title: Pt3R1 [RNA-seq]

description:
Organism: Poncirus trifoliata (L.) Raf.
processed data file: All_gene_fpkm.xls

data_processing:
Clean reads (high quality reads) of 18 transcriptome libraries were filtered from raw reads by removing low-quality reads with ambiguous nucleotides and adaptor sequences, and Tophat2 (Kim et al., 2013) was used to map clean reads to the reference genome C. sinensis (Xu et al., 2013). Gene expression levels were calculated by the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method using the RSEM tool (Li and Dewey, 2011). Differential expression analysis was performed using the DESeq R package (1.10.1) (Anders and Huber, 2010). The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value (FDR) < 0.05 found by DESeq were assigned as differentially expressed genes.
Genome_build: Citrus sinensis Annotation Project (CAP) (http://citrus.hzau.edu.cn/).
Supplementary_files_format_and_content: All_gene_fpkm.xls: File was generated by Microsoft Excel, FPKM represents the expression of genes.

source_name: seedling

extract_protocol:
Approximately 2 to 3 g of powdered material was subjected to each RNA extraction, including 10 mL buffer extraction, 5 mL chloroform-isoamylalcohol extraction (twice), 5 mL isopropanol precipitation, 5 mL 75% ethanol cleaning and RNA purification as described by Camacho-Villasana YM et al.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: root

tag: ph treatment


title: Pt3R3 [RNA-seq]

status: Public on Mar 18 2019

type: SRA

city: Wuhan

first: Juxun

last: Wu

state: Hubei

address: No.1 of Shizishan street, Hongshan District

country: China

institute: Huazhong Agricultral University

library_source: transcriptomic

molecule: total RNA

organism: Citrus trifoliata

growth_protocol: The seeds of Cj and Pt were surface-sterilized and their germination accelerated. The seedlings were grown in a growth chamber until they had four leaves. Then, the seedlings were selected by uniform size and transferred into hydroponics with 4 L solution in a green house.

treatment_protocol: Three different pH gradients (6.5, 8.0 and 9.5) were set up. Because most natural soils have a weak acidity, we set pH 6.5 as the normal condition. After 8 weeks of culture, three biological replicates (three seedling plants per replicate) were harvested randomly for each treatment.

tag: tissue


title: resistant_OMM1_3B_DMSO_2

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

country: USA

institute: HUMC

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq (version 1.8.4) for converting BCL to FASTQ format, coupled with adaptor trimming.
The reads were mapped to the human reference genome using Tophat with 4 mismatches and 10 maximum multiple hits
The relative expression level of genes was estimate by FPKM using Cufflinks with default settings
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: tab-delimited matix of gene-level FPKM estimates, annotated for the gene ID (gene_id), gene symbol (gene_short_name), TSS ID (tss_id), and gene coodinates (locus).

molecule: polyA RNA

organism: Homo sapiens

source_name: uveal melanoma cell line

growth_protocol: The cells were cultured in RPMI medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 100µg/ml streptomycin, and maintained at 37°C in 5% CO2. The resistant cell lines were derived from the corresponding parental cell lines after at least 8 weeks of exposure to escalating doses of PLX51107. The surviving cells were then routinely grown in 0.2-0.5 μM PLX51107. PLX51107 and PLX8573 were from Plexxikon, Inc. JQ1 and QNZ (EVP4593) were from Selleck Chemicals.

extract_protocol:
Total RNA was extracted using the RNeasyMini kit (Qiagen) according to the manufacturer's instructions.
Poly-A pull-down was used to enrich for mRNAs, and libraries were prepared using the Illumina TruSeq RNA kit according to Illumina's instructions.

treatment_protocol: Parental and naive cells were treated with DMSO or 0.5 μM PLX51107 for 24 hours.

tag: cell line

value: BETI-resistant OMM1.3B

tag: treatment

value: DMSO

value: uveal melanoma cell line


title: Pt3R2 [RNA-seq]


title: resistant_OMM1_3B_DMSO_1


title: X37-9_shH3F3A_H3K4me3_ChIP-seq

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

library_source: genomic

data_processing:
We used BWA (version 0.7.12, default parameter) to align the reads to the human hg19 + mouse mm9 + drosophila
marked duplicated reads with Picard with only nonduplicated reads kept by samtools
Only mapped human reads were extracted by samtools for quality contol and peak calling
To control the quality of the data and estimate the fragment size, the nonduplicated version of SPP (version 1.11) was used to draw cross-correlation with support of R (version 2.14.0)
peaks were called using MACS2 (for narrow peak histone marks) or Sicer V1.1 (for broad peak marks)
bam was converted to BigWig using bedtools (v2.25.0) and UCSC tools (20150811). Read coverage was scaled according to normalization factor using mouse contaminant reads as internal reference
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing locations of defined peaks
Supplementary_files_format_and_content: bigWig files containing normalized read coverage

molecule: genomic DNA

source_name: SJ-DIPGx37 (PDX)

growth_protocol: human xenografts grown as implants in nude mouse brain

extract_protocol:
ChIP and library construction for SJDIPGX7 xenografts using H3K27me3 (Millipore 07-449), H3K27ac (Active Motif 39133) and H3K4me3 (Active Motif 39159) was performed by Active Motif.  All other ChIP was performed at St. Jude using the following method.  Xenograft tumors were snap frozen and ground to a powder before fixation.  Single cell suspensions were generated from cultured cells then fixed. For histone ChIP, samples were fixed for 5 minutes with 1% paraformaldehyde in PBS (from a frozen stock) at room temperature.  For BMI1 and RNF2 ChIP, samples were fixed with 2mM disuccinimidyl glutarate in PBS for 45 minutes at room temperature followed by 1% paraformaldehyde in PBS for 15 minutes at room temperature following the method established in Gargiulo et al. (van Lohuizen lab, 2013 Cancer Cell 23:660-676). Bare nuclei were sheared on a Covaris M220.  For histone mark ChIPs, the reads arising from mouse cells entrapped within the xenograft to normalize the post ChIP samples to the human/mouse read ratio obtained for the pre-ChIP material (input library).  For some experiments, chromatin from drosophila S2 cells was also spiked-in and used to validate the use of mouse reads for normalization.  ChIP reactions were performed using a modified Upstate Biotechnology protocol. Antibodies used were (μl antibody per IP shown): H3K27me3 (Cell Signaling 9733, lot 8; 4 μl), H3K27ac (Cell Signaling 8173, lot 1; 4 μl), H3K4me3 (Cell Signaling 9751, lot 8; 5 μl), BMI1 (Bethyl A301-694A, lot 4; 5 μl) and RNF2 (Bethyl A302-869A, lot 1; 5 μl).
Libraries were prepared from 5-10 ng of DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext Q5 Hot Start HiFi PCR Master Mix according to the manufacturer’s instructions (New England Biolabs) with the following modifications: a second 1:1 Ampure cleanup was added after adaptor ligation. The Ampure size selection step prior to PCR was eliminated. Completed libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (Perkin Elmer).  Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies), Kapa Library Quantification kit (Kapa Biosystems) or low pass sequencing on a MiSeq Nano v2 run (Illumina).

treatment_protocol: Xenografts dissected from mouse brain, cells dissociated and for each experiment, the same pool of cells was transduced with lentivirus expressing non-silencing control or specific shRNA, then cultured for 12 days under puro selection. Transduced cells were reimplanted into multiple mouse brains for each shRNA construct. The resulting tumors were dissected for ChIP-seq and RNAseq.

tag: cell source

value: in vivo xenograft dissected from mouse brain

tag: experiment id

tag: shRNA id

value: H3F3A shRNA #2

tag: shRNA backbone

value: miRE

tag: chip antibody

value: H3K4me3(Cell Signaling, #9751, lot 8)


title: X37-9_shH3F3A_H3K27me3_ChIP-seq

value: H3K27me3 (Cell Signaling, #9733, lot 8)


title: GSC20

type: genomic

city: Houston

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

institute: Baylor College of Medicine

hyb_protocol: According to Illumina default protocol and recommendations

data_processing:
.idat files were processed using R bioconductor with the Minfi package. Signal from CpG probes were pre-processed with background correction and dye-bias normalization using the 'preprocessNoob' method (Triche et al., 2013). Following pre-processing, probes found to contain SNPs or found withing chromosome X and Y were removed for downstream analysis.
Matrices are provided for all samples as processed Beta values: GBM_GSC_i850K_beta_formatted.txt, Methylated signal: GBM_GSC_i850K_meth_formatted.txt, unmethylated signal: GBM_GSC_i850K_unmeth_formatted.txt, p-values: GBM_GSC_i850K_pvals_formatted.txt

extract_protocol: DNA was extracted using the Invitrogen PureLink Genomic DNA kit, and quantity assesed with Nanodrop and Picogreen quantification. Genomic DNA was submitted to McGill University and Genomic Quebec Innovation center for bisulphite treatment and  subsequent array hybridization according to Illumina recommendations.

tag: cell type

value: glioblastoma stem cell model


title: GSC2

scan_protocol: According to Illumina default protocol and recommendations


title: X37-6_shH3F3A_H3K4me3_ChIP-seq

value: H3F3A shRNA #1


title: Pt2R2 [RNA-seq]


title: resistant_92_1_PLX51107_3

value: BETI-resistant 92.1

value: 0.5 μM PLX51107 for 24 hours


title: X37-6_shH3F3A_H3K27me3_ChIP-seq


title: GSC19

label_protocol: According to Illumina default protocol and recommendations


title: Pt2R1 [RNA-seq]


title: GSC18


title: resistant_92_1_PLX51107_2


title: resistant_92_1_PLX51107_1


title: X37-5_Ctl_H3K4me3_ChIP-seq

value: non silencing shRNA


title: Pt1R3 [RNA-seq]


title: X37-5_Ctl_H3K27me3_ChIP-seq


title: Pt1R2 [RNA-seq]


title: resistant_92_1_DMSO_3


title: GSC17


title: Pt2R3 [RNA-seq]


title: resistant_92_1_DMSO_1


title: GSC16


title: H4_R2

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

data_processing:
RNASeq data were aligned on the P. communis genome using the new Tuxedo protocol. Alignment was carried out with HiSAT2, while read counting analysis was performed with StringTie. For the analysis fo the genes differentially expressed was used DEseq2.
Genome_build: Pyrus communis Genome v1.0 Draft Assembly & Annotation at Genome Database for Rosaceae: https://www.rosaceae.org/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Pyrus communis

source_name: harvest week4_pear flesh

extract_protocol:
RNA extraction was performed, for each of the three biological replicates with the Spectrum Plant total RNA kit (Sigma-Aldrich Co., St. Luis, MO, USA). RNA was quantified using a NanoDrop ND-8000 spectrophotometer (Thermo Scientific, Waltham, MA, USA), while its purity and integrity was assessed with a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
For each replicate/sample, 3 mg of RNA was used for the construction of a non-directional Illumina RNA-seq library, using TrySeq RNA sample preparation kits, v2 (Illumina, San Diego, CA, USA). Libraries were quantified using quantitative PCR and quality control was performed with the DNA 1000 series II chip bioanalyzer (Agilent, Santa Clara, CA, USA). Sequencing of libraries was performed with an Illumina HiSeq 1000 Sequencer using TruSeq SBS v3-HS kit (100 cycles) and TruSeq SR Cluster v3-cBot-HS kits (Illumina, San Diego, CA, USA) generating 100-bp reads.

