title: sFRP2OE D0 MSCs, 1

description:
sFRP2 overexpression in mesenchymal stem cells derived from WT iPSCs
S9


title: LFS D17 pre-osteoblasts, 2

status: Public on Jan 01 2019

type: SRA

city: New York

first: Seungyeul

last: Yoo

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
LFS D17 pre-osteoblasts derived from LFS iPSCs
S24

library_source: transcriptomic

data_processing:
Sequence reads were aligned to human transcript reference (RefSeq Genes, hg19) for the expression analysis at gene levels using TopHat (Trapnell et al., 2009) and HTSeq softwares (Anders et al., 2015). The rawcount of reads aligned to each gene was further normalized by Reads Per Kilobase of transcript per Million (RPKM) as gene expression abundance measurement.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including RPKM values of each gene
Supplementary_files_format_and_content: log2 transformed RPKM

molecule: total RNA

organism: Homo sapiens

source_name: LFS Pre-osteoblasts

extract_protocol:
Total RNA (1-3μg/sample) extracted from MSCs or pre-osteoblasts in vitro culture were submitted to Novogene for quality control analysis. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, and double stranded cDNA synthesized using random hexamers
cDNA was synthesized using random hexamers, M-MuLV Reverse Transcriptase (RNase H), and DNA Polymerase I. NEBNext Adaptor with hairpin loop structure were ligated to the cDNA in preparation for hybridization. The library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA)

tag: cell type

value: pre-osteoblasts derived from LFS iPSCs


title: WT D14 pre-osteoblasts, 1

description:
Wild type D14 pre-osteoblasts derived from WT iPSCs
S5

source_name: WT Pre-osteoblasts

value: pre-osteoblasts derived from WT iPSCs


title: EpiLC_cyt_rep2

city: Shanghai

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

country: China

institute: Fudan University

description:
EPI_cyt_2_0
Processed data file: EPI_genes.fpkm_table.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
We trimmed and mapped reads to the mouse mm10 reference assembly (GRCm38) by the Tophat2 software (Kim et al., 2013). We used default parameters except that we reduced maximum insertion and deletion length to 2bp, and kept only uniquely mapping, “no mixed” and “no discordant” reads.
We quantified gene expression levels in each sample by cuffnorm (Trapnell et al., 2012) with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_genes.fpkm_table.txt: Tab-delimited text files include FPKM values for each replicate.

organism: Mus musculus

source_name: EpiLC, cytoplasmic

growth_protocol: mESCs (E14) were cultured in serum-free N2B27 medium containing 2i (MEK and GSK inhibitor, PD0325901 and CHIR99021) and LIF. The nESC-to-EpiLC transition was conducted as described (Hayashi et al., 2011) with minor modifications. Briefly, mouse nESCs cells were plated at a density of 1x10e4 per cm2 in gelatin-coated plates with N2B27 medium containing activin A (20 ng/ml) and bFGF (12 ng/ml). The medium was changed every day. The converted EpiLCs were collected at day 3.

extract_protocol:
Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HiSeq system (lllumina).

treatment_protocol: Cellular fractionation was prepared as described (Pandya-Jones and Black, 2009), with minor changes. 1x10e7 cells (E14) were gently trypsinized from plate and centrifugation. As for isolation of nuclei, the lysate was layered on to 500 ul cold sucrose buffer.

tag: originating cell line

value: EpiLC

tag: subcellular fraction

value: cytoplasmic


title: EpiLC_sol_rep3

description:
EPI_sol_3_0
Processed data file: EPI_genes.fpkm_table.txt

source_name: EpiLC, nucleoplasmic

value: nucleoplasmic


title: EpiLC_chr_rep1

description:
EPI_chr_1_0
Processed data file: EPI_genes.fpkm_table.txt

source_name: EpiLC, chromatin

value: chromatin


title: WT D17 pre-osteoblasts, 1

description:
Wild type D17 pre-osteoblasts derived from WT iPSCs
S7


title: EpiLC_sol_rep2

description:
EPI_sol_2_0
Processed data file: EPI_genes.fpkm_table.txt


title: WT D17 pre-osteoblasts, 2

description:
Wild type D17 pre-osteoblasts derived from WT iPSCs
S8


title: WT D14 pre-osteoblasts, 2

description:
Wild type D14 pre-osteoblasts derived from WT iPSCs
S6


title: EpiLC_chr_rep2

description:
EPI_chr_2_0
Processed data file: EPI_genes.fpkm_table.txt


title: WT D0 MSCs, 2

description:
Wild type mesenchymal stem cells derived from WT iPSCs
S2

source_name: WT mesenchymal stem cells

value: MSCs derived from WT iPSCs


title: EpiLC_cyt_rep1

description:
EPI_cyt_1_0
Processed data file: EPI_genes.fpkm_table.txt


title: EpiLC_sol_rep1

description:
EPI_sol_1_0
Processed data file: EPI_genes.fpkm_table.txt


title: WT D7 pre-osteoblasts, 1

description:
Wild type D7 pre-osteoblasts derived from WT iPSCs
S3


title: EpiLC_chr_rep3

description:
EPI_chr_3_0
Processed data file: EPI_genes.fpkm_table.txt


title: nESC_tol_rep3

description:
ES_tol3_0
Processed data file: ES_genes.fpkm_table.txt

source_name: nESC, total

value: nESC

value: total


title: 18-TC35 normoxy

city: strasbourg

first: Anne-Florence

last: Blandin

state: bas-rhin

address: 3 avenue molière

department: Hautepierre hospital

country: France

institute: University of Strasbourg

data_processing:
Base calling : Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto hg38 assembly of human genome using Tophat v2.0.14 with bowtie v2.1.0.
Quantification : gene expression was quantified using HTSeq v0.6.1 and intersection-nonempty mode.
Normalization : Data normalization was performed with DESeq2 v1.6.3 Bioconductor package
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a tabulated text with the following columns : Ensembl gene id, Gene name and one column for each sample containing the normalized read counts

source_name: primary cell line derived from biospy

growth_protocol: Neurosphere cell culture were maintained in F12 medium supplemented with B27 and growth factors. Monolayer cell culture were obtained using a medium to promote cell differentiation (F12 medium supplemented with serum 10% and w/o growth factors).

