Mmu vascular smooth muscle cells-exosome treated3

city: Guangzhou

first: Xiaoyu

last: Zhang

address: number 58, Zhongshan er road

institute: The first affiliated hospital of sun yat-sen unversity

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2).
The clean reads were mapped to the reference genome GRCm39 using HISAT2.
The expression level of gene was calculated by RSEM
The differential expression analysis was performed using the DESeq
Genome_build: GRCm39
Supplementary_files_format_and_content: xls, gene expression data

source_name: vascular smooth muscle cells

growth_protocol: Mouse vascular smooth muscle cells were cultivated by Dulbecco’s modified Eagle’s medium (Gibco) supplemented with 10% FBS (Australia)

extract_protocol:
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

treatment_protocol: The cells were treated with HucMSC-Exo 24 hours

value: Mouse aorta vascular smooth muscle cells

tag: sample type

value: exosome derived from umbilical  cord mesenchymal stem cells by ultracentrifugation


title: Mmu vascular smooth muscle cells-control1

value: media layer of the aorta


title: Mmu vascular smooth muscle cells-exosome treated2


title: Mmu vascular smooth muscle cells-exosome treated1


title: Input DNA


title: Reverb_a


title: Liver, MIER1 PHx 24 h

source_name: Liver

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
A total amount of 50 ng DNA per sample was used as input material for the ChIP sample preparations.The purified  DNA was end prepared.After end preparation, the Adaptor were ligated to prepare for hybridization.Then the Adaptor liagted DNA was puried by DNA clean beads.The PCR was performed with PCR primers and Index Primers for library amplification.At last,PCR products were purified and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Liver

tag: infection

value: PHx 24 h

value: anti-FLAG M2 (Sigma, A2220)


title: Normal heart 2

status: Public on Dec 29 2022

city: Zunyi

first: Song

last: Cao

state: China

address: 149 Dalian Street

institute: Affiliated Hospital of Zunyi Medical University

data_processing:
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left. miRDeep2 software was used to predict the novel miRNAs with these trimmed reads
Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression
When comparing the differentially expressed miRNA profiles between two groups, fold change and p-value were calculated and used to identify significant differentially expressed miRNAs
Assembly: miRBase v21

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
RNA was harvested using Trizol reagent
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: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).The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq per the manufacturer's instructions.library strategy

tag: tissue

value: Heart

value: WT

value: control


title: Left anterior descending coronary artery ligation and reperfusion heart 1

tag: treatment

value: ischemia-reperfusion


title: Left anterior descending coronary artery ligation and reperfusion heart 3

tag: genotype


title: C2206

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is D. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).


title: Liver, MIER1 PHx 0 h

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were mapped to the mm10 genome assembly using bowtie2 version 2.2.9
Sam files were converted to Bam format using Samtools version 1.8
Peak calling was done using MACS2 version 2.1.0
big wig files was done using deeptools version 3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: big wig files include read count data

tag: strain

value: PHx 0 h


title: Reverb_b

tag: cell type

value: programmed Th1 cells

value: C57BL/6, wild-type

value: Nr1d1 antibody (sc-47626 X, Santa Cruz Biotechnology)


title: Mmu vascular smooth muscle cells-control2


title: Liver, Input


title: C3207

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is I. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).

value: tadpole

value: Cool (22C)

value: Depleted


title: C3204

description: Processed data file is a matrix of read counts for all expressed genes (row names) across all samples (column names). This sample's matrix column is G. Gene ID names come from the Bullfrog reference genome used (GenBank accession number GCA_002284835.2).

value: Gut


title: Liver, Empty control

value: AAV-LUCIFERASE


title: Left anterior descending coronary artery ligation and reperfusion heart 2


title: Normal heart 3


title: Normal heart 1


title: Mmu vascular smooth muscle cells-control3

value: Mouse aorta vascular smooth muscle cells

value: media layer of the aorta


title: Patient31Post-treatment

city: Houston

first: Jin

middle: S

last: Im

state: Texas

address: 1515 Holcombe Blvd, Unit 900

institute: The University of Texas M.D. Anderson Cancer Center

hyb_protocol: Up to 100 ng amplified RNAs were hybridized with target-specific, fluorescence-labeled 594 CodeSet and reporter probes from the nCounter Immunology panel (Human v2 – NanoString, Seattle, WA) for 20 h, and added to the robotic nCounter Prep Station for automated sample processing for the remaining steps.