tag: cultivar

value: cv. Abate Fetel

tag: Stage

value: harvest week4

value: pear flesh


title: resistant_92_1_DMSO_2


title: X37-4_Ctl_H3K27me3_ChIP-seq


title: H4_R3


title: GSC15


title: X37-3_Ctl_H3K4me3_ChIP-seq


title: GSC14


title: GSC13


title: parental_UM004_PLX51107_3

value: parental UM004


title: H4_R1


title: X37-3_Ctl_H3K27me3_ChIP-seq


title: parental_UM004_PLX51107_2


title: H3_R3

source_name: harvest week3_pear flesh

value: harvest week3


title: X37-2_Ctl_H3K4me3_ChIP-seq


title: GSC12


title: GSC11


title: H3_R2


title: X37-2_Ctl_H3K27me3_ChIP-seq


title: parental_UM004_DMSO_3

value: DMSO


title: X37-4_Ctl_H3K4me3_ChIP-seq


title: Pt1R1 [RNA-seq]

value: root


title: H3_R1


title: X37-1_Ctl_H3K4me3_ChIP-seq

value: in vivo xenograft dissected from mouse brain


title: GSC10


title: Dieldrin_ribominus

city: Paris cedex 15

first: Christian

last: MUCHARDT

address: 25 rue du Dr-Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur Paris

data_processing:
Reads were aligned with STAR on human genome version Hg19 without patches, allowing only single alignments. Transcriptome analysis on poly(dA)-enriched libraries was performed with edgeR with TMM normalization.
Genome_build: Hg19
Supplementary_files_format_and_content: Transcriptome_analysis.xlsx: Transcriptome analysis listing all genes and their score when comparing dieldrin to DMSO and PMA to DMSO
Supplementary_files_format_and_content: DMSO_sites_of_divergent_transcription.bed: List of sites showing divergent transcription in the DMSO ribominus data
Supplementary_files_format_and_content: Dieldrin_sites_of_divergent_transcription.bed: List of sites showing divergent transcription in the dieldrin ribominus data

source_name: Jurkat cells + dieldrin 30 min.

growth_protocol: Jurkat cells were cultured in RPMI-1640, all with 10% decomplemented fetal bovine serum (FBS) and 100 U.ml−1 penicillin-streptomycin at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA from Jurkat cells was extracted with Phenol-chloroform methods and quantified with an ND-1000 (Nanodrop).
poly(A) enrichment was replaced by rRNA depletion.

treatment_protocol: Jurkat cells were treated with phorbol myristate acetate (PMA) or dieldrin in DMSO at 100 µM for 30 min.

value: Jurkat, Clone E6-1 (ATCC TIB-152)

tag: library type

value: Ribominus


title: parental_MEWO_PLX51107_2

source_name: cutaneous melanoma cell line

value: parental MEWO

value: cutaneous melanoma cell line


title: parental_UM004_DMSO_1

value: uveal melanoma cell line


title: GBM81

value: primary glioblastomas


title: H2_R2

source_name: harvest week2_pear flesh

value: harvest week2


title: H2_R1


title: PMA_3

source_name: Jurkat cells + PMA 30 min.

extract_protocol:
Total RNA from Jurkat cells was extracted with Phenol-chloroform methods and quantified with an ND-1000 (Nanodrop).
Samples were enriched in mRNA (with poly(A) tails) using oligo(dT) beads. After enrichment, the RNAs were fragmented into 250-400 bp fragments and the cDNA was synthesized with random hexamer primers and amplified

value: poly(A) enriched


title: PMA_2


title: DMSO_ribominus

source_name: Jurkat cells + DMSO 30 min.


title: parental_OMM1_PLX51107_2

value: parental OMM1

value: 0.5 μM PLX51107 for 24 hours


title: parental_UM004_PLX51107_1


title: GBM79


title: H1_R3

source_name: harvest week1_pear flesh

value: cv. Abate Fetel

value: harvest week1


title: PMA_1


title: H1_R2

value: pear flesh


title: GBM78


title: parental_OMM1_PLX51107_1


title: H1_R1


title: Dieldrin_3


title: parental_OMM1_DMSO_2


title: GBM76


title: parental_UM004_DMSO_2

value: parental UM004


title: Dieldrin_2


title: parental_OMM1_DMSO_3

value: DMSO


title: GSC1


title: H2_R3


title: parental_OMM1_DMSO_1


title: Patent 16 Recurrent

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description:
Sample name:
48
Post treatment

data_processing:
QA/QC of raw fastq files was performed using FastQC v 0.10.1
Raw fastq sequences were aligned to the hg38 genome using tophat2 v2.0.13 using the Ensembl gtf
Genome_build: hg38
Supplementary_files_format_and_content: FPKM_geneMatrix_NORMALIZED.txt represents normalized FPKM values using cuffnorm v2.2.1

source_name: Epidermis

extract_protocol:
RNAs were isolated using a Qiagen RNeasy kit according to the manufacturer’s instructions (Qiagen) or TRIzol (Invitrogen). After total RNA extraction, magnetic beads with oligo dT were used to isolate polyA enriched mRNA.
Libraries were constructed by BGI using their standard RNA transcriptome sequencing protocol.

treatment_protocol: All patients had not been treated systemically for at least 4 weeks or topical treatment for at least 2 weeks prior to the study entry. Patients were treated with topical halomethasone monohydrate 0.05% cream daily for 2 weeks. Skin lesion severity was evaluated by PASI (psoriasis area and severity index) score. Typical lesions that represented the overall skin condition before and after treatment as well as relapse (4 weeks after treatment) were taken.

value: Epidermis

tag: treatment stage

value: Post treatment


title: GBM75


title: parental_OMM1_PLX51107_3


title: Dieldrin_1

value: Jurkat, Clone E6-1 (ATCC TIB-152)


title: parental_OMM1_3B_PLX51107_3

value: parental OMM1.3B


title: DMSO_3


title: DMSO_2


title: parental_OMM1_3B_PLX51107_2


title: GBM80


title: GBM74_1


title: DMSO_1


title: parental_OMM1_3B_PLX51107_1


title: Patient 11 Recurrent

description:
Sample name:
43
Post treatment


title: GBM73


title: GBM72


title: Patient 8 Recurrent

description:
Sample name:
40
Post treatment


title: parental_OMM1_3B_DMSO_3


title: Patient 7 Recurrent

description:
Sample name:
39
Post treatment


title: GBM71


title: parental_OMM1_3B_DMSO_2


title: Patient 6 Recurrent

description:
Sample name:
38
Post treatment


title: parental_OMM1_3B_DMSO_1


title: GBM69


title: GBM70


title: Patient 5 Recurrent

description:
Sample name:
37
Post treatment


title: Patient 15 Recurrent

description:
Sample name:
47
Post treatment


title: GBM67


title: parental_92_1_PLX51107_2

value: parental 92.1


title: GBM74_2


title: GBM66


title: parental_92_1_PLX51107_3


title: parental_92_1_PLX51107_1


title: Patient 12 Recurrent

description:
Sample name:
44
Post treatment


title: Patient 3 Recurrent

description:
Sample name:
35
Post treatment


title: Patient 4 Recurrent

description:
Sample name:
36
Post treatment


title: parental_92_1_DMSO_3


title: GBM64


title: Patient 2 Recurrent

description:
Sample name:
33
Post treatment


title: Patent 16 Posttreatment

description:
Sample name:
32
Glucocorticoid treatment

value: Glucocorticoid treatment


title: GBM63


title: GBM62


title: parental_92_1_DMSO_1

value: uveal melanoma cell line


title: Patient 10 Recurrent

description:
Sample name:
42
Post treatment


title: Patient 15 Posttreatment

description:
Sample name:
31
Glucocorticoid treatment


title: GBM57

value: primary glioblastomas


title: GBM59


title: Patient 12 Posttreatment

description:
Sample name:
28
Glucocorticoid treatment


title: GBM56


title: GBM55


title: Patient 11 Posttreatment

description:
Sample name:
27
Glucocorticoid treatment


title: Patient 10 Posttreatment

description:
Sample name:
26
Glucocorticoid treatment


title: GBM52


title: GBM54


title: Patient 8 Posttreatment

description:
Sample name:
24
Glucocorticoid treatment


title: GBM53


title: Patient 4 Posttreatment

description:
Sample name:
20
Glucocorticoid treatment


title: Patient 6 Posttreatment

description:
Sample name:
22
Glucocorticoid treatment


title: Patient 5 Posttreatment

description:
Sample name:
21
Glucocorticoid treatment


title: GBM51


title: parental_92_1_DMSO_2


title: GBM49


title: Patient 3 Posttreatment

description:
Sample name:
19
Glucocorticoid treatment


title: Patent 16 Pretreatment

description:
Sample name:
17
Pre treatment

value: Pre treatment


title: GBM48


title: Patient 15 Pretreatment

description:
Sample name:
16
Pre treatment


title: Patient 12 Pretreatment

description:
Sample name:
13
Pre treatment


title: GBM47


title: GBM4


title: Patient 11 Pretreatment

description:
Sample name:
12
Pre treatment


title: GBM46


title: Cj3R3 [RNA-seq]

description:
Organism: Citrus junos Sieb. ex Tanaka
processed data file: All_gene_fpkm.xls

organism: Citrus junos

value: root


title: Patient 10 Pretreatment

description:
Sample name:
11
Pre treatment


title: Cj3R2 [RNA-seq]


title: Patient 7 Posttreatment

description:
Sample name:
23
Glucocorticoid treatment


title: Patient 8 Pretreatment

description:
Sample name:
8
Pre treatment


title: DRAIC_3

city: Copenhagen N

first: Imke

last: Tiessen

address: Ole Maaløes Vej 5

department: Biotech Research and Innovation Centre (BRIC)

country: Denmark

institute: University of Copenhagen

data_processing:
Raw RNA-seq data was subjected to quality control filters applying threshold of Phred (quality) >= 25.
Prior to mapping, Illumina adapters were removed and the reads were trimmed using cutadapt.
Read mapping was performed with bowtie2 (version 2.2.4).
Counting of reads was performed using Bam files in HTSeq (using gencode hg19 gene annotations). Read counts were analysed by DESeq2in R environment.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files containing RNA seq peaks

source_name: MCF-7 cells

growth_protocol: MCF-7 cells (stably expressing with eGFP-LC3) were cultured in RPMI L-Glutamine media, supplemented with 6 % FBS.

extract_protocol:
Total RNA from three biological replicates was purified and depleted for ribosomal RNA using the Illumina Ribo-Zero Magnetic Gold rRNA removal kit (MRZG12324).
Libraries were built using the Illumina TruSeq kit (RPHMR12126) according to the manufacturer’s protocol.

treatment_protocol: Cells were reverse transfected for 72 h with 10 nM silencer-select siRNAs against DRAIC or scramble using Lipofectamine2000. Media was renewed after 24 h.

