title: Sample_15_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_10_longRNA

status: Public on Sep 06 2019

type: SRA

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

country: USA

institute: Mount Sinai School of Medicine

description:
Sperm_RNAseq
RPKMgenomic.txt

library_source: transcriptomic

data_processing:
For long RNA samples, paired-end reads were trimmed of adaptors and low-quality bases using Trimmomatic (version 0.36) [217], using default parameters (2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15), and requiring a minimum read length of 50 bp (MINLEN:50). The TruSeq Universal adaptor (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) was used as input to Trimmomatic.
For long RNA samples, trimmed paired and unpaired reads were aligned to the consensus human ribosomal RNA (GenBank: U13369.1) using HISAT2 (version 2.0.6) and the non-default parameters (-p10 --max-seeds 30 -k 2), then aligned to the human genome (hg38) and exogenous RNA spike-in sequences, using the same HISAT2 parameters. Reads without alignments in either U13369.1, the human genome (hg38), or an exogenous RNA were further assessed for alignments to repeat sequences (RepBase, February 2017 release), using HISAT2, with the following parameters (-p10 --no-spliced-alignment --max-seeds 10 -k 3). Reads without alignments in either U13369.1, hg38, an exogenous RNA, or RepBase were aligned to bacterial and viral genomes using Kraken (version 0.10.5-beta) and Jellyfish (version 1.1.10), implementing the full Kraken library and filtering alignments with a threshold of 0.15. Read alignments to the human genome, exogenous RNAs, and U13369.1 were processed to remove duplicated reads using Picardtools MarkDuplicates (version 1.129).
For long RNA samples, RNA element (RE) discovery algorithm (REDa) was applied to genomic read alignments, and expression in Reads Per Kilobase per Million (RPKM) for the RE loci was calculated. Due to the use of REs, rather than whole transcripts, Paired-end read alignments were treated as individual (single) reads, and the common FPKM value was replace by RPKM. Depending on a read pair’s insert size and RE length, this approach ran the risk of inflating the read count for a given RE. To mitigate this risk, read counts were assessed for the forward and reverse reads separately, with the read count from single (non-paired due to mate loss during quality control) reads were added to the forward and reverse read counts. The averaged read count between the forward and reverse reads were then used for generating the RPKM values.
For small RNA libraries, reads were trimmed of adaptors and low-quality bases, followed by removal of reads smaller than 13 bp. sncRNAbench (version 10.14) was used for assigning reads to small RNA species and repeat classes, followed by a custom code for generating normalized expression values (RPM- Reads Per Million).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text files include RPKM values for long RNA libraries and RPM values for small RNA libraries

molecule: total RNA

organism: Homo sapiens

source_name: Ejaculated spermatozoa

extract_protocol:
Sperm samples were brought up to 1ml volume with PureSperm Buffer (Nidacon) and laid onto a 50% PureSperm (Nidacon) gradient, then centrifuged at 300xg for 20 minutes. The pellet was removed and washed in PureSperm Buffer. Each sample was added to a 2ml tube containing 500ul RLT buffer (Qiagen) with 7.5ul BME (14.3M), 100mg 0.2mm nuclease free SS beads. The sample were homogenized, 500ul Qiazol (Qiagen) added and homogenized again. 200ul chloroform (0.124M) was added and samples shaken by hand then centrifuged at 12,000xg for 20 minutes at 4⁰C and the upper aqueous layer removed. RNA was isolated from the aqueous layer using a customized Qiacube (Qiagen) protocol. RNA samples were treated with 4U Turbo DNase (Ambion) for 20 minutes at room temperature.  Samples were tested for DNA contamination by RT-PCR and intron spanning PRM1 primers. Samples still containing DNA were treated a second time and tested again by RT-PCR. The RNA samples void of DNA were quantified with a fluorescent assay as described. An aliquot of RNA (5 ng or 10 ng) of each sample was used to make cDNA with SuperScript III RT (Invitrogen). The cDNAs were used as template for RT-PCR with intron spanning PRM1 primers providing verification of RNA.
Two nanograms of RNA per sample was used with the Seqplex (Sigma-Aldrich) amplification kit prior to library construction. Fifty nanograms of Seqplex cDNA product was used with the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) to create sequencing libraries. Complete barcoded libraries were quantified and pooled for sequencing at a concentration of 2 nM per sample. All samples were subject to paired-end sequencing using either the NextSeq 500 (Illumina) sequencer, HiSeq 2500 (Illumina) sequencer or the HiSeq 4000 (Illumina) sequencer. One nanogram of small RNA per sample was used with the NEXTflex Small RNA-Seq Kit v2 (Bioo Scientific) to create sequencing libraries. Complete barcoded libraries were quantified and pooled for sequencing. Samples were subject to paired-end sequencing using the MiSeq (Illumina) sequencer.

tag: cell type

value: spermatozoa

tag: study subject

tag: visit number

tag: visit type

value: Crossover

tag: dbp level

tag: rna fraction

value: long RNA


title: Sample_4_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_7_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_8_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Baseline


title: Sample_2_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_1_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_20_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Crossback


title: 27_019_IL5

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description:
Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
Nelson_raw_counts.txt
Nelson_TPM.txt

data_processing:
RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg38
Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count

molecule: polyA RNA

source_name: Venous blood

growth_protocol: No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.

extract_protocol:
Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).

treatment_protocol: Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.

tag: tissue

value: Venous blood

value: Eosinophils

tag: stimulation


title: 28_019_GMCSF

value: GMCSF


title: 24_018_GMCSF


title: 26_019_IL3


title: Sample_14_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: 21_018_NegCtrl

value: NegCtrl


title: 19_002_IL5


title: 20_002_GMCSF


title: 23_018_IL5


title: V583 ΔtdcΔagdi (test) compared to V583 (reference) Replicate 2

type: RNA

city: Villaviciosa

first: Victor

last: Ladero

state: Select if applicable

address: Paseo Rio Linares S/N

department: Technology and Biotechnology of dairy products

country: Spain

institute: IPLA-CSIC

description: Biological replicate 2 of 2.

hyb_protocol: Nine hundred ng of DyLight 550- and nine hundred ng of DyLight 650-labelled cDNA were mixed and hybridized for 17 h at 60°C in the E. faecalis V583 DNA microarray using the In situ Hybridization Kit Plus, the Hybridization Gasket Slide and the Agilent G2534A Microarray Hybridization Chamber (Agilent Technologies). Slides were washed using the washing buffers indicated by the manufacturer.

scan_protocol: Microarrays were scanned using a GenePix 4200A Microarray Scanner (Molecular Devices, Sunnyvale, CA)

data_processing: Slide images were analyzed using GenePix Pro v.6.0 software. Background subtraction and LOWESS (locally weighted scatterplot smoothing) normalization were done using the standard routines provided by GENOME2D software available at http://server.molgenrug.nl/index.php/analysis-pipeline.

label: DyLigth 550

organism: Enterococcus faecalis

source_name: Enterococcus faecalis V583  delta-tdc delta-agdi

label_protocol: Total cDNA was synthesized from 20 µg of RNA using the SuperScript® III Reverse Transcriptase kit (Life Technologies, Bleiswijk, Netherlands). The cDNA was purified using the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nager, Landsmeer, The Netherlands) following the manufacturer instructions. Twenty µg of the purified cDNA was immediately labeled with DyLight 550 or DyLight 650 using the DyLight® Amine-Reactive Dyes kit (Thermo Scientific) as the manufacturer indicated. Quality and quantity of cDNA and DyLight 550 and DyLight 650 labelling were checked on a NanoDrop spectrophotometer (Thermo Scientific, Landsmeer, The Netherlands).

growth_protocol: Both strains E. faecalis V583 and E. faecalis V583 ΔtdcΔagdi were grown in 30 mL of M17 culture medium (Oxoid, UK) supplemented with 0.5% glucose (w/v) (GM17) for 7 h at 37°C without aereation. After a centrifugation at 16,000 x g for 1 min at 4˚C, the supernatants were discarded and cell pellets were frozen in liquid nitrogen and stored at -80°C.

extract_protocol: Cell pellets were resuspended in 400 µl of TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8.0) and 50 µl of 10% SDS, 500 µl of phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma-Aldrich), 500 mg of glass beads (75–150 µm) (Sigma-Aldrich), and 175 µl of Macaloid suspension (Bentone MA, Rheox Inc., Scotland, United Kingdom) were added. Cells were mechanically disrupted in a bead beater at 4˚C with two cycles of 60 s. During the shaking intervals the cells were kept on ice for 1 min. The samples were then centrifuged at 16,000 x g for 1 min at 4˚C. The upper phase was transferred to fresh tubes containing 500 µl chloroform: isoamyl alcohol (24:1) and centrifuged for 5 min at 4˚C. Total RNA was isolated with the High Pure RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany) following the instructions provided by the manufacturer. The concentration and quality of the RNA was determined on a NanoDrop spectrophotometer (Thermo Scientific, Landsmeer, The Netherlands).

tag: strain

value: V583  delta-tdc delta-agdi

tag: tyramine and putrescine producer

value: No

label: DyLigth 650

source_name: Enterococcus faecalis V583

value: Yes


title: 17_002_NegCtrl


title: 14_006_IL3


title: 18_002_IL3


title: 15_006_IL5


title: Sample_5_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: 16_006_GMCSF


title: Sample_3_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: 12_007_GMCSF


title: 13_006_NegCtrl


title: 25_019_NegCtrl


title: UMUC3_Vector

city: Wuhan

first: Feng

last: Liu

state: Hubei

address: Air Road 13

country: China

institute: Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Low-complexity or low-quality sequence of the original data were filtered to obtain high-quality clean data, which were then compared to the reference genome of human species to obtain comprehensive transcript information using bowtie v0.12.2.
We took RPKM (Reads per Kilobase per Million Reads) as A measure of gene expression (Mortazavi a. et al. 2008).
The differentially expressed genes were screened from the difference multiples and the significant levels. Here, we use the absolute value of logFC >1 and pvalue<0.05 as the standard to indicate that the gene is a differentially expressed gene.

