title: ALL_388r1


title: ALL_680

status: Public on Aug 11 2021

type: SRA

city: Linköping

first: Shumaila

last: Sayyab

address: Campus US, Building 420, Entrance 68

department: Biomedical and Clinical Sciences (BKV)

country: Sweden

institute: Linköping University

library_source: transcriptomic

data_processing:
*** Raw data not provided due to patient privacy concerns ***
Filtering or Preprocess:The raw RNA-seq reads were pre-processed using cutadopt v3.1
Alignment: The RNA reads were aligned to reference genome hg19 using STAR v2.7.2.
Processing data: Gene expression levels in fragments per kilobase per million mapped reads (FPKM) was calculated using Cufflinks v2.2.0, and Cuffdiff was used to detect differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: Bone marrow

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: diagnosis

tag: tissue

value: Bone marrow

tag: rna prep

value: ScriptSeq

tag: source

value: Marincevic-Zuniga et al., 2017.


title: KO-sedentary group mouse 4

city: Charlestown

first: Christiane

last: Wrann

state: MA

address: 149 13th Street

country: USA

institute: Massachusetts General Hospital

data_processing:
Sequenced reads were aligned to the UCSC mm10 reference genome assembly
Gene counts were quantified using STAR (v2.5.1b)
Normalized read counts (FPKM) were calculated using cufflinks (v2.2.1)
RNAseq analysis was performed using the VIPER snakemaker pipeline
Genome_build: mm10
Supplementary_files_format_and_content: STAR normalized counts for all mice in different groups and all genes.

organism: Mus musculus

source_name: microdisected hippocampus sample

extract_protocol:
Hippocampi were micro-dissected, flash frozen on dry ice, and the nuclei were isolated. The isolated nuclei were stained woth Vybrant Ruby dye and Ruby+/GFP+ nuclei were FACS-sorted.
The cDNA was synthesized from sorted cells using Takara SmartSeq v4 reagents according to manufacturer's protocol with modification: 1μl of 2X Reaction buffer was used with 1μl of CDS primer and 18 cycles of PCR were used for the cDNA amplification step. Full length cDNA was fragmented to a mean size of 150bp with a Covaris M220 ultrasonicator and Illumina libraries were prepared from 2ng of sheared cDNA using Rubicon Genomics Thruplex DNAseq reagents according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced with single-end 75bp reads on an Illumina NextSeq500 run by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

tag: strain

value: Global Fndc5 Knock out mice (C57BL/6 background)

tag: genotype

value: Knock-out

tag: treatment

value: Injected with GFP-reporter retrovirus

tag: running or sedentary

value: Sedentary group

value: Hippocampus


title: KO-running group mouse 4

value: Voluntery free wheel running group


title: KO-running group mouse 3


title: ALL_317

value: TruSeq stranded total RNA

value: Current study


title: ALL_358r1

value: first relapse


title: ALL_257r1


title: WT-sedentary group mouse 4

value: Wild-type


title: ALL_380r1


title: ALL_839r1

value: TruSeq RNA Access


title: KO-running group mouse 2


title: WT-sedentary group mouse 3


title: ALL_257


title: KO-running group mouse 1


title: ALL_839


title: STARR-seq plasmid input DNA

city: Ann Arbor

first: Stephen

middle: C. J.

last: Parker

state: MI

address: 100 Washtenaw Ave

department: Computational medicine and Bioinformatics

institute: University of Michigan

description: We sequenced input STARR-seq plasmid library

library_source: genomic

data_processing:
Library strategy: STARR-seq
Quantifying Barcode counts from STARR-seq: The STARR-seq barcode sequencing data included the input DNA barcode library along with three cDNA barcode libraries representing three biological replicated. We processed this data through a custom pipeline which quantified barcode counts while accounting for sequencing errors. We extracted the DNA barcodes from the input DNA library (first 16 bp of the read-1 fastq file) and clustered these at an edit distance of 0 followed by computing the DNA counts for each read group of DNA sequencing files. We then aggregated the read groups and collapsed counts for barcodes using the sequence clustering algorithm Starcode (https://github.com/gui11aume/starcode) [DOI: 10.1093/bioinformatics/btv053]. We repeated this process for the cDNA barcode counts for each replicate, with the added step of removing PCR-duplicated barcodes using the UMI information (UMI sequence was the reverse complement of the first 6bp of the read-2 fastq file). The pipeline is shared at https://github.com/ParkerLab/STARR-seq-Analysis-Pipeline.
Tetsing for CAGE element transcriptional activity: We matched the barcodes with CAGE inserts using results from CAGE insert-barcode pairing experiment (Supplementary data “cage_insert_barcode_pairing.txt”). We first retained barcodes with at least 10 DNA counts, and further retained CAGE elements that had at least two such qualifying barcodes. This was the set of N=3,446 CAGE elements quantifiable in our assay. To quantify STARR-seq activities from these count-based data, we used the tool MPRAnalyze (version 1.3.1) (https://github.com/YosefLab/MPRAnalyze}) [DOI 10.1101/527887] that models DNA and RNA counts in a negative binomial generalized linear model. This approach is more robust than using metrics such as the aggregated ratio, which is the ratio of the sum of RNA counts across barcodes divided by the sum of DNA counts across barcodes and loses the statistical power provided by multiple barcodes per tested element; and the mean ratio, which is the mean of the observed RNA/DNA ratios across barcodes which can be quite sensitive to low counts and noise. We corrected for library depth for the three replicates using upper quartile normalization via the ‘estimateDepthFactors’ function in MPRAnalyze. STARR-seq activity is quantified by estimating the transcription rate for each element in the dataset, followed by identifying active elements that induce a higher transcription by testing against a null. MPRAnalyze fits two nested generalized linear models - the DNA model estimates plasmid copy numbers, and the RNA model is estimates transcription rate. We included barcode information in the DNA model which allows different estimated counts for each barcode, and increases the statistical power of the model. Replicate information was included in the RNA model. MPRAnalyze then tests the transcriptional activity of each element against a null distribution and computing Z and Median-Absolute-Deviation (MAD) scores. The null is based on the assumption that the mode of the distribution of transcription rate estimates is the center of the null distribution, and that values lower than the mode all belong to the null. Thus, values lower than the mode are used to estimate the variance of the null.
Genome_build: not applicable since the synthetic barcode sequences and not mapped to any genome
Supplementary_files_format_and_content: File "cage_insert_barcode_pairing.tsv" is a tab separated values (tsv) files containing the hg19 coordinates of the CAGE elements tested in the STARR-seq experiment and the corresponding barcode sequences. These sequenced barcodes represent the STARR-seq experiment readout. File "cage_insert_starrseq_counts_filtered.tsv" includes CAGE elements hg19 coordinates, corresponding barcode sequences, the DNA count and the RNA counts for the three replicates for the barcode sequences. CAGE elements in this file are what were selected for statistically testing the STARR-seq transcriptional activity. Specifically, we selected barcodes that had a minimum of 10 DNA counts, and selected CAGE elements that had minimum 2 such qualifying barcodes.

molecule: genomic DNA

organism: synthetic construct

source_name: STARR-seq plasmid library containing synthetic oligos created (Agilent) from human sequences

extract_protocol:
We electroporated 10 ug of barcoded STARR-seq library into 25 million the 832/13 rat insulinoma cell line for each biological replicate (3 replicates), and harvested the cells twenty-fours later. We isolated total RNA using TRIZOL reagent (Life Technologies) following the manufacturer’s protocol up to phase separation. After phase separation, we transferred the aqueous phase of the solution to a new 1.5 mL Eppendorf tube, added 1:1 volume of 100\% ethanol, and then column-purified using the Direct-zol RNA Miniprep Kit (Zymo) following the manufacturer’s protocol. We further purified mRNA using Dynabeads oligo(dT) beads (Thermo Fisher). We treated 2 ug of mRNA with RNase-free DNaseI (invitrogen) to eliminate possible plasmid DNA contamination, and then reverse transcribed it into cDNA using the SuperScript III First-Strand Synthesis kit (invitrogen) with a custom primer that specifically recognizes ‘STARR transcripts’ (i.e. mRNA that had been transcribed from the STARR-seq plasmids). To eliminate any residual plasmid contamination in cDNA samples, we treated cDNA with DpnI (NEB), and purified the reaction using the DNA Clean and Concentrator-5 kit (Zymo).
We constructed Illumina sequencing library via two serial rounds of PCR. In the first round, we used a primer set to specifically amplify STARR transcripts using cDNA as starting material. In the second round, we used a primer set to append the P5/P7 Illumina sequences using the PCR product from the first round as starting material. In both rounds, we PCR-amplified the fragments until the amplification curve reached a mid-log phase, and then purified the products for subsequent steps using the DNA Clean and Concentrator-5 kit (Zymo). To identify the barcodes corresponding to each CAGE element in the STARR-seq plasmid, 1ng of each library constructed was used in a polymerase chain reaction with primers flanking the allele and the barcode to generate fragments which were subsequently gel verified and extracted using Zymo gel extraction kit (Zymo). 25ng of the purified product was subjected to self-ligation at 16 °C overnight in a total volume of 50uls and column purified using Qiagen (Qiagen) PCR purification kit as per manufacturers recommendations. The purified fragments were subsequently treated with 10U of Plasmid-Safe ATP-Dependent DNase for 1 hour in the presence of 25mM ATP to remove unligated linear DNA fragments. 1ul of the recircularized fragments were subjected to another round of PCR resulting in a smaller fragment. Briefly an aliquot of this product was diluted 1:10 in DNAse/RNase free water and amplified in a PCR reaction, with Illumina P5 and P7 adapters, until saturation to generate libraries. The libraries were subsequently column purified, quantified and sequenced.

tag: cell line


title: RNAseq IGF2BP3 KO CD11b rep3

city: Los Angeles

first: Dinesh

last: Rao

address: 650 Charles E Young Dr S

department: Pathology & Lab Medicine

institute: UCLA

description:
biological rep
IM8-5

data_processing:
mapping to mm10 with STAR (v 2.5.3a)
repeatmasking with bowtie2
peak calling - CLIPper with default parameters
differential expression with DESeq2 on all genes with non-zero counts
Genome_build: mm10

source_name: CD11b+ cells

growth_protocol: Lin- cells were obtained by harvesting the BM from mice, lysing in red blood cell lysis buffer, and staining with a cocktail of biotinylated antibodies for lineage depletion by MACS (Miltenyi). Lin- cells were spin-infected with the MSCV-MLL-flag-Af4 retroviral supernatant four times at 30°C for 45 minutes in the presence of polybrene. Cells were selected with 400 μg/ml of G418 for 7 days.