scan_protocol: The cartridge was then moved to the nCounter Digital Analyzer MAX (nanoString) where the samples were scanned and fluorescent targets counted.

data_processing: The nSolver software version 4 (NanoString, Seattle, WA, USA) was used for preprocessing of raw counts, subsequent normalization, and downstream analysis.

source_name: Myelodysplastic syndrome

label_protocol: RNA was further amplified using a NanoString Low Input Amplification Kit (NanoString, Seattle, WA, USA).

extract_protocol: Total RNAs were isolated from previously cryopreserved PBMC using the RNeasy Plus Micro Kit (Qiagen, Germantown, MD, USA).

tag: patient diagnosis

value: Myelodysplastic syndrome

value: Peripheral blood

value: Hypomethylating agent

tag: response

value: Non-response

tag: sampling time

value: Post-treatment


title: Patient4Post-treatment


title: Patient56Post-treatment

value: Response


title: Patient27Post-treatment


title: Patient30Post-treatment


title: Patient77Pre-treatment

value: Pre-treatment


title: Patient49Post-treatment


title: Patient64Pre-treatment


title: Patient37Post-treatment


title: Patient77Post-treatment


title: Patient49Pre-treatment


title: Patient9Pre-treatment


title: Patient9Post-treatment


title: Patient56Pre-treatment


title: Patient37Pre-treatment


title: Patient51Post-treatment


title: Patient54Post-treatment


title: Patient64Post-treatment


title: Patient32Post-treatment


title: Patient30Pre-treatment


title: Patient27Pre-treatment


title: Patient51Pre-treatment


title: Patient4Pre-treatment


title: Patient54Pre-treatment


title: Patient78Post-treatment

value: Immunotherapy


title: Patient31Pre-treatment


title: Patient74Post-treatment

value: Immunotherapy + Hypomethylating agent


title: Patient59Post-treatment


title: Patient72Post-treatment


title: Patient63Post-treatment


title: Patient62Post-treatment


title: Patient53Post-treatment


title: Patient68Post-treatment


title: Patient15Post-treatment


title: Patient73Post-treatment


title: Patient76Post-treatment


title: Patient32Pre-treatment


title: Patient78Pre-treatment


title: Patient55Post-treatment


title: Patient68Pre-treatment


title: Patient62Pre-treatment


title: Patient3Post-treatment


title: Patient61Post-treatment


title: Patient52Post-treatment


title: Patient76Pre-treatment


title: Patient15Pre-treatment


title: Patient53Pre-treatment


title: Patient8Post-treatment


title: Patient43Post-treatment


title: Patient42Post-treatment


title: Patient72Pre-treatment


title: Patient3Pre-treatment


title: Patient74Pre-treatment


title: Patient43Pre-treatment


title: AC2

city: Tianjin

first: Pengju

last: Wang

address: 32 West Seventh Road, Airport Economic Zone, Dongli District

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to E.coli MG1655 genome using Bowtie 2 (version 2.3.4.3)
Fragments Per Kilobase of gene per Megabase of library size (FPKM) were calculated
Detailed parameters for reads mapping: bowtie2 -x MG1655 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam
Genome_build: E.coli MG1655
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

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

source_name: E. coli cells

growth_protocol: cells of haploid and diploid E.coli grown overnight were inoculated into 50 ml LB medium and cultured for 3~4 hours to the logarithmic growth phase (OD600= 0.5~0.8).

extract_protocol:
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were collected by centrifugation at 6000g for 5 minutes. After washing twice with phosphate buffer saline (PBS),  the E.coli cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction.