source_name: UMUC3 cell in control group

growth_protocol: All the cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated from cell lines with RNeasy Mini kit (QIAGEN, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: T24T and UMUC3 cells was stably transfected with BCUC-1 overexpression plasmid or vector, respectively.

value: bladder cancer cell line

tag: cell line


title: Sample_87_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: UMUC3_BCUC-1

source_name: BCUC-1-overexpressed UMUC3 cell


title: T24T_Vector

source_name: T24T cell in control group


title: T24T_BCUC-1

source_name: BCUC-1-overexpressed T24T cell


title: 22_018_IL3


title: 10_007_IL3


title: Homo rep3

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Drive, MC 0412

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
STAR2.6.0a was used to align reads to the genome with default parameters
Kallisto0.44.0 was used to quantify transcripts abundance in terms of TPM
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values

organism: Mus musculus

source_name: Subcutaneous adipose tissue

extract_protocol:
subcutaneous adipose tissue was harvested,  frozen by liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Subcutaneous adipose tissue

tag: age

value: 24 weeks

tag: genotype

value: Homo KO


title: 09_007_NegCtrl


title: Homo rep2


title: neg_control_008


title: Hete rep2

value: Hete KO


title: Homo rep1


title: Hete rep1


title: Hete rep3


title: neg_control_005


title: WT rep1

value: WT


title: WT rep2


title: MF02

city: NanNing

first: Chen

last: Ying

address: Daxuedaling street, number 98

institute: Guangxi academy of science

description: transcriptome

data_processing:
Illumina Casava1.8 package was used for basecalling.
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: saccharomyces cerevisiae genome (ftp://ftp.ensembl.org/pub/release-85/gtf/saccharomyces_cerevisiae)
Supplementary_files_format_and_content: FPKM values for each Sample

organism: Saccharomyces cerevisiae

source_name: saccharomyces cerevisiae

extract_protocol:
Cells was collected, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ DNA Library Prep Kit for Illumina® was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: wild-type MF02

tag: condition

value: high glucose

tag: growth phase

value: mid-exponential


title: IL3_008


title: Sample_167_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

value: spermatozoa

value: Crossover

value: small RNA


title: IL5_008

value: Venous blood

value: Eosinophils


title: UV02_HG

description: transcriptome


title: WT rep3


title: 11_007_IL5


title: IL3_005


title: Sample_107_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Baseline

value: long RNA


title: Sample_166_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

value: Crossback


title: Sample_164_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_165_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: GMCSF_005

value: GMCSF


title: Sample_162_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_163_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_161_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_160_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: IL5_005


title: Sample_156_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_157_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: HGEP_3 H3K4me3 (biological replicate 2)

city: Buffalo

first: Michael

last: Buck

address: 701 Ellicott St

department: Biochemistry

institute: SUNY at Buffalo

description:
IPed DNA
Histone H3K4me3 IP from HGEP

library_source: genomic

data_processing:
Raw reads were analyzed for quality purposes with FASTQC (v 0.10.0
Aligned against the GRCh37 (hg19) reference genome with Bowtie (v 1.1.1) and default parameters except the option –m 1
Aligned reads were quality controlled by examining alignment statistics with SAMtools (v 0.1.19), generating cross-correlation plots with Phantompeakqualtools and filtering of duplicate reads with Picard tools
Genome_build: GRCh37
Supplementary_files_format_and_content: broadPeak

molecule: genomic DNA

source_name: cultured cells

growth_protocol: The established human HNSCC epithelial oral cell line SCC25 (HPV-) and the primary human gingival epithelial cell line HGEP (single donor) were used in all experiments. SCC25 was purchased from American Type Culture Collection (ATCC® CRL-1628TM, Manassas, VA) and HGEP was purchased from CELLnTEC (Switzerland) and used as the healthy control in our experiments. SCC25 was grown in Dulbecco Modified Eagle Medium/F12 (1:1) supplemented with 10% fetal bovine serum (GIBCO, Life Technologies), 1% penicillin/streptomycin (100 IU/ml) (GIBCO, Life Technologies), and 400 ng/ml hydrocortisone (Sigma) at 37°C in an atmosphere of 5% CO2. HGEP cells were grown in CnT-24 media. Cells were harvested upon reaching 80% confluence using 0.25% trypsin-EDTA (GIBCO, Life Technologies).

extract_protocol:
SCC25 and HGEP cells were fixed with 1% formaldehyde for 10 min. For histone ChIP-seq we used the Chromatin Shearing Optimization Kit-Low SDS (Diagenode) with 10 million cells per cell line and 40 cycles sonication (30 sec ON, 30 sec OFF, High) in the Bioruptor Plus (Diagenode). After RNase and proteinase K incubation, chromatin shearing was confirmed as a DNA smear between 100-300 bp on a 1.5% agarose gel. Histone ChIP DNA was prepared with the Auto Histone ChIP-seq kit protein G Kit (Diagenode), with 3 μg H3K4me1, 2 μg H3K4me3, 2.4 μg H3K27ac, 2 μg H3K27me3 and 2.4 μg H3K36me3 premium polyclonal antibody (Diagenode) per 1 million cells with the SX-8G IP-Star® Compact System (Diagenode). 1% input sample for each cell line was used as a control for background experimental noise.
ChIP and input DNA were quantified with the Quant-iT PicoGreen ds DNA Assay Kit (Invitrogen). ChIP-seq libraries were made with the ThruPLEXTM-FD Prep Kit (Rubicon Genomics), purified and size-selected with a 2% agarose Pippin cassette (Sage Science). Libraries were quantified with the Quant-iT PicoGreen ds DNA Assay Kit (Invitrogen) and the KAPA Library Quantification Kit (Kapa Biosystems). Quality control was performed with the Agilent Technologies 2100 Bioanalyzer. Libraries were normalized based on qPCR and pooled with the TruSeq SR Cluster Kit v3-cBot-HS (Illumina). Pooled samples were multiplexed and sequenced with the HiSeq 2500 v3 (Illumina).

value: HGEP

tag: experiment type

value: ChIP-seq

tag: ip-target


title: Sample_155_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: cell type

tag: study subject


title: Sample_154_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: visit number

tag: visit type


title: Sample_153_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: dbp level

tag: rna fraction


title: HGEP_3 Input (biological replicate 2)

description:
Input DNA
Input for IP experiments

value: primary human gingival epithelial cell line

value: Input


title: GMCSF_008

tag: tissue

tag: stimulation


title: HGEP_3 H3K27me3 (biological replicate 2)

description:
IPed DNA
Histone H3K27me3 IP from HGEP


title: HGEP_3 H3K36me3 (biological replicate 2)

description:
IPed DNA
Histone H3K36me3 IP from HGEP


title: Sample_148_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_150_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_152_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: HGEP_3 H3K4me1 (biological replicate 2)

description:
IPed DNA
Histone H3K4me1 IP from HGEP


title: Sample_149_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_145_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: HGEP_3 H3K27ac (biological replicate 2)

description:
IPed DNA
Histone H3K27ac IP from HGEP


title: Sample_144_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_146_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_143_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_158_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_159_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_140_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: HGEP_2 H3K27me3 (biological replicate 1)

description:
IPed DNA
Histone H3K27me3 IP from HGEP


title: HGEP_2 H3K36me3 (biological replicate 1)

description:
IPed DNA
Histone H3K36me3 IP from HGEP


title: Sample_138_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: HGEP_3mock_rabbit IgG (biological replicate 2)

description:
Mock DNA
Mock IP from HGEP

value: rabbit IgG


title: Sample_136_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: HGEP_2 mock_rabbit IgG (biological replicate 1)

description:
Mock DNA
Mock IP from HGEP

value: mock_rabbit IgG


title: Sample_126_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: HGEP_2 H3K27ac (biological replicate 1)

description:
IPed DNA
Histone H3K27ac IP from HGEP


title: Sample_118_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_119_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_142_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_133_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: HGEP_2 Input (biological replicate 1)

description:
Input DNA
Input for IP experiments


title: Sample_132_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_141_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_134_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: HGEP_2 H3K4me3 (biological replicate 1)

description:
IPed DNA
Histone H3K4me3 IP from HGEP


title: HGEP_2 H3K4me1 (biological replicate 1)

description:
IPed DNA
Histone H3K4me1 IP from HGEP


title: Sample_125_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_117_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_121_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: SCC25_2 Input (biological replicate 2)

description:
Input DNA
Input for IP experiments

value: head and neck sequamous cell carcinoma cell line


title: SCC25_2 H3K27me3 (biological replicate 2)

description:
IPed DNA
Histone H3K27me3 IP from SCC25


title: SCC25_2 H3K36me3 (biological replicate 2)

description:
IPed DNA
Histone H3K36me3 IP from SCC25


title: SCC25_2 mock_rabbit IgG (biological replicate 2)

description:
Mock DNA
Mock IP from SCC25


title: Sample_114_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: SCC25_2 H3K4me3 (biological replicate 2)

description:
IPed DNA
Histone H3K4me3 IP from SCC25


title: Sample_112_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: SCC25_2 H3K4me1 (biological replicate 2)