extract_protocol:
CD11b+ cells were obtained by harvesting the splenic tumors from the WT/MLL-Af4 or I3/MLL-Af4 mice, lysing in red blood cell lysis buffer, and staining with a CD11b biotinylated antibody for positive selection by MACS (Miltenyi). RNA from both cell types was collected using QIAzol Lysis Reagent and purified using the miRNeasy Mini Kit (217004; Qiagen). The Agilent 2100 Bioanalyzer using RNA pico chip was utilized to quality check total RNA. The Nugen Universal plus mRNA-Seq Kit was used to generate strand-specific RNA-seq libraries. Samples were subjected to poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mixture of random and oligo(dT) priming. The cDNA samples were then subjected to end repair to generate blunt ends, adapter ligation, strand selection, and PCR amplification to generate the final library. To mulitplex samples in one sequencing lane, different index adapters were used. Single-end, strand-specific RNA sequencing was performed on the Illumina HiSeq3000 system for the Lin- and CD11b+ samples, resulting in 15-20 million reads per sample, at the the UCLA Technology Center for Genomics & Bioinformatics.
Nugen Universal plus mRNA-Seq Kit (RNA-seq) and Eclipse BioInnovations Inc eCLIP kit (eCLIP)

value: IGF2BP3 KO

tag: cell type

value: CD11b+ cells

value: no treatment


title: RNAseq IGF2BP3 KO CD11b rep2

description:
biological rep
IM5-5


title: WT-sedentary group mouse 2


title: RNAseq wild type CD11b rep3

description:
biological rep
WM8-4

value: wild type


title: ALL_244r1

value: Bone marrow


title: ALL_244

value: diagnosis


title: RNAseq IGF2BP3 KO CD11b rep1

description:
biological rep
IM1-5


title: RNAseq wild type CD11b rep1

description:
biological rep
WM2-5


title: RNAseq wild type CD11b rep2

description:
biological rep
WM6-4


title: RNAseq IGF2BP3 KO Lin- rep3

description:
biological rep
IM-7

source_name: Lin- cells

value: Lin- cells


title: WT-sedentary group mouse 1

value: Global Fndc5 Knock out mice (C57BL/6 background)


title: WT-running group mouse 3

value: Injected with GFP-reporter retrovirus


title: WT-running group mouse 4


title: ALL_210r1

value: ScriptSeq

value: Marincevic-Zuniga et al., 2017.


title: RNAseq IGF2BP3 KO Lin- rep2

description:
biological rep
IM-4


title: ALL_210


title: RNAseq IGF2BP3 KO Lin- rep1

description:
biological rep
IM-1


title: WT-running group mouse 2

value: Voluntery free wheel running group

value: Hippocampus


title: RNAseq wild type Lin- rep3

description:
biological rep
WM-6


title: RNAseq wild type Lin- rep2

description:
biological rep
WM-3


title: T-cells (CD3+)_899

source_name: Peripheral Blood

value: Healthy control

value: Peripheral Blood


title: WT-running group mouse 1

value: Wild-type


title: ALL_205


title: RNAseq wild type Lin- rep1

description:
biological rep
WM-1


title: treatP3C

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

country: China

institute: Northeast Agricultural University

description: cultivars "Compound raceme"; Full bloom

data_processing:
BGI500 own software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni .
Genome_build: GCF_000188115.4_SL3.0
Supplementary_files_format_and_content: Excels include FPKM values for each Sample

organism: Solanum lycopersicum

source_name: flower

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

treatment_protocol: The two cultivars (monomaker, raceme) had three different flowering stages (budlet, Flower bud, Full bloom) for transcriptome sequencing

value: flower

tag: cultivar

value: Compound raceme

tag: flowering stage

value: Full bloom


title: ALL_205r1

value: first relapse

value: TruSeq stranded total RNA

value: Current study


title: treatP3B

description: cultivars "Compound raceme"; Full bloom


title: LD [Sample9_TCR]

city: Chicago

first: Pablo

last: Penaloza-Macmaster

state: Illinois

address: 303 E. Chicago Avenue

department: Microbiology-Immunology

institute: Northwestern University

data_processing:
Sequencing data was demultiplexed using cellranger mkfastq version 4.0.0
FASTQ files for gene expression (GEX) were aligned and counted to mm10 (10X Genomics transcript version mm10-2020-A) using cellranger count version 4.0.0
FASTQ files for TCR were aligned and counted to mm10 VDJ regions (10X Genomics transcript version vdj_GRCm38_alts_ensembl-5.0.0) using cellranger vdj version 4.0.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited matrix output files from cellranger count

source_name: splenic CD8 T cell

growth_protocol: samples were harvested in RPMI with 10% FBS, P/S, BME, L-Glu

extract_protocol:
For isolation, splenic CD8 T cells were negatively selected using MACS, then FACS-sorted (CD8+, CD44+, and Kb VNFNFNGL tetramer+) to 99% purity, and delivered to the NU Seq core
Library preparation by the NUSeq core at the Northwestern University Feinberg School of Medicine using the 10x Genomics Chromium platform for gene expression (GEX) and VDJ. Libraries were then sequenced using a NextSeq 500 instrument.

treatment_protocol: SARS CoV-2 specific CD8 T cells (KbVNFNFNGL+) were generated by vaccinating mice with an adenovirus serotype 5-based vector expressing SARS CoV-2 spike protein

value: spleen

tag: dose

value: low dose (LD 10^6 PFU)

tag: agent

value: SARS CoV-2 vaccine (Ad5-SARS CoV-2 spike)


title: ALL_202r1

value: TruSeq RNA Access


title: treatP3A

description: cultivars "Compound raceme"; Full bloom


title: ALL_202

value: diagnosis


title: LD [Sample9_GEX]


title: SD [Sample6_TCR]

value: standard dose (SD, 10^9 PFU)


title: treatP2A

description: cultivars "Compound raceme"; Flower bud

value: Flower bud


title: controlM3C

description: cultivars "monomaker"; Full bloom

value: monomaker


title: treatP2C

description: cultivars "Compound raceme"; Flower bud


title: ALL_128r2

value: second relapse

value: Bone marrow


title: treatP2B

description: cultivars "Compound raceme"; Flower bud


title: treatP1A

description: cultivars "Compound raceme"; budlet

value: budlet


title: Ypel4+/+ #4 Ortho-E

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

institute: BMC

data_processing:
Fastq files were processed using the nf-core Nexflow pipeline for RNAseq nf-core/rnaseq v1.4.2
Reads were mapped against GRCm38
Differentiallly expressed genes were found using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts and gene IDs.

source_name: Steady-state bone marrow

extract_protocol:
Total RNA was extracted from cells using RNeasy Kit (QIAGEN) according to manufacturer’s protocol. Genomic DNA was removed using DNase I on-column digestion (QIAGEN). RNA concentration and integrity were measured using Agilent RNA Pico Kit on a Bioanalyzer Instrument (Agilent Genomics).
RNA sequencing libraries were prepared using TruSeq RNA Library Preparation Kit v2 (Illumina) according to manufacturer’s standard protocol and the sequencing was performed using NextSeq 500/550 Mid Output v2 Kit, 150 cycle (Illumina).

treatment_protocol: Bone marrows were homogenized and filtered to single cell suspensions prior to fluorescence activated cell sorting (FACS). For cell sorting, the following antibodies against murine epitopes were used: CD44 (BioLegend) and Ter119 (eBioscience). Fc receptor block (BD Biosciences) was used for sorting samples and dead cells were excluded using propidium iodide (PI; ThermoFisher Scientific). FACS was performed on BD FACS Aria III (Becton Dickinson). FACS gating was based on the strategy defined by Chen et al. Proc Natl Acad Sci U S A. 2009.

value: Wild-type

value: Orthochromatic erythroblast


title: SD [Sample6_GEX]


title: treatP1C

description: cultivars "Compound raceme"; budlet

value: flower

value: Compound raceme


title: Ypel4+/+ #4 Poly-E

value: Polychromatic erythroblast


title: controlM2B

description: cultivars "monomaker"; Flower bud


title: ALL_124r1

source_name: Bone marrow+Peripheral blood

value: first relapse

value: Bone marrow+Peripheral blood

value: Current study


title: Ypel4+/+ #3 Ortho-E


title: controlM3B

description: cultivars "monomaker"; Full bloom

value: Full bloom


title: ALL_838r1

value: TruSeq RNA Access


title: controlM3A

description: cultivars "monomaker"; Full bloom


title: treatP1B

description: cultivars "Compound raceme"; budlet


title: Fndc5 knock-out mouse 3

source_name: microdisected dentate gyrus sample_KO

extract_protocol:
Dentate gyri were micro-dissected and the RNA was isloated using trizol and the Qiagen RNAeasy mini kit.
Libraries were prepared from 500 ng of purified total RNA using the Illumina TruSeq stranded mRNaseq kit according to the manufacturer’s protocol. Pooled, uniquely indexed libraries were sequenced on an Illumina NextSeq500 with single-end 75-bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

tag: strain background

tag: genotype/variation

value: Global Fndc5 Knock out

value: Dentate Gyrus


title: controlM2C

description: cultivars "monomaker"; Flower bud

value: Flower bud


title: ALL_109r2


title: ALL_838

value: diagnosis


title: controlM1C

description: cultivars "monomaker"; budlet

value: monomaker


title: controlM2A

description: cultivars "monomaker"; Flower bud


title: Ypel4+/+ #3 Poly-E

value: Bone marrow


title: ALL_128r1


title: controlM1B

description: cultivars "monomaker"; budlet

value: budlet


title: controlM1A

description: cultivars "monomaker"; budlet


title: ALL_27r2

value: second relapse

value: Peripheral Blood

value: TruSeq stranded total RNA


title: Ypel4+/+ #2 Ortho-E

value: Wild-type

value: Orthochromatic erythroblast


title: ALL_48r1

value: first relapse


title: ALL_109r1


title: ALL_27

value: ScriptSeq

value: Marincevic-Zuniga et al., 2017.