tag: sirna

value: DRAIC


title: GBM50


title: GBM5


title: Cj2R3 [RNA-seq]


title: GBM32


title: GBM31


title: Cj2R2 [RNA-seq]


title: Patient 7 Pretreatment

description:
Sample name:
7
Pre treatment


title: GBM30


title: Cj2R1 [RNA-seq]


title: Patient 6 Pretreatment

description:
Sample name:
6
Pre treatment


title: GBM28


title: Patient 5 Pretreatment

description:
Sample name:
5
Pre treatment


title: siCTRL_2

value: control siRNA


title: Cj1R3 [RNA-seq]


title: GBM21


title: Patient 4 Pretreatment

description:
Sample name:
4
Pre treatment


title: Patient 3 Pretreatment

description:
Sample name:
3
Pre treatment


title: siCTRL_1


title: Cj1R1 [RNA-seq]


title: Mouse_IVD_Col2Cre_Control_RNAseq_replicaC3

status: Public on Mar 17 2019

city: San Francisco

first: Nadav

last: Ahituv

state: CA

address: 1550 4th Street

institute: UCSF

data_processing:
star (STAR_2.5.3a) --genomeDir mm10 --outSAMtype BAM SortedByCoordinate
htseq-count -s yes -r pos -t gene -f bam -i gene_name Mus_musculus.GRCm38.78.gtf
DESeq2 R library
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include reads count and normalized values for each Sample ...

organism: Mus musculus

source_name: Intervertebral disc

extract_protocol:
Intervertebral discs from the thoracic and lumbar spine (T8-L5) of the 20-day-old Col2Cre; Adgrg6f/f and wild type control mice were isolated in cold PBS, snap frozen in liquid N2 and pulverized in liquid nitrogen. Each biological replicate contains itervertebral discs isolated from 2-3 mice.Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analyzed on Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Total RNA was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). RNA fragments were reverse-transcribed to create the final cDNA libraries following the NEBNext® Ultra™ RNA Library Prep Kit (Illumina, San Diego, USA).

tag: strain

tag: age

value: postnatal day 20

tag: genotype

value: wild type

value: intervertebral disc


title: Mouse_IVD_Col2Cre;Gpr126 f/f_Mutant_RNAseq_replicaM3

value: Col2Cre; Adgrg6f/f

tag: tissue


title: Mouse_IVD_Col2Cre;Gpr126 f/f_Mutant_RNAseq_replicaM2


title: Mouse_IVD_Col2Cre_Control_RNAseq_replicaC2


title: DRAIC_1

tag: cell line


title: Mouse_IVD_Col2Cre;Gpr126 f/f_Mutant_RNAseq_replicaM1


title: Smeg_normoxia_mock Rep2

city: Worcester

first: Scarlet

last: Shell

state: MA

address: 60 Prescott St

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

description:
wildtype Smegmatis mc2155. Normoxia 5' end mapping library, mock treated, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80

data_processing:
bwa and samtools were used to generate .bam and .sam files from fastq files
Read pairs that were not correctly oriented with respect to each other were filtered out, unpaired reads were filtered out, and the region encoding the rRNA was filtered out
For expression libraries, coverage at each genome coordinate and RPKMs were calculated.
For 5' end libraries, the coverage of each position at the M. smegmatis genome was calculated.
Genome_build: NC_008596
Supplementary_files_format_and_content: RPKM files contain RPKM data from RNAseq expression libraries
Supplementary_files_format_and_content: DEseq excel file contains output from DEseq2 differential expression analysis (normoxia vs hypoxia)
Supplementary_files_format_and_content: Coverage files for RNAseq libraries contain coverage at every nt acrosss the genome (not normalized)
Supplementary_files_format_and_content: 5-prime-end coverage files contain read depth at each RNA 5' end identified in 5' end mapping libraries (not normalized)
Supplementary_files_format_and_content: 5-prime-end excel file contains normalized coverage at 5' ends that met filtering criteria as detailed in Martini et al 2019 Frontiers in Microbiology

organism: Mycolicibacterium smegmatis

source_name: Bacteria

growth_protocol: Bacteria were grown in Middlebrook 7H9 supplemented with ADC (Albumin Dextrose Catalase, final concentrations 5 g/L bovine serum albumin fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L catalase), 0.2% glycerol and 0.05% Tween 80. For the exponential phase experiment (Dataset 1), 50 ml conical tubes containing  5 ml of 7H9 were inoculated with M. smegmatis to have an initial OD = 0.01. Cultures were grown at 37◦C and 200 rpm.

extract_protocol:
RNAseq 5' end mapping library. There was no treatment to 5' ends before adapter ligation.
RNA was extracted as follows: frozen cultures stored at −80◦C were thawed on ice and centrifuged at 4,000 rpm for 5 min at 4◦C. The pellets were resuspended in 1 ml Trizol  Life Technologies) and placed in tubes containing Lysing Matrix B (MP Bio). Cells were lysed by bead-beating twice for 40 s at 9 m/sec in a FastPrep 5G instrument (MP Bio). 300 µl chloroform was added and samples were centrifuged for 15 min at 4,000 rpm at 4◦C. The aqueous phase was collected and RNA was purified using Direct-Zol RNA miniprep kit (Zymo) according to the manufacturer’s instructions. Samples were then treated with DNase Turbo (Ambion) for 1 h and purified with an RNA Clean & Concentrator-25 kit (Zymo) according to the manufacturer’s instructions
RNA samples from each biological replicate were split in three, in order to generate two 50 -end differentially treated libraries and one RNAseq expression library. RNA for library 1 (“converted” library) was treated either with RNA 50 pyrophosphohydrolase RPPH (NEB) (exponential phase experiment), or with 50 polyphosphatase (Epicenter) (hypoxia experiment and normoxia controls), in order to remove the native 50 triphosphates of primary transcripts, whereas RNA for Library 2 (“nonconverted” library) was subject to mock treatment. Thus, the converted libraries capture both 50 triphosphates (converted to monophosphates) and native 50 monophosphate transcripts, while non-converted libraries capture only native 50 monophosphates. Library construction was performed as described by Shell et al. (2015). For RNA expression libraries, KAPA stranded RNA-Seq library preparation kit and NEBNext Ultra RNA library prep kit for Illumina (NEB) were used for Dataset 1 and Dataset 2, respectively, according to manufacturer’s instructions. The following major  odifications were introduced into the protocols: (i) For RNA fragmentation, in order to obtain fragments around 300 nt, RNA was mixed with the corresponding buffer and placed at 85◦C for 6 min (Dataset 1), or at 94◦C for 12 min (Dataset 2). (ii) For library amplification, 10 or 19–23 PCR cycles were used for Dataset 1 and Dataset 2, respectively. The number of cycles was chosen according to the amount of cDNA obtained for each sample.

treatment_protocol: For hypoxia experiments, a protocol similar to the Wayne model (Wayne and Hayes, 1996) was implemented. Briefly, 60 ml serum bottles (Wheaton, product number 223746, actual volume to top of rim 73 ml) were inoculated with 36.5 ml of M. smegmatis culture with an initial OD = 0.01. The bottles were sealed with rubber caps (Wheaton, W224100-181 Stopper, 20 mm) and aluminum caps (Wheaton, 20 mm aluminum seal) and cultures were grown at 37◦C and 125 rpm to generate hypoxic conditions. Samples were taken at an early stage of oxygen depletion when growth had slowed but not completely stopped (15 h) and at a later stage when a methylene blue indicator dye was fully decolorized and growth had ceased (24 h).

tag: growth phase

value: Aerobic log phase


title: siCTRL_3


title: Smeg_normoxia_mock Rep1

description:
wildtype Smegmatis mc2155. Normoxia 5' end mapping library, mock treated, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80


title: Smeg_hypoxia 24 h_mock Rep2

description:
wildtype Smegmatis mc2155. Hypoxia 24 hours, 5' end mapping library, mock treated, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80

value: Hypoxia 24 hours after sealing Wayne model vials


title: Patient 2 Posttreatment

description:
Sample name:
18
Glucocorticoid treatment

value: Epidermis


title: Smeg_hypoxia 15 h_mock Rep2

description:
wildtype Smegmatis mc2155. Hypoxia 15 hours, 5' end mapping library, mock treated, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80

value: Hypoxia 15 hours after sealing Wayne model vials


title: Smeg_hypoxia 24 h_mock Rep1

description:
wildtype Smegmatis mc2155. Hypoxia 24 hours, 5' end mapping library, mock treated, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80


title: Patient 2 Pretreatment

description:
Sample name:
2
Pre treatment


title: Smeg_hypoxia 15 h_mock Rep1

description:
wildtype Smegmatis mc2155. Hypoxia 15 hours, 5' end mapping library, mock treated, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80


title: Cj1R2 [RNA-seq]

tag: ph treatment


title: Smeg_hypoxia 15 h_polyphosphatase Rep2

description:
wildtype Smegmatis mc2155. Hypoxia 15 hours 5' end mapping library, treated with polyphosphatase, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80

extract_protocol:
RNAseq 5' end mapping library. 5' triphosphates were converted to 5' monophosphates by 5' Polyphosphatase before adapters were ligated to RNA 5' ends.
RNA was extracted as follows: frozen cultures stored at −80◦C were thawed on ice and centrifuged at 4,000 rpm for 5 min at 4◦C. The pellets were resuspended in 1 ml Trizol  Life Technologies) and placed in tubes containing Lysing Matrix B (MP Bio). Cells were lysed by bead-beating twice for 40 s at 9 m/sec in a FastPrep 5G instrument (MP Bio). 300 µl chloroform was added and samples were centrifuged for 15 min at 4,000 rpm at 4◦C. The aqueous phase was collected and RNA was purified using Direct-Zol RNA miniprep kit (Zymo) according to the manufacturer’s instructions. Samples were then treated with DNase Turbo (Ambion) for 1 h and purified with an RNA Clean & Concentrator-25 kit (Zymo) according to the manufacturer’s instructions
RNA samples from each biological replicate were split in three, in order to generate two 50 -end differentially treated libraries and one RNAseq expression library. RNA for library 1 (“converted” library) was treated either with RNA 50 pyrophosphohydrolase RPPH (NEB) (exponential phase experiment), or with 50 polyphosphatase (Epicenter) (hypoxia experiment and normoxia controls), in order to remove the native 50 triphosphates of primary transcripts, whereas RNA for Library 2 (“nonconverted” library) was subject to mock treatment. Thus, the converted libraries capture both 50 triphosphates (converted to monophosphates) and native 50 monophosphate transcripts, while non-converted libraries capture only native 50 monophosphates. Library construction was performed as described by Shell et al. (2015). For RNA expression libraries, KAPA stranded RNA-Seq library preparation kit and NEBNext Ultra RNA library prep kit for Illumina (NEB) were used for Dataset 1 and Dataset 2, respectively, according to manufacturer’s instructions. The following major  odifications were introduced into the protocols: (i) For RNA fragmentation, in order to obtain fragments around 300 nt, RNA was mixed with the corresponding buffer and placed at 85◦C for 6 min (Dataset 1), or at 94◦C for 12 min (Dataset 2). (ii) For library amplification, 10 or 19–23 PCR cycles were used for Dataset 1 and Dataset 2, respectively. The number of cycles was chosen according to the amount of cDNA obtained for each sample.