extract_protocol:
RNA extraction from fresh cell pellet using TRIzol reagent. Precipitating of RNA using Sodium Acetate.
Libraries suitable for high throughput sequencing were generated from 500 ng of total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina, Part Numbers RS-122-2101/RS-122-2102). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94°C for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C) to create the cDNA library. After removing surplus PCR primers by purification using AMPure XP beads (Beckman Coulter), DNA libraries were checked for quality and quantified using a Fragment Analyzer automated CE system (Advanced Analytical Technologies, Inc.).

treatment_protocol: Two-day-old monolayer and neurosphere cell culture were exposed to low level of oxygen (hypoxia 1%O2) or maintained in normoxic atmosphere (21%O2) for 48hours.

tag: diagnosis

value: glioblastoma

tag: location

value: thalamic

tag: passages

tag: cell culture condition

value: monolayer

tag: treatment

value: normoxy


title: WT D7 pre-osteoblasts, 2

description:
Wild type D7 pre-osteoblasts derived from WT iPSCs
S4


title: nESC_cyt_rep3

description:
ES_cyt3_0
Processed data file: ES_genes.fpkm_table.txt

source_name: nESC, cytoplasmic


title: nESC_tol_rep2

description:
ES_tol2_0
Processed data file: ES_genes.fpkm_table.txt


title: nESC_cyt_rep2

description:
ES_cyt2_0
Processed data file: ES_genes.fpkm_table.txt


title: nESC_sol_rep3

description:
ES_sol3_0
Processed data file: ES_genes.fpkm_table.txt

source_name: nESC, nucleoplasmic


title: 23-TC68 normoxy

value: DIPG

value: pons

value: neurosphere


title: 16-TC35 hypoxia

value: hypoxia


title: 10-TC83 normoxy


title: 20-TC83 normoxy


title: nESC_sol_rep2

description:
ES_sol2_0
Processed data file: ES_genes.fpkm_table.txt


title: WT D0 MSCs, 1

description:
Wild type mesenchymal stem cells derived from WT iPSCs
S1


title: nESC_cyt_rep1

description:
ES_cyt1_0
Processed data file: ES_genes.fpkm_table.txt


title: 8-TC83 hypoxia


title: nESC_sol_rep1

description:
ES_sol1_0
Processed data file: ES_genes.fpkm_table.txt


title: 6-TC69 normoxy


title: nESC_chr_rep3

description:
ES_chr3_0
Processed data file: ES_genes.fpkm_table.txt

source_name: nESC, chromatin


title: pTpA_1E8_YPD_MNase_A1

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

description: 20171006_MNaseData.sorted.withSeqs.txt.gz

library_source: genomic

data_processing:
Sequencing reads of 76 bp were mapped to all known promoters in any pTpA library using Bowtie2.
Only promoters with at least 20 reads in the input DNA and 1 read in the MNase data were kept for subsequent analysis. Input and MNase counts were scaled within each sample to yield a CPM per promoter and the log ratio of MNase to input was compared between replicates and to the model’s predicted occupancy, corresponding to log(1-predicted accessibility).
Supplementary_files_format_and_content: compressed text file with sequence IDs, sequences, and log (Mnase/input) ratios for each replicate

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Random promoter library

growth_protocol: Aliquots of the pTpA library, theoretically corresponding to ~100,000 (sample A) or ~200,000 (sample B) cells were cultured in duplicate (Rep 1 and 2) in YPD for ~16 hours to an OD of ~0.4-1.0.

extract_protocol:
For each sample, 0.5mL of culture was pelleted and frozen to prepare input genomic DNA, and 3 mL of culture was crosslinked with 1% formaldehyde, washed twice with 1mL H2O supplemented with protease inhibitors cocktail, and the pellet frozen for MNase treatment. The MNase pellets were sphaeroplasted using zymolyase, and spheroplasts lysed in NP buffer (10 mM Tris pH 7.4, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail) at a concentration of 2*10^6 cells/ul of NP buffer. 0.125 units of Worthington MNase were added per 10 ul of lysed spheroplasts and MNase digestion was preformed at 37C for 20 minutes. MNase digestion was stopped by addition of equal volume of 2X MNase Stop Buffer (220 mM NaCl, 0.2% SDS, 0.2% sodium deoxycholate, 10 mM EDTA, 2%,Triton X-100, EDTA-free protease inhibitor cocktail). MNased chromatin samples were treated with RNase A, and proteinase K, reverse cross linked, separated on a 4% agarose gel and mononucleosome bands were isolated. Genomic DNA was prepared using the Masterpure yeast genomic DNA preparation kit (Epicenter).
For both MNase and genomic DNA, the variable region of the promoter library was amplified, and adaptors added for sequencing.

tag: media

value: YPD

tag: libraryid

tag: replicate

tag: material

value: MNase


title: 4-TC69 normoxy


title: nESC_chr_rep2

description:
ES_chr2_0
Processed data file: ES_genes.fpkm_table.txt


title: 2-TC69 hypoxia


title: nESC_tol_rep1

description:
ES_tol1_0
Processed data file: ES_genes.fpkm_table.txt


title: 21-TC68 hypoxia


title: pTpA_1E8_YPD_input_B1

value: input


title: pTpA_1E8_YPD_input_A2


title: pTpA_1E8_YPD_MNase_A2


title: pTpA_1E8_YPD_input_A1


title: pTpA_1E8_YPD_MNase_B1


title: 14T3, Treatment rep3

city: Conway

first: Arijit

last: Mukherjee

state: AR

address: 201 Donaghey Avenue, UCA

department: Biology

institute: University of Central Arkansas

data_processing:
Fastq files were merged by sample by read across lanes followed by alignment to the genome via Rsubread.
Read summarization at the exon level was performed via the function featureCounts.
Genome_build: Oryza Sativa MSU Genome v7
Supplementary_files_format_and_content: tab-delimited text file containing raw counts per sample

organism: Oryza sativa

growth_protocol: For studies in rice, we used Oryza sativa cv. Nipponbare  for NLS studies and RNA-seq experiments. The seeds of the above-mentioned rice genotypes were surface-sterilized in 2% (v/v) sodium hypochlorite solution for 30 minutes, rinsed five times with distilled water and then allowed to imbibe in the distilled water for 24 hours. Following the 24-hour period, the seeds were transferred under sterile conditions to 9-cm petri plates lined with germination paper. Plates were sealed with parafilm, wrapped completely in aluminum foil, and then allowed to germinate at room temperature (25°C) for approximately 72–96 hours. Germinated seedlings were transferred to 15-cm petri plates containing low-N Fahraeus medium and allowed to grow for 7 days in a Percival growth chamber (#CU-22L, Iowa, USA) with a 16-h, 22°C day and 8-h, 24°C night cycle and 150 to 200 μmol m–2s–1 light intensity, and relative humidity of 65% prior to hormone treatment.