description:
IPed DNA
Histone H3K4me1 IP from SCC25


title: Cxcl12CE_D7_ABL#2

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

description: FACS-sorted at 7 days after bone marrow ablation

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1000 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Genome_build: mm10_trans_nono
Supplementary_files_format_and_content: raw_feature_bc_matrix/barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz

source_name: Femurs

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. 6,500~14,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v2 (Sample_114020/114021) or v3 (Sample_137724/137725)
10X Genomic Chromium Single Cell 3' v2 (Sample_114020/114021) or v3 (Sample_137724/137725) Libraries

value: Cxcl12-iCreER; R26R(tdTomato/+)

tag: cells

value: tdTomato+ bone marrow mesenchymal cells

tag: treatment

value: 7 days after bone marrow ablation, tamoxifen injection at 7 days before ablation


title: Cxcl12CE_D7_CONT#2


title: Sample_115_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

value: spermatozoa

value: small RNA


title: SCC25_1 Input (biological replicate 1)

description:
Input DNA
Input for IP experiments

tag: cell line


title: pr2_sp2: ovary_primary vs spheroid_2

city: Seongnam-si

first: Hyun

last: Park

address: Bundang-gu, Yatap-dong

department: Obstetrics and Gynecology

country: South Korea

institute: CHA university, CHA Bundang Medical Center

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

source_name: ovarian high grade serous adenocarcinoma

label_protocol: 25ng of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: Serum-free DMEM/F12 medium supplemented with 20 ng/ml epidermal growth factor,10 ng/ml basic fibroblast growth factor, 0.4% bovine serum albumin, and 5 µg/mL insulin.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: isolated spheroid-forming cell

value: primary ovarian cancer cell


title: pr3_sp3: ovary_primary vs spheroid_4


title: Sample_111_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: miR-455-3p rep3

city: Tianjin

first: Yan

last: Wang

address: #22 Qixiangtai Road

department: Department of Biochemistry and Molecular Biology

institute: Tianjin Medical University

data_processing:
SOAPnuke (version: v1.5.2) was used for filter reads, parameters: -1 15 -q 0.5 -n 0.1.
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
HISAT (version: v2.0.4) was used to align clean reads to the mouse genome, parameters: -p 8 --phred64 --sensitive -I 1 -X 10000.
RSEM (version: v1.2.12) was used for abundance measurement, parameters: default.
FPKM method was used in calculated expression level.
Genome_build: hg 19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Human breast cancer cell line

growth_protocol: MCF-7 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol:
Total RNA was extracted from the MCF-7 cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: miRNA was transfected into MCF-7 cells using Lipofectamine RNAiMAX (Invitrogen).

value: MiR-455-3p mimics


title: Sample_107_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

value: Baseline


title: Sample_109_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

value: Crossover


title: SCC25_2 H3K27ac (biological replicate 2)

description:
IPed DNA
Histone H3K27ac IP from SCC25


title: SCC25_1 H3K27me3 (biological replicate 1)

description:
IPed DNA
Histone H3K27me3 IP from SCC25


title: Sample_110_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_105_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: SCC25_1 H3K36me3 (biological replicate 1)

description:
IPed DNA
Histone H3K36me3 IP from SCC25


title: miR-455-3p rep1


title: Cxcl12GFPCxcl12CE#1

description: FACS-sorted at P28

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~18,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v3
10X Genomic Chromium Single Cell 3' v3 Libraries

tag: genotype

value: GFP+ bone marrow mesenchymal cells

value: Postnatal day 28, tamoxifen injection at P21


title: Cxcl12GFPCxcl12CE#2

description: FACS-sorted at P28


title: SCC25_1 mock_rabbit IgG (biological replicate 1)

description:
Mock DNA
Mock IP from SCC25

value: ChIP-seq


title: Patient 1 Scar

city: Crawley

first: Andrew

middle: William

last: Stevenson

state: Western Australia

address: Room 112b, Curnow Building, Hackett Drive Carpark Entrance 2, UWA

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

description: Gene expression data from normal human scar dermal fibroblasts cultured to passage 2

hyb_protocol: Following fragmentation, cRNAs were hybridized for 16 hr at 45C on HuGene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Processing of the data was carried out using the statistical software R (Team, 2015) and the Oligo and Limma packages (Carvalho and Irizarry, 2010, Smyth, 2004). Data was imported from .CEL files using Oligo and then normalised and corrected for background. Gene expression levels were calculated using the Robust Multichip Average (RMA) function of the Limma package. Samples were compared pairwise using a moderated paired t-test from the linear model, using a 5% false discovery rate (FDR) with a Benjamini-Hochtberg (B-H) correction for multiple testing (Benjamini and Hochberg, 1995)

label: Biotin

source_name: Patient 1 Scar

label_protocol: Biotinylated cRNA was prepared using the GeneChip™ WT Terminal Labeling Kit as per manufacturer's instructions

growth_protocol: 3mm punch biopsies were taken from the forearm scar site and a matched site on the uninjured forearm by the attendant physician. Tissue was transported to the lab where it was placed in a petri dish and sliced into three equal sized potions. Pieces of the biopsy were then placed dermis side down in a T-25 (25 cm2) (Greiner Bio-One, Germany) culture flask without any media, and a drop of 100% foetal bovine serum (FBS) added to the surface of each piece. They were then cultured in DMEM with 10% FBS and 5% pen/strep until passage 2, at which point DNA and RNA was extracted.

extract_protocol: RNA was prepared using the RNeasy mini kit (Cat. No. 74104, QIAGEN, Netherlands), as per manufacturer's instructions

treatment_protocol: There were no treatments applied to the scar and control cells

tag: individual

value: Patient 1

tag: Sex

value: Male

tag: age (years)

tag: time since injury (years)


title: Patient 4 Scar

source_name: Patient 4 Scar

value: Patient 4

value: normal human scar dermal fibroblasts cultured to passage 2


title: Patient 6 Scar

source_name: Patient 6 Scar

value: Patient 6


title: pr1_sp1: ovary_primary vs spheroid_1


title: miR-455-3p rep2


title: Control rep3

value: control


title: Sample_99_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

source_name: Ejaculated spermatozoa


title: SCC25_1 H3K4me3 (biological replicate 1)

description:
IPed DNA
Histone H3K4me3 IP from SCC25

value: head and neck sequamous cell carcinoma cell line

tag: experiment type

tag: ip-target


title: Patient 2 Scar

source_name: Patient 2 Scar

value: Patient 2

tag: cell type


title: Control rep2


title: Sample_97_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

value: spermatozoa

tag: study subject

tag: visit number

value: Crossback

value: small RNA


title: Control rep1


title: Patient 5 Scar

source_name: Patient 5 Scar

value: Patient 5


title: pr5_sp5: ovary_primary vs spheroid_3

value: isolated spheroid-forming cell

value: primary ovarian cancer cell


title: Sample_89_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: visit type

value: Crossover

tag: dbp level


title: SCC25_1 H3K27ac (biological replicate 1)

description:
IPed DNA
Histone H3K27ac IP from SCC25


title: Patient 3 Scar

source_name: Patient 3 Scar

value: Patient 3


title: Sample_91_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: rna fraction


title: Patient 6 Control

description: Gene expression data from normal human dermal fibroblasts cultured to passage 2

source_name: Patient 6 Control


title: SCC25_1 H3K4me1 (biological replicate 1)

description:
IPed DNA
Histone H3K4me1 IP from SCC25

value: ChIP-seq


title: Sample_86_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

value: Baseline


title: Sorted SOX17/GFP- cells

city: NEW YORK

first: Qing

last: Li

address: 1275 YORK AVE

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Library strategy: Amplicon Sequencing
Raw FASTQ files demultiplexed by MSKCC IGO were further processed to contain only the unique gRNA sequences, and the processed reads were aligned to the designed gRNA sequences from the library using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
The read counts were further normalized to total reads of that sample to offset differences in Hi-Seq depth.
Genome_build: GECKO v2 library B (Addgene, 1000000049)

source_name: HUES8 human embryonic stem cells (hESCs)

growth_protocol: Undifferentiated human ES and iPS cells were maintained in the chemically defined feeder-free E8 condition (Thermo Fisher Scientific, A1517001) at 37oC with 5% CO2, and routinely confirmed to be mycoplasma-free by the MSKCC Antibody and Bioresource Core Facility.

extract_protocol:
SOX17GFP+ and SOX17GFP- cells are sorted by fluorescence activated cell sorting. Genmoic DNA were extracted by using Qiagen Maxi Kit (Qiagen 13362)
A two-step PCR method was performed to amplify the gRNA sequence for Hi-Seq. For the first step, 380 _g of DNA per sample (6.6 _g of genomic DNA per 1 million cells) was used to perform PCR using Herculase II fusion DNA polymerase (Agilent, 600679) in order to achieve a 1,000-fold converge of the GECKO library containing 58,028 gRNAs. In total, we performed 38 separate 100 _l reaction with 10 _g genomic DNA per sample for 18 cycles and combined the resulting amplicons. For the second step, 5 _l of the product from the first PCR was used in a 100 _l PCR reaction for 24 cycles with primers to attach Illumina adaptors for barcoding. Gel purified amplicons from the second PCR were quantified, mixed and sequenced using a HiSeq 2500 (Illumina) at MKSCC Integrated Genomics Operation (IGO).