value: Contain two chromosomes

tag: culture

value: LB medium, pH=7.0


title: AC1


title: Patient73Pre-treatment


title: AC3


title: WT1

value: Contain one chromosome


title: Patient63Pre-treatment


title: Patient8Pre-treatment


title: Patient59Pre-treatment


title: Patient61Pre-treatment


title: Patient55Pre-treatment


title: WT3


title: Patient23Post-treatment


title: WT2


title: Patient22Post-treatment


title: Patient42Pre-treatment


title: Patient52Pre-treatment


title: CX001, stems, bolting stage

city: Shenyang

first: chuanhong

last: liu

address: No. 120 Dongling Road, Shenhe District

institute: Shenyang Agricultural University

data_processing:
After the sample was sequenced on the computer, the image file was obtained, which was converted by the software of the sequencing platform to generate the original data of FASTQ
Further filter the sequencing data
Use the upgraded version of TopHat2 HISAT2 software to compare the filtered Reads to the reference genome
Assembly: Brapa_sequence_v3.0.fasta（http://brassicadb.cn/#/Download/）
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

organism: Brassica rapa subsp. chinensis

source_name: CX001, stems, bolting stage, 3 reps

growth_protocol: In the autumn of 2020 (mid-July), the seeds were sown in the experimental base of the  Shenyang Agricultural University.

extract_protocol:
RNA extraction kit
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: no

value: stems

tag: cultivar

tag: Stage

value: bolting

tag: phenotype

value: wax-less


title: FT, stems, bolting stage

source_name: FT, stems, bolting stage, 3 reps

value: FT

value: control


title: Patient21Post-treatment

value: Myelodysplastic syndrome


title: Patient12Post-treatment

value: Peripheral blood


title: pet 3

city: shenyang

first: jun

last: zhang

address: liaoning

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: BRAD_Brara_V3.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Brassica rapa

source_name: petiole

growth_protocol: The leaves and petioles of baby Chinese cabbage were sampled at maturity

extract_protocol:
The total RNA of ‘leaf’ and ‘pet’ was isolated and purified by Trizol reagent (Invitrogen, CA, USA).
For mRNA, lncRNA and circRNA, the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA) was used to remove ribosomal RNA and construct the chain-specific library.For miRNA, the six small RNA library was prepared by TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA).

treatment_protocol: No

value: petiole

value: inbred line

value: No


title: leaf 3

source_name: leaf

value: leaf


title: pet 2


title: pet 1


title: Patient48Post-treatment

value: Response

value: Post-treatment


title: Patient44Post-treatment

value: Immunotherapy + Hypomethylating agent

value: Non-response


title: Patient39Post-treatment


title: leaf 1


title: leaf 2


title: Patient38Post-treatment

value: Immunotherapy


title: Patient5Post-treatment


title: Patient40Post-treatment


title: Patient34Post-treatment


title: RD10_3

city: Hangzhou

first: Xu

last: Ping

state: Zhejiang

address: 866 Yuhangtang Road

department: Tea Research Institute

institute: Zhejiang University

data_processing:
The sequencing data were first filtered to remove adaptors, low-quality data, and contamination using Trimmomatic v 0.38
Filtered high quality reads were then mapped to C. sinensis reference genome using default parameter with HISAT2 v 2.1.0
The transcript sequence assembly and abundance calculation were performed using StringTie v1.3.4d with default parameter
Differentially expressed genes (DEGs) were analyzed by DESeq2 method (v 1.26.0). The genes with fold change ≥ 2.0 and pvalue ≤ 0.05 were defined as DEGs
Genome_build: Teaplant_CSS_version2 from TPIA (http://tpia.teaplant.org/download.html)

organism: Camellia sinensis

source_name: the leaves samples picked up on May 20, 2019 after five consecutive days shading and followed 5-day regaining light

growth_protocol: The five-year old albino tea plants of Camellia sinensis cv. ‘Yujinxiang’ were planted in the Tea Research Institute of Hangzhou Academy of Agricultural Sciences, Hangzhou, China (30º11'7.21"N, 120º03'52.45”)

extract_protocol:
Total RNA was isolated by using Omega E.Z.N.A.® Plant RNA Kit (Omega Bio-Tek Inc, Norcross, GA, USA)
The cDNA library was constructed using TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) and SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) referring to the kit instructions

treatment_protocol: Shading treatment was started on May 10, 2019 in five consecutive days using a single-layer black shade net with shading rate of 65%. After 5-day shading (SD) and followed 5-day regaining (RD) light treatment.The non-shaded leaves corresponding with the days of the treatment were collected as control