extract_protocol:
For this study, total RNA was extracted from untreated plant roots and 50μM 2,4-D treated plant roots at 1, 7, and 14 days post treatment (dpt). Specifically for treatment samples at 7dpt and 14dpt, RNA was extracted only from plant roots containing NLS. Total RNA was extracted using Qiagen RNeasy® Plant Mini Kit (Cat #74904, California, USA) per manufacturer’s protocol. We included three biological replicates for each sample.
RNA sequencing including RNA quantification and library preparation was performed at the Research Technology Support Facility (RTSF), Michigan State University, East Lansing, MI. The RNA was checked for integrity before library preparation and sequencing using a Bioanalyzer (Agilent Technologies). Briefly, multiplex sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit LT. After QC, all 6 libraries (3 treatment and 3 controls) were combined into a single pool. This pool was loaded on one lane of an Illumina HiSeq 2500 Rapid Run flow cell (v1). Sequencing was performed in a PE100 format with Rapid SBS reagents. Base calling was done by Illumina Real Time Analysis (RTA) v1.17.21.3 and output of RTA was de-multiplexed and converted to Fastq format with Illumina Bcl2fastq v1.8.4.

treatment_protocol: Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22°C day and 8-h, 24°C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.

tag: cultivar

value: cv. Nipponbare

value: auxin (50μM 2,4-D)

tag: contains nls

value: Yes

tag: time post treatment

value: 14 days

tag: tissue

value: Rice roots

tag: sequencing batch


title: 14T2, Treatment rep2


title: 14T1, Treatment rep1


title: 14C2, Control rep 2

value: mock

value: No


title: 14C3, Control rep 3


title: 7C3, Control rep 3

value: 7 days


title: 7T1, Treatment rep1


title: 7T2, Treatment rep2


title: 7C2, Control rep 2


title: 7C1, Control rep 1


title: pTpA_1E8_YPD_input_B2


title: 1T3, Treatment rep3

value: 1 day


title: 1T2, Treatment rep2


title: 1C3, Control rep 3


title: 1T1, Treatment rep1


title: nESC_chr_rep1

description:
ES_chr1_0
Processed data file: ES_genes.fpkm_table.txt

tag: cell type

value: nESC

value: chromatin


title: 14C1, Control rep 1


title: 1C2, Control rep 2


title: T8_repeat3

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

description: high-throughput profiling of transcriptome in T8_repeat3

data_processing:
The paired-end reads were aligned to the moso bamboo genome using tophat-2.0.11 with anchor length more than 8nt for spliced alignments (Kim et al. 2013).
Genome_build: P.heterocycla-v1.0
Supplementary_files_format_and_content: bigwig files were generated using wig2bw program

organism: Phyllostachys edulis

growth_protocol: For materials used for RNA-Seq analysis, Culms were collected with the length of 0.2, 0.5, 1, 2, 3, 4, 5, 6, 7, 8m .

extract_protocol:
Total RNA from bamboo culms  was extracted using the RNAprep Pure Plant Kit (QIAGEN, China) according to the manufacturer’s instructions.
In total, there were 24 strand-specific RNA-Seq libraries that were sequenced in this study using dUTP method (Parkhomchuk et al. 2009).

treatment_protocol: The middle part of culms  with different length  were dissected for RNA extraction

tag: development stage


title: T8_repeat2

description: high-throughput profiling of transcriptome in T8_repeat2


title: T7_repeat2

description: high-throughput profiling of transcriptome in T7_repeat2


title: T7_repeat3

description: high-throughput profiling of transcriptome in T7_repeat3


title: pTpA_1E8_YPD_MNase_B2


title: T8_repeat1

description: high-throughput profiling of transcriptome in T8_repeat1


title: T7_repeat1

description: high-throughput profiling of transcriptome in T7_repeat1


title: T6_repeat3

description: high-throughput profiling of transcriptome in T6_repeat3


title: T6_repeat2

description: high-throughput profiling of transcriptome in T6_repeat2


title: T6_repeat1

description: high-throughput profiling of transcriptome in T6_repeat1


title: T5_repeat3

description: high-throughput profiling of transcriptome in T5_repeat3


title: T4_repeat3

description: high-throughput profiling of transcriptome in T4_repeat3


title: T5_repeat2

description: high-throughput profiling of transcriptome in T5_repeat2


title: T4_repeat1

description: high-throughput profiling of transcriptome in T4_repeat1


title: T3_repeat2

description: high-throughput profiling of transcriptome in T3_repeat2


title: T3_repeat3

description: high-throughput profiling of transcriptome in T3_repeat3


title: T4_repeat2

description: high-throughput profiling of transcriptome in T4_repeat2


title: T2_repeat3

description: high-throughput profiling of transcriptome in T2_repeat3


title: T3_repeat1

description: high-throughput profiling of transcriptome in T3_repeat1


title: 1C1, Control rep 1


title: T2_repeat1

description: high-throughput profiling of transcriptome in T2_repeat1


title: T2_repeat2

description: high-throughput profiling of transcriptome in T2_repeat2


title: T1_repeat1

description: high-throughput profiling of transcriptome in T1_repeat1


title: Gerbil wounded skin 3 days after wound

city: Seoul

first: Eun-Jung

last: Kim

address: 50 Yonsei-ro

department: Department of Oral Biology

country: South Korea

institute: Yonsei Universiry

description: Gerbil 3days 1ea 160616

data_processing:
Basecalls performed using CASAVA version v2.17.1.14
Data were filtered using the following configurations: 1) Reads contain more than 10% of skipped bases (marked as ‘N’s), 2) Reads contain more than 40% of bases whose quality scores are less than 20, 3) Reads of which average quality scores of each read is less than 20
RNA-seq reads were aligned to the GRCm38.p2 genome assembly using STAR version 2.4.0b with default configurations.
Excel file generated using rsem-1.2.19 with default configurations and cufflinks-2.2.1 with the following configurations: multi-read-correction & frag-bias-correct.
Genome_build: GRCm38.p2
Supplementary_files_format_and_content: gene_unigene_result.xlsx

organism: Meriones unguiculatus

source_name: Gerbil wounded skin 3 days after wound

extract_protocol:
Total RNA was extracted from skin wound samples using a TRIZOL reagent (Invitrogen, CA, USA). After DNase I (Roche, Basel, Switzerland) treatment, the RNA was purified with RNeasy kit (Qiagen, Hilden, Germany).
Illumina TruSeq RNA Library Prep Kit