title: Ypel4+/+ #2 Poly-E

value: Polychromatic erythroblast


title: Ypel4+/+ #1 Ortho-E


title: Ypel4-/- #4 Poly-E

value: Homozygous mutant


title: Ypel4-/- #4 Ortho-E


title: Ypel4+/+ #1 Poly-E


title: ALL_27r1


title: ALL_837

value: TruSeq RNA Access

value: Current study


title: ALL_837r1


title: Ypel4-/- #3 Poly-E


title: ALL_24

source_name: Blood

value: Blood


title: B-cells (CD19+)_867

value: Healthy control


title: Fndc5 knock-out mouse 5

value: Global Fndc5 Knock out

value: Dentate Gyrus


title: Ypel4-/- #2 Ortho-E

value: Bone marrow


title: TR7_8hr

type: RNA

city: Yahaba-cho

first: Reiko

last: Tsutsumi

state: Iwate Prefecture

address: Idaidori 1-1-1

country: Japan

institute: Iwate Medical University

description: Gene expression after 8hr after influenza virus inoculation

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and Agilent blocking agent according to the manufacturers instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Canine Oligo DNA Microarray ver.2 (Agilent-015067) for 17 hours at 65°C in a rotating Agilent DNA Microarray Hybridization Oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent Technologies) using default parameters (protocol GE1-v5_95 and Grid: 015067_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities. The Feature extracted data were imported into GeneSpring GX Software 7.3.1 (Agilent Technologies) for the analysis of gene expression. Transformation and Normalization of the data were performed with default settings described in the user manual (Data transformation: Set measurements less than 0.01 to 0.01, Per Chip normalization: Normalize to 50th percentile, Per Gene normalization: Normalize to Specific Samples).

organism: Canis lupus familiaris

source_name: TR7 Cells, 8hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low RNA Input Fluorescent Linear Amplification Kit PLUS, One-Color Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy Mini Kit column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (Thermo Fisher Scientific).

growth_protocol: MDCK and TR7 Cells were grown in 25T flasks (approximately 3 million cells) in MEM containing 10% FBS.

extract_protocol: Total RNA was extracted from the adherent cells and cell pellets using the NucleoSpin® RNA II Kit (Macherey-Nagel). RNA was quantified using a NanoDrop Spectrophotometer (Thermo Fisher Scientific) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were infected with A/Panama/H3N2 at MOI 0.5 or mock infected with PBS. Cells adhering to the flask were rinsed with PBS at 2, 4, 6, 8, 12 and 16 hpi. All floating cells were recovered as cell pellets by centrifugation at 1,500 g for 10 min in 15 mL conical tubes.

value: Cultured TR7 cells

tag: time point


title: day1_sal rep2

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v1.4.8, RTA 1.12.4.2. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Reads were mapped to mm9 with the Bowtie alignment program with setting --Best
Genome_build: mm9 with UCSC known genes annotation
Supplementary_files_format_and_content: tab delimited text file of FPKM values

molecule: polyA RNA

source_name: striatum of both hemispheres

growth_protocol: Groups of age-matched, sex-matched, and group-housed sibling mice

extract_protocol:
The striatum of both hemispheres, dorsal to the anterior commissure, were dissected on a cold plate and frozen on dry ice. Frozen tissue samples were homogenized in Tri Reagent (Sigma), and RNA was precipitated using chloroform and isopropanol. RNA was purified with the RNEasy kit (Qiagen, Inc.) and DNAse-treated (Qiagen, Inc.), according to the manufacturer’s instructions.
Illumina TruSeq SBS Kit v3

value: 129Sv/Jae S4

value: 0.9% saline was injected, i.p.

tag: time

value: day 1

value: striatum of both hemispheres


title: day21_amph rep3

value: D-amphetamine hemisulfate salt (Sigma) was dissolved in 0.9% saline just prior to use and injected, i.p., at 10 ml/kg for a total daily dose of 7 mg/kg.

value: day 21

tag: tissue


title: MDCK_16hr

description: Gene expression after 16hr after influenza virus inoculation

source_name: MDCK Cells, 16hr

value: Cultured MDCK cells


title: TR7_12hr

description: Gene expression after 12hr after influenza virus inoculation

source_name: TR7 Cells, 12hr


title: TR7_4hr

description: Gene expression after 4hr after influenza virus inoculation

source_name: TR7 Cells, 4hr


title: TR7_2hr

description: Gene expression after 2hr after influenza virus inoculation

source_name: TR7 Cells, 2hr


title: Ypel4-/- #3 Ortho-E

value: Orthochromatic erythroblast


title: Ypel4-/- #2 Poly-E

value: Homozygous mutant

value: Polychromatic erythroblast


title: ALL_836

tag: disease state

value: diagnosis

tag: rna prep

value: TruSeq RNA Access

value: Current study


title: MDCK_4hr

source_name: MDCK Cells, 4hr


title: MDCK_8hr

source_name: MDCK Cells, 8hr


title: day7_sal rep2

tag: strain

value: day 7


title: day7_amph rep3


title: Ypel4-/- #1 Ortho-E

tag: genotype


title: TR7_0hr

description: Gene expression after 0hr after influenza virus inoculation

source_name: TR7 Cells, 0hr


title: ALL_8r1

value: first relapse

value: Blood

tag: source


title: TR7_16hr

source_name: TR7 Cells, 16hr

value: Cultured TR7 cells


title: day1_amph rep3

value: 129Sv/Jae S4

tag: treatment


title: day21_sal rep1

value: 0.9% saline was injected, i.p.


title: day1_sal rep3

value: day 1


title: day1_amph rep1

value: striatum of both hemispheres


title: Ypel4-/- #1 Poly-E

value: Bone marrow


title: ALL_836r1


title: MDCK_6hr

description: Gene expression after 6hr after influenza virus inoculation

source_name: MDCK Cells, 6hr


title: MDCK_12hr

source_name: MDCK Cells, 12hr


title: ALL_8

value: ScriptSeq

value: Marincevic-Zuniga et al., 2017.


title: MDCK_2hr

source_name: MDCK Cells, 2hr

value: Cultured MDCK cells


title: TR7_6hr

source_name: TR7 Cells, 6hr


title: day21_sal rep2

value: day 21


title: ALL_5r2

source_name: Bone marrow

value: second relapse


title: ALL_5

value: diagnosis


title: day21_amph rep1

value: D-amphetamine hemisulfate salt (Sigma) was dissolved in 0.9% saline just prior to use and injected, i.p., at 10 ml/kg for a total daily dose of 7 mg/kg.


title: day7_sal rep3


title: day7_amph rep1


title: day1_amph rep2


title: normoxia + 2h PBS; replicate 3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.39; parameters:ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 AVGQUAL:20 TRAILING:20 MINLEN:33
Data were mapped to the mm10 reference genome with bwa mem (v0.7.17)
sam files of mapped reads were converted to position sorted bam format with samtools (v1.10)
peak calling was done with HOMER requiring a fold enrichment over local background and control of 4x or more (-F and -L parameters) and with 50 or more tags per peak
Genome_build: mm10
Supplementary_files_format_and_content: text files with called peaks per samples and bigwig fileswith per condition coverage

source_name: normoxia + 2h PBS

growth_protocol: Mice were housed in a temperature-controlled, specific pathogen free (SPF) air-conditioned animal house with 14 and 10h light/dark cycles and received food and water ad libitum

extract_protocol:
Chip was performed on snapfrozen liver samples derived from mice that were injected with PBS or 10 mg/kg DEX. 200mg of tissue was homogenized in PBS and then crosslinked with 2% formaldehyde in PBS for 20 min at RT while rotating. This reaction was stopped by adding 125mM glycine for 10min at RT. Tissue was then collected in ice-cold PBS and subsequently lysed in lysis buffer (0.1% SDS, 1% Triton X-100, 0.15M NaCl, 1mM EDTA and 20mM Tris pH8, supplemented with protease inhibitors). Lysates were sonicated at 4°C to yield 200-800bp DNA fragments. IP was performed on 100µl lysates diluted 1:3 in incubation buffer (0.15% SDS, 1% Triton X-100, 0.15M NaCl, 1mM EDTA and 20mM HEPES) with 5µg of rabbit anti-GR antibody (H300, sc-8992; Santa Cruz) or normal rabbit IgG (10500C; Invitrogen) as negative control at 4°C overnight. After two hours BSA blocked nProtein sepharose beads (GE Healthcare) were added to the lysates. The following day, beads were washed in WBI, WBII, LiCl buffer and twice in EDTA/HEPES buffer (0.5M EDTA and 1M HEPES). Chromatin was eluted in 200µl elution buffer (0,1M NaHCO3 and 10% SDS) supplemented with proteinase K. Next, proteins were decrosslinked by raising the incubation temperature to 65°C for 16h and DNA purified using the PCR purification kit (Qiagen), and eluting in 50µl of Qiagen Elution Buffer
Fifteen ng of purified DNA was used to generate ChIP-seq libraries according to manufacturer’s protocol using NEBNext Ultra II DNA Library Prep Kit (E7645L, NEB).

treatment_protocol: mice were placed in a hypoxic chamber and exposed to 7% oxygen (93% nitrogen) for 6 hours (6h hypoxia group), 24 hours (24h hypoxia group), or kept in normal conditions (normoxia group). Half of each group were given 10 mg/kg DEX, the other half were given PBS, and mice in the hypoxia group were placed back at 7% oxygen. Mice were sampled 2 hours post injection

value: 21% O2 + PBS injection

value: liver

tag: chip antibody


title: MDCK_0hr

source_name: MDCK Cells, 0hr

tag: cell type


title: normoxia + 2h PBS; replicate 1

value: anti-GR antibody (H300, sc-8992; Santa Cruz)


title: day21_sal rep3


title: ALL_834r2

source_name: Bone marrow+Peripheral blood

value: Bone marrow+Peripheral blood

value: TruSeq RNA Access

value: Current study


title: day21_amph rep2

source_name: striatum of both hemispheres

value: 129Sv/Jae S4


title: day7_amph rep2

value: day 7


title: normoxia + 2h PBS; replicate 2


title: normoxia + 2h DEX; replicate 3

source_name: normoxia + 2h DEX

value: 21% O2 with 2h of DEX stimulation (10 mg/kg i.p.)


title: day7_sal rep1

value: 0.9% saline was injected, i.p.

value: striatum of both hemispheres


title: ALL_834


title: day1_sal rep1

value: day 1


title: ALL_834r1

value: first relapse


title: normoxia + 2h DEX; replicate 2


title: ALL_833r2

value: TruSeq stranded total RNA


title: normoxia + 2h DEX; replicate 1


title: ALL_833


title: 24h hypoxia input control

source_name: 24h hypoxia input control

value: 7% O2 for 24 hours


title: 6h hypoxia input control

source_name: 6h hypoxia input control

value: 7% O2 for 6 hours


title: ALL_832r2

value: second relapse


title: ALL_832r1


title: 24h hypoxia + 2h PBS; replicate 3

source_name: 24h hypoxia + 2h PBS

value: 7% O2 for 24 hours (+ PBS injection)


title: ALL_831

value: diagnosis


title: normoxia input control

source_name: normoxia input control

value: liver


title: 24h hypoxia + 2h DEX; replicate 3

source_name: 24h hypoxia + 2h DEX

value: 7% O2 for 24 hours combined with 2h of DEX stimulation (10 mg/kg i.p.)