treatment_protocol: Human ES or iPS cells were cultured in E8 medium and routinely passaged by EDTA. When cells reached 80-90% confluence, cells were treated with TrypLE Select to dissociate them as single cells for passaging. Typically, 0.15 million human ES or iPS cells were plated in one well of the six-well plates with 10 μM ROCK inhibitor in 2 ml E8 media. 24 hours later, cells were washed with PBS once and culture medium was changed to Advanced RPMI (Thermo Fisher Scientific, 12633012) with penicillin/streptomycin (Thermo Fisher Scientific, 15070063), GlutaMAX (Thermo Fisher Scientific, 35050079), 0.003% BSA (Thermo Fisher Scientific, 15260037), 5 μM CHIR-99021 (Tocris, 4423) and 100 ng/ml Activin A (PeperoTech ,12014E). Over the next 2 days, culture medium was changed to Advanced RPMI with penicillin/streptomycin, GlutaMAX, 0.2% FBS and 100 ng/ml Activin A.

tag: genotype/variation

value: SOX17-GFP knockin


title: Sample_83_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sorted SOX17/GFP+ cells


title: 48h rep2

data_processing:
STAR2.6.0a was used to align reads to the genome with default parameters
Kallisto0.44.0 was used to quantify transcripts abundance in terms of TPM
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values

source_name: Human microvascular endothelial cells

growth_protocol: cells were cultured in human microvascular endothelial growth media (Cell Applications, Inc

extract_protocol:
phenol-chloroform (RNA grade)
RNA underwent reverse transcription, cDNA size selection, circularization, linearization, and library amplification.

treatment_protocol: Cells were cultured under or 2% oxygen at 37C for 0 12, 24, and 48hr.

tag: time point

tag: condition

value: hypoxia

value: Passage 3-4


title: Cxcl12CE_D7_ABL#1

value: Cxcl12-iCreER; R26R(tdTomato/+)

tag: cells

value: tdTomato+ bone marrow mesenchymal cells

tag: treatment

value: 7 days after bone marrow ablation, tamoxifen injection at 7 days before ablation


title: Sample_81_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: 48h rep1

tag: genotype


title: Sample_80_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: JRY11540 (DSSY347), native MNase-seq

city: Berkeley

first: Daniel

last: Saxton

state: CA

address: 100 University Ave

department: MCB

institute: University of California Berkeley

data_processing:
Basecalls and alignment performed using Bowtie2
Python was used to:
eliminate reads less than 140bp and greater than 180bp in length
plot midpoints of reads
use a 25bp rolling mean to smooth out resulting peaks
Genome_build: S. cerevisiae S288C Genome (Genbank Accession number GCA_000146045.2)
Supplementary_files_format_and_content: Tab-delimited .txt file

growth_protocol: Grown in CSM overnight, then to log phase over the course of 4 hours.

extract_protocol:
Cells were spheroplasted and nuclei were purified. Nuclei were treated with Mnase.
Libraries were prepared with NEBnext UltraII library preparation kit.

tag: hml genotype

value: hml∆

tag: hmr genotype

value: HMRα, hmrα2∆::CRE (N7)


title: JRY11536 (DSSY343), native MNase-seq

value: HMRα, hmrα2∆::CRE (N9)


title: JRY11259 (DSSY66), native MNase-seq

value: hmlα2∆::Cre (N22)

value: hmr∆


title: JRY11538 (DSSY345), native MNase-seq

value: HMRα, hmrα2∆::CRE (N12)


title: Cxcl12CE_D7_CONT#1


title: 24h rep1


title: Patient 3 Control

source_name: Patient 3 Control

tag: individual

tag: Sex

value: Male

tag: age (years)

tag: time since injury (years)

value: normal human dermal fibroblasts cultured to passage 2


title: Patient 4 Control

source_name: Patient 4 Control

value: Patient 4

tag: cell type


title: Sample_65_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

value: spermatozoa

tag: study subject

tag: visit number

value: Crossover

value: small RNA


title: 12h rep2

value: hypoxia


title: Sample_68_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: visit type

tag: dbp level


title: 24h rep2

value: Passage 3-4


title: Patient 1 Control

source_name: Patient 1 Control

value: Patient 1


title: Cxcl12CE_D14

description: FACS-sorted at 14 days after bone marrow ablation

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 500 genes per cell and with more than 20% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Genome_build: mm10_trans_nono
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. 6,500~14,000 cells cells were loaded onto 10X Genomic Chromium Single Cell Solution v2 (Sample_114020/114021) or v3 (Sample_137724/137725)
10X Genomic Chromium Single Cell 3' v2 Libraries

value: Cxcl12-iCreER; R26R(tdTomato/+)

value: tdTomato+ bone marrow mesenchymal cells

value: 14 days after bone marrow ablation, tamoxifen injection at 7 days before ablation


title: Patient 2 Control

source_name: Patient 2 Control

value: Patient 2


title: Patient 5 Control

source_name: Patient 5 Control

value: Patient 5


title: JRY11471 (DSSY278), native MNase-seq

value: hml∆

value: HMRα, hmrα2∆::CRE (N14)


title: 12h rep1


title: 0h rep2


title: Sample_61_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: rna fraction


title: Sample_59_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

value: Baseline


title: 0h rep1

tag: time point


title: Blood_trained_A2_1_90_rep1

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

description: blood-borne miRNA sequencing

hyb_protocol: Agilent protocols.

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

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil-normalized and log2 transformed.

label: Cyanine 3

source_name: Peripheral blood, trained, A2, 1_90, replicate 1

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

extract_protocol: Whole blood samples were collected in PAXGene Blood RNA Tubes (BD Biosciences). Total RNA including miRNAs was isolated using the PAXGene Blood miRNA kit (Qiagen) according to manufacturers recommendations.

tag: tissue

value: whole blood

tag: gender

value: female

tag: age

tag: participant

tag: timepoint

tag: rin-value

tag: cho-first-round(y/n)

value: y


title: Blood_untrained_E2_1_89_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_89, replicate 1


title: Blood_trained_A1_1_88_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_88, replicate 1


title: Blood_untrained_E1_1_87_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_87, replicate 1


title: Sample_62_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

extract_protocol:
Sperm samples were brought up to 1ml volume with PureSperm Buffer (Nidacon) and laid onto a 50% PureSperm (Nidacon) gradient, then centrifuged at 300xg for 20 minutes. The pellet was removed and washed in PureSperm Buffer. Each sample was added to a 2ml tube containing 500ul RLT buffer (Qiagen) with 7.5ul BME (14.3M), 100mg 0.2mm nuclease free SS beads. The sample were homogenized, 500ul Qiazol (Qiagen) added and homogenized again. 200ul chloroform (0.124M) was added and samples shaken by hand then centrifuged at 12,000xg for 20 minutes at 4⁰C and the upper aqueous layer removed. RNA was isolated from the aqueous layer using a customized Qiacube (Qiagen) protocol. RNA samples were treated with 4U Turbo DNase (Ambion) for 20 minutes at room temperature.  Samples were tested for DNA contamination by RT-PCR and intron spanning PRM1 primers. Samples still containing DNA were treated a second time and tested again by RT-PCR. The RNA samples void of DNA were quantified with a fluorescent assay as described. An aliquot of RNA (5 ng or 10 ng) of each sample was used to make cDNA with SuperScript III RT (Invitrogen). The cDNAs were used as template for RT-PCR with intron spanning PRM1 primers providing verification of RNA.
Two nanograms of RNA per sample was used with the Seqplex (Sigma-Aldrich) amplification kit prior to library construction. Fifty nanograms of Seqplex cDNA product was used with the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) to create sequencing libraries. Complete barcoded libraries were quantified and pooled for sequencing at a concentration of 2 nM per sample. All samples were subject to paired-end sequencing using either the NextSeq 500 (Illumina) sequencer, HiSeq 2500 (Illumina) sequencer or the HiSeq 4000 (Illumina) sequencer. One nanogram of small RNA per sample was used with the NEXTflex Small RNA-Seq Kit v2 (Bioo Scientific) to create sequencing libraries. Complete barcoded libraries were quantified and pooled for sequencing. Samples were subject to paired-end sequencing using the MiSeq (Illumina) sequencer.

value: spermatozoa

value: Crossback


title: Normoxia-2

data_processing:
CLIPSeqTool0.1.8 was used to trim the adapaters, align the reads to the genome and perform deduplications
Kallisto0.44.0 was used to quantify transcripts abundance in terms of TPM
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values

growth_protocol: cells were cultured in human microvascular endothelial growth media (Cell Applications, Inc)

treatment_protocol: Cells were cultured under 20% oxygen (with 5% CO2) or 2% oxygen at 37C for 12, 24, and 48hr.