value: wounding

tag: time

value: 3 days after wound

value: wounded dermis


title: DRB

status: Public on Dec 31 2018

city: Rochester

first: jinlong

last: lu

address: 213 Hutchinson Hall

institute: University of Rochester

data_processing:
Basecalls performed using CASAVA version
Sequenced reads were trimmed for barcode sequence
Nucleolar retrieved DNA-Seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.2.3 with the default parameters
Peaks of each sample were called using MACS v. 1.4.2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: cj9 mES cells

growth_protocol: Wild-type (cj9) and infected embryonic stem cells (ESCs) were cultured on gelatin coated plates in standard ESC medium consisting of DMEM (Cellgro) supplemented with 15% heat-inactivated fetal bovine serum (Hyclone), 1% Glutamax (GIBCO), 1% Penicillin/Streptomycin (Cellgro), 1% nucleoside (Millipore), 0.1mM  2-mercaptoethanol  (GIBCO),  1%  MEM  nonessential  amino  acids  (Cellgro),  and  1000U/ml  recombinant leukemia inhibitory factor (Millipore).

extract_protocol:
Treated cells (4X15 cm dishes)  were harvested by trypsinization and rinsed twice by PBS. Then the cells were treated by 10ml Buffer A (10mM Hepes, pH 7.9, 10mM KCl, 1.5mM MgCl2, 0.5mM DTT) on ice for 5min followed by 10X Dounce homogenization. Centrifuge the cells at 218g for 5min at 4C. Then resuspend the pellet with 3 ml S1 solution (0.25M sucrose, 10mM MgCl2) and layered over 3ml S2 solution (0.35M sucrose, 0.5mM MgCl2) and centrifuged at 1430g for 5min at 4C. Resuspend the pellet with 3ml of S2 solution and sonicate to break the nuclei. Layered the sonicated sample over 3ml of S3 solution (0.88M Sucrose, 0.5mM MgCl2) and centrifuge at 3000g for 10min at 4 C. Resuspended the nucleoli with 500ul of S2 solution and centrifuged for another 5min. The pellet was resuspended and purified by phenol-chloroform extraction.
Nucleolar retrieved DNA-seq were prepared by library preparation modules (New England Biolabs)

treatment_protocol: The cells were treated with DMSO, Actinomycin D (1ug/ml) and DRB (100uM) for 2hrs

value: embryonic stem cells

value: DRB

tag: strain


title: DMSO

value: DMSO


title: 7T3, Treatment rep3

value: cv. Nipponbare


title: WT #6 RPF

first: F.

middle: Nina

last: Papavasiliou

state: New York

address: 1230 York Ave.

institute: Rockefeller University

description:
allGenes_resultsDESeq2_batchCorrected.txt
top25percent_resultsDESeq2_batchCorrected.txt

data_processing:
Library strategy: Ribo-seq
Library strategy: Ribo-seq
Libraries were trimmed for adapters and quality using Trim Galore!.
The resulting reads were initially aligned to mouse ribosomal RNA using bowtie (v1.1.2). The remaining unmapped reads were then aligned to mm10 (using the reference sequences and annotations provided by iGenomes (Illumina)) using Tophat2 (v.2.1.0) and the following parameters: –bowtie1, –no- novel-juncs, –read-realign-edit-dist=0 (default settings for the remaining parameters).
Total RNA reads were counted using HTseq in intersection-strict mode, and RPF reads were counted using a custom script provided by Xiao et al. [doi :10.1038/ncomms11194], which used
Cufflinks ( v2.2.1) was also run on the total RNA sequencing to estimate transcript abundances with default parameters. Both cufflinks and HTSeq were run using the genes.gtf file from iGenomes UCSC mm10.
DESeq2 was then used to assess changes in translational efficiency (TE), defined here as the ratio of RPF to mRNA reads, between the two genotypes. This was achieved with the design ~ assay + genotype + batch + assay:genotype, and analysis run as follows: dds <- DESeq(dds, test='LRT', full=design(dds), reduced = ~ assay + genotype + batch), where assay indicates if the library was mRNA or RPF, genotype indicates if the sample was WT or KO, and batch indicates the batch that the library was prepared with. Data was combined from three separate experiments, resulting in n=6 for each genotype in total. DESeq2 was run on the full list of transcripts, and the top 25% expressed coding transcripts based on the cufflinks results.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 results contain log2FC in translational efficiency from the ribosome profiling data for all replicates; genes.fpkm_tracking files contain FPKM values for genes from sequencing total RNA; HTSeq counts contain counts for either total RNA or RPFs, using the parameters described above

source_name: Bone-marrow derived macrophages

growth_protocol: C57BL6 littermate or age-matched mice were used at 6-12 weeks of age. Apobec1-/- mice were a gift from N.O. Davidson (Washington University School of Medicine). Mouse femurs were removed and flushed with cold PBS onto a cell strainer. Precursor cells were plated onto untreated 10cm dishes and incubated in a humidified 37°C/5% CO2 incubator for 7 days in DMEM, 10% FBS 1% Non-essential amino acids (Invitrogen), 0.1% BME, 20ng/mL M-CSF (Peprotech), replacing half of the media (with complete media plus 40ng/mL M-CSF) every 3 days. Macrophage surface markers: F4/80 (Invitrogen) and Cd11b (BD biosciences) were confirmed via flow cytometry on a FACS Calibur flow cytometer after the 7-day maturation.