value: five consecutive days shading

value: Yujinxiang

value: leaf sample

tag: age

value: five-year old albino tea plants

tag: geography

value: planted in Hangzhou, China (30º11'7.21"N, 120º03'52.45”)


title: RD10_2


title: RD10_1


title: Patient33Post-treatment


title: Patient22Pre-treatment

value: Pre-treatment


title: D10_2

source_name: the leaves samples picked up on May 20, 2019 without treatment


title: Patient16Post-treatment

value: Myelodysplastic syndrome


title: D10_3


title: SD5_2

source_name: the leaves samples picked up on May 15, 2019 after five consecutive days shading


title: Patient20Post-treatment

value: Peripheral blood


title: SD5_1


title: D10_1


title: SD5_3


title: Patient14Post-treatment


title: Patient11Post-treatment


title: Patient17Post-treatment


title: D5_3

source_name: the leaves samples picked up on May 15, 2019 without treatment


title: Patient13Post-treatment


title: Patient39Pre-treatment


title: Patient34Pre-treatment


title: diseased bee 6

city: Beltsville

first: Judy

last: Chen

email: judy.chen@usda.gov, george.liu@usda.gov

state: Maryland

address: 306 Powder Mill Road

department: Agriculture

institute: USDA-ARS-BARC

description: Overwintering

data_processing:
First, after trimming and quality control of the generated sequences, transcriptomic analysis was performed with TopHat (version 1.4.1 at https://ccb.jhu.edu/software/tophat/index.shtml) by mapping sequencing reads and counting the reads across genes and transcripts based on annotated reference genes from the honey bee reference assembly Amel_4.5. During the alignment, three mismatches with maximum 100 multiple hits for a read were allowed.
Second, from the mapped reads, a list of differentially expressed genes was generated by running DEgene (one of R/Bioconductor packages version 3.8) under its default settings. Genes with a fold-change value >2 and an FDF-adjusted p-value < 0.05 by the Benjamini & Hochberg method were considered differentially expressed genes (DEGs). The gene expression volcano plot was generated using the web tool, which is freely available at https://paolo.shinyapps.io/ShinyVolcanoPlot/. Using PANTHER (Version 14.0 at http://www.pantherdb.org/) and DAVID (Bioinformatics Resources 6.8, https://david.ncifcrf.gov/), gene ontology (GO) enrichment analysis was performed on FlyBase orthologs of bee differentially expressed genes (DEGs). The terms with gene count more than five and P-value < 0.05 after the false discovery rate (FDR) correction for multiple testing were considered.
Third, the unmapped reads for each sample were processed using Metaphlan2 (version 2.0 at http://huttenhower.sph.harvard.edu/metaphlan2).
Finally, in order to better explore exogenous pathogen transcripts, unmapped reads by removing reads which aligned to the Apis rRNA sequence from http://www.rna.icmb.utexas.edu/ using Bowtie2 (version2.2.3 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) with its default parameters were further filtered. The remaining unmapped reads were then aligned against nr/nt (NCBI non-redundant nucleotide database) using megaBLAST (with an option of -W 16, i.e. a word size of 16). The matches in megaBLAST results were parsed into a taxonomic representation listing using KronaTool (a set of computer scripts at https://github.com/marbl/Krona/wiki/KronaTools) to represent the LCA (lowest common ancestor). These lists were formatted into a HTML style of files (Krona charts), containing the percentage of reads that match a specific organism. Krona charts allow hierarchical data to be interactively visualized and explored in multi-layered pie charts with zooming (https://github.com/marbl/Krona/wiki) in a web browser like Google Chrome or Internet Explorer.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: *.transcripts.gtf: Normalized abundance measurements, output from CUFFLINK.
Supplementary_files_format_and_content: *.counts_sorted.txt: Normalized counts sorted, output from Metaphlan2.