tag: condition

value: Normoxia

tag: antibody

tag: passage


title: Normoxia-1


title: Sample_57_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

data_processing:
For long RNA samples, paired-end reads were trimmed of adaptors and low-quality bases using Trimmomatic (version 0.36) [217], using default parameters (2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15), and requiring a minimum read length of 50 bp (MINLEN:50). The TruSeq Universal adaptor (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) was used as input to Trimmomatic.
For long RNA samples, trimmed paired and unpaired reads were aligned to the consensus human ribosomal RNA (GenBank: U13369.1) using HISAT2 (version 2.0.6) and the non-default parameters (-p10 --max-seeds 30 -k 2), then aligned to the human genome (hg38) and exogenous RNA spike-in sequences, using the same HISAT2 parameters. Reads without alignments in either U13369.1, the human genome (hg38), or an exogenous RNA were further assessed for alignments to repeat sequences (RepBase, February 2017 release), using HISAT2, with the following parameters (-p10 --no-spliced-alignment --max-seeds 10 -k 3). Reads without alignments in either U13369.1, hg38, an exogenous RNA, or RepBase were aligned to bacterial and viral genomes using Kraken (version 0.10.5-beta) and Jellyfish (version 1.1.10), implementing the full Kraken library and filtering alignments with a threshold of 0.15. Read alignments to the human genome, exogenous RNAs, and U13369.1 were processed to remove duplicated reads using Picardtools MarkDuplicates (version 1.129).
For long RNA samples, RNA element (RE) discovery algorithm (REDa) was applied to genomic read alignments, and expression in Reads Per Kilobase per Million (RPKM) for the RE loci was calculated. Due to the use of REs, rather than whole transcripts, Paired-end read alignments were treated as individual (single) reads, and the common FPKM value was replace by RPKM. Depending on a read pair’s insert size and RE length, this approach ran the risk of inflating the read count for a given RE. To mitigate this risk, read counts were assessed for the forward and reverse reads separately, with the read count from single (non-paired due to mate loss during quality control) reads were added to the forward and reverse read counts. The averaged read count between the forward and reverse reads were then used for generating the RPKM values.
For small RNA libraries, reads were trimmed of adaptors and low-quality bases, followed by removal of reads smaller than 13 bp. sncRNAbench (version 10.14) was used for assigning reads to small RNA species and repeat classes, followed by a custom code for generating normalized expression values (RPM- Reads Per Million).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text files include RPKM values for long RNA libraries and RPM values for small RNA libraries

tag: cell type

value: Crossover

value: small RNA


title: Hypoxia-1

value: Hypoxia

value: Passage 3-4


title: Sample_55_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: study subject


title: Sample_58_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: visit number


title: Blood_trained_A2_1_86_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_86, replicate 1

value: male

value: n


title: Hypoxia-2


title: Blood_untrained_E2_1_85_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_85, replicate 1


title: Blood_trained_A1_1_84_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_84, replicate 1


title: Sample_51_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

source_name: Ejaculated spermatozoa

tag: visit type


title: Sample_47_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: dbp level


title: Blood_untrained_E2_1_79_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_79, replicate 1


title: Blood_untrained_E1_1_83_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_83, replicate 1


title: Blood_untrained_E1_1_80_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_80, replicate 1


title: Blood_untrained_E2_1_82_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_82, replicate 1


title: Blood_trained_A1_1_81_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_81, replicate 1


title: Sample_48_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: rna fraction


title: Sample_42_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Cancer_Stem_cell_4T1_S

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

country: Japan

institute: kyushu university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: cancer stem cell, 4T1, S

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Non treatment cultured cell

extract_protocol: The total RNA was isolated from cells using ReliaPrep TM  RNA Cell Miniprep System (Promega) according to the manufacturer's instructions.

treatment_protocol: Non treatment cultured cell

tag: strain

value: BALB/C

tag: cell

value: cancer stem cell


title: Anti_Cancer_Stem_cell_4T1_NS

source_name: anti cancer stem cell, 4T1, NS

value: anti cancer stem cell


title: Sample_35_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Wild-type IL-4

city: Shanghai

first: Tao

last: Yu

state: Shanghai

address: 320 Yueyang Road

institute: Chinese Academy of Science

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (GRCm38/mm10) using Bowtie.
Gene expression levels were quantified using the RSEM software package.
Differentially expressed genes were subsequently analyzed using the DAVID bioinformatics platformand IPA and GraphPad.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data were txt format and all gene FPKM of each sample were contained in each txt file.

source_name: Peritoneal macrophage

growth_protocol: 4% thioglycolate was intraperitoneally injected into wild-type and TIF1a myliod-cells-conditional deficient mice, 4 days later, mice were sacrificed, and the peritoneal cavity was lavaged with DMEM medium. Macrophages were allowed to adhere for 4 h, washed with fresh medium to remove unattached cells and starved with DMEM containing 0.5% FBS.

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Nontreat or stimulated with mouse IL-4(20ng/mL) for 6 h.

tag: genotype

value: Wild-type

tag: treatment

value: Stimulated with IL-4 for 6h


title: Blood_trained_A1_1_78_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_78, replicate 1

tag: tissue

value: whole blood

tag: gender

tag: age

tag: participant


title: Sample_33_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_46_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

value: Baseline


title: FRC_Stim2

city: Boston

first: Kevin

last: Bi

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: Following labeling, biotinylated cRNA was hybridized to the Mouse Genome 430 2.0 GeneChips® for 16 hr at 45C in an Affymetrix HybridizationOven 645. GeneChips® were washed and stained in the Affymetrix Fluidics Station 450 using the GeneChip® Hybridization, Wash, and Stain Kit.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Fibroblastic Reticular Cells (FRCs)

label_protocol: The targets were prepared using the NuGeN Ovation® RNA Amplification System V2 assay and labeled using the NuGEN Encore® Biotin Module. The Ovation kit generates DNA/RNA heteroduplexes and uses SPIA® Amplification to create cDNA.

growth_protocol: In vitro expanded FRCs were cultured alone or with splenocytes activated with soluble antibody (0.25μg/ml) against CD3 (anti-CD3) and anti-CD28 for 16 hours.

extract_protocol: RNA was isolated from cell pellets using the Qiagen RNeasy Mini kit according to the manufacturer’s instructions. Extracted RNA was amplified and prepared for hybridization to the Mouse Genome 430 2.0 GeneChip using the Ovation RNA Amplification System V2 Assay in accordance with manufacturer’s instructions.

treatment_protocol: FRCs were briefly trypsinized and sorted from cultures as previously described (Malhotra et al., Nature Immunology, 2012)

value: Fibroblastic Reticular Cells (FRCs)

value: cultured with activated splenocytes for 16 hours


title: FRC_Stim1


title: TIF1a-KO IL-4


title: TIF1a-KO nontreat


title: FRC_1

value: cultured alone for 16 hours


title: FRC_2


title: Blood_trained_A2_1_75_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_75, replicate 1

tag: timepoint

tag: rin-value

tag: cho-first-round(y/n)


title: TK6 cells, microgravity + ionizing radiation

city: Beijing

first: Changhui

last: Ge

email: chge502@163.com, chge88@sina.com

address: 27 Taiping Rd., Haidian Dist.

department: Department of Experimental Hematology and Biochemistry

institute: Beijing institute of Radiation Medicine

description: miRNA, lncRNA and mRNA expression data from human lymphoblastoid TK6 cells cultured for 24 hours in in simulated microgravity condition after ionizing radiation.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization,Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization   Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station  450 (Cat#00‐0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s  instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00‐00212, Affymetrix,  Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA,  US) with default settings.

data_processing: Raw data were normalized by Expression console.

source_name: Human lymphoblastoid TK6 cells cultured for 24 hours in simulated microgravity condition after ionizing radiation

label_protocol: Total RNA were amplified, labeled and purified by using Ambion WT Expression   Kit (Cat#411973, Ambion, US) and GeneChip WT Terminal Labeling Kit (Cat#900671,  Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain  biotin labeled cDNA.

growth_protocol: Human lymphoblastoid TK6 cells were incubated in RPMI-1640 medium supplemented with 10% fetal bovine serum and maintained in 5% CO2 at 37 °C.

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

treatment_protocol: The cells were cultured for 24 h in static condition without (Control) or with irradiation (IR), rotating condition to simulate microgravity in space using Rotary Cell Culture Systems (Synthecon, Houston, TX, US), or rotating condition after irradiation with 2 Gy γ-rays (MG + IR). IR was performed using a Co60 gamma-ray source (Beijing Institute of Radiation Medicine, Beijing, China) with a total dose of 2 Gy at a dose rate of 128.67 cGy/min.

value: spleen, lymphoblast

value: 5 years


title: Sample_56_shortRNA

city: New York

first: Molly

last: Estill

address: 1 Gustave L. Levy Place

institute: Mount Sinai School of Medicine

description:
Sperm_RNAseq
sRNA_expression.txt

tag: cell type

value: spermatozoa

value: small RNA


title: Sample_24_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: study subject


title: Sample_18_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: visit number

value: Crossover


title: Blood_untrained_E1_1_72_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_72, replicate 1

value: male


title: Blood_trained_A1_1_73_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_73, replicate 1

value: n


title: Sample_54_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

tag: visit type


title: Blood_trained_A2_1_76_rep2

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_76, replicate 2


title: sp3: ovary_spheroid_3

description: miRNA expression of spheroid-forming cell

hyb_protocol: desalted labeled RNA were hybridized to the Agilent miRNA expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: spheroid-forming cell, cultured for 8 days

label_protocol: Desalted Labeled RNA were prepared from 100ng total RNA Agilent’s miRNA Complete Labeling and Hyb Kit

value: ovarian adenocarcinoma

tag: type

value: high grade serous


title: Blood_untrained_E2_1_74_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_74, replicate 1


title: sp4: ovary_spheroid_4

source_name: spheroid-forming cell, cultured for 9 days


title: Sample_32_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

source_name: Ejaculated spermatozoa

value: Crossback

tag: dbp level

tag: rna fraction


title: Blood_untrained_E1_1_77_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_77, replicate 1


title: sp2: ovary_spheroid_1

source_name: spheroid-forming cell, cultured for 6 days


title: Blood_trained_A2_1_71_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_71, replicate 1

value: female

value: y


title: Blood_untrained_E2_1_70_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_70, replicate 1

value: whole blood


title: Sample_29_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt

value: Baseline


title: WT IL-4

description: IL-4 6h

source_name: Peritoneal macrophages

growth_protocol: 4% thioglycolate was intraperitoneally injected into WT and Trim24 myliod-cells-conditional deficient mice, 4-5 days later, mice were sacrificed, and the peritoneal cavity was lavaged with DMEM medium. Macrophages were allowed to adhere for 4 h, washed with fresh medium to remove unattached cells and starved with DMEM containing with 0.5%FBS.