value: anti-GR antibody (H300, sc-8992; Santa Cruz)


title: 24h hypoxia + 2h PBS; replicate 2


title: ALL_831r1

value: Bone marrow+Peripheral blood

value: TruSeq RNA Access

value: Current study


title: 24h hypoxia + 2h PBS; replicate 1


title: 24h hypoxia + 2h DEX; replicate 2


title: 6h hypoxia + 2h PBS; replicate 3

source_name: 6h hypoxia + 2h PBS

value: 7% O2 for 6 hours (+ PBS injection)


title: 6h hypoxia + 2h PBS; replicate 2


title: 6h hypoxia + 2h PBS; replicate 1


title: 24h hypoxia + 2h DEX; replicate 1


title: 6h hypoxia + 2h DEX; replicate 3

source_name: 6h hypoxia + 2h DEX

value: 7% O2 for 6 hours combined with 2h of DEX stimulation (10 mg/kg i.p.)


title: 6h hypoxia + 2h DEX; replicate 2


title: genomic DNA from semen 39

type: genomic

city: Krakow

first: Aleksandra

last: Pisarek-Pacek

state: Malopolska

address: Gronostajowa 7A

department: Malopolska Centre of Biotechnology

country: Poland

institute: Jagiellonian University

description:
DNA isolated without preferential lysis
SAMPLE.39

hyb_protocol: Epigenome-wide methylation analysis was carried out using Illumina’s Infinium MethylationEPIC BeadChip array by the specialized Human Genomics Facility of Erasmus MC University Medical Center Rotterdam, The Netherland

data_processing: Basic QC analysis was performed by the specialized Human Genomics Facility of Erasmus MC University Medical Center Rotterdam, The Netherland. Subsequently, Infinium MethylationEPIC Array BeadChip data were pre-processed with R Bioconductor packages: “minfi”, “IlluminaHumanMethylationEPICanno.ilm10b4.hg19” and lluminaHumanMethylationEPICmanifest”. In the next step, methylation data were normalized with the SWAN method.

label: Cy5 and Cy3

source_name: semen 39

label_protocol: Standard Illumina Protocol

growth_protocol: Semen samples were collected from patients of fertility centers.

extract_protocol: DNA was extracted from semen using Sherlock AX Kit (A&A Biotechnology, Gdansk, Poland) according to the manufacturer’s protocol.

treatment_protocol: Semen sample was frozen and stored at -20°C until DNA extraction.

tag: age


title: genomic DNA from semen 35

description:
DNA isolated without preferential lysis
SAMPLE.35

scan_protocol: Epigenome-wide methylation analysis was carried out using Illumina’s Infinium MethylationEPIC BeadChip array by the specialized Human Genomics Facility of Erasmus MC University Medical Center Rotterdam, The Netherland

source_name: semen 35


title: genomic DNA from semen 20

description:
DNA isolated without preferential lysis
SAMPLE.20

source_name: semen 20


title: genomic DNA from semen 31

description:
DNA isolated without preferential lysis
SAMPLE.31

source_name: semen 31


title: genomic DNA from semen 40

description:
DNA isolated without preferential lysis
SAMPLE.40

source_name: semen 40


title: genomic DNA from semen 19

description:
DNA isolated without preferential lysis
SAMPLE.19

source_name: semen 19


title: genomic DNA from semen 21

description:
DNA isolated without preferential lysis
SAMPLE.21

source_name: semen 21


title: genomic DNA from semen 28

description:
DNA isolated without preferential lysis
SAMPLE.28

source_name: semen 28


title: 7d 10nM MT rep2

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for base calling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. 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. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of MT or IAA treatment vs control (two biological replicates) was performed using the Edge R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized with 2%(v/v) sodium hypochlorite (NaClO) containing 0.1%(v/v) TritonX-100 for 3 minutes, then washed for five times with sterile water and sown on plates containing Murashige and Skoog (MS) medium with 3%（w/v) sucrose and 0.8% (w/v) agar. After 3 days stratification at 4oC in the dark, plates were transferred to a growth chamber. The growth chamber was set at 23oC with 16 hours light and 8 hours dark cycles, 100 µmol photons m−2 s−1 light intensity and 60% relative humidity.

extract_protocol:
The seedlings of control and MT or IAA treated Col plants were collected for RNA isolation following the standard Qiagen RNeasy mini kit protocol. RNA purity and integrity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MT and IAA were dissolved in 100% ethanol (v/v) to obtain stock concentrations which were further diluted to the desired working concentrations. Ethanol with the final concentration of 0.1% was used as control treatment.  Four-day-old Arabidopsis seedlings on control MS medium plates were transferred to MS plates containing MT or IAA.

value: seedlings

tag: treatment time

value: 7d after MT treatment

value: WT


title: genomic DNA from semen 17

description:
DNA isolated without preferential lysis
SAMPLE.17

source_name: semen 17


title: genomic DNA from semen 23

description:
DNA isolated without preferential lysis
SAMPLE.23

source_name: semen 23


title: genomic DNA from semen 38

description:
DNA isolated without preferential lysis
SAMPLE.38

source_name: semen 38


title: genomic DNA from semen 12

description:
DNA isolated without preferential lysis
SAMPLE.12

source_name: semen 12


title: genomic DNA from semen 34

description:
DNA isolated without preferential lysis
SAMPLE.34

source_name: semen 34


title: genomic DNA from semen 29

description:
DNA isolated without preferential lysis
SAMPLE.29

source_name: semen 29


title: 6h hypoxia + 2h DEX; replicate 1


title: genomic DNA from semen 22

description:
DNA isolated without preferential lysis
SAMPLE.22

source_name: semen 22


title: 7d 10nM MT rep1


title: genomic DNA from semen 27

description:
DNA isolated without preferential lysis
SAMPLE.27

source_name: semen 27


title: genomic DNA from semen 26

description:
DNA isolated without preferential lysis
SAMPLE.26

source_name: semen 26


title: 7d 1nM IAA rep2

value: 7d after IAA treatment


title: genomic DNA from semen 36

description:
DNA isolated without preferential lysis
SAMPLE.36

source_name: semen 36


title: genomic DNA from semen 25

description:
DNA isolated without preferential lysis
SAMPLE.25

source_name: semen 25


title: genomic DNA from semen 16

description:
DNA isolated without preferential lysis
SAMPLE.16

source_name: semen 16


title: genomic DNA from semen 30

description:
DNA isolated without preferential lysis
SAMPLE.30

source_name: semen 30


title: genomic DNA from semen 13

description:
DNA isolated without preferential lysis
SAMPLE.13

source_name: semen 13


title: normoxia control rep3

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.39 parameters:ILLUMINACLIP:PE_adapters.fa:2:30:10 RAILING:20
Data were mapped to the mm10 reference genome with hisat2 v2.0.4 with Ensembl release 95 derived splice sites (--known-splicesite-infile)
mapped read were stired as position sorted bam files by diretly piping hisat output through samtools (| samtools view -bu - | samtools sort -@ 4 -o out.bam )
read counting was performed with featurecounts (-a Ensemb95.gtf -s 2 -T 6 --primary *.bam)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: processed files are a count matrix containg the counts output from featurecounts for all samples

source_name: liver

extract_protocol:
Total RNA was isolated with Aurum total RNA mini kit (Biorad) according to the manufacturer’s instructions
The 24h library was constructed using the TruSeq Stranded mRNA Library Prep kit (Illumina) according to the manufacturer’s instructions

treatment_protocol: mice were placed in a hypoxic chamber end exposed to 7% oxygen (93% nitrogen) for 24hours (hypoxia group), or kept in normal conditions (hypoxia group). Half of each group were given 10 mg/kg DEX, the other half were given PBS, and mice in the hypoxia group were placed back at 7% oxygen. Mice were sampled 2 hours post injection

value: 21percent O2 for 24 hours (+ PBS injection)


title: 7d 1nM IAA rep1


title: genomic DNA from semen 18

description:
DNA isolated without preferential lysis
SAMPLE.18

source_name: semen 18


title: genomic DNA from semen 14

description:
DNA isolated without preferential lysis
SAMPLE.14

source_name: semen 14


title: normoxia control rep2


title: genomic DNA from semen 33

description:
DNA isolated without preferential lysis
SAMPLE.33

source_name: semen 33


title: genomic DNA from semen 32

description:
DNA isolated without preferential lysis
SAMPLE.32

source_name: semen 32


title: genomic DNA from semen 15

description:
DNA isolated without preferential lysis
SAMPLE.15

source_name: semen 15


title: 7d control rep1

source_name: seedlings

value: 7d without treatment


title: normoxia 10 mg/kg DEX rep2

value: 21percent O2 for 24 hours combined with 2h of DEX stimulation (10 mg/kg i.p.)


title: normoxia control rep1


title: normoxia 10 mg/kg DEX rep1


title: Low milk protein percentage phenotype in non-lactating period_rep2

city: Beijing

first: Wentao

last: Cai

address: No2. Yuanmingyuan West Road

institute: Chinese Academic of Agricultural Science

data_processing:
Quality trimming and adaptor removal of the Illumina reads were carried out using Cutadapt and Trimmomatic
The matching sequences ranged from 18 nt to 30 nt were used to align against the miRBase 22.0 (http://www.mirbase.org/) to identify known miRNAs by miRDeep2 with a quantifier.pl module
Genome_build: ARS-UCD 1.2
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

organism: Bos taurus

source_name: Mammary gland

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Twelve small RNA libraries from RNA integrity and concentration were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
All RNA samples had an RNA integrity number of at least 7.5. 15% agarose gels separated total RNA to extract the small RNA (18-30 nt). After precipitated by ethanol and centrifugal enrichment of small RNA sample, the library was prepared according to the method and process of Small RNA Sample Preparation Kit (Illumina, RS-200-0048). RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 2.0 to preliminary quantify and then dilute to 1 ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). After the insert size consistent with expectations, the qualified insert size was accurate quantitative using the Taqman fluorescence probe of AB Step One Plus Real-Time PCR system (Library valid concentration>2 nM). The qualified libraries were sequenced by an Illumina Hiseq 2500 platform and generate 50 bp single-end reads.

tag: breed

value: Chinese Holstein

value: Mammary gland

tag: phenotype

value: low protein in non-lactating


title: normoxia 10 mg/kg DEX rep3


title: Low milk protein percentage phenotype in non-lactating period_rep3


title: 7d control rep2


title: 24h of hypoxia rep3

value: 7percent O2 for 24 hours (+ PBS injection)


title: 24h of hypoxia rep2


title: genomic DNA from semen 24

description:
DNA isolated without preferential lysis
SAMPLE.24

source_name: semen 24


title: Low milk protein percentage phenotype in non-lactating period_rep1


title: High milk protein percentage phenotype in non-lactating period_rep3

value: high protein in non-lactating


title: genomic DNA from semen 37

description:
DNA isolated without preferential lysis
SAMPLE.37

source_name: semen 37


title: 24h of hypoxia rep1


title: High milk protein percentage phenotype in non-lactating period_rep2


title: 24h of hypoxia + 10 mg/kg DEX rep3

value: 7percent O2 for 24 hours combined with 2h of DEX stimulation (10 mg/kg i.p.)