title: GBM1


title: Smeg_hypoxia 24 h_polyphosphatase Rep1

description:
wildtype Smegmatis mc2155. Hypoxia 24 hours 5' end mapping library, treated with polyphosphatase, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80


title: DRAIC_2


title: Smeg_normoxia_expression Rep2

description:
wildtype Smegmatis mc2155. Normoxia (log phase) 15 hours, used to compare hypoxia to log phase, expression library, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Expression libraries_DEseq_hypoxia.xlsx

extract_protocol:
RNAseq strand-specific expression library
RNA was extracted as follows: frozen cultures stored at −80◦C were thawed on ice and centrifuged at 4,000 rpm for 5 min at 4◦C. The pellets were resuspended in 1 ml Trizol  Life Technologies) and placed in tubes containing Lysing Matrix B (MP Bio). Cells were lysed by bead-beating twice for 40 s at 9 m/sec in a FastPrep 5G instrument (MP Bio). 300 µl chloroform was added and samples were centrifuged for 15 min at 4,000 rpm at 4◦C. The aqueous phase was collected and RNA was purified using Direct-Zol RNA miniprep kit (Zymo) according to the manufacturer’s instructions. Samples were then treated with DNase Turbo (Ambion) for 1 h and purified with an RNA Clean & Concentrator-25 kit (Zymo) according to the manufacturer’s instructions
RNA samples from each biological replicate were split in three, in order to generate two 50 -end differentially treated libraries and one RNAseq expression library. RNA for library 1 (“converted” library) was treated either with RNA 50 pyrophosphohydrolase RPPH (NEB) (exponential phase experiment), or with 50 polyphosphatase (Epicenter) (hypoxia experiment and normoxia controls), in order to remove the native 50 triphosphates of primary transcripts, whereas RNA for Library 2 (“nonconverted” library) was subject to mock treatment. Thus, the converted libraries capture both 50 triphosphates (converted to monophosphates) and native 50 monophosphate transcripts, while non-converted libraries capture only native 50 monophosphates. Library construction was performed as described by Shell et al. (2015). For RNA expression libraries, KAPA stranded RNA-Seq library preparation kit and NEBNext Ultra RNA library prep kit for Illumina (NEB) were used for Dataset 1 and Dataset 2, respectively, according to manufacturer’s instructions. The following major  odifications were introduced into the protocols: (i) For RNA fragmentation, in order to obtain fragments around 300 nt, RNA was mixed with the corresponding buffer and placed at 85◦C for 6 min (Dataset 1), or at 94◦C for 12 min (Dataset 2). (ii) For library amplification, 10 or 19–23 PCR cycles were used for Dataset 1 and Dataset 2, respectively. The number of cycles was chosen according to the amount of cDNA obtained for each sample.


title: Smeg_normoxia_polyphosphatase Rep2

description:
wildtype Smegmatis mc2155. Normoxia 5' end mapping library, treated with polyphosphatase, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80


title: Smeg_normoxia_expression Rep1

description:
wildtype Smegmatis mc2155. Normoxia (log phase) 15 hours, used to compare hypoxia to log phase, expression library, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Expression libraries_DEseq_hypoxia.xlsx


title: Smeg_hypoxia 24 h_expression Rep2

description:
wildtype Smegmatis mc2155. Hypoxia 24 hours, expression library, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Expression libraries_DEseq_hypoxia.xlsx


title: Smeg_hypoxia 15 h_polyphosphatase Rep1

description:
wildtype Smegmatis mc2155. Hypoxia 15 hours 5' end mapping library, treated with polyphosphatase, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80


title: Smeg_hypoxia 24 h_expression Rep1

description:
wildtype Smegmatis mc2155. Hypoxia 24 hours, expression library, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Expression libraries_DEseq_hypoxia.xlsx


title: M82 Rep2

city: Portici

first: Daniela

last: D'Esposito

address: Via Università 100

department: Department of Agriculture

institute: University of Naples Federico II

description: M82II_TAGCTT_L001_R1_002_BH0RBDADXX.filt

data_processing:
Base calling was performed with CASAVA 1.8.2
Data filtering (trimming and clipping) was performed with Trimmomatic (minimum quality 25 and minimum length 35bp)
Read alignment was performed with TopHat2.
Variant calling was performed with SAMtools v1.9
Read count was performed usign HT-seq with default setting.
Normalized aboundance measurement was performed using the R package CQN (conditional quantile normalization)
Differential expression analysis was performed using the R package edgeR
Genome_build: SL2.50
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for samples IL2-6 (Rep1, Rep2, Rep3) IL3-2 (Rep1, Rep2, Rep3) and variant calling for M82 Rep2

organism: Solanum lycopersicum

growth_protocol: Plants were grown in the field in natural conditions

extract_protocol:
Total RNA was extracted from leaf tissue using the Spectrum plant total RNA Kit (Sigma) and treated with DNase I (Sigma) to remove contaminant DNA. All RNA samples were quantified with NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE, USA) and RNA quality (integrity) was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Single end libraries were prepared using Illumina TruSeq Standard mRNA kit. Stranded paired-end libraries were prepared with Illumina TruSeq Stranded mRNA Kit

tag: line

value: control M82

value: leaf


title: IL3-2 Rep3

description: 3-2III_ACTGAT_L001_R1_001_AH0NUHADXX.filt

organism: Solanum lycopersicum x Solanum pennellii

value: introgression line IL3-2


title: Smeg_hypoxia 15 h_expression  Rep1

description:
wildtype Smegmatis mc2155. Hypoxia 15 hours, expression library, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Expression libraries_DEseq_hypoxia.xlsx


title: Smeg_log phase_expression Rep2

description:
wildtype Smegmatis mc2155. Log phase expression library, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Expression libraries_log phase_RPKM.xlsx


title: IL3-2 Rep2

description: 3-2II_CTTGTA_L001_R1_001_AH0NUHADXX.filt


title: Smeg_log phase_mock Rep2

description:
wildtype Smegmatis mc2155. Log phase 5' end mapping library, mock treated, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Normalized_filtered_5-prime_ends_coverage_and_ratios.xlsx


title: IL3-2 Rep1


title: IL2-6 Rep2

value: introgression line IL2-6

tag: phenotype

value: enhanced biomass production


title: Smeg_log phase_polyphosphatase Rep3

description:
wildtype Smegmatis mc2155. Log phase 5' end mapping library, treated with polyphosphatase, replicate 3
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Normalized_filtered_5-prime_ends_coverage_and_ratios.xlsx

extract_protocol:
RNAseq 5' end mapping library. 5' triphosphates were converted to 5' monophosphates by RppH before adapters were ligated to RNA 5' ends.
RNA was extracted as follows: frozen cultures stored at −80◦C were thawed on ice and centrifuged at 4,000 rpm for 5 min at 4◦C. The pellets were resuspended in 1 ml Trizol  Life Technologies) and placed in tubes containing Lysing Matrix B (MP Bio). Cells were lysed by bead-beating twice for 40 s at 9 m/sec in a FastPrep 5G instrument (MP Bio). 300 µl chloroform was added and samples were centrifuged for 15 min at 4,000 rpm at 4◦C. The aqueous phase was collected and RNA was purified using Direct-Zol RNA miniprep kit (Zymo) according to the manufacturer’s instructions. Samples were then treated with DNase Turbo (Ambion) for 1 h and purified with an RNA Clean & Concentrator-25 kit (Zymo) according to the manufacturer’s instructions
RNA samples from each biological replicate were split in three, in order to generate two 50 -end differentially treated libraries and one RNAseq expression library. RNA for library 1 (“converted” library) was treated either with RNA 50 pyrophosphohydrolase RPPH (NEB) (exponential phase experiment), or with 50 polyphosphatase (Epicenter) (hypoxia experiment and normoxia controls), in order to remove the native 50 triphosphates of primary transcripts, whereas RNA for Library 2 (“nonconverted” library) was subject to mock treatment. Thus, the converted libraries capture both 50 triphosphates (converted to monophosphates) and native 50 monophosphate transcripts, while non-converted libraries capture only native 50 monophosphates. Library construction was performed as described by Shell et al. (2015). For RNA expression libraries, KAPA stranded RNA-Seq library preparation kit and NEBNext Ultra RNA library prep kit for Illumina (NEB) were used for Dataset 1 and Dataset 2, respectively, according to manufacturer’s instructions. The following major  odifications were introduced into the protocols: (i) For RNA fragmentation, in order to obtain fragments around 300 nt, RNA was mixed with the corresponding buffer and placed at 85◦C for 6 min (Dataset 1), or at 94◦C for 12 min (Dataset 2). (ii) For library amplification, 10 or 19–23 PCR cycles were used for Dataset 1 and Dataset 2, respectively. The number of cycles was chosen according to the amount of cDNA obtained for each sample.


title: IL2-6 Rep3


title: Smeg_log phase_mock Rep3

description:
wildtype Smegmatis mc2155. Log phase 5' end mapping library, mock treated, replicate 3
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Normalized_filtered_5-prime_ends_coverage_and_ratios.xlsx


title: IL2-6 Rep1


title: Smeg_log phase_polyphosphatase Rep2

description:
wildtype Smegmatis mc2155. Log phase 5' end mapping library, treated with polyphosphatase, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Normalized_filtered_5-prime_ends_coverage_and_ratios.xlsx


title: Cj3R1 [RNA-seq]

description:
Organism: Citrus junos Sieb. ex Tanaka
processed data file: All_gene_fpkm.xls


title: Smeg_log phase_expression Rep1

description:
wildtype Smegmatis mc2155. Log phase expression library, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Expression libraries_log phase_RPKM.xlsx


title: Plasma_39

status: Public on Mar 16 2019

city: Turin

first: Alessio

last: Naccarati

address: Via Nizza 52

institute: Italian Institute for Genomic Medicine

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of AGATCGGAAGAGCACACGTCT. exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files contain RPM read counts for miRNAs (miRBase version 21) / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

source_name: Plasma

extract_protocol:
Exosomes were isolated from plasma using the ExoQuick exosome precipitation solution according to the manufacturer's instructions with minor modifications. The mixture was then further centrifuged at 1500 g for 30 min. The exosome pellet was dissolved in nuclease free water; RNA was extracted immediately from the solution.
Library preparation was performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs Inc., USA). For each library, 6 μL of RNA (min 35 ng) were used in all the experimental procedures as starting material. Each library was prepared with a unique indexed primer so that the libraries could all be pooled into one sequencing lane. Multiplex adaptor ligations, reverse transcription primer hybridization, reverse transcription reaction and PCR amplification were performed according to the protocol for library preparation (Protocol E7330, New England BioLabs Inc., USA). After PCR amplification, the cDNA constructs were purified with the QIAQuick PCR Purification Kit (Qiagen, Germany) following the modifications suggested by the NEBNext Multiplex Small RNA Library Prep Protocol and loaded on the Bioanalyzer 2100 (Agilent, Germany) using the DNA High Sensitivity Kit (Agilent, Germany) according to the manufacturer's protocol. Libraries were pooled together (24plex) and further purified with a gel size selection.