extract_protocol:
total RNA and RPFs were extracted following manufacturer's instructions from the TruSeq Ribo Profile kit (formerly ARTseq) from Illumina
Libraries were prepared with the TruSeq Ribo Profile kit (formerly ARTseq) from Illumina, according to manufacturer's instructions

tag: genotype

value: wildtype

tag: batch

tag: molecule type

value: ribosome protected fragment (RPFs)


title: WT #5 total RNA

data_processing:
Library strategy: Ribo-seq
Libraries were trimmed for adapters and quality using Trim Galore!.
The resulting reads were initially aligned to mouse ribosomal RNA using bowtie (v1.1.2). The remaining unmapped reads were then aligned to mm10 (using the reference sequences and annotations provided by iGenomes (Illumina)) using Tophat2 (v.2.1.0) and the following parameters: –bowtie1, –no- novel-juncs, –read-realign-edit-dist=0 (default settings for the remaining parameters).
Total RNA reads were counted using HTseq in intersection-strict mode, and RPF reads were counted using a custom script provided by Xiao et al. [doi :10.1038/ncomms11194], which used
Cufflinks ( v2.2.1) was also run on the total RNA sequencing to estimate transcript abundances with default parameters. Both cufflinks and HTSeq were run using the genes.gtf file from iGenomes UCSC mm10.
DESeq2 was then used to assess changes in translational efficiency (TE), defined here as the ratio of RPF to mRNA reads, between the two genotypes. This was achieved with the design ~ assay + genotype + batch + assay:genotype, and analysis run as follows: dds <- DESeq(dds, test='LRT', full=design(dds), reduced = ~ assay + genotype + batch), where assay indicates if the library was mRNA or RPF, genotype indicates if the sample was WT or KO, and batch indicates the batch that the library was prepared with. Data was combined from three separate experiments, resulting in n=6 for each genotype in total. DESeq2 was run on the full list of transcripts, and the top 25% expressed coding transcripts based on the cufflinks results.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 results contain log2FC in translational efficiency from the ribosome profiling data for all replicates; genes.fpkm_tracking files contain FPKM values for genes from sequencing total RNA; HTSeq counts contain counts for either total RNA or RPFs, using the parameters described above

value: total RNA


title: T1_repeat2

description: high-throughput profiling of transcriptome in T1_repeat2


title: Control

tag: treatment


title: WT #5 RPF


title: KO #6 RPF

value: Apobec1 -/-


title: KO #5 RPF


title: WT #6 total RNA


title: WT #4 total RNA


title: WT #4 RPF


title: KO #4 RPF


title: KO #3 total RNA


title: KO #5 total RNA


title: T1_repeat3

description: high-throughput profiling of transcriptome in T1_repeat3


title: T5_repeat1

description: high-throughput profiling of transcriptome in T5_repeat1


title: KO #2 total RNA


title: KO #2 RPF


title: WT #3 RPF


title: WT #2 total RNA


title: WT #3 total RNA


title: WT #1 total RNA


title: WT #1 RPF


title: WT #2 RPF


title: KO #1 total RNA


title: ACTD

value: Actinomycin D


title: V6.5 Rsf1 KO #1 [MNase-Seq]

city: Richmond

first: Hengbin

last: Wang

state: VA

address: 401 College Street

department: Massey Cancer Institute

institute: Virginia Commonwealth University

description: MnaseSeq

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were trimmed to remove adapters and low quality bases
Reads were mapped to mm10 or hg19 with TopHat (tophat -p 12 --mate-inner-dist=200 --mate-std-dev=40 --no-mixed --no-coverage-search) for RNAseq or BWA samse for ChIPseq
Transcripts were assembled with Cufflinks.
Differential gene expression was performed by Cuffdiff
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Gene expression values are a direct output of Cuffdiff. Bedgraph files were scaled to 10 million reads

source_name: V6.5 Rsf1 KO #1

extract_protocol:
 HeLa cells (3X105) were treated with either scrambled siRNA, or RNF2 siRNA, or RSF1 siRNA. 48 hrs later, cells were harvested and total RNA was extracted with Trizol. For mouse ESC, total RNA was extracted directly from wild type and RSF1 KO cells. For ChIP sequencing experiments, ChIP was performed with anti-FLAG antibody in a mouse ESC line stably expressing FLAG-RSF1.
RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP and Mnase libraries were prepared for sequencing using standard illumina protocols

tag: cell line


title: KO #1 RPF


title: V6.5 Rsf1 KO #2 [MNase-Seq]

description: MnaseSeq

source_name: V6.5 Rsf1 KO #2


title: KO #6 total RNA


title: V6.5 Control [MNase-Seq]

description: MnaseSeq

source_name: V6.5 Control


title: V6.5 Control [RNA-Seq]

description:
polyA RNAseq
mESC_V6.5_gene_differential_expression_testing].tabular


title: V6.5 Rsf1 KO 1-4 [RNA-Seq]


title: KO #3 RPF


title: V6.5 Rsf1 KO 2-7 [RNA-Seq]


title: KO #4 total RNA


title: V6.5 FLAG-Rsf1 [ChIP-Seq]

description: ChIP

source_name: V6.5 FLAG-Rsf1


title: E142i diff3 D0  [mRNA]

city: Lyngby

first: Federico

last: De Masi

address: Kemitorvet 208

department: Institute of Systems Biology

country: Denmark

institute: Technical University of Denmark

description:
E14.diff3.d0
E14 (male) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_E14.txt
Processed data file: mRNA_norm_E14.txt
Processed data file: mRNA_vsd_E14.txt

data_processing:
Basecalls performed with CASAVA-1.8.2.
Quality control, alignment to genome, transcript identification and raw counts calculations were performed using Cuffdiff.
Data normalization and differential expression analysis performed with DESeq2.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Data matrices containing raw counts (mRNA_raw.txt), DESeq2 normalized values (mRNA_norm.txt), DESeq2 Variance Stabilisation Transformed values (mRNA_vsd.txt).
Supplementary_files_format_and_content: mRNA_raw_E14.txt: Raw Counts for male ESC.
Supplementary_files_format_and_content: mRNA_norm_E14.txt: Normalized Counts for male ESC.
Supplementary_files_format_and_content: mRNA_vsd_E14.txt: Variance Stabilized Counts for male ESC.
Supplementary_files_format_and_content: mRNA_raw_PGK.txt: Raw Counts for female ESC.
Supplementary_files_format_and_content: mRNA_norm_PGK.txt: Normalized Counts for female ESC.
Supplementary_files_format_and_content: mRNA_vsd_PGK.txt: Variance Stabilized Counts for female ESC.

source_name: Mouse ESCs-EpiSCs, male, D0

growth_protocol: ES cells (cultured in 2i medium) are differentiated in EpiSC by plating them in mouse EpiSC medium (N2B27/Activin A (20ng/ul) /Fgf2 (12ng/ul)) on 10ug/ml fibronectin at a density of 2x10^5/well. 4 days after switching from ESC to EpiSC medium, the well should be confluent and be split with Accutase. We continue to split them every 2 days until 30 days.

extract_protocol:
We extract RNA by phenol:chloroform protocol and we did a step of DNase treatment, do a quantification and a gel.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: We recover the time point with Trizol, store them at -80°C.