title: 24h of hypoxia + 10 mg/kg DEX rep2


title: genomic DNA from semen 11

description:
DNA isolated without preferential lysis
SAMPLE.11

source_name: semen 11


title: Low milk protein percentage phenotype in lactation_rep3

value: low protein in lactation


title: 24h of hypoxia + 10 mg/kg DEX rep1


title: High milk protein percentage phenotype in non-lactating period_rep1


title: Low milk protein percentage phenotype in lactation_rep2


title: genomic DNA from semen 10

description:
DNA isolated without preferential lysis
SAMPLE.10

source_name: semen 10


title: Low milk protein percentage phenotype in lactation_rep1


title: genomic DNA from semen 9

description:
DNA isolated without preferential lysis
SAMPLE.9

source_name: semen 9


title: control rep2

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.39 parameters:ILLUMINACLIP:PE_adapters.fa:2:30:10 RAILING:20
Data were mapped to the mm10 reference genome with hisat2 v2.0.4 with Ensembl release 95 derived splice sites (--known-splicesite-infile) and an only concordantly mapping reads were kept
mapped read were stired as position sorted bam files by diretly piping hisat output through samtools (| samtools view -bu - | samtools sort -@ 4 -o out.bam )
read counting was performed with featurecounts (-a Ensemb95.gtf -s 2 -T 6 --primary *.bam)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: processed files are a count matrix containg the counts output from featurecounts for all samples

extract_protocol:
Total RNA was isolated with Aurum total RNA mini kit (Biorad) according to the manufacturer’s instructions
The 24h library was constructed using a Stranded nextseq high output mRNA Library Prep kit (2x150p) according to the manufacturer’s instructions

treatment_protocol: mice were placed in a hypoxic chamber end exposed to 7% oxygen (93% nitrogen) for 6 hours (hypoxia group), or kept in normal conditions (hypoxia group). Half of each group were given 10 mg/kg DEX, the other half were given PBS, and mice in the hypoxia group were placed back at 7% oxygen. Mice were sampled 2 hours post injection

value: 21percent O2 for 6 hours (+ PBS injection)


title: genomic DNA from semen 8

description:
DNA isolated without preferential lysis
SAMPLE.8

source_name: semen 8


title: genomic DNA from semen 6

description:
DNA isolated without preferential lysis
SAMPLE.6

source_name: semen 6


title: genomic DNA from ovarian cancer tissues [G674]

city: Pokfulam

first: David

middle: Wai

state: Hong Kong

address: L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road

department: Obs. & Gyn.

country: Hong Kong

institute: The Uniersity of Hong Kong

description:
Ovarian tumor tissue
R07C01

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina iScan System

data_processing: Genome Studio Version 2011.1 and Methylation Fenome Studio Module v1.9

source_name: Tumor Tissues

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: Sex

value: female

tag: Stage

tag: grade

tag: tumour subtypes

tag: tumour subtypes2

value: clear cell

tag: primary chemotherapy treatment

value: carboplatin/pacelitaxel

tag: recurrence

tag: doot

tag: dodx

tag: survivial status


title: control rep3

tag: strain

tag: treatment


title: genomic DNA from ovarian cancer tissues [G667]

description:
Ovarian tumor tissue
R05C01

value: endometrioid


title: genomic DNA from ovarian cancer tissues [G657]

description:
Ovarian tumor tissue
R04C01

value: mucinous


title: High milk protein percentage phenotype in lactation_rep3

tag: tissue

value: high protein in lactation


title: genomic DNA from ovarian cancer tissues [G677]

description:
Ovarian tumor tissue
R08C01

tag: age


title: genomic DNA from semen 7

description:
DNA isolated without preferential lysis
SAMPLE.7

source_name: semen 7


title: genomic DNA from semen 1

description:
DNA isolated without preferential lysis
SAMPLE.1

source_name: semen 1


title: genomic DNA from ovarian cancer tissues [G662]

description:
Ovarian tumor tissue
R01C01

value: no chemotherapy


title: High milk protein percentage phenotype in lactation_rep2


title: genomic DNA from semen 4

description:
DNA isolated without preferential lysis
SAMPLE.4

source_name: semen 4


title: control rep1

source_name: liver


title: genomic DNA from ovarian cancer tissues [G661]

description:
Ovarian tumor tissue
R08C01


title: genomic DNA from ovarian cancer tissues [G663]

description:
Ovarian tumor tissue
R02C01

value: carboplatin


title: genomic DNA from ovarian cancer tissues [G658]

description:
Ovarian tumor tissue
R05C01

value: mixed clear cell and endometrioid


title: genomic DNA from ovarian cancer tissues [G670]

description:
Ovarian tumor tissue
R06C01

value: serous


title: genomic DNA from ovarian cancer tissues [G664]

description:
Ovarian tumor tissue
R03C01

value: carboplatin/taxol+avastin


title: 10 mg/kg DEX rep3

value: 21percent O2 for 6 hours combined with 2h of DEX stimulation (10 mg/kg i.p.)


title: genomic DNA from semen 3

description:
DNA isolated without preferential lysis
SAMPLE.3

source_name: semen 3


title: genomic DNA from ovarian cancer tissues [G666]

description:
Ovarian tumor tissue
R04C01


title: High milk protein percentage phenotype in lactation_rep1

value: Chinese Holstein

value: Mammary gland


title: genomic DNA from ovarian cancer tissues [G655]

description:
Ovarian tumor tissue
R02C01


title: 10 mg/kg DEX rep1


title: 10 mg/kg DEX rep2


title: genomic DNA from semen 2

description:
DNA isolated without preferential lysis
SAMPLE.2

source_name: semen 2


title: genomic DNA from semen 5

description:
DNA isolated without preferential lysis
SAMPLE.5

source_name: semen 5


title: genomic DNA from ovarian cancer tissues [G650]

description:
Ovarian tumor tissue
R07C01


title: spt4-2_NETseq

city: Boston

first: Mary

middle: T

last: Couvillion

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: nascent RNA isolated by IP against Rpb3-3x FLAG affinity label

data_processing:
Library strategy: NET-seq
Library strategy: NET-seq
For NET-seq, libraries were sequenced in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net). The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts. Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read. Only the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, is recorded with a custom python script using HTSeq package in python.
Genome_build: sacCer3
Supplementary_files_format_and_content: Bedgraph with 4 columns: Chromosome, Start, End, Score

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.

extract_protocol:
For NET-seq, frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004).
For NET-seq, a preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScriptsIII (Invitrogen)) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~8-10 cycles) by band extraction from a polyacrylamide gel. DNA was sequenced on the Illumina NextSeq 500 according to the manufacturer’s instructions in 75 base pair reads.

tag: genotype/variation

value: RPB3::RPB3-3xFLAG NAT, SPT4::HIS3

tag: rna fraction

value: Nascent RNA

tag: ip

value: IP against 3xFLAG affinity label


title: ubp8-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, UBP8::HIS3


title: rpb4-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, RPB4::HIS3


title: swr1-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, SWR1::HIS3


title: 6h of hypoxia rep3

value: 7percent O2 for 6 hours (+ PBS injection)


title: 6h of hypoxia rep2


title: 6h of hypoxia rep1


title: genomic DNA from ovarian cancer tissues [G652]

description:
Ovarian tumor tissue
R08C01

tag: Sex

value: female

value: mixed endometrioid, clear cell

value: carboplatin/pacelitaxel


title: genomic DNA from ovarian cancer tissues [G656]

description:
Ovarian tumor tissue
R03C01

tag: Stage

value: mixed endometrioid and clear cell


title: genomic DNA from ovarian cancer tissues [G653]

description:
Ovarian tumor tissue
R01C01

tag: grade

value: mucinous

value: no chemotherapy


title: 6h of hypoxia + 10 mg/kg DEX rep3

value: 7percent O2 for 6 hours combined with 2h of DEX stimulation (10 mg/kg i.p.)


title: rad6-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, RAD6::HIS3


title: genomic DNA from ovarian cancer tissues [G651]

description:
Ovarian tumor tissue
R06C01

tag: tumour subtypes

value: endometrioid


title: 6h of hypoxia + 10 mg/kg DEX rep2


title: rco1-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, RCO1::HIS3


title: dst1-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, DST1::HIS3


title: 6h of hypoxia + 10 mg/kg DEX rep1


title: genomic DNA from ovarian cancer tissues [G659]

description:
Ovarian tumor tissue
R06C01

tag: tumour subtypes2

value: seromucinous borderline tumour with a small focus of clear cell carcinoma and another focus of mixed endoemtrioid and mucinous tumour


title: ccr4-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, CCR4::HIS3

value: Nascent RNA

value: IP against 3xFLAG affinity label


title: genomic DNA from ovarian cancer tissues [G660]

description:
Ovarian tumor tissue
R07C01

value: serous

tag: primary chemotherapy treatment


title: genomic DNA from ovarian cancer tissues [G649]

description:
Ovarian tumor tissue
R05C01

value: clear cell

tag: recurrence


title: bye1-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, BYE1::HIS3


title: CAPs-treated endothelial progenitor cells rep3 [miRNA-seq]

city: Louisville

first: Timothy

last: O'Toole

state: KY

address: 302E. Muhammad Ali Blvd

institute: University of Louisville

data_processing:
Illumina RTA (v2.4.11) and bcl2fastq2 (20.0.422) softwares were used for basecalling.
Sequencing run were concatenated into one single-end .fastq file using the unix cat command. The Sequenced reads were trimmed for adaptor sequence and quality using Trimmomatric v0.33.
The trimmed data were further analyzed using mirDeep2 and DESeq2. Briefly, the trimmed sequence reads were directly mapped to the mouse  mm10 reference genome assembly using mirDeep2 package (v 0.07) implementing bowtie mapper (v 1.1.1).The aligned sequences were then used as inputs into mirSeep2 along with the mirBase release 22 mature miRNA and miRNA hairpin sequences. After quantification, the resulting counts for each miRNA in each sample were combined into a reads matrix.
Using the counts table resulting from the previous step, differentially expressed miRNAs were determined using DESeq2
Genome_build: mm10 and mirBase
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: EPCs isolated from the bone marrow were cultured for 12 days

extract_protocol:
RNAs were isolated with the miRNeasy kit (Qiagen)
libraries were prepared according to Illumina standard protocols using QIAseq miRNA Library Kit and QIAseq miRNA NGS beads.