tag: condition

value: Healthy Control

tag: anatomical location

value: Entire body system

tag: rna source

value: extracellular exosome

tag: rna isolation kit

value: miRNeasy (Qiagen)

tag: study


title: Urine_18

source_name: Urine

extract_protocol:
Urine samples from each participant were collected in the morning, stored at 4°C until the processing consisting of centrifugation at 3,000g for 10 min. The urine supernatant aliquots were then transferred in tubes and stored at -80°C until use.
Library preparation was performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs Inc., USA). For each library, 6 μL of RNA (min 35 ng) were used in all the experimental procedures as starting material. Each library was prepared with a unique indexed primer so that the libraries could all be pooled into one sequencing lane. Multiplex adaptor ligations, reverse transcription primer hybridization, reverse transcription reaction and PCR amplification were performed according to the protocol for library preparation (Protocol E7330, New England BioLabs Inc., USA). After PCR amplification, the cDNA constructs were purified with the QIAQuick PCR Purification Kit (Qiagen, Germany) following the modifications suggested by the NEBNext Multiplex Small RNA Library Prep Protocol and loaded on the Bioanalyzer 2100 (Agilent, Germany) using the DNA High Sensitivity Kit (Agilent, Germany) according to the manufacturer's protocol. Libraries were pooled together (24plex) and further purified with a gel size selection.

value: Urinary system structure

value: total cell-free biofluid RNA

value: Urine microRNA Purification kit (Norgen Biotek Corp)


title: Plasma_50


title: Plasma_100


title: Plasma_118


title: Plasma_59


title: Smeg_log phase_mock Rep1

description:
wildtype Smegmatis mc2155. Log phase 5' end mapping library, mock treated, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Normalized_filtered_5-prime_ends_coverage_and_ratios.xlsx


title: Urine_27


title: Plasma_9


title: Stool_16

source_name: Stool specimen

extract_protocol:
Stool samples were collected in special tubes with RNA stabilizing solution, returned at the time of performing colonoscopy and stored at-80°C until RNA extraction.
Library preparation was performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs Inc., USA). For each library, 6 μL of RNA (min 35 ng) were used in all the experimental procedures as starting material. Each library was prepared with a unique indexed primer so that the libraries could all be pooled into one sequencing lane. Multiplex adaptor ligations, reverse transcription primer hybridization, reverse transcription reaction and PCR amplification were performed according to the protocol for library preparation (Protocol E7330, New England BioLabs Inc., USA). After PCR amplification, the cDNA constructs were purified with the QIAQuick PCR Purification Kit (Qiagen, Germany) following the modifications suggested by the NEBNext Multiplex Small RNA Library Prep Protocol and loaded on the Bioanalyzer 2100 (Agilent, Germany) using the DNA High Sensitivity Kit (Agilent, Germany) according to the manufacturer's protocol. Libraries were pooled together (24plex) and further purified with a gel size selection.

value: Digestive tract structure

value: Stool Total RNA Purification Kit (Norgen Biotek Corp)


title: Urine_4


title: Urine_44


title: Plasma_82


title: Urine_5


title: Plasma_114


title: Urine_6


title: Stool_32


title: Plasma_13


title: Plasma_74


title: Stool_31


title: Plasma_83


title: Plasma_57


title: Plasma_31


title: Stool_5


title: Plasma_65


title: Plasma_42


title: Plasma_14


title: Plasma_22


title: Stool_38


title: Urine_11


title: Plasma_89


title: Plasma_3


title: Plasma_116


title: Plasma_107


title: Urine_10


title: Plasma_99


title: Urine_25


title: Urine_42


title: Urine_26


title: Plasma_125


title: Plasma_37


title: Plasma_94


title: Urine_43


title: Stool_21


title: Stool_22


title: Urine_17


title: Urine_34


title: Urine_12


title: Plasma_108


title: Stool_23


title: Plasma_38


title: Smeg_hypoxia 15 h_expression Rep2

description:
wildtype Smegmatis mc2155. Hypoxia 15 hours, expression library, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Expression libraries_DEseq_hypoxia.xlsx


title: Plasma_104


title: Plasma_48


title: Plasma_121


title: Plasma_81


title: Plasma_122


title: Plasma_29


title: Plasma_72


title: Plasma_64


title: Plasma_123


title: Stool_36


title: Stool_14


title: Stool_4


title: Plasma_55


title: Plasma_21


title: Smeg_normoxia_polyphosphatase Rep1

description:
wildtype Smegmatis mc2155. Normoxia 5' end mapping library, treated with polyphosphatase, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80

value: Aerobic log phase


title: Stool_3


title: Plasma_87


title: Stool_19


title: Stool_37


title: Plasma_12


title: GBM33

tag: cell type

value: primary glioblastomas


title: Plasma_73


title: Plasma_56


title: Stool_28


title: Plasma_106


title: Urine_9


title: Plasma_97


title: Plasma_40


title: Plasma_2


title: Urine_15


title: Stool_8


title: Plasma_115


title: Urine_16


title: Urine_33


title: Plasma_98


title: Urine_41


title: Plasma_27


title: Urine_24


title: Plasma_19


title: Plasma_88


title: Stool_30


title: Stool_13


title: Plasma_28


title: Plasma_47


title: Plasma_71


title: Stool_11


title: Plasma_7


title: Plasma_112


title: Plasma_36


title: Plasma_111


title: Plasma_86


title: Urine_48

extract_protocol: Library preparation was performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs Inc., USA). For each library, 6 μL of RNA (min 35 ng) were used in all the experimental procedures as starting material. Each library was prepared with a unique indexed primer so that the libraries could all be pooled into one sequencing lane. Multiplex adaptor ligations, reverse transcription primer hybridization, reverse transcription reaction and PCR amplification were performed according to the protocol for library preparation (Protocol E7330, New England BioLabs Inc., USA). After PCR amplification, the cDNA constructs were purified with the QIAQuick PCR Purification Kit (Qiagen, Germany) following the modifications suggested by the NEBNext Multiplex Small RNA Library Prep Protocol and loaded on the Bioanalyzer 2100 (Agilent, Germany) using the DNA High Sensitivity Kit (Agilent, Germany) according to the manufacturer's protocol. Libraries were pooled together (24plex) and further purified with a gel size selection.


title: Urine_3


title: Plasma_113


title: Stool_2


title: Plasma_54


title: Stool_26


title: Stool_27


title: Plasma_30


title: Mouse_IVD_Col2Cre_Control_RNAseq_replicaC1

value: postnatal day 20

value: wild type

value: intervertebral disc


title: Plasma_11


title: Plasma_80


title: Urine_39


title: Stool_9


title: Plasma_96


title: Urine_40


title: Plasma_78


title: Plasma_76


title: Plasma_1


title: Plasma_26


title: Stool_35


title: Plasma_105


title: Urine_14


title: Stool_12


title: Plasma_91


title: Urine_23


title: Urine_31


title: Plasma_17


title: Stool_29


title: Plasma_63


title: Plasma_35


title: Plasma_93


title: Plasma_46


title: Plasma_18


title: Stool_18


title: Plasma_101


title: Urine_2


title: Stool_20


title: Stool_1


title: Smeg_hypoxia 24 h_polyphosphatase Rep2

description:
wildtype Smegmatis mc2155. Hypoxia 24 hours 5' end mapping library, treated with polyphosphatase, replicate 2
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80

value: Hypoxia 24 hours after sealing Wayne model vials


title: Plasma_120


title: Plasma_103


title: Plasma_79


title: Plasma_70


title: Plasma_62


title: Smeg_log phase_polyphosphatase Rep1

description:
wildtype Smegmatis mc2155. Log phase 5' end mapping library, treated with polyphosphatase, replicate 1
Middlebrook 7H9 supplemented with ADC (Albumin Dextrose  Catalase, final concentrations 5 g/L bovine serum albumin  fraction V, 2 g/L dextrose, 0.85 g/L sodium chloride, and 3 mg/L  catalase), 0.2% glycerol and 0.05% Tween 80
Normalized_filtered_5-prime_ends_coverage_and_ratios.xlsx


title: Stool_34


title: Urine_29


title: RM_FB_S_R1

city: Szeged

first: Laszlo

middle: G.

last: Nagy

state: Csongrad

address: Temesvari krt 62

department: Institute of Biochemistry, Synthetic and Systems Biology Unit

country: Hungary

institute: Biological Research Centre, Hungarian Academy of Sciences

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 10.0.1). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package v 2.15 of CLC Genomics Workbench Tool (v. 10.0.1) allowing intergenic mapping.  Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8.  mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Linear modeling with empirical Bayes moderation was built in limma. Package: limma, Version: 3.18.13
Genome_build: Rickenella mellea v1.0 SZMC22713 (Ricmel1), JGI project ID:1075324
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool

organism: Rickenella mellea

source_name: fruiting body, stipe

growth_protocol: Rickenella mellea SZMC22713 was cultured on Fries Agar for harvesting vegetative mycelium for RNA extraction. Fruiting body stages were collected in November 2016 from Kistelek, Hungary (approx. coordinates: 46.546309, 19.954507). Stage 1 primordium was defined as an approximately 1 mm tall, shaft-like, pear-shaped structure, without any visible cap initial, stage 2 primordium was described as a 2-3 mm tall structure with a small cap initial, young fruiting body was defined by the 5-15 mm tall structure with a 1-2 mm wide cap, and the fruiting body was characterized by a fully expanded cap on the top of a 20-32 mm tall stipe.

extract_protocol:
After harvesting, samples were immediately placed on liquid nitrogen and stored at -80 °C until use.  10-20 mg frozen tissue was placed in a pre-chilled mortar and ground to a fine powder. Quick-RNA Miniprep Kit (Zymo Research) was used according to manufacturer«s instructions.
Whole transcriptome sequencing was performed using the TrueSeq RNA Library Preparation Kit v2 (Illumina) according to the manufacturer’s instructions. Briefly, RNA quality and quantity measurements were performed using RNA ScreenTape and Reagents on TapeStation (all from Agilent) and Qubit (ThermoFisher); only high quality (RIN >8.0) total RNA samples were processed. Next, RNA was DNaseI (ThermoFisher) treated and the mRNA was purified and fragmented. First strand cDNA synthesis was performed using SuperScript II (ThermoFisher) followed by second strand cDNA synthesis, end repair, 3’-end adenylation, adapter ligation and PCR amplification. All of the purification steps were performed using AmPureXP Beads (Backman Coulter). Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation (all from Agilent). Concentration of each library was determined using either the QPCR Quantification Kit for Illumina (Agilent) or the KAPA Library Quantification Kit for Illumina (KAPA Biosystems)

tag: group

value: CALKCANXX

value: fruiting body, stipe


title: RM_FB_S_R4


title: Urine_47

value: Healthy Control


title: Chinese horse breeds_Series 4: NQ4

city: Beijing

first: Hongying

last: Ma

address: yuanmingyuan road NO.2

institute: China agriculture university

description: Genomic DNA extracted from blood was genotyped with the Illumina Equine SNP70 Bead Array

hyb_protocol: Not provided

scan_protocol: After allele-specific staining BeadChip arrays  and scanned on  Illumina BeadScand..

data_processing:
Genomic DNA extracted from blood was genotyped using the Illumina Equine SNP70 Bead Array.
Image data was analyzed using GenomeStudio Software.