tag: differentiation days

value: ESCs-EpiSCs

tag: Sex

value: male

tag: experiment name


title: E14cEpiSC diff3 D10  [mRNA]

description:
E14.diff3.d10
E14 (male) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_E14.txt
Processed data file: mRNA_norm_E14.txt
Processed data file: mRNA_vsd_E14.txt

source_name: Mouse ESCs-EpiSCs, male, D10


title: E14cEpiSC diff3 D19  [mRNA]

description:
E14.diff3.d19
E14 (male) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_E14.txt
Processed data file: mRNA_norm_E14.txt
Processed data file: mRNA_vsd_E14.txt

source_name: Mouse ESCs-EpiSCs, male, D19


title: PGKcEpiSC diff3 D4  [mRNA]

description:
PGK.diff3.d4
PGK (female) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_PGK.txt
Processed data file: mRNA_norm_PGK.txt
Processed data file: mRNA_vsd_PGK.txt

source_name: Mouse ESCs-EpiSCs, female, D4

value: PGK

value: female


title: PGKcEpiSC diff3 D10  [mRNA]

description:
PGK.diff3.d10
PGK (female) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_PGK.txt
Processed data file: mRNA_norm_PGK.txt
Processed data file: mRNA_vsd_PGK.txt

source_name: Mouse ESCs-EpiSCs, female, D10


title: PGKcEpiSC diff3 D29  [mRNA]

description:
PGK.diff3.d29
PGK (female) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_PGK.txt
Processed data file: mRNA_norm_PGK.txt
Processed data file: mRNA_vsd_PGK.txt

source_name: Mouse ESCs-EpiSCs, female, D29


title: PGKcEpiSC diff3 D21  [mRNA]

description:
PGK.diff3.d21
PGK (female) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_PGK.txt
Processed data file: mRNA_norm_PGK.txt
Processed data file: mRNA_vsd_PGK.txt

source_name: Mouse ESCs-EpiSCs, female, D21


title: PGKcEpiSC diff2 D23  [mRNA]

description:
PGK.diff2.d23
PGK (female) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_PGK.txt
Processed data file: mRNA_norm_PGK.txt
Processed data file: mRNA_vsd_PGK.txt

source_name: Mouse ESCs-EpiSCs, female, D23


title: PGK2i diff3 D0  [mRNA]

description:
PGK.diff3.d0
PGK (female) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_PGK.txt
Processed data file: mRNA_norm_PGK.txt
Processed data file: mRNA_vsd_PGK.txt

source_name: Mouse ESCs-EpiSCs, female, D0


title: E14 EpiSC D10 GEI-98 [mRNA]

description:
E14.diff2.d10
E14 (male) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_E14.txt
Processed data file: mRNA_norm_E14.txt
Processed data file: mRNA_vsd_E14.txt


title: E14cEpiSC diff2 D27  [mRNA]

description:
E14.diff2.d27
E14 (male) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_E14.txt
Processed data file: mRNA_norm_E14.txt
Processed data file: mRNA_vsd_E14.txt

source_name: Mouse ESCs-EpiSCs, male, D27


title: E14 EpiSC D4 GEI-96 [mRNA]

description:
E14.diff2.d4
E14 (male) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_E14.txt
Processed data file: mRNA_norm_E14.txt
Processed data file: mRNA_vsd_E14.txt

source_name: Mouse ESCs-EpiSCs, male, D4


title: E14 2i P30+2 GEI-95 [mRNA]

description:
E14.diff2.d0
E14 (male) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_E14.txt
Processed data file: mRNA_norm_E14.txt
Processed data file: mRNA_vsd_E14.txt

source_name: Mouse ES cells, male, D0

value: embryonic stem cells (ESCs)


title: PGK EpiSC D4 GEI-93 [mRNA]

description:
PGK.diff2.d4
PGK (female) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_PGK.txt
Processed data file: mRNA_norm_PGK.txt
Processed data file: mRNA_vsd_PGK.txt


title: PGKcEpiSC diff2 D29  [mRNA]

description:
PGK.diff2.d29
PGK (female) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_PGK.txt
Processed data file: mRNA_norm_PGK.txt
Processed data file: mRNA_vsd_PGK.txt


title: E14cEpiSC diff3 D30 GEI-130 [miRNA]

description:
E14.diff3.d30
E14 (male) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_E14.txt
Processed data file: miRNA_norm_E14.txt
Processed data file: miRNA_vsd_E14.txt

data_processing:
Basecalls performed with CASAVA-1.8.2.
Quality control, alignment to genome, miRNA calls and raw counts calculations were performed using the ncPRO web application (Chen C et al. ncPRO-seq: a tool for annotation and profiling analysis of ncRNAs from small RNA-seq. Bioinformatics (2012)).
Data normalization and differential expression analysis performed with DESeq2.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Data matrices containing raw counts (miRNA_raw.txt), DESeq2 normalized values (miRNA_norm.txt), DESeq2 Variance Stabilisation Transformed values (miRNA_vsd.txt).
Supplementary_files_format_and_content: miRNA_raw_E14.txt: Raw Counts for male ESC.
Supplementary_files_format_and_content: miRNA_norm_E14.txt: Normalized Counts for male ESC.
Supplementary_files_format_and_content: miRNA_vsd_E14.txt: Variance Stabilized Counts for male ESC.
Supplementary_files_format_and_content: miRNA_raw_PGK.txt: Raw Counts for female ESC.
Supplementary_files_format_and_content: miRNA_norm_PGK.txt: Normalized Counts for female ESC.
Supplementary_files_format_and_content: miRNA_vsd_PGK.txt: Variance Stabilized Counts for female ESC.