tag: cell type

value: endothelial progenitor cells

value: bone marrow

value: CAPS exposure


title: CAPs-treated endothelial progenitor cells rep2 [miRNA-seq]


title: CAPs-treated endothelial progenitor cells rep1 [miRNA-seq]


title: wt-H4K12Ac_ChIPnexus

description: genomic DNA isolated by IP against histone H4K12Ac

data_processing:
Library strategy: ChIP-nexus
For NET-seq, libraries were sequenced in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net). The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts. Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read. Only the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, is recorded with a custom python script using HTSeq package in python.
For ChIP-nexus, all reads were filtered for the presence of the fixed barcode (CTGA), beginning at position 6 of the read. Next, the adapter sequence was trimmed using cutadapt with the following parameters: cutadapt -f fastq -a AGATCGGAAGAGCACACGTCT -O 3 -m 22 --length-tag ‘length=’. Lastly, before alignment to the genome, the molecular barcode was removed using custom python scripts. As the ChIP-nexus samples were spiked with S. pombe, the reads were aligned to a combined genome containing both the S. cerevisiae and S. pombe genomes. Reads were aligned using Bowtie version 1.1.1 (Langmead et al., 2009) with the following parameters: -v 2 -M 1 --best -S. Plus and minus strand coverage were then combined and coverage files were then generated using BEDtools version 2.23.0 with the following parameters: genomeCoverageBed -d -5. Only the 5’ end of the read, which corresponds to the point of crosslinking is recorded. The S. cerevisiae and S. pombe data were then separated and S. cerevisiae coverage files were normalized by the total number of mapped S. pombe reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: Bedgraph with 4 columns: Chromosome, Start, End, Score

extract_protocol:
For NET-seq, frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004). For ChIP-nexus cells were crosslinked in 1% formaldehyde, lysed by bead beating, and sonicated. Chomatin was isolated via immunoprecipitation using antibodies: for H3 (Abcam, ab1791), H4 (Abcam, ab10158), H3K23Ac (Millipore, 07-355), and H4K12Ac (Millipore, 07-595), IPs, 12 µg of each antibody were added to 100 µL of Protein G Dynabeads (Thermo Fischer Scientific) previously washed 3 times with 1 mL of 0.5% BSA in PBS.
For NET-seq, a preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScriptsIII (Invitrogen)) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~8-10 cycles) by band extraction from a polyacrylamide gel. DNA was sequenced on the Illumina NextSeq 500 according to the manufacturer’s instructions in 75 base pair reads. Preparation of ChIP-nexus libraries was done as described in (He et al., 2015) with the following modifications made to adapt the protocol to yeast: Frozen cell pellets were thawed on ice 1600µL of LB 140 (50 mM HEPES pH 7.4, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1X protease inhibitors (Roche, cOmplete EDTA free)) was added to the pellet. The samples were then split into two screw-cap tubes and acid-washed glass beads (Sigma) were added to the meniscus. Cells were lysed by bead beating for a total of 8 minutes, beating for 1 minute at 4˚C followed by resting for 2 minutes on ice. Chromatin was then removed from the tubes by using a 25G needle to pierce the bottom of the tube. The tubes were then placed inside a 15 mL conical and spun for 1 minute at 1000 xg at 4˚C. The samples were then transferred to a 1.5 mL eppendorf tube and spun at 14,000 rpm for 5 minutes at 4˚C. Pellets were next washed in 800 µL of LB 140 and collected again by centrifuging at 14,000 rpm for 5 minutes at 4˚C. 800 µL of LB 140 was added to the sample and the suspension was transferred to a 15 mL polystyrene tube. 600 µL of LB 140 was used to wash the empty eppendorf tube and then added to the 15 mL tube. Chromatin was then sonicated using Diagenode Bioruptor. Six cycles of sonication were done, each for 5 minutes and 30 seconds ON and 30 seconds OFF for a total sonication time of 15 minutes. After sonication, the chromatin was spun at 20,000 xg for 20 minutes at 4˚C. The supernatant was transferred to a new tube and the concentration of the chromatin was assayed by a Modified Lowry assay (Pierce). The size of the sonicated chromatin was confirmed on a 1.5% agarose gel to be between 100 - 400 bp. For each IP, 3 mg of chromatin extract was used, spiked with 5% (by protein concentration) of S. pombe chromatin. Samples were diluted up to 10 mL using WB 140 (50mM HEPES pH 7.4, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate). For H3 (Abcam, ab1791), H4 (Abcam, ab10158), H3K23Ac (Millipore, 07-355), and H4K12Ac (Millipore, 07-595), IPs, 12 µg of each antibody were added to 100 µL of Protein G Dynabeads (Thermo Fischer Scientific) previously washed 3 times with 1 mL of 0.5% BSA in PBS. After the final was, the supernatant was removed and the chromatin was added to the beads in a 15 mL conical tube. Samples were incubated overnight at 4˚C with rotation. The remainder of the library construction was done exactly as described in (He et al., 2015). The only modifications were changes made to the four wash buffers to adapt them to yeast. Wash buffer A consisted of 10mM TE and 0.1% Triton X-100. Wash buffer B consisted of 50mM HEPES pH 7.4, 140mM NaCl, 1mM EDTA, 1% Triton X-100, and 0.1% sodium deoxycholate. Wash buffer C is the same as wash buffer B, but with 250mM NaCl. Wash buffer D consisted of 10mM Tris pH 7.5, 250 mM lithium chloride, 10 mM EDTA, 0.5% NP40, 0.1% sodium deoxycholate.

value: RPB3::RPB3-3xFLAG NAT

value: IP against histone H4K12Ac (Millipore, 07-595)


title: genomic DNA from ovarian cancer tissues [G648]

description:
Ovarian tumor tissue
R04C01

value: female

value: carboplatin/pacelitaxel

tag: doot

tag: dodx


title: genomic DNA from ovarian cancer tissues [G645]

description:
Ovarian tumor tissue
R01C01

value: endometrioid

value: carboplatin

tag: survivial status


title: genomic DNA from ovarian cancer tissues [G634]

description:
Ovarian tumor tissue
R06C01

value: mucinous


title: genomic DNA from ovarian cancer tissues [G646]

description:
Ovarian tumor tissue
R02C01

value: carboplatin/pacelitaxel, topotecan, liposomal doxorubicin


title: wt-H4_ChIPnexus

description: genomic DNA isolated by IP against histone H4

tag: strain

value: IP against histone H4 (Abcam, ab10158)


title: genomic DNA from ovarian cancer tissues [G626].

description:
Ovarian tumor tissue
R06C01


title: Air-treated endothelial progenitor cells rep2 [miRNA-seq]

tag: tissue

tag: treatment

value: Air exposure


title: Air-treated endothelial progenitor cells rep3 [miRNA-seq]


title: genomic DNA from ovarian cancer tissues [G590]

description:
Ovarian tumor tissue
R04C01

tag: age

value: no chemotherapy


title: wt-H3K23Ac_ChIPnexus

description: genomic DNA isolated by IP against histone H3K23Ac

tag: genotype/variation

value: IP against histone H3K23Ac (Millipore, 07-355)


title: genomic DNA from ovarian cancer tissues [G585]

description:
Ovarian tumor tissue
R08C01

value: mixed mucinous and serous


title: genomic DNA from ovarian cancer tissues [G588]

description:
Ovarian tumor tissue
R02C01

value: serous


title: Air-treated endothelial progenitor cells rep1 [miRNA-seq]

value: endothelial progenitor cells


title: bur2-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, BUR2::HIS3

tag: rna fraction

value: Nascent RNA

tag: ip

value: IP against 3xFLAG affinity label


title: wt-H3_ChIPnexus

description: genomic DNA isolated by IP against histone H3

value: RPB3::RPB3-3xFLAG NAT

value: IP against histone H3 (Abcam, ab1791)


title: CAPs-treated endothelial progenitor cells rep3 [mRNA-seq]

data_processing:
Illumina RTA (v2.4.11) and bcl2fastq2 (20.0.422) softwares were used for basecalling.
Sequenced reads were trimmed for adaptor sequence. Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1) for each sequencing sample. All the samples have a phred score above 28, which were considered to be  good quality and sequencing trimming is unnessary.
The concatenated sequences were directly aligned to the mm10 reference genome assembly using STAR (version 2.6). The alignment rate for each of the six samples are above 99%.
Raw counts were obtained from the STAR aligned bam format files using HTSeq version 0.10.0. The reverse option was used to indicate strand orientation. Illumina's TruSeq Stranded mRNA protocol was used to sequence the data and produces libraries where the first read is on the opposite strand to the RNA molecule. The raw counts were normalized using the Relative Log Expression (RLE) method with the aid of DESeq2.
Differentially expressed genes were identified by comparison of CAPs vs. Air using DESeq2 package.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: endothelial progenitor cells

extract_protocol:
RNAs were isolated with the miRNeasy kit (Qiagen)
libraries were prepared according to Illumina standard protocols using the TruSeq Stranded mRNA library Prep kit and Agencourt AMPure XP Beads.

value: bone marrow

value: CAPS exposure


title: gcn5-H4K12Ac_ChIPnexus

value: RPB3::RPB3-3xFLAG NAT, GCN5::HIS3

value: IP against histone H4K12Ac (Millipore, 07-595)


title: genomic DNA from ovarian cancer tissues [G589]

description:
Ovarian tumor tissue
R03C01

tag: Sex

value: female

tag: Stage

value: carboplatin/pacelitaxel


title: genomic DNA from ovarian cancer tissues [G582]

description:
Ovarian tumor tissue
R06C01

tag: grade

tag: tumour subtypes

value: carboplatin


title: genomic DNA from ovarian cancer tissues [G572].