label: not provided

organism: Equus caballus

source_name: Naqu horse

label_protocol: Not provided

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction. Integrity and purity of DNA verified by agarose gel electrophoresis and A260/280 ratio.

treatment_protocol: The samples were obtained following the principles approved by the Animal Care and Use Committee of China Agricultural University (Permit Number: XK257)

tag: gender

value: unknown

value: blood

value: 3 years


title: Chinese horse breeds_Series 2: NQ2


title: Chinese horse breeds_Series 1: NQ1


title: Chinese horse breeds_Series 3: NQ3


title: Plasma_61

value: Entire body system

value: extracellular exosome

value: miRNeasy (Qiagen)


title: Urine_38

value: Urinary system structure

value: total cell-free biofluid RNA

value: Urine microRNA Purification kit (Norgen Biotek Corp)


title: RM_FB_C_R2

source_name: fruiting body, cap

tag: strain

value: fruiting body, cap


title: Chinese horse breeds_Series 5: NQ5

tag: age


title: RM_FB_C_R3


title: Plasma_53


title: RM_FB_C_R1


title: Urine_7


title: Urine_46


title: RM_YFB_R3

source_name: young fruiting body

value: young fruiting body


title: Stool_25

value: Digestive tract structure

value: Stool Total RNA Purification Kit (Norgen Biotek Corp)


title: Plasma_8


title: RM_YFB_R2


title: RM_YFB_R1


title: Stool_33


title: Plasma_20


title: RM_P2_R1

source_name: primordium

value: primordium


title: RM_P1_R2

value: CALKCANXX


title: RM_VM_R3

source_name: vegetative mycelium

value: vegetative mycelium


title: Plasma_66

value: Healthy Control


title: Plasma_95


title: Stool_17


title: Plasma_77


title: Plasma_33


title: Urine_13


title: Urine_30


title: Stool_7


title: Jinjinag horse samples_Series 24: JJ1-37

source_name: Jinjiang horse

value: unknown


title: Jinjinag horse samples_Series 23: JJ1-30

value: blood


title: Jinjinag horse samples_Series 21: JJ1-22

value: 3 years


title: Plasma_16

value: Entire body system


title: Plasma_85

value: extracellular exosome


title: Plasma_34

value: miRNeasy (Qiagen)


title: Jinjinag horse samples_Series 22: JJ1-28


title: Plasma_44


title: Plasma_68


title: Jinjinag horse samples_Series 20: JJ1-19


title: Jinjinag horse samples_Series 19: JJ1-18


title: RM_P2_R3


title: Urine_21

value: Urinary system structure


title: Jinjinag horse samples_Series 18: JJ1-14


title: Urine_32

value: total cell-free biofluid RNA


title: Jinjinag horse samples_Series 17: JJ1-11


title: Plasma_5


title: RM_VM_R2


title: RM_VM_R1


title: Jinjinag horse samples_Series 16: JJ1-5


title: Jinjinag horse samples_Series 15: JJ1-2


title: Plasma_25


title: Plasma_45


title: Plasma_4


title: Stool_10


title: Plasma_92


title: Plasma_119


title: Plasma_51


title: Jinjinag horse samples_Series 10: JJ24


title: Jinjinag horse samples_Series 12: JJ28


title: Jinjinag horse samples_Series 11: JJ25


title: Plasma_102


title: Jinjinag horse samples_Series 14: JJ34


title: Jinjinag horse samples_Series 13: JJ31


title: Jinjinag horse samples_Series 9: JJ23


title: Urine_28

value: Urine microRNA Purification kit (Norgen Biotek Corp)


title: Urine_1


title: Jinjinag horse samples_Series 5: JJ13


title: Jinjinag horse samples_Series 7: JJ15


title: Jinjinag horse samples_Series 8: JJ22


title: Urine_36


title: Urine_45


title: Jinjinag horse samples_Series 4: JJ12


title: Jinjinag horse samples_Series 3: JJ11


title: Plasma_52


title: Jinjinag horse samples_Series 2: JJ3


title: Jinjinag horse samples_Series 1: JJ2


title: Stool_24


title: Plasma_60


title: Additional horse samples_Series 24: DZLV268

organism: Equus asinus

source_name: Dezhou donkey


title: Plasma_69


title: Plasma_6


title: Urine_19


title: Additional horse samples_Series 23: CK47

source_name: Chakouyi horse


title: Plasma_110


title: Jinjinag horse samples_Series 6: JJ14


title: Urine_37


title: Additional horse samples_Series 19: CK64


title: Additional horse samples_Series 21: Z250

organism: Equus przewalskii

source_name: przewalskii


title: Additional horse samples_Series 20: DZLV304


title: Additional horse samples_Series 18: DZLV110


title: Plasma_84


title: Stool_15


title: Plasma_10


title: Additional horse samples_Series 17: CK39


title: Stool_6


title: Plasma_75


title: Plasma_67


title: Additional horse samples_Series 15: JJ60


title: Additional horse samples_Series 14: DA135

source_name: Daan horse


title: Additional horse samples_Series 13: GZ36

source_name: Guizhou horse


title: Plasma_23


title: Additional horse samples_Series 12: DA186


title: Stool_39


title: Additional horse samples_Series 9: GZ10


title: Additional horse samples_Series 22: DZLV167


title: Additional horse samples_Series 8: BS48（BS27）

source_name: Baise horse


title: Plasma_124


title: Additional horse samples_Series 5: N33

source_name: Debao horse


title: Additional horse samples_Series 7: N7


title: Additional horse samples_Series 11: GZ17


title: Plasma_24

source_name: Plasma


title: Plasma_43


title: Plasma_32


title: Plasma_90


title: Urine_20

source_name: Urine


title: Additional horse samples_Series 6: BS38


title: Additional horse samples_Series 16: LV3


title: Urine_22


title: Additional horse samples_Series 3: D34


title: Plasma_58


title: Plasma_117


title: Plasma_109


title: Additional horse samples_Series 2: CK52


title: Additional horse samples_Series 10: DA123


title: Plasma_15


title: Additional horse samples_Series 1: BS48


title: Chinese horse breeds_Series 264: DA27


title: Additional horse samples_Series 4: BS60


title: Chinese horse breeds_Series 262: DA46


title: Chinese horse breeds_Series 261: DA219


title: EXR-MBITZ1CTOT2SAMPB24A20-BS: CTOT04_02_Urine_24-20

city: Ann Arbor

first: Markus

last: Bitzer

state: MI

address: 1500 E Medical Center Dr SPC 5361

institute: University of Michigan

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

extract_protocol:
450 ul biofluid sample were mixed with 105 ul buffer P, digested with 28 ul Proteinase K working solution at 65C for 8 minutes, extracted with 517 ul ED2 working solution, cooled to 10C, phase separation was induced after adding 110 ul chloroform, approx. 600 ul aqueous supernatants were mixed with 1200 ul buffer VB2G, loaded on Zymo-I 96-well silica matrix plate, washed twice with 970 ul EWL, once with 970 ul 100% ethanol, twice with 500 ul 80% ethanol and eluted into 20 ul TrisHCl pH 7.5. Protocol was executed on epMotion 5075 liquid handling system. Low speed centrifugation (1200 g x 10 minutes) was performed for cell removal.
No Kit was used. Multiplexed Small RNA library preparation protocol developed by Tuschl lab. Adenylated DNA adapters each containing a unique 5-nt barcode sequence were ligated to the 3end of the RNA overnight at 4C.The barcoded adapters allow 24 individual RNA samples to be pooled into one lane.The pooled samples were purified on a 15% polyacrylamide gel and size-selection was guided by radiolabeled RNA markers corresponding to a sRNA size of 19-30 nt. Next, a 26-nt RNA adapter compatible with Illumina sequencing was ligated to the 5end of the RNA at 37C for 1 hour and samples were purified on a 12% polyacrylamide gel.  The cDNA libraries were then generated by reverse transcription and amplified using up to 20 PCR cycles, and the final libraries ranging from 90-101 nt were purified on a 2.5% agarose gel and sequenced in a single Illumina HiSeq lane.

tag: diagnosis

value: nephrotic syndrome

value: urine

value: Transplanted kidney present

tag: 3' adapter sequence

value: TTCATTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A24-BS: CTOT04_02_Urine_24-24

tag: tissue

value: TGCCATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A22-BS: CTOT04_02_Urine_24-22

value: TTGTATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A21-BS: CTOT04_02_Urine_24-21

value: TTGACTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 260: DA77


title: EXR-MBITZ1CTOT2SAMPB24A19-BS: CTOT04_02_Urine_24-19

value: TTATTTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A18-BS: CTOT04_02_Urine_24-18

value: TAGCCTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 257: DA32

value: unknown

value: blood


title: Chinese horse breeds_Series 259: DA68

value: 3 years


title: Chinese horse breeds_Series 256: DA15


title: Chinese horse breeds_Series 258: DA52


title: EXR-MBITZ1CTOT2SAMPB24A17-BS: CTOT04_02_Urine_24-17

value: TACTCTCGTATGCCGTCTTCTGCTTG


title: Urine_35

value: Healthy Control


title: EXR-MBITZ1CTOT2SAMPB24A23-BS: CTOT04_02_Urine_24-23

value: Urinary system structure

value: TGTTATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A16-BS: CTOT04_02_Urine_24-16

value: total cell-free biofluid RNA

value: TTACATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A15-BS: CTOT04_02_Urine_24-15

value: nephrotic syndrome

value: urine

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 255: DA89


title: EXR-MBITZ1CTOT2SAMPB24A14-BS: CTOT04_02_Urine_24-14

value: Transplanted kidney present

value: TATCATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A12-BS: CTOT04_02_Urine_24-12

value: TAATATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A13-BS: CTOT04_02_Urine_24-13

value: TAGAGTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 253: DA100


title: Chinese horse breeds_Series 252: DA51


title: Chinese horse breeds_Series 263: DA39


title: Chinese horse breeds_Series 251: DA51


title: EXR-MBITZ1CTOT2SAMPB24A11-BS: CTOT04_02_Urine_24-11

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A10-BS: CTOT04_02_Urine_24-10

value: TTAAGTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 250: DA3

value: unknown

value: blood


title: Chinese horse breeds_Series 249: DA74

value: 3 years


title: EXR-MBITZ1CTOT2SAMPB24A9-BS: CTOT04_02_Urine_24-9

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A8-BS: CTOT04_02_Urine_24-8

value: Urinary system structure

value: TCTAGTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 245: DA78


title: Chinese horse breeds_Series 247: DA112


title: EXR-MBITZ1CTOT2SAMPB24A6-BS: CTOT04_02_Urine_24-6

value: total cell-free biofluid RNA

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A5-BS: CTOT04_02_Urine_24-5

value: nephrotic syndrome

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 246: DA42


title: EXR-MBITZ1CTOT2SAMPB24A3-BS: CTOT04_02_Urine_24-3

value: urine

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A24-BS: CTOT04_02_Urine_23-24

value: Transplanted kidney present

value: TGCCATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A7-BS: CTOT04_02_Urine_24-7

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A20-BS: CTOT04_02_Urine_23-20

value: TTCATTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB24A2-BS: CTOT04_02_Urine_24-2