treatment_protocol: non-treated (NT) or stimulated for 6 h with mouse IL-4

tag: strain

value: wild type

value: bone marrow


title: Distal lung cells

city: London

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
cellranger count (v2.1.1)
Filtering and re-clustering using the Monocle package in R-3.4.1
Tagging of clusters with marker genes and extraction of co-expressed genes (R-3.4.1, see methods for details)
Genome_build: mm10
Supplementary_files_format_and_content: Gzipped Tab delimted text file containing raw count data for each cell and annotated gene after primary filtering.

source_name: Lung

extract_protocol:
Lung tissues were dissociated as described in Malanchi I., et al., Nature, 2011.
Library generation for Genomics were performed following the Chromium Single Cell 3ʹ Reagents Kits and sequenced on an Hiseq4000 (Illumina), to achieve an average of 50,000 reads per cell.

tag: cells


title: Sample_13_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Niche cells


title: Blood_trained_A1_1_69_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_69, replicate 1


title: TK6 cells, static culture

description: miRNA, lncRNA and mRNA expression data from human lymphoblastoid TK6 cells cultured for 24 hours in static condition.

source_name: Human lymphoblastoid TK6 cells cultured for 24 hours in static condition

tag: genotype


title: Sample_11_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: TK6 cells, 2Gy ionizing radiation

description: miRNA, lncRNA and mRNA expression data from human lymphoblastoid TK6 cells cultured for 24 hours in static condition after ionizing radiation.

source_name: Human lymphoblastoid TK6 cells cultured for 24 hours after ionizing radiation

tag: tissue


title: TK6 cells, microgravity

description: miRNA, lncRNA and mRNA expression data from human lymphoblastoid TK6 cells cultured for 24 hours in simulated microgravity condition.

source_name: Human lymphoblastoid TK6 cells cultured for 24 hours in simulated microgravity condition


title: pr4: ovary_primay_4

description: miRNA expression of primary ovarian cancer cells

source_name: primary ovarian cancer cell


title: WT NT

description: NT


title: Wild-type nontreat

source_name: Peritoneal macrophage

value: Wild-type

tag: treatment


title: Sample_15_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Sample_9_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: Blood_trained_A2_1_67_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_67, replicate 1

tag: gender

tag: age


title: Sample_6_shortRNA

description:
Sperm_RNAseq
sRNA_expression.txt


title: sp1: ovary_spheroid_2

source_name: spheroid-forming cell, cultured for 7 days


title: Blood_untrained_E1_1_68_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_68, replicate 1

tag: participant

tag: timepoint


title: pr1: ovary_primay_2


title: pr3: ovary_primay_3


title: pr2: ovary_primay_1


title: rtel1-3_INPUT

first: Jinkui

last: Cheng

address: No.2 Yuanmingyuan West Road

institute: China Agricultural University

data_processing:
For ChIP-seq analysis, paired-end clean reads were mapped to the reference genome sequence of Arabidopsis thaliana (TAIR10) with Bowtie2. Only uniquely mapped reads were retained. The alignments were converted to WIG files and enriched domains were called using MACS. All sets of defined regions were significant by fold change >2 and p value <0.00001.
For RNA-seq process,trimmed reads were mapped to the reference genome sequence of Arabidopsis thaliana (TAIR10) using TopHat (http://tophat.cbcb.umd.edu/) with the default settings Differential gene expression analysis was performed using Cufflinks
For Bisulfite-seq analysis,  paired-end clean reads were mapped to the reference genome sequence of Arabidopsis thaliana (TAIR10) using Bismark. Only uniquely mapped reads were retained. PCR duplicates were removed. The reference genome was divided into 100-bp bins. Bins with at least four cytosines and covered by at least four reads were retained.
Genome_build: tair10
Supplementary_files_format_and_content: peaks files for ChIP-seq processed data; excel files for RNA-seq processed data; txt files for bisulfite-seq processed data.

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana seeds were grown on Murashige and Skoog (MS) medium  16  containing 0 406 .8% (w/v) agar and 2% (w/v) sucrose. After 3 days at 4°C, the plates were transferred to a growth chamber at 22°C with 16 h of light and 8 h of darkness.

extract_protocol:
Genomic DNA was extracted from seedlings using the DNeasy Plant Mini Kit (QIAGEN)；total RNA was extracted from seedlings using the RNeasy Plant Mini Kit (QIAGEN)
For ChIP-seq, 10 ng DNA was used to prepare a high-throughput sequencing library. Sequencing was carried out with single-end 50-bp reads using HiSeq 2000 (Illumina).
For bisulfite sequencing, 2 µg DNA was used for bisulfite treatment and library construction, and sequencing was carried out using HiSeq 2000 (Illumina)
For RNA-seq, 2 µg  RNA was used for library construction.

treatment_protocol: 10-day-old seedlings germinated on MS or MS containing 1 mg/L zebularine (Sigma, Z4775) were used for RNA sequencing.

tag: ecotype background

value: Col

tag: genotype/variation

value: rtel1-3 mutant

tag: developmental stage

value: 10-day-old whole seedlings


title: WT TAM2

description: WT

source_name: B16 bearing mice

growth_protocol: B16-F10 cells were subcutaneously injected into the abdomen of 6-8-week-old WT and Trim24 myliod-cells-conditional deficient mice. 16 days later, mice were sacrificed,CD45+ CD11b+ F4/80+ tumor-associated macrophage(TAM) were sorted from tumors by FACS.

treatment_protocol: RNA were harvest directly from sorted TAM.

tag: cell population

tag: cell type


title: KO TAM1

value: CD45+ CD11b+ F4/80+ tumor-associated macrophage


title: Blood_untrained_E2_1_66_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_66, replicate 1

tag: rin-value

tag: cho-first-round(y/n)


title: rtel1-3_H3

tag: chip antibody


title: WT TAM1

description: WT

tag: strain


title: KO TAM2


title: rtel1-3_H3K9me2


title: rtel1-3_H3K27me3


title: rtel1-3_H3K4me3

value: H3K4me3 (Millipore,07-473)


title: Blood_untrained_E1_1_64_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_64, replicate 1


title: Blood_trained_A1_1_65_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_65, replicate 1


title: L119_H3


title: Blood_trained_A2_1_63_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_63, replicate 1

value: male


title: L119_INPUT


title: Blood_untrained_E1_1_60_rep1

description: blood-borne miRNA sequencing

label: using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp

source_name: Peripheral blood, untrained, E1, 1_60, replicate 1

value: n


title: Blood_untrained_E2_1_62_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_62, replicate 1


title: Blood_trained_A1_1_61_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_61, replicate 1


title: L119_H3K4me3


title: L119_H3K9me2


title: Blood_untrained_E2_1_58_rep2

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_58, replicate 2


title: HR627.AZA

type: genomic

city: Singapore

first: Zhiyong

last: Poon

address: 20 College Road

country: Singapore

institute: Singapore General Hospital

description: Genomic data from MDS-MSCs with 5-Aza treatment

hyb_protocol: The microarray service was provided by Macrogen Inc. (South Korea)

data_processing: Raw DNA methylation data was processed by first applying quality control (“minfi” R-package), followed by normalization with the beta-mixture quantile normalization (BMIQ) method (“wateRmelon” R-package). Finally, probe-wise differential methylation analysis (“limma” R-package) was conducted to filter out all probes that had a less than 10% average methylation rate and less than 0.106455 (M-value) fold change between untreated and 5-aza treated samples.

label: Cy3 and Cy5

source_name: Bone marrow

growth_protocol: For MSCs, the culture reagents used were: Dulbecco’s Modified Eagle’s Medium (DMEM) - low glucose (Gibco) supplemented with 10% fetal bovine serum (FBS) (Hyclone) and 50 U/ml penicillin and streptomycin (Gibco), subsequently referred to as D10 media. To derive MSCs, 2.0 - 3.0 × 105 cells/cm2 of BM derived mononuclear cells were inoculated in D10 media that was changed completely after 3 days and subsequently replaced twice a week until confluence and cryopreserved for experiments at P1. MDS patient derived mononuclear cells (1.0 × 106 – 1.0 × 107 cells/ml) were also inoculated in D10 media in a T75 flask. Non-adherent cells were removed after 3 days with subsequent media change twice a week. MDS-MSCs were further expanded, frozen down and all experiments were carried out using MSCs derived from P1 - P2.

extract_protocol: DNA was extracted from cells using the DNeasy Blood and Tissue Kit (Qiagen).

treatment_protocol: Subconfluent MSCs at P1 - P2 were treated with 1 µM AZA (Sigma-Aldrich) for up to 48 h. After exposure to AZA, cells were washed with PBS and replaced with drug free media. The drug-treated MSCs were then maintained in AZA free media for further experimentation.