source_name: Mouse ESCs-EpiSCs, male, D30


title: E14cEpiSC diff3 D19 GEI-129 [miRNA]

description:
E14.diff3.d19
E14 (male) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_E14.txt
Processed data file: miRNA_norm_E14.txt
Processed data file: miRNA_vsd_E14.txt


title: E14cEpiSC diff2 D21  [mRNA]

description:
E14.diff2.d21
E14 (male) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_E14.txt
Processed data file: mRNA_norm_E14.txt
Processed data file: mRNA_vsd_E14.txt

source_name: Mouse ESCs-EpiSCs, male, D21


title: V6.5 FLAG [ChIP-Seq]

description: ChIP

source_name: V6.5 FLAG


title: E14cEpiSC diff3 D30  [mRNA]

description:
E14.diff3.d30
E14 (male) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_E14.txt
Processed data file: mRNA_norm_E14.txt
Processed data file: mRNA_vsd_E14.txt


title: PGK EpiSC D10 GEI-94 [mRNA]

description:
PGK.diff2.d10
PGK (female) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_PGK.txt
Processed data file: mRNA_norm_PGK.txt
Processed data file: mRNA_vsd_PGK.txt


title: E14cEpiSC diff3 D10 GEI-128 [miRNA]

description:
E14.diff3.d10
E14 (male) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_E14.txt
Processed data file: miRNA_norm_E14.txt
Processed data file: miRNA_vsd_E14.txt


title: PGKcEpiSC diff3 D10 GEI-121 [miRNA]

description:
PGK.diff3.d10
PGK (female) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_PGK.txt
Processed data file: miRNA_norm_PGK.txt
Processed data file: miRNA_vsd_PGK.txt


title: E14cEpiSC diff3 D4 GEI-126 [miRNA]

description:
E14.diff3.d4
E14 (male) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_E14.txt
Processed data file: miRNA_norm_E14.txt
Processed data file: miRNA_vsd_E14.txt


title: PGKcEpiSC diff3 D29 GEI-124 [miRNA]

description:
PGK.diff3.d29
PGK (female) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_PGK.txt
Processed data file: miRNA_norm_PGK.txt
Processed data file: miRNA_vsd_PGK.txt


title: E142i diff3 D0 GEI-125 [miRNA]

description:
E14.diff3.d0
E14 (male) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_E14.txt
Processed data file: miRNA_norm_E14.txt
Processed data file: miRNA_vsd_E14.txt


title: PGKcEpiSC diff3 D4 GEI-119 [miRNA]

description:
PGK.diff3.d4
PGK (female) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_PGK.txt
Processed data file: miRNA_norm_PGK.txt
Processed data file: miRNA_vsd_PGK.txt


title: PGKcEpiSC diff3 D21 GEI-123 [miRNA]

description:
PGK.diff3.d21
PGK (female) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_PGK.txt
Processed data file: miRNA_norm_PGK.txt
Processed data file: miRNA_vsd_PGK.txt


title: E14cEpiSC diff3 D4  [mRNA]

description:
E14.diff3.d4
E14 (male) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_E14.txt
Processed data file: mRNA_norm_E14.txt
Processed data file: mRNA_vsd_E14.txt


title: PGK 2i P26+2 GEI-92 [mRNA]

description:
PGK.diff2.d0
PGK (female) cells.
Stranded mRNA STD
Processed data file: mRNA_raw_PGK.txt
Processed data file: mRNA_norm_PGK.txt
Processed data file: mRNA_vsd_PGK.txt

source_name: Mouse ES cells, female, D0


title: PGKcEpiSC diff2 D29 GEI-113 [miRNA]

description:
PGK.diff2.d29
PGK (female) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_PGK.txt
Processed data file: miRNA_norm_PGK.txt
Processed data file: miRNA_vsd_PGK.txt


title: E14 EpiSC D4 GEI-96 [miRNA]

description:
E14.diff2.d4
E14 (male) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_E14.txt
Processed data file: miRNA_norm_E14.txt
Processed data file: miRNA_vsd_E14.txt


title: E14 EpiSC D10 GEI-98 [miRNA]

description:
E14.diff2.d10
E14 (male) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_E14.txt
Processed data file: miRNA_norm_E14.txt
Processed data file: miRNA_vsd_E14.txt


title: PGKcEpiSC diff2 D23 GEI-112 [miRNA]

description:
PGK.diff2.d23
PGK (female) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_PGK.txt
Processed data file: miRNA_norm_PGK.txt
Processed data file: miRNA_vsd_PGK.txt


title: E14 2i P30+2 GEI-95 [miRNA]

description:
E14.diff2.d0
E14 (male) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_E14.txt
Processed data file: miRNA_norm_E14.txt
Processed data file: miRNA_vsd_E14.txt


title: E14cEpiSC diff2 D21 GEI-114 [miRNA]

description:
E14.diff2.d21
E14 (male) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_E14.txt
Processed data file: miRNA_norm_E14.txt
Processed data file: miRNA_vsd_E14.txt


title: PGK 2i P26+2 GEI-92 [miRNA]

description:
PGK.diff2.d0
PGK (female) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_PGK.txt
Processed data file: miRNA_norm_PGK.txt
Processed data file: miRNA_vsd_PGK.txt


title: PGK2i diff3 D0 GEI-118 [miRNA]

description:
PGK.diff3.d0
PGK (female) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_PGK.txt
Processed data file: miRNA_norm_PGK.txt
Processed data file: miRNA_vsd_PGK.txt


title: PGK EpiSC D10 GEI-94 [miRNA]

description:
PGK.diff2.d10
PGK (female) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_PGK.txt
Processed data file: miRNA_norm_PGK.txt
Processed data file: miRNA_vsd_PGK.txt


title: DIFOX2_Dex2

city: Athens

first: Zhihua

last: Hua

state: Ohio

address: 22 Richland Ave

department: Department of Environmental and Plant Biology

institute: Ohio University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were processed for quality control by Trimmomatic to remove adapter and low quality sequences (phred=33, minimum length=36).  Processed sequences were aligned to the A. thaliana Col-0 genomic sequence (TAIR10) via TOPHAT2 to identify accepted hits, which were then used to generate an absolute expression level (counts) of each locus by HTSeq.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include CPKM values for each Sample.

organism: Arabidopsis thaliana

growth_protocol: Seeds harvested from plants subjected to the same growth conditions were vapor-phase surface sterilized for 3-5 hr with 50 ml NaOCl (bleach) supplemented with 3 ml HCl.  Seeds were germinated and grown on 0.6% (w/v) agar plates containing Gamborg’s B-5 basal medium (GM, Sigma-Aldrich), 1% (w/v) sucrose (Suc), 0.05% N-morpholinoethansulphonic acid (MES; pH 5.7) supplemented with or without 10 μM Dex under a long-day (LD) photoperiod (16-hr light [100 μmol white light m-2 s-1]/8-hr dark at 21°C/19°C, respectively).

extract_protocol:
Seedlings with 4 open true leaves were harvested, immediately frozen in liquid nitrogen, and kept at -80°C until RNA extraction.  RNA was extracted and purified using the RNeasy plant mini kit (Qiagen) as according to the manufacturer’s protocol. The Illumina TruSeq RNA Sample Prep Kit was used with 1 µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Seedlings were treated with either 0.1% ethanol (control) or 0.1% ethanol with 10 μM Dex (treatment) directly added into the GM-Suc media.