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 244: DA80

value: unknown


title: EXR-MBITZ1CTOT2SAMPB23A21-BS: CTOT04_02_Urine_23-21

value: TTGACTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A19-BS: CTOT04_02_Urine_23-19

value: TTATTTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 243: DA26

value: blood

value: 3 years


title: Chinese horse breeds_Series 242: JJ1-42


title: Chinese horse breeds_Series 241: JJ1-41


title: EXR-MBITZ1CTOT2SAMPB23A22-BS: CTOT04_02_Urine_23-22

value: Urinary system structure

value: TTGTATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A23-BS: CTOT04_02_Urine_23-23

value: total cell-free biofluid RNA

value: TGTTATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 248: DA16


title: EXR-MBITZ1CTOT2SAMPB24A4-BS: CTOT04_02_Urine_24-4

value: nephrotic syndrome

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: RKO_rep2

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan 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 hg38 whole genome using Hisat2
mRNA and lncRNA annotated in NCBI were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Cell line

extract_protocol:
Cellular RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using mRNA-seq protocols

tag: cell line

value: RKO

value: colorectal cancer

tag: genotype/variation

value: control


title: RKO_cTAZ_KO_rep2

value: cTAZ KO


title: RKO_cTAZ_KO_rep1


title: RKO_KO_putback_rep2

value: cTAZ putback


title: RKO_KO_putback_rep1


title: Chinese horse breeds_Series 254: DA75


title: Chinese horse breeds_Series 240: JJ1-40


title: EXR-MBITZ1CTOT2SAMPB23A18-BS: CTOT04_02_Urine_23-18

value: urine

value: Transplanted kidney present

value: TAGCCTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A17-BS: CTOT04_02_Urine_23-17

value: TACTCTCGTATGCCGTCTTCTGCTTG


title: RKO_rep1


title: Chinese horse breeds_Series 239: JJ1-39

value: unknown

value: blood


title: EXR-MBITZ1CTOT2SAMPB23A15-BS: CTOT04_02_Urine_23-15

value: Urinary system structure

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A14-BS: CTOT04_02_Urine_23-14

value: total cell-free biofluid RNA

value: TATCATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A16-BS: CTOT04_02_Urine_23-16

value: nephrotic syndrome

value: TTACATCGTATGCCGTCTTCTGCTTG


title: d7

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

data_processing:
BAM files were converted to FASTQ with Picard Tools
FASTQ files were aligned to the mouse genome with Bismark using bowtie
Methylation call files were computed with Bismark
Genome_build: mm10
Supplementary_files_format_and_content: Text (Bismark methylation call file: chromosome, coordinate, coverage, percent methylated, percent unmethylated, tab separated)

source_name: Nucleus accumbens

extract_protocol: Genomic DNA was extracted from frozen nAcc punches using Qiagen DNA micro kit (Qiagen, Cat# 56304.) following the kit protocol. On-column RNaseA treatment was performed during DNA extraction to reduce RNA contamination. WGBS libraries were prepared using Pico Methyl-seq library prep kit (Cat# D5456, Zymo research)

treatment_protocol: 8-week-old male C57BL/6J mice were subjected to ten daily defeats by a novel CD1 retired male breeder aggressor mouse that had been previously screened for aggressive behavior.

value: Susceptible

value: Nucleus accumbens


title: Chinese horse breeds_Series 238: JJ1-38

value: 3 years


title: EXR-MBITZ1CTOT2SAMPB23A12-BS: CTOT04_02_Urine_23-12

value: TAATATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 237: JJ1-36


title: d6


title: EXR-MBITZ1CTOT2SAMPB23A8-BS: CTOT04_02_Urine_23-8

value: TCTAGTCGTATGCCGTCTTCTGCTTG


title: d3


title: EXR-MBITZ1CTOT2SAMPB23A13-BS: CTOT04_02_Urine_23-13

value: urine

value: TAGAGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A9-BS: CTOT04_02_Urine_23-9

value: Transplanted kidney present

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 236: JJ1-32

value: unknown


title: EXR-MBITZ1CTOT2SAMPB23A11-BS: CTOT04_02_Urine_23-11

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: d2


title: Chinese horse breeds_Series 235: JJ1-31

value: blood


title: C8

value: Control


title: EXR-MBITZ1CTOT2SAMPB23A7-BS: CTOT04_02_Urine_23-7

value: Urinary system structure

value: total cell-free biofluid RNA

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A5-BS: CTOT04_02_Urine_23-5

value: nephrotic syndrome

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: C5

value: Nucleus accumbens


title: Chinese horse breeds_Series 233: JJ1-27

value: 3 years


title: EXR-MBITZ1CTOT2SAMPB23A6-BS: CTOT04_02_Urine_23-6

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A1-BS: CTOT04_02_Urine_23-1

value: TCACTTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A3-BS: CTOT04_02_Urine_23-3

value: urine

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A10-BS: CTOT04_02_Urine_23-10

value: Transplanted kidney present

value: TTAAGTCGTATGCCGTCTTCTGCTTG


title: C4


title: EXR-MBITZ1CTOT2SAMPB22A24-BS: CTOT04_02_Urine_22-24

value: TGCCATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 232: JJ1-25

value: unknown


title: C3


title: Chinese horse breeds_Series 231: JJ1-23

value: blood


title: EXR-MBITZ1CTOT2SAMPB22A23-BS: CTOT04_02_Urine_22-23

value: TGTTATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 234: JJ1-29


title: EXR-MBITZ1CTOT2SAMPB22A21-BS: CTOT04_02_Urine_22-21

value: Urinary system structure

value: TTGACTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 230: JJ1-21


title: EXR-MBITZ1CTOT2SAMPB22A22-BS: CTOT04_02_Urine_22-22

value: total cell-free biofluid RNA

value: TTGTATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB23A4-BS: CTOT04_02_Urine_23-4

value: nephrotic syndrome

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB22A18-BS: CTOT04_02_Urine_22-18

value: TAGCCTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB22A20-BS: CTOT04_02_Urine_22-20

value: TTCATTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB22A19-BS: CTOT04_02_Urine_22-19

value: TTATTTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 229: JJ1-20

value: 3 years


title: C2

extract_protocol: Genomic DNA was extracted from frozen nAcc punches using Qiagen DNA micro kit (Qiagen, Cat# 56304.) following the kit protocol. On-column RNaseA treatment was performed during DNA extraction to reduce RNA contamination. WGBS libraries were prepared using Pico Methyl-seq library prep kit (Cat# D5456, Zymo research).

value: Control

value: Nucleus accumbens


title: EXR-MBITZ1CTOT2SAMPB22A17-BS: CTOT04_02_Urine_22-17

value: urine

value: Transplanted kidney present

value: TACTCTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 228: JJ1-16

value: unknown

value: blood


title: EXR-MBITZ1CTOT2SAMPB22A14-BS: CTOT04_02_Urine_22-14

value: Urinary system structure

value: TATCATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB22A13-BS: CTOT04_02_Urine_22-13

value: total cell-free biofluid RNA

value: TAGAGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB22A16-BS: CTOT04_02_Urine_22-16

value: nephrotic syndrome

value: TTACATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 227: JJ1-15


title: EXR-MBITZ1CTOT2SAMPB22A11-BS: CTOT04_02_Urine_22-11

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB22A12-BS: CTOT04_02_Urine_22-12

value: TAATATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 226: JJ1-10


title: EXR-MBITZ1CTOT2SAMPB22A10-BS: CTOT04_02_Urine_22-10

value: TTAAGTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 225: JJ1-8

value: 3 years


title: EXR-MBITZ1CTOT2SAMPB22A9-BS: CTOT04_02_Urine_22-9

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 224: JJ1-4


title: EXR-MBITZ1CTOT2SAMPB22A8-BS: CTOT04_02_Urine_22-8

value: TCTAGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB22A7-BS: CTOT04_02_Urine_22-7

value: urine

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB22A15-BS: CTOT04_02_Urine_22-15

value: Transplanted kidney present

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 223: JJ1-3

value: unknown

value: blood


title: Chinese horse breeds_Series 221: JJ35


title: EXR-MBITZ1CTOT2SAMPB22A2-BS: CTOT04_02_Urine_22-2

value: Urinary system structure

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 222: JJ1-1


title: Chinese horse breeds_Series 220: JJ30


title: EXR-MBITZ1CTOT2SAMPB22A4-BS: CTOT04_02_Urine_22-4

value: total cell-free biofluid RNA

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB22A6-BS: CTOT04_02_Urine_22-6

value: nephrotic syndrome

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB22A5-BS: CTOT04_02_Urine_22-5

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB19A23-BS: CTOT04_02_Urine_19-23

value: TGTTATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB22A1-BS: CTOT04_02_Urine_22-1

value: TCACTTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB19A24-BS: CTOT04_02_Urine_19-24

value: TGCCATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB19A22-BS: CTOT04_02_Urine_19-22

value: TTGTATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 218: JJ26

value: 3 years


title: Chinese horse breeds_Series 219: JJ27


title: Chinese horse breeds_Series 217: JJ9


title: EXR-MBITZ1CTOT2SAMPB19A20-BS: CTOT04_02_Urine_19-20

value: urine

value: TTCATTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB19A19-BS: CTOT04_02_Urine_19-19

value: Transplanted kidney present

value: TTATTTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB19A18-BS: CTOT04_02_Urine_19-18

value: TAGCCTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB19A17-BS: CTOT04_02_Urine_19-17

value: Urinary system structure

value: TACTCTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 216: JJ8

value: unknown

value: blood


title: Placental tissue ID 1478

type: RNA

city: Diepenbeek

first: Tim

middle: S

last: Nawrot

address: Agoralaan building D

department: Centre for Environmental Sciences

country: Belgium

institute: Hasselt University

hyb_protocol: Cyanine-3 labelled cRNA was hybridized onto Agilent Whole Human Genome 8 x 60K microarrays.

scan_protocol: Microarray signals were detected using the Agilent DNA G2505C Microarray Scanner (Agilent Technologies). Scan images were converted into TXT files using the Agilent Feature Extraction Software (Version 10.7.3.1, Agilent Technologies, Amstelveen, The Netherlands).

data_processing: An in-house developed quality control pipeline in R software was used to preprocess raw data as follows: local background correction, omission of controls, flagging of bad spots and spots with too low intensity, log2 transformation and quantile normalization using arrayQC. More information about the flagging and the R-scripts of the pipeline are available at https://github.com/BiGCAT-UM/arrayQC_Module . Further preprocessing included removal of probes showing >30% flagged data, merging of replicate probes based on the median, and imputation of missing values by means of K-nearest neighbor imputation (K = 15). Batch effects were corrected for by using an empirical Bayes method (ComBat) (Johnson et al., 2007). For genes with multiple probes, the probe with the largest interquartile range was selected. From the resulting 18,847 probes, only those with expression levels above 6 (in the log2 scale) in a minimum of 30 samples were kept, leaving 14,040 genes for further analysis.

source_name: Placental tissue

label_protocol: 0.2 μg total RNA was used to synthesize fluorescent cyanine-3-labeled cRNA following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies).