organism: Apis mellifera

source_name: Whole bee

extract_protocol:
RNA samples that were extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) were further processed with a Qiagen RNeasy purification kit (Germantown, MD) according to the manufacturer's instructions. The quantity and purity of RNA samples were measured using a NanoDrop 8000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE). The integrity of RNA samples was evaluated using Agilent Bioanalyzer 2100 (Santa Clara, CA). Only RNA samples with an RNA integrity number (RIN) value of over eight were used to generate first and second-strand cDNAs using random hexamer primers and the reverse transcriptase Superscript II (Invitrogen, Carlsbad, CA) following manufacturer's instructions. The overall level of ribosomal RNA present in total RNA samples was reduced prior to library construction using the Ribo-Zero™ Magnetic (Human/Mouse/Rat) rRNA Removal Kit (Epicentre Technologies, Madison, WI).
The TruSeq RNA Sample Prep kit (Illumina, San Diego, CA) per manufacturer’s protocol.

tag: diagnosis

value: Diseased

value: Whole body


title: diseased bee 1

description: Overwintering


title: Patient44Pre-treatment


title: healthy bee 3

description: Overwintering

value: Healthy


title: Patient23Pre-treatment


title: D5_2


title: Patient38Pre-treatment


title: healthy bee 1

description: Overwintering


title: healthy bee 2

description: Overwintering


title: Patient5Pre-treatment


title: Patient21Pre-treatment


title: RNA CNS (recipient), CD45.2+CD88+CD317+ myeloid cells, Day15

city: Dallas

first: Victor

last: Salinas

address: 5323 Harry Hines Blvd.

department: Neurology

institute: University of Texas Southwestern Medical Center

description: 10X Genomics

data_processing:
Sample demultiplexing, alignment, filtering, barcode counting, and UMI counting were conducted on CellRanger software (10X Genomics).
Assembly: mm10
Supplementary files format and content: Gzipped TSV files of MEX format data (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices)

source_name: CNS

extract_protocol:
Bone marrow chimeric mice (BL/6) were generated by injecting CD45.1+ bone marrow cells into irradiated CD45.2+ mice. These subsequently underwent induction with active experimental autoimmune encephalopathy (EAE). At peak of disease (day 15 post induction), cell suspensions from brain and spinal cord were sorted for CD88, CD317, and either CD45.1 or CD45.2 expression. Cell populations were subjected to single cell analysis using the 10X Multiomics platform.
Library was prepared according to the manufacturer's instructions for the 10X Single Cell Multiome ATAC + Gene Expression kit

value: CNS

value: Myeloid

value: EAE induction

tag: antibody


title: Patient16Pre-treatment

value: Immunotherapy + Hypomethylating agent

value: Response


title: diseased bee 2

description: Overwintering


title: Patient17Pre-treatment


title: D5_1


title: RNA CNS (donor), CD45.1+CD88+CD317+ myeloid cells, Day15

description: 10X Genomics


title: Patient14Pre-treatment


title: Patient20Pre-treatment


title: ATAC CNS (recipient), CD45.2+CD88+CD317+ myeloid cells, Day15

description: 10X Genomics

data_processing:
Sample demultiplexing, alignment, filtering, barcode counting, and UMI counting were conducted on CellRanger software (10X Genomics).
Assembly: mm10
Supplementary files format and content: BED-like tabular file (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/fragments)


title: Patient13Pre-treatment


title: Patient33Pre-treatment

value: Non-response


title: ZFP251 KO eWAT Sample 2

city: Seoul

first: Han Geuk

last: Seo

address: 120 Neungdong-ro, Gwangjin-gu

institute: Konkuk University

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to mm10 whole genome using STAR (version 2.5.4) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Epididymal white adipose tissue

growth_protocol: Epididymal white adipose tissue (eWAT) isolated from 20-week-old male mice

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
The quantity and quality of the total RNA were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeqStranded mRNA Sample Preparation kit (Illumina), according to the manufacturer's protocol.

value: Epididymal white adipose tissue

value: 20 wk

value: ZFP251 KO

value: Normal Diet

tag: gender

value: male


title: Patient12Pre-treatment

tag: tissue

value: Immunotherapy

value: Pre-treatment


title: ZFP251 KO eWAT Sample 1

tag: treatment


title: Patient40Pre-treatment

value: Myelodysplastic syndrome

value: Peripheral blood


title: Wild Type eWAT Sample 2

tag: genotype

value: Wild


title: Patient11Pre-treatment