tag: drug

tag: disease state

value: MDS


title: Blood_untrained_E2_1_57_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_57, replicate 1

tag: tissue


title: HR768.AZA

scan_protocol: The microarray service was provided by Macrogen Inc. (South Korea)


title: Blood_trained_A1_1_56_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_56, replicate 1


title: HR775.AZA

label_protocol: The microarray service was provided by Macrogen Inc. (South Korea)


title: HR400.AZA


title: Blood_trained_A2_1_59_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_59, replicate 1


title: HR305.AZA


title: Blood_untrained_E1_1_55_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_55, replicate 1


title: HR325.AZA


title: L119_H3K27me3


title: HR261.AZA


title: HR613.AZA


title: Blood_trained_A2_1_54_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_54, replicate 1


title: hMSC5.AZA

description: Genomic data from healthy MSCs with 5-Aza treatment

value: healthy


title: hMSC4.AZA


title: hMSC3.AZA


title: Blood_untrained_E2_1_53_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_53, replicate 1


title: rtel1-3_zebularine_RNA_rep1_R1_R2


title: hMSC2.AZA


title: L119_zebularine_RNA_rep1_R1_R2


title: L119_zebularine_RNA_rep2_R1_R2


title: Blood_trained_A1_1_52_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_52, replicate 1


title: rtel1-3_zebularine_RNA_rep2_R1_R2


title: L119_bisulfite sequencing-R1_R2

source_name: L119_bisulfite sequencing-R1_R2


title: rtel1-3_bisulfite sequencing-R1_R2

source_name: rtel1-3_bisulfite sequencing-R1_R2


title: rtel1-3_RNA_rep1_R1_R2


title: rtel1-3_RNA_rep2_R1_R2


title: WT_HC25_LNv_ZT16

city: Evanston

first: Ravi

last: Allada

state: IL

address: 2205 Tech Drive

department: Neurobiology

institute: Northwestern University

data_processing:
Sequence reads were processed to calculate TPM and estimated counts by kallisto.
Estimated counts were used to identify differential expressed genes by DEseq2.
Genome_build: dmel-all-transcript-r6.10
Supplementary_files_format_and_content: *_kallisto_abundance.txt: Tab-delimited text files containing TMP and estimated counts for each sample.

organism: Drosophila melanogaster

source_name: LNv neurons

growth_protocol: Flies were raised at 25°C on standard 1.5x sucrose-yeast (SY) food.

extract_protocol:
Fly brains were dissected at certain time points and processed as previously described (Kula-Eversole et al., 2010; Nagoshi et al., 2010). RNA from FACS sorted LNvs were extracted with PicoPure Kits. We synthesized 1st and 2nd strand cDNA from RNA first with Superscript III and DNA polymerase. Then we amplified the RNA by synthesizing more RNA from the cDNA template with T7 RNA polymerase. After the second round of cDNA synthesis from amplified RNA, the cDNA was submitted to HGAC at the University of Chicago for library preparation and sequencing.
Library construction and sequencing followed the protocol at HGAC at University of Chicago.

tag: strain/background

value: WT

value: Female

value: LNv neurons

tag: condition

tag: time point


title: WT_HC25_LNv_ZT14

tag: gender


title: L119_RNA_rep2_R1_R2


title: L119_RNA_rep1_R1_R2


title: Blood_trained_A2_1_50_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_50, replicate 1

value: whole blood

value: female

tag: age

tag: participant

tag: timepoint

value: y


title: hMSC1.AZA


title: WT_HC25_LNv_ZT04

tag: genotype/variation


title: Blood_untrained_E1_1_51_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_51, replicate 1


title: WT_HC25_LNv_ZT02


title: WT_HC25_LNv_ZT12


title: ESRP2_KD_3

city: Newcastle upon Tyne

first: David

last: Elliott

address: International Centre for Life

institute: Institute of Genetic Medicine

data_processing:
Quality control of reads was performed using FastQC. Reads were mapped to the hg38 transcriptome using Salmon. Differential gene expression analysis was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Normalised gene counts in tab-delimited text

growth_protocol: LNCaP cells (CRL-1740, ATCC) were grown routinely in RPMI-1640 with L-Glutamine (PAA Laboratories, R15-802) supplemented with 10% Fetal Bovine Serum (FBS) (PAA Laboratories, A15-101) at 37°C in 5% CO2.

extract_protocol:
RNA was extracted 72 hours after siRNA treatment using the Qiagen RNAeasy kit (Cat No. 74104) as per the manufacturer's instructions
TruSeq Stranded mRNA Sequencing NextSeq High-Output 2 x 75 bp reads (total of 6 samples)

treatment_protocol: For each condition: 500,000 cells were seeded onto a six well plate and allowed to adhere overnight. siRNA treatment was then performed using Lipofectamine RNAiMax as per the manufacturer's instructions. siRNAs were purchased from IDT: (hs.Ri.ESRP1.13.1); ESRP1 siRNA2 (hs.Ri.ESRP1.13.2); ESRP2 siRNA 1(hs.Ri.ESRP2.13.1); ESRP2 siRNA 2 (hs.Ri.ESRP2.13.2) and negative control siRNA  (IDT (51-01-14-04).

tag: cell line

value: LNCaP

tag: passage

value: passage 19

tag: treatment

value: siRNAs targeting ESRP1 and ESRP2


title: HR768.UT

description: Genomic data from MDS-MSCs without 5-Aza treatment


title: Blood_untrained_E2_1_49_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_49, replicate 1

tag: rin-value

tag: cho-first-round(y/n)


title: ESRP2_KD_2


title: Blood_untrained_E2_1_45_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_45, replicate 1


title: Blood_trained_A1_1_44_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_44, replicate 1


title: Blood_trained_A1_1_48_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_48, replicate 1


title: HR627.UT

source_name: Bone marrow


title: HR613.UT


title: ESRP2_KD_1


title: HR400.UT


title: HR305.UT


title: Blood_untrained_E1_1_47_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_47, replicate 1


title: HR775.UT


title: ESRP2_control_3

value: control siRNAs


title: Blood_trained_A2_1_46_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_46, replicate 1


title: HR325.UT


title: HR261.UT


title: ESRP2_control_2


title: Blood_untrained_E1_1_43_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_43, replicate 1


title: WT_HC25_LNv_ZT24

tag: cell type


title: hMSC5.UT

description: Genomic data from healthy MSCs without 5-Aza treatment

tag: drug


title: ESRP2_control_1


title: Blood_trained_A2_1_42_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_42, replicate 1


title: tyf(e) ZT16 2

value: tyf(e)


title: tyf(e) ZT16 1


title: tyf(e) ZT04 1


title: tyf(e) ZT04 2


title: Atx2 KD ZT12 2

value: Atx2 KD


title: Sample_152_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

source_name: Ejaculated spermatozoa

value: spermatozoa

tag: study subject

tag: visit number

tag: visit type

value: Crossback

tag: dbp level

tag: rna fraction

value: long RNA


title: Blood_untrained_E2_1_41_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_41, replicate 1

tag: tissue

tag: gender

value: n


title: Blood_trained_A1_1_40_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_40, replicate 1

tag: age

tag: participant


title: Atx2 KD ZT00 2

tag: strain/background

tag: genotype/variation

tag: condition

tag: time point


title: Atx2 KD ZT00 1


title: Blood_untrained_E1_1_39_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_39, replicate 1

tag: timepoint

tag: rin-value


title: hMSC1.UT

tag: disease state

value: healthy


title: Blood_trained_A1_1_37_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_37, replicate 1

value: male

tag: cho-first-round(y/n)


title: Blood_trained_A2_1_38_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_38, replicate 1


title: Sample_141_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: cell type

tag: study subject


title: hMSC3.UT

tag: drug


title: Sample_138_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: visit number

tag: visit type

value: Baseline

tag: dbp level


title: hMSC4.UT


title: Atx2 KD ZT12 1

source_name: LNv neurons

tag: gender

value: Female

value: LNv neurons


title: Sample_136_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: rna fraction


title: Blood_untrained_E1_1_36_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_36, replicate 1

tag: tissue

value: whole blood

tag: age

tag: participant


title: HC18_LNv_ZT22

data_processing:
Sequence reads were processed to calculate TPM and estimated counts by kallisto.
TPM values were used as input for booteJTK to identify cycling genes.
Genome_build: dmel-all-transcript-r6.14
Supplementary_files_format_and_content: PDF_abundance_transcripts.csv: This is a summary file for transcript abundance for all the conditions and time points for which raw data files are deposited.
Supplementary_files_format_and_content: PDF_all.cmn_eJTKprep_10-2017.xlsx: This is a summary file for gene level TPM for all the conditions and time points for which raw data files are deposited.
Supplementary_files_format_and_content: SUMMARY_LNv_BeJTK_results_10-04-17.xlsx: This results from booteJTK for HC25 and 3 conditions data.

growth_protocol: Flies were raised at standard 1.5x sucrose-yeast (SY) food at 25°C, 1.5xSY at 18°C, or 0.5xSY at 25°C.

tag: strain/background

tag: genotype/variation

value: WT

tag: condition


title: hMSC2.UT


title: HC18_LNv_ZT20

tag: time point


title: Sample_150_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Crossover


title: Sample_148_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: HC18_LNv_ZT18


title: Blood_trained_A2_1_35_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_35, replicate 1

value: female

tag: timepoint

tag: rin-value


title: Blood_untrained_E2_1_34_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_34, replicate 1

tag: cho-first-round(y/n)


title: HC18_LNv_ZT24

tag: cell type


title: Blood_trained_A1_1_33_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_33, replicate 1


title: PianpKO hypothalamus biological rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
Gene expression data of Pianp-deficient murine hypothalamus.
Hypothalamus_KO_156

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: PianpKO biological rep2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Pianptm1a(KOMP)Wtsi mice were crossed with B6N.Cg-Tg(ACTFLPe)9205Dym/CjDswJ mice to generate Pianp floxed mice (FL). These mice were further bred with B6.C-Tg(CMV-cre)1Cgn/J mice to generate constitutive knockout mice, denoted as PianpKO (KO).

extract_protocol: Total RNA was extracted from dissected brain region tissue using the RNeasy Mini Kit (Qiagen).

treatment_protocol: The whole brain from experimentally naive male mice was cut coronally and manually microdissected into the respective regions using brain punches. Allen mouse brain atlas (version 2, 2011, https://www.brain-map.org/) was used for identification of the different brain areas.