extract_protocol: Total RNA was extracted from one placental tissue biopsy using the miRNeasy mini kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s protocol. RNase-Free DNase treatment was performed on RNA samples according to the manufacturer’s instructions (Qiagen, Venlo, The Netherlands). RNA quantity and purity were assessed by spectrophotometry (Nanodrop 1000, Isogen Life Science, De Meern, the Netherlands) and RNA integrity by Agilent 2100 Bioanalyzer (Agilent Technologies, Amstelveen, the Netherlands). Samples with RNA Integrity Number below 6 were excluded from further analysis.

treatment_protocol: Placental tissue was collected within 1 hour after delivery. Four standardized biopsies were taken from the fetal side, at fixed locations across the middle point of the placenta around 4 cm distance from the umbilical cord (Janssen et al., 2017). The collected biopsies were stored in RNA later (ThermoFisher Scientific, Massachusetts, USA) at 4°C for at least 12 hours and maximally 24 hours, followed by storage at -20°C.

value: Placenta

tag: labeling date

tag: hybridization date

tag: date delivery

tag: maternal pre-pregnancy bmi

tag: birth weight (gram)

tag: Sex

value: Male

tag: gestational age (month)

tag: ethnicity

value: 0 (European)

tag: parity

value: 2 (2 children)

tag: maternal age (year)

tag: maternal smoking

value: 0 (never smoked)

tag: gestational weight gain (kilogram)

tag: gestational diabetes

value: 1 (yes)

tag: gestational hypertension


title: Placental tissue ID 1492

tag: tissue

value: Female

value: 1 (stopped smoking before pregnancy)


title: Placental tissue ID 1500

value: 1 (1 child)


title: Placental tissue ID 1511


title: EXR-MBITZ1CTOT2SAMPB19A16-BS: CTOT04_02_Urine_19-16

tag: diagnosis

value: nephrotic syndrome

value: urine

tag: condition

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

tag: 3' adapter sequence

value: TTACATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB19A15-BS: CTOT04_02_Urine_19-15

value: Transplanted kidney present

value: Urinary system structure

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: Placental tissue ID 1498

tag: labeling date

tag: hybridization date

tag: date delivery

tag: maternal pre-pregnancy bmi


title: EXR-MBITZ1CTOT2SAMPB19A14-BS: CTOT04_02_Urine_19-14

value: TATCATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB19A13-BS: CTOT04_02_Urine_19-13

value: TAGAGTCGTATGCCGTCTTCTGCTTG


title: Placental tissue ID 1501

value: Placenta

tag: birth weight (gram)

tag: Sex

value: Male

tag: gestational age (month)

tag: ethnicity

value: 3 (3 children)


title: Chinese horse breeds_Series 214: JJ6

tag: gender

value: unknown

value: blood

tag: age

value: 3 years


title: Placental tissue ID 1445

value: Female

value: 0 (European)

tag: parity

value: 2 (2 children)

tag: maternal age (year)

tag: maternal smoking

value: 1 (stopped smoking before pregnancy)

tag: gestational weight gain (kilogram)

tag: gestational diabetes

tag: gestational hypertension


title: EXR-MBITZ1CTOT2SAMPB19A21-BS: CTOT04_02_Urine_19-21

tag: diagnosis

value: nephrotic syndrome

tag: tissue

value: urine

tag: condition

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

tag: 3' adapter sequence

value: TTGACTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB19A11-BS: CTOT04_02_Urine_19-11

value: Transplanted kidney present

value: Urinary system structure

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: Placental tissue ID 1469

value: Placenta

tag: labeling date

tag: hybridization date

tag: date delivery

tag: maternal pre-pregnancy bmi

tag: birth weight (gram)

tag: Sex

value: 1 (non-European)

value: 0 (never smoked)


title: Chinese horse breeds_Series 215: JJ7

tag: gender

value: unknown

tag: age


title: EXR-MBITZ1CTOT2SAMPB19A12-BS: CTOT04_02_Urine_19-12

value: TAATATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 213: JJ5

value: blood

value: 3 years


title: EXR-MBITZ1CTOT2SAMPB19A10-BS: CTOT04_02_Urine_19-10

value: TTAAGTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 212: JJ4


title: EXR-MBITZ1CTOT2SAMPB19A8-BS: CTOT04_02_Urine_19-8

value: TCTAGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB19A7-BS: CTOT04_02_Urine_19-7

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: Placental tissue ID 1429

value: Female

tag: gestational age (month)

tag: ethnicity

value: 0 (European)

tag: parity

value: 2 (2 children)

tag: maternal age (year)

tag: maternal smoking

tag: gestational weight gain (kilogram)


title: Placental tissue ID 1443

tag: tissue

value: 3 (3 children)

tag: gestational diabetes

tag: gestational hypertension


title: Chinese horse breeds_Series 210: ZT26

source_name: Zhaotong horse


title: EXR-MBITZ1CTOT2SAMPB19A4-BS: CTOT04_02_Urine_19-4

tag: diagnosis

value: nephrotic syndrome

value: urine

tag: condition

value: Transplanted kidney present

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

tag: 3' adapter sequence

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB19A2-BS: CTOT04_02_Urine_19-2

value: Urinary system structure

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: Placental tissue ID 1439

value: Placenta

tag: labeling date

tag: hybridization date

tag: date delivery

tag: maternal pre-pregnancy bmi

tag: birth weight (gram)

tag: Sex

value: 0 (never smoked)


title: EXR-MBITZ1CTOT2SAMPB19A5-BS: CTOT04_02_Urine_19-5

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: Placental tissue ID 1444

tag: gestational age (month)

tag: ethnicity

tag: parity

value: 1 (1 child)

tag: maternal age (year)


title: Placental tissue ID 1427

tag: tissue

value: Male

value: 1 (non-European)

tag: maternal smoking

tag: gestational weight gain (kilogram)

tag: gestational diabetes


title: Placental tissue ID 1428

value: 2 (smoked during pregnancy)

tag: gestational hypertension


title: Chinese horse breeds_Series 209: ZT13

tag: gender

value: unknown

value: blood

tag: age

value: 3 years


title: EXR-MBITZ1CTOT2SAMPB19A9-BS: CTOT04_02_Urine_19-9

tag: diagnosis

value: nephrotic syndrome

tag: condition

tag: anatomical location

tag: rna source

tag: 3' adapter sequence

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 211: JJ1


title: Chinese horse breeds_Series 208: ZT12


title: EXR-MBITZ1CTOT2SAMPB17A21-BS: CTOT04_02_Urine_17-21

value: urine

value: Transplanted kidney present

value: TTGACTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB17A20-BS: CTOT04_02_Urine_17-20

value: Urinary system structure

value: total cell-free biofluid RNA

value: TTCATTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB17A23-BS: CTOT04_02_Urine_17-23

value: TGTTATCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB17A22-BS: CTOT04_02_Urine_17-22

value: TTGTATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 207: ZT3


title: EXR-MBITZ1CTOT2SAMPB17A18-BS: CTOT04_02_Urine_17-18

value: TAGCCTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB17A17-BS: CTOT04_02_Urine_17-17

value: TACTCTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 206: ZT31


title: EXR-MBITZ1CTOT2SAMPB19A3-BS: CTOT04_02_Urine_19-3

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: Placental tissue ID 1424

value: Placenta

tag: labeling date

tag: hybridization date

tag: date delivery

tag: maternal pre-pregnancy bmi

tag: birth weight (gram)

tag: Sex

value: Male

value: 0 (European)

value: 3 (3 children)

value: 1 (stopped smoking before pregnancy)


title: EXR-MBITZ1CTOT2SAMPB17A19-BS: CTOT04_02_Urine_17-19

value: nephrotic syndrome

tag: tissue

value: TTATTTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB17A16-BS: CTOT04_02_Urine_17-16

value: urine

value: Transplanted kidney present

value: TTACATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 205: ZT6

value: unknown

value: blood

value: 3 years


title: EXR-MBITZ1CTOT2SAMPB17A15-BS: CTOT04_02_Urine_17-15

value: Urinary system structure

value: total cell-free biofluid RNA

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: Placental tissue ID 1423

tag: gestational age (month)

tag: ethnicity

tag: parity

value: 1 (1 child)

tag: maternal age (year)

tag: maternal smoking

tag: gestational weight gain (kilogram)


title: EXR-MBITZ1CTOT2SAMPB17A24-BS: CTOT04_02_Urine_17-24

tag: diagnosis

tag: condition

value: TGCCATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 204: ZT4

tag: gender

tag: age


title: EXR-MBITZ1CTOT2SAMPB17A14-BS: CTOT04_02_Urine_17-14

tag: anatomical location

tag: rna source

tag: 3' adapter sequence

value: TATCATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 203: ZT5


title: Placental tissue ID 1400

value: Placenta

tag: labeling date

tag: hybridization date

tag: date delivery

tag: maternal pre-pregnancy bmi

value: Male

value: 0 (European)

value: 0 (never smoked)

tag: gestational diabetes

tag: gestational hypertension


title: EXR-MBITZ1CTOT2SAMPB17A13-BS: CTOT04_02_Urine_17-13

value: nephrotic syndrome

tag: tissue

value: TAGAGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB17A12-BS: CTOT04_02_Urine_17-12

value: urine

value: Transplanted kidney present

value: TAATATCGTATGCCGTCTTCTGCTTG


title: Placental tissue ID 1409

tag: birth weight (gram)

tag: Sex

value: Female

tag: gestational age (month)

tag: ethnicity

tag: parity

tag: maternal age (year)

value: 1 (stopped smoking before pregnancy)


title: Placental tissue ID 1410

value: 2 (2 children)

tag: maternal smoking

tag: gestational weight gain (kilogram)


title: Chinese horse breeds_Series 202: ZT7

tag: gender

value: unknown

value: blood

tag: age

value: 3 years


title: EXR-MBITZ1CTOT2SAMPB17A11-BS: CTOT04_02_Urine_17-11

tag: diagnosis

tag: condition

tag: anatomical location

value: Urinary system structure

tag: rna source

value: total cell-free biofluid RNA

tag: 3' adapter sequence

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB17A10-BS: CTOT04_02_Urine_17-10

value: TTAAGTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 201: ZT22


title: EXR-MBITZ1CTOT2SAMPB17A9-BS: CTOT04_02_Urine_17-9

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB17A7-BS: CTOT04_02_Urine_17-7

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 200: ZT17


title: Placental tissue ID 1385

value: Placenta

tag: labeling date

tag: hybridization date

tag: date delivery

tag: maternal pre-pregnancy bmi

value: Male

value: 1 (non-European)

value: 3 (3 children)

value: 0 (never smoked)

tag: gestational diabetes

value: 1 (yes)

tag: gestational hypertension


title: EXR-MBITZ1CTOT2SAMPB17A6-BS: CTOT04_02_Urine_17-6

value: nephrotic syndrome

tag: tissue

value: urine

value: Transplanted kidney present

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: EXR-MBITZ1CTOT2SAMPB17A5-BS: CTOT04_02_Urine_17-5

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 199: ZT8

value: unknown

value: blood

value: 3 years


title: Placental tissue ID 1377

tag: birth weight (gram)

tag: Sex

tag: gestational age (month)

tag: ethnicity

value: 0 (European)

tag: parity

value: 2 (2 children)

tag: maternal age (year)