description:
Ovarian tumor tissue
R07C01

tag: tumour subtypes2

tag: primary chemotherapy treatment

value: no chemotherapy


title: CAPs-treated endothelial progenitor cells rep2 [mRNA-seq]


title: genomic DNA from ovarian cancer tissues [G591]

description:
Ovarian tumor tissue
R05C01

value: mixed endometrioid and serous

tag: recurrence


title: gcn5-H4_ChIPnexus

value: IP against histone H4 (Abcam, ab10158)


title: CAPs-treated endothelial progenitor cells rep1 [mRNA-seq]


title: gcn5-H3K23Ac_ChIPnexus

value: IP against histone H3K23Ac (Millipore, 07-355)


title: genomic DNA from ovarian cancer tissues [G581]

description:
Ovarian tumor tissue
R05C01

value: at least 1A

value: seromucinous

tag: doot


title: genomic DNA from ovarian cancer tissues [G647]

description:
Ovarian tumor tissue
R03C01

value: mucinous

tag: dodx


title: genomic DNA from ovarian cancer tissues [G577]

description:
Ovarian tumor tissue
R04C01

tag: survivial status


title: genomic DNA from ovarian cancer tissues [G587]

description:
Ovarian tumor tissue
R01C01

value: mixed clear cell and serous


title: genomic DNA from ovarian cancer tissues [G584]

description:
Ovarian tumor tissue
R07C01

value: clear cell


title: genomic DNA from ovarian cancer tissues [G550]

description:
Ovarian tumor tissue
R07C01

value: endometrioid


title: genomic DNA from ovarian cancer tissues [G563]

description:
Ovarian tumor tissue
R01C01

value: high grade

value: serous


title: genomic DNA from ovarian cancer tissues [G576]

description:
Ovarian tumor tissue
R03C01


title: Air-treated endothelial progenitor cells rep3 [mRNA-seq]

value: bone marrow

tag: strain

value: Air exposure


title: gcn5-H3_ChIPnexus

value: RPB3::RPB3-3xFLAG NAT, GCN5::HIS3

value: IP against histone H3 (Abcam, ab1791)


title: genomic DNA from ovarian cancer tissues [G548]

description:
Ovarian tumor tissue
R05C01

value: female

value: carboplatin/pacelitaxel


title: genomic DNA from ovarian cancer tissues [G556]

description:
Ovarian tumor tissue
R08C01

value: no chemotherapy


title: Air-treated endothelial progenitor cells rep2 [mRNA-seq]

tag: tissue


title: genomic DNA from ovarian cancer tissues [G707]

description:
Ovarian tumor tissue
R08C01


title: Air-treated endothelial progenitor cells rep1 [mRNA-seq]

tag: treatment


title: genomic DNA from ovarian cancer tissues [G709]

description:
Ovarian tumor tissue
R02C01

tag: age

value: mixed serous endometrioid


title: Aire-KO rep 3 (mouse)

city: Bethesda

first: Michail

last: Lionakis

address: 9000 Rockville Pike

institute: National Institutes of Health

description:
CPM_TMM_counts.txt
RawCountFile.txt

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCm38.p3 mouse genome using STAR v2.5.2a in  single-pass mode. With the following parameters:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Genome_build: Custom mm10/GRCm38.vM11+ERCCs
Supplementary_files_format_and_content: Tab delimited files include a raw counts and TMM-normalized expression matrices.

source_name: Oral epithelial cells

extract_protocol:
Sorted tongue epithelial cells were lysed in Trizol prior to extraction with the Norgen Biotek RNA Clean-up and Concentration Micro-Elute Kit (cat. # 61000)
Sequencing libraries were prepared by the Illumina Nextera method, following manufacturer's recommendations and sequenced in a NextSeq500 instrument in 150 bp end mode

value: Non-obese diabetic (NOD)

tag: cell source

value: Tongue epithelium

value: 8 weeks

value: Male

tag: genotype

value: Aire-/-


title: eaf1-H4_ChIPnexus

tag: genotype/variation

value: RPB3::RPB3-3xFLAG NAT, EAF1::HIS3

tag: ip

value: IP against histone H4 (Abcam, ab10158)


title: genomic DNA from ovarian cancer tissues [G549]

description:
Ovarian tumor tissue
R06C01

tag: Sex

tag: Stage

value: at least 3A2

value: endometrioid


title: genomic DNA from ovarian cancer tissues [G570]

description:
Ovarian tumor tissue
R02C01

value: unstaged

tag: grade

tag: tumour subtypes


title: genomic DNA from ovarian cancer tissues [G710]

description:
Ovarian tumor tissue
R03C01

tag: tumour subtypes2

value: mucinous

tag: primary chemotherapy treatment


title: eaf1-H3K23Ac_ChIPnexus

value: IP against histone H3K23Ac (Millipore, 07-355)


title: genomic DNA from ovarian cancer tissues [G711]

description:
Ovarian tumor tissue
R04C01

tag: recurrence

tag: doot


title: Aire-KO rep 2 (mouse)

description:
CPM_TMM_counts.txt
RawCountFile.txt


title: genomic DNA from ovarian cancer tissues [G702]

description:
Ovarian tumor tissue
R06C01

tag: dodx

tag: survivial status


title: genomic DNA from ovarian cancer tissues [G708]

description:
Ovarian tumor tissue
R01C01


title: eaf1-H3_ChIPnexus

tag: strain

value: IP against histone H3 (Abcam, ab1791)


title: wt-3_NETseq

data_processing:
Library strategy: NET-seq
For NET-seq, libraries were sequenced in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net). The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts. Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read. Only the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, is recorded with a custom python script using HTSeq package in python.
For ChIP-nexus, all reads were filtered for the presence of the fixed barcode (CTGA), beginning at position 6 of the read. Next, the adapter sequence was trimmed using cutadapt with the following parameters: cutadapt -f fastq -a AGATCGGAAGAGCACACGTCT -O 3 -m 22 --length-tag ‘length=’. Lastly, before alignment to the genome, the molecular barcode was removed using custom python scripts. As the ChIP-nexus samples were spiked with S. pombe, the reads were aligned to a combined genome containing both the S. cerevisiae and S. pombe genomes. Reads were aligned using Bowtie version 1.1.1 (Langmead et al., 2009) with the following parameters: -v 2 -M 1 --best -S. Plus and minus strand coverage were then combined and coverage files were then generated using BEDtools version 2.23.0 with the following parameters: genomeCoverageBed -d -5. Only the 5’ end of the read, which corresponds to the point of crosslinking is recorded. The S. cerevisiae and S. pombe data were then separated and S. cerevisiae coverage files were normalized by the total number of mapped S. pombe reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: Bedgraph with 4 columns: Chromosome, Start, End, Score

value: RPB3::RPB3-3xFLAG NAT

tag: rna fraction

value: Nascent RNA

value: IP against 3xFLAG affinity label


title: WT rep 2 (mouse)

description:
CPM_TMM_counts.txt
RawCountFile.txt

tag: age

value: WT


title: WT rep 3 (mouse)

description:
CPM_TMM_counts.txt
RawCountFile.txt

value: Non-obese diabetic (NOD)

tag: cell source


title: genomic DNA from ovarian cancer tissues [G703]

description:
Ovarian tumor tissue
R07C01

value: female

value: mixed serous endometrioid


title: genomic DNA from ovarian cancer tissues [G698]

description:
Ovarian tumor tissue
R03C01

value: serous


title: wt-4_NETseq


title: eaf1-H4K12Ac_ChIPnexus

value: IP against histone H4K12Ac (Millipore, 07-595)


title: genomic DNA from ovarian cancer tissues [G701]

description:
Ovarian tumor tissue
R05C01

value: carboplatin/pacelitaxel


title: genomic DNA from ovarian cancer tissues [G691]

description:
Ovarian tumor tissue
R07C01

value: no chemotherapy


title: WT rep 1 (mouse)

description:
CPM_TMM_counts.txt
RawCountFile.txt

value: Tongue epithelium

value: 8 weeks

value: Male

tag: genotype


title: genomic DNA from ovarian cancer tissues [G697]

description:
Ovarian tumor tissue
R02C01

value: endometrioid

value: carboplatin


title: wt-1_NETseq

tag: genotype/variation


title: wt-2_NETseq

tag: ip


title: Cerebellar tissue - 84Q+IGF1_rep3 [22_2_1]

city: Changhua

first: Chin-San

last: Liu

address: 135 Nan-Hsiao Street

country: Taiwan

institute: Changhua Christian Hospital

data_processing:
Basecalls performed using bcl2fastq version 2.20.
Both adaptor clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach
RNAseq reads were aligned to the mm10 genome assembly using hisat2 version 2.2.0 with default setting
Genome_build: mm10
Supplementary_files_format_and_content: raw counts files were generated using featureCounts implemented in Rsubread v1.22.2

source_name: Cerebellar tissue - 84Q+IGF1

growth_protocol: Tissue was harvest from 18-month old mice.

extract_protocol:
Total RNA was extracted using Trizol® Reagent (Invitrogen, USA) according to the instruction manual. Purified RNA was quantified at OD260nm using a ND-1000 spectrophotometer (Nanodrop Technology,USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 LabChip kit (Agilent Technology, USA).
Samples with very high RNA integrity numbers were selected for library construction, and the libraries were constructed using Agilent's SureSelect Strand-Specific RNA Library Preparation Kit followed by AMPure XP beads (Beckman Coulter, USA) size selection. Libraries were sequenced as paired-end 150 bp reads on an Illumina HiSeq 2500 (Illumina, San Diego, USA) with a depth of ~20 million reads each. Sequencing data (FASTQ reads) were generated using Welgene Biotech's pipeline based on Illumina's base-calling program bcl2fastq v2.20.

treatment_protocol: The SCA3 15Q and 84Q transgenic mice were administered intraperitoneal injections of PBS(0.01 M) or IGF1(50 mg/kg) weekly from the postnatal age of 9 months to 18 months.

tag: strain background

tag: treatment

value: treated with IGF1(50 mg/kg) per week

tag: cell type

value: cerebellar tissue


title: Aire-KO rep 1 (mouse)

description:
CPM_TMM_counts.txt
RawCountFile.txt

tag: Sex

value: Aire-/-


title: genomic DNA from ovarian cancer tissues [G690]

description:
Ovarian tumor tissue
R06C01

tag: Stage

tag: grade

tag: tumour subtypes

tag: tumour subtypes2

value: mucinous


title: Cerebellar tissue - 84Q+IGF1_rep2 [22_1_1]


title: genomic DNA from ovarian cancer tissues [G696]

description:
Ovarian tumor tissue
R01C01

tag: primary chemotherapy treatment

tag: recurrence

tag: doot

tag: dodx


title: vps34-2_NETseq

tag: strain

value: RPB3::RPB3-3xFLAG NAT, VPS34::HIS3

tag: rna fraction

value: Nascent RNA

value: IP against 3xFLAG affinity label


title: genomic DNA from ovarian cancer tissues [G688]

description:
Ovarian tumor tissue
R04C01

value: female

tag: age

value: carboplatin/pacelitaxel, topotecan

tag: survivial status


title: vps34-1_NETseq

tag: genotype/variation

tag: ip


title: genomic DNA from ovarian cancer tissues [G692]

description:
Ovarian tumor tissue
R08C01

value: mixed endoemtrioid and serous

value: carboplatin/taxol+avastin


title: vps15-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, VPS15::HIS3


title: genomic DNA from ovarian cancer tissues [G686]

description:
Ovarian tumor tissue
R03C01

value: serous


title: vps15-1_NETseq


title: m6A-seq FTO mutant root IP rep2

first: Shun

state: IL

address: 929 E. 57th. Street

department: Chemistry

institute: University of Chicago

description:
FTOmut_root_rep2_gene_MeTPeak.txt
FTOmut_root_rep2_repeat_MeTPeak.txt