value: Hypothalamus

tag: genotype

value: KO


title: PianpKO hypothalamus biological rep4

description:
Gene expression data of Pianp-deficient murine hypothalamus.
Hypothalamus_KO_165

source_name: PianpKO biological rep4


title: PianpKO hypothalamus biological rep3

description:
Gene expression data of Pianp-deficient murine hypothalamus.
Hypothalamus_KO_157

source_name: PianpKO biological rep3


title: Sample_132_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: study subject

tag: visit number


title: PianpKO hypothalamus biological rep5

description:
Gene expression data of Pianp-deficient murine hypothalamus.
Hypothalamus_KO_168

source_name: PianpKO biological rep5


title: Control hypothalamus biological rep5

description:
Gene expression data of control murine hypothalamus.
Hypothalamus_FL_122

source_name: Control biological rep5

value: FL


title: HC18_LNv_ZT16


title: Sample_119_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: visit type

tag: dbp level


title: HC18_LNv_ZT14

tag: gender


title: Blood_untrained_E1_1_32_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_32, replicate 1

tag: tissue


title: Sample_117_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

source_name: Ejaculated spermatozoa

tag: rna fraction


title: HC18_LNv_ZT12


title: Sample_134_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_115_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_99_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Control hypothalamus biological rep3

description:
Gene expression data of control murine hypothalamus.
Hypothalamus_FL_112

source_name: Control biological rep3


title: Blood_trained_A1_1_29_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_29, replicate 1

tag: age

tag: participant

value: y


title: Control hypothalamus biological rep2

description:
Gene expression data of control murine hypothalamus.
Hypothalamus_FL_111

source_name: Control biological rep2


title: HC18_LNv_ZT10

tag: strain/background

tag: genotype/variation


title: Blood_untrained_E2_1_30_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_30, replicate 1


title: Sample_97_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: spermatozoa


title: HC18_LNv_ZT06

tag: condition

tag: time point


title: Blood_untrained_E1_1_28_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_28, replicate 1

tag: timepoint

tag: rin-value


title: Sample_91_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: cell type

value: Crossback


title: HC18_LNv_ZT08

source_name: LNv neurons


title: HC18_LNv_ZT04


title: Sample_89_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: long RNA


title: HC18_LNv_ZT02


title: Blood_trained_A2_1_31_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_31, replicate 1

tag: cho-first-round(y/n)


title: Sample_86_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: study subject


title: Blood_trained_A2_1_27_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_27, replicate 1

value: n


title: Blood_untrained_E2_1_26_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_26, replicate 1


title: LC25_LNv_ZT24


title: Blood_trained_A1_1_25_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_25, replicate 1


title: Control hypothalamus biological rep1

description:
Gene expression data of control murine hypothalamus.
Hypothalamus_FL_110

source_name: Control biological rep1

tag: genotype


title: Control hypothalamus biological rep4

description:
Gene expression data of control murine hypothalamus.
Hypothalamus_FL_113

source_name: Control biological rep4


title: PianpKO hippocampus biological rep5

description:
Gene expression data of Pianp-deficient murine hippocampus.
Hippocampus_KO_168

value: Hippocampus


title: Sample_83_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: visit number

tag: visit type


title: LC25_LNv_ZT22

tag: gender


title: Sample_81_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: dbp level


title: Blood_untrained_E1_1_24_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_24, replicate 1

tag: tissue

value: male


title: LC25_LNv_ZT20


title: PianpKO hippocampus biological rep3

description:
Gene expression data of Pianp-deficient murine hippocampus.
Hippocampus_KO_157

source_name: PianpKO biological rep3


title: Blood_trained_A1_1_22_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_22, replicate 1

tag: age


title: Sample_68_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: rna fraction


title: PianpKO hippocampus biological rep2

description:
Gene expression data of Pianp-deficient murine hippocampus.
Hippocampus_KO_156

source_name: PianpKO biological rep2


title: Sample_80_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

source_name: Ejaculated spermatozoa

value: Baseline


title: PianpKO hippocampus biological rep4

description:
Gene expression data of Pianp-deficient murine hippocampus.
Hippocampus_KO_165

source_name: PianpKO biological rep4


title: PianpKO hippocampus biological rep1

description:
Gene expression data of Pianp-deficient murine hippocampus.
Hippocampus_KO_155

source_name: PianpKO biological rep1


title: Control hippocampus biological rep5

description:
Gene expression data of control murine hippocampus.
Hippocampus_FL_122

source_name: Control biological rep5


title: LC25_LNv_ZT16

tag: strain/background

value: Female


title: Control hippocampus biological rep4

description:
Gene expression data of control murine hippocampus.
Hippocampus_FL_113


title: Sample_61_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_56_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: LC25_LNv_ZT12

tag: genotype/variation

value: LNv neurons


title: Control hippocampus biological rep3

description:
Gene expression data of control murine hippocampus.
Hippocampus_FL_112

source_name: Control biological rep3


title: LC25_LNv_ZT14

tag: condition


title: Blood_untrained_E1_1_21_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_21, replicate 1

value: whole blood

tag: participant


title: Sample_55_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Blood_untrained_E2_1_19_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_19, replicate 1

tag: timepoint


title: Blood_trained_A1_1_18_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_18, replicate 1

tag: rin-value


title: LC25_LNv_ZT18

source_name: LNv neurons

value: WT

tag: cell type

tag: time point


title: Blood_untrained_E2_1_23_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_23, replicate 1

tag: cho-first-round(y/n)


title: Sample_51_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: study subject


title: Sample_54_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: visit number


title: LC25_LNv_ZT08


title: LC25_LNv_ZT06


title: Sample_48_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: visit type


title: Blood_untrained_E1_1_17_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_17, replicate 1

tag: gender


title: Blood_untrained_E2_1_15_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_15, replicate 1


title: LC25_LNv_ZT04


title: Blood_trained_A2_1_20_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_20, replicate 1


title: PianpKO cortex biological rep5

description:
Gene expression data of Pianp-deficient murine cortex.
Cortex_KO_168

source_name: PianpKO biological rep5

value: Cortex

tag: genotype


title: Sample_47_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Crossover

tag: dbp level


title: PianpKO cortex biological rep4

description:
Gene expression data of Pianp-deficient murine cortex.
Cortex_KO_165

tag: tissue


title: Sample_46_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: rna fraction


title: PianpKO cortex biological rep3

description:
Gene expression data of Pianp-deficient murine cortex.
Cortex_KO_157

source_name: PianpKO biological rep3


title: Control hippocampus biological rep1

description:
Gene expression data of control murine hippocampus.
Hippocampus_FL_110

source_name: Control biological rep1


title: PianpKO cortex biological rep2

description:
Gene expression data of Pianp-deficient murine cortex.
Cortex_KO_156

source_name: PianpKO biological rep2


title: LC25_LNv_ZT02

tag: strain/background


title: Blood_untrained_E1_1_13_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_13, replicate 1

value: female

tag: age


title: HC25_LNv_ZT24

tag: genotype/variation

tag: condition


title: PianpKO cortex biological rep1

description:
Gene expression data of Pianp-deficient murine cortex.
Cortex_KO_155

value: KO


title: Blood_trained_A2_1_12_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_12, replicate 1

tag: participant

tag: timepoint


title: Sample_35_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

source_name: Ejaculated spermatozoa

tag: cell type


title: HC25_LNv_ZT22

tag: time point


title: Blood_trained_A2_1_16_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_16, replicate 1

tag: rin-value

tag: cho-first-round(y/n)


title: Sample_32_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: study subject

tag: visit number


title: Control cortex biological rep5

description:
Gene expression data of control murine cortex.
Cortex_FL_122

source_name: Control biological rep5

value: FL


title: Blood_untrained_E2_1_11_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_11, replicate 1

tag: gender


title: PianpKO hypothalamus biological rep1

description:
Gene expression data of Pianp-deficient murine hypothalamus.
Hypothalamus_KO_155

source_name: PianpKO biological rep1

value: Hypothalamus

tag: genotype


title: Control cortex biological rep4

description:
Gene expression data of control murine cortex.
Cortex_FL_113

source_name: Control biological rep4


title: Blood_trained_A1_1_14_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_14, replicate 1


title: Control hippocampus biological rep2

description:
Gene expression data of control murine hippocampus.
Hippocampus_FL_111

source_name: Control biological rep2


title: HC25_LNv_ZT18

source_name: LNv neurons


title: Control cortex biological rep2

description:
Gene expression data of control murine cortex.
Cortex_FL_111


title: Sample_18_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: spermatozoa

tag: visit type

tag: dbp level


title: Blood_trained_A1_1_10_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_10, replicate 1

tag: tissue


title: Blood_untrained_E1_1_9_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_9, replicate 1


title: LC25_LNv_ZT10

tag: strain/background


title: HC25_LNv_ZT16


title: Control cortex biological rep3

description:
Gene expression data of control murine cortex.
Cortex_FL_112

source_name: Control biological rep3


title: Sample_13_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Crossback

tag: rna fraction


title: HC25_LNv_ZT20

tag: genotype/variation


title: Control cortex biological rep1

description:
Gene expression data of control murine cortex.
Cortex_FL_110


title: HC25_LNv_ZT14

tag: condition


title: PianpKO amygdala biological rep5

description:
Gene expression data of Pianp-deficient murine amygdala.
Amygdala_KO_168

source_name: PianpKO biological rep5

value: Amygdala


title: Blood_trained_A2_1_8_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_8, replicate 1

tag: age

tag: participant

value: y


title: Blood_untrained_E2_1_7_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_7, replicate 1

tag: timepoint


title: HC25_LNv_ZT12

tag: cell type

tag: time point


title: Sample_11_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: long RNA