data_processing:
Library strategy: m6A-seq
Adapters of raw reads were clipped by Cutadapt v1.15. Reads longer than 15 nt after trimming were mapped to the rice genome (MSU 7.0) using HISAT2 v2.1.0 with default parameters. mRNA and repeat annotation were downloaded from the Rice Genome Annotation Project and the Rice Annotation Project (RAP-DB), respectively.
For RNA-seq, reads on genes were counted by featureCounts (-t exon -g gene_id -C -M -O --fraction -T 24 -s 2 -p) from from Subread v1.6.4.
For m6A-seq, mapped reads were separated by strands and then MeTPeak was used to detect m6A peaks respectively with the mRNA and repeat anotation (FRAGMENT_LENGTH=200, READ_LENGTH=150, PEAK_CUTOFF_FDR=0.05, WINDOW_WIDTH=50, SLIDING_STEP=10, FOLD_ENRICHMENT=2).
Genome_build: MSU 7.0
Supplementary_files_format_and_content: Raw counts and peaks of mRNAs and repeats were present in tab-delimited plain text files

organism: Oryza sativa

source_name: FTO transgenic mutant rice root

growth_protocol: Nipp and FTO rice were grown in Kimura B solutionKimura B solution  a 12-h light (26 °C)/12-h dark (22 °C) photoperiod, 50–60% relative humidity and 700 μmol m-2 s-1 light. 15 days old plants were harvested for experiment

extract_protocol:
For RNA-seq, 15-day-old seedlings of the Nipp and FTO plant were used for sequencing. Before purified non-ribosomal RNA with Ribo-Zero rRNA Removal Kit (Illumina), ERCC RNA spike-in control (Ambion) was added to each sample (0.1 μl per 5 ug total RNA). Library preparation was performed by using the NEBNext® Ultra™ I Directional RNA Library Prep Kit for Illumina® (NEB #E7420S) according to the manufacturer’s protocols. Sequencing was performed on an Illumina HiSeq machine in pair-end mode with 150 bp per read (Genewiz company, China). For m6A-seq, 1 g of 15-day-old seedlings of the Nipp, FTOmut and FTO plants from hydroponic experiments were used to isolate poly(A) RNA for m6A sequencing. 5 pg spike-ins for m6A seq mixture containing 3 diverse 20% m6A modified and 3 diverse non-m6A modified poly(A) spike-ins (see Supplementary Table 6) which synthesized in vitro used the MEGAscript ® Kit (AM1333, Thermo Fisher Scientific, USA) was added to the poly(A) RNA, followed by fragmented into ~100 nt using RNA Fragmentation Reagents (Ambion, USA) according to the manufacturer’s protocol.  m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocol. Library preparation was performed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s protocol. Sequencing was performed on an Illumina HiSeq 4000 machine in pair-end mode with 150 bp per read (Genewiz, China).
For RNA-seq, library preparation was performed by using the NEBNext® Ultra™ I Directional RNA Library Prep Kit for Illumina® (NEB #E7420S) according to the manufacturer’s protocols. Sequencing was performed on an Illumina HiSeq machine in pair-end mode with 150 bp per read (Genewiz company, China). For m6A-seq, library preparation was performed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB #E7760S) according to the manufacturer’s protocols. Sequencing was performed on an Illumina HiSeq machine in pair-end mode with 150 bp per read (Genewiz company, China).

tag: ecotype

value: Nipponbare (Nipp)

tag: genotype

value: FTO homogeneous transgenic mutant

tag: ip antibody

value: anti-m6A (NEB, monoclonal,  rabbit,Cat. No. E1617S)

tag: tissue

value: root


title: Cerebellar tissue - 84Q_rep3 [22_2_4]

source_name: Cerebellar tissue - 84Q

tag: strain background

tag: treatment

value: untreated

tag: cell type


title: Cerebellar tissue - 84Q+IGF1_rep1 [18_2_1]

value: treated with IGF1(50 mg/kg) per week

value: cerebellar tissue


title: genomic DNA from ovarian cancer tissues [G699]

description:
Ovarian tumor tissue
R04C01

tag: Sex

tag: Stage

tag: grade

tag: tumour subtypes

tag: tumour subtypes2

value: mixed serous endometrioid

tag: primary chemotherapy treatment


title: genomic DNA from ovarian cancer tissues [G681]

description:
Ovarian tumor tissue
R01C01

tag: age

value: clear cell

tag: recurrence

tag: doot

tag: dodx


title: genomic DNA from ovarian cancer tissues [G680]

description:
Ovarian tumor tissue
R08C01

value: carboplatin+paclitaxel

tag: survivial status


title: m6A-seq FTO mutant root IP rep1

description:
FTOmut_root_rep1_gene_MeTPeak.txt
FTOmut_root_rep1_repeat_MeTPeak.txt

tag: ecotype

tag: genotype

value: anti-m6A (NEB, monoclonal,  rabbit,Cat. No. E1616S)


title: genomic DNA from ovarian cancer tissues [G679]

description:
Ovarian tumor tissue
R07C01

value: female


title: ubp8-1_NETseq

tag: strain

tag: genotype/variation

value: RPB3::RPB3-3xFLAG NAT, UBP8::HIS3

tag: rna fraction

value: Nascent RNA

tag: ip

value: IP against 3xFLAG affinity label


title: genomic DNA from ovarian cancer tissues [G678]

description:
Ovarian tumor tissue
R06C01

tag: Sex


title: genomic DNA from ovarian cancer tissues [G689]

description:
Ovarian tumor tissue
R05C01

tag: Stage

value: endometrioid

value: carboplatin/pacelitaxel


title: swr1-1_NETseq

value: RPB3::RPB3-3xFLAG NAT, SWR1::HIS3


title: genomic DNA from ovarian cancer tissues [G673]

description:
Ovarian tumor tissue
R04C01

tag: grade


title: genomic DNA from ovarian cancer tissues [G671]

description:
Ovarian tumor tissue
R02C01

tag: tumour subtypes


title: m6A-seq FTO mutant shoot IP rep2

description:
FTOmut_shoot_rep2_gene_MeTPeak.txt
FTOmut_shoot_rep2_repeat_MeTPeak.txt

source_name: FTO transgenic mutant rice shoot

value: Nipponbare (Nipp)

value: FTO homogeneous transgenic mutant

tag: ip antibody

value: anti-m6A (NEB, monoclonal,  rabbit,Cat. No. E1615S)

tag: tissue

value: shoot


title: Cerebellar tissue - 15Q_rep3 [Q15_5_3]

source_name: Cerebellar tissue - 15Q

tag: strain background

tag: treatment

value: untreated

tag: cell type


title: genomic DNA from ovarian cancer tissues [G676]

description:
Ovarian tumor tissue
R05C01

tag: age

tag: tumour subtypes2

tag: primary chemotherapy treatment

tag: recurrence

tag: doot

tag: dodx


title: Cerebellar tissue - 15Q_rep2 [Q15_3_5]

tag: genotype/variation

value: cerebellar tissue


title: genomic DNA from ovarian cancer tissues [G665]

description:
Ovarian tumor tissue
R08C01

tag: survivial status


title: spt4-1_NETseq

tag: strain

value: RPB3::RPB3-3xFLAG NAT, SPT4::HIS3

tag: rna fraction

tag: ip


title: m6A-seq FTO mutant root input rep2

tag: ecotype

tag: genotype

value: root


title: Cerebellar tissue - 15Q_rep1 [Q15_2_1]


title: set3-3_NETseq

value: RPB3::RPB3-3xFLAG NAT, SET3::HIS3


title: set3-2_NETseq


title: m6A-seq FTO mutant shoot IP rep1

description:
FTOmut_shoot_rep1_gene_MeTPeak.txt
FTOmut_shoot_rep1_repeat_MeTPeak.txt

tag: ip antibody

value: anti-m6A (NEB, monoclonal,  rabbit,Cat. No. E1614S)

tag: tissue


title: m6A-seq FTO mutant root input rep1


title: genomic DNA from ovarian cancer tissues [G654]

description:
Ovarian tumor tissue
R07C01

tag: Sex

value: female

tag: Stage

tag: grade

tag: tumour subtypes

value: serous


title: genomic DNA from ovarian cancer tissues [G694]

description:
Ovarian tumor tissue
R05C01

tag: age

tag: tumour subtypes2

value: clear cell

tag: primary chemotherapy treatment


title: genomic DNA from ovarian cancer tissues [G672]

description:
Ovarian tumor tissue
R03C01

value: carboplatin+paclitaxel

tag: recurrence

tag: doot

tag: dodx


title: set3-1_NETseq

tag: strain

tag: genotype/variation

value: Nascent RNA

value: IP against 3xFLAG affinity label


title: genomic DNA from ovarian cancer tissues [G695]

description:
Ovarian tumor tissue
R06C01

value: carboplatin/pacelitaxel

tag: survivial status


title: set2-4_NETseq

value: RPB3::RPB3-3xFLAG NAT, SET2::HIS3

tag: rna fraction

tag: ip


title: genomic DNA from ovarian cancer tissues [G687]

description:
Ovarian tumor tissue
R04C01


title: m6A-seq FTO mutant shoot input rep1

tag: ecotype

value: Nipponbare (Nipp)

tag: genotype

value: FTO homogeneous transgenic mutant

tag: ip antibody


title: genomic DNA from ovarian cancer tissues [G682]

description:
Ovarian tumor tissue
R01C01

tag: Sex

tag: Stage


title: RNA-seq FTO mutant root rep2

description:
non-ribosomal RNA
root_gene_featureCounts.txt
root_repeat_featureCounts.txt

data_processing:
Adapters of raw reads were clipped by Cutadapt v1.15. Reads longer than 15 nt after trimming were mapped to the rice genome (MSU 7.0) using HISAT2 v2.1.0 with default parameters. mRNA and repeat annotation were downloaded from the Rice Genome Annotation Project and the Rice Annotation Project (RAP-DB), respectively.
For RNA-seq, reads on genes were counted by featureCounts (-t exon -g gene_id -C -M -O --fraction -T 24 -s 2 -p) from from Subread v1.6.4.
For m6A-seq, mapped reads were separated by strands and then MeTPeak was used to detect m6A peaks respectively with the mRNA and repeat anotation (FRAGMENT_LENGTH=200, READ_LENGTH=150, PEAK_CUTOFF_FDR=0.05, WINDOW_WIDTH=50, SLIDING_STEP=10, FOLD_ENRICHMENT=2).
Genome_build: MSU 7.0
Supplementary_files_format_and_content: Raw counts and peaks of mRNAs and repeats were present in tab-delimited plain text files

tag: tissue


title: set2-3_NETseq