tag: ecotype background

tag: age

value: 12 days post germination

value: seedlings with 4 open true leaves


title: DIFOX2_Dex1


title: dal2_GMSUC1

value: 20 days post germination


title: Col0_GMSUC2

value: WT


title: DIFOX2_GMSUC2


title: ICC8261 Genotype sample 3

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

data_processing:
Trimmomatic command line was used to remove low quality reads.
High quality filtered reads were aligned to the Chickpea referemce genome (Cicer arietinum ASM33114v1) (Varshney et al., 2013) TopHat v2.1.1
To analyse gene expression, a consensus reference-guided assembly of the transcriptome data from all samples will be generated using Cufflinks (v2.0.2) and the genes exhibiting a significant difference between treatment and control samples (at least two-fold change with P-value ≤ 0.05) considered to be differentially expressed.
To process data from high-throughput sequencing the read count was performed by HTseq python package
To analyse the gene expression of leaf tissue samples two different R programming analysis methods were used, DESeq2 (Love et al. 2014a) and EdgeR (Robinson et al. 2010). A stringent cut-off (q –value  0.001 and log2 fold change  1.0), was used for selecting differentially expressed genes.
Genome_build: ASM33114v1
Supplementary_files_format_and_content: RNAseq.gene.counts, DESeq2 and EdgeR data

organism: Cicer arietinum

source_name: Cicer arietinum L. Chickpea Leaf tissue

growth_protocol: In this study, two different chickpeas (Cicer arietinum L.) genotypes ICC8261 (Drought tolerant) and ICC283 (Drought sensitive) seeds were grown in a glasshouse under controlled conditions. The field capacity of soils for control samples was 80% and 20% for drought. Plants were grown in 20 cm polypropylene pots containing 4 kg of soil under controlled environmental conditions with air temperature regulated between 23C and 28C (night/day). The experiment was a 3 X 2 X 2 completely randomised block design one-time point (Shoot apical meristem), two genotypes, and two treatment conditions). For each genotype, 6 pots were used and randomly designated to one of two treatments: Well-watered (WW) control and drought-stressed (DS).

extract_protocol:
RNA was extracted using Qiagen Rneasy mini kit
The sequencing for leaf samples was performed by Illumina HiSeq 1000 in one lane each to generate 2×150 base pair paired-end reads

treatment_protocol: Total RNA was extracted from leaf tissues using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions. The quality and quantity of isolated RNA were confirmed by using Nanodrop spectrophotometer (NanoDrop Technologies) and Agilent Bioanalyzer

value: Shoot apical meristem stage

value: Drought stressed (DS)


title: ICC8261 Genotype sample 1


title: DIFOX2_GMSUC1


title: Col0_GMSUC1


title: ICC8261 Genotype control 1

value: well watered (WW)


title: ICC283 Genotype sample 2


title: ICC8261 Genotype sample 2


title: ICC8261 Genotype control 3


title: ICC283 Genotype sample 3


title: E14cEpiSC diff2 D27 GEI-115 [miRNA]

description:
E14.diff2.d27
E14 (male) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_E14.txt
Processed data file: miRNA_norm_E14.txt
Processed data file: miRNA_vsd_E14.txt


title: PGK EpiSC D4 GEI-93 [miRNA]

description:
PGK.diff2.d4
PGK (female) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_PGK.txt
Processed data file: miRNA_norm_PGK.txt
Processed data file: miRNA_vsd_PGK.txt


title: ICC283 Genotype sample 1


title: dal2_GMSUC2

value: 21 days post germination


title: 4moRAGECS2

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

data_processing:
Fastq data files were aligned to the mouse Mm10 Ensembl genome with Novoalign read aligner version 2.08.02
Novoaligned SAM files were parsed into binary BAM files and differentially expressed genes identified using the RNASeq application from USeq software version 8.7.4
RNASeq application calculates fraction of reads that are exonic, intronic and intergenic and makes normalized read data tracks (FPKM) for visualization in the Integrated Genome Browser
RNASeq application runs DefinedRegionsDifferentialSeq for calculating differential expression using Anders DESeq2 negative binomial statistics and Benjamini and Hochberg mulitple testing correction
Genome_build: Ensembl Mus musculus Mm10
Supplementary_files_format_and_content: Excel file with Ensembl IDs, chromosome coordinates, individual sample raw read counts, FPKM counts, Log2 ratio and false discovery rate

source_name: Alveolar macrophages

extract_protocol:
Qiagen RNAeasy mini kit
Illumina TruSeq RNA sample prep with oligo dT selection

value: RAGE null

tag: exposure

value: cigarette smoke

tag: time point


title: 4moRAGEnull3

value: control


title: ICC283 Genotype control 1

tag: tissue


title: 4moRAGECS1


title: ICC283 Genotype control 2


title: 4moRAGEnull1


title: 4moRAGECS3


title: 4moRAGECS0


title: 7dayRAGECS2


title: 4moRAGEnull0


title: 7dayRAGECS3


title: 7dayRAGEnull2


title: 7dayRAGECS0


title: 7dayRAGECS1


title: 7dayRAGEnull1


title: 7dayRAGEnull3


title: 4moC57CS3

value: Wild-type


title: 4moC57CS2


title: 4moC57CS1


title: BV2_siTet2_LPS-2

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.3.3 with default parameters.
Trimmed reads were mapped to mm9 using Tophat v2.0.9.
Raw read counts for each gene were generated in Seqmonk with the RNA-seq quantitation pipeline. Normalized gene expression values were calculated with the variance stabilizing transformation in DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file containing normalized gene expression values (log2) for each sample.

molecule: polyA RNA

growth_protocol: Murine microglial BV2 cells were grown in DMEM-based medium containing 10% fetal calf serum.

extract_protocol:
RNA was extracted using TRIzol (Sigma) following the manufacturer's instructions.
Directional mRNA-seq libraries were prepared from 1 µg of total RNA using the Dynabeads mRNA purification kit (ThermoFisher Scientific) and the low input ScriptSeq Complete Gold Kit (Epicentre).

treatment_protocol: Cells were transfected with Tet2-specific siRNAs or a non-targetting control using Lipofectamine 3000. After 48 hours cells were switched to 5% FCS medium and treated with 1 µg/ml LPS for 3 hours.

value: microglial cell line BV2

tag: sirna

value: Tet2 depletion

value: LPS


title: ICC283 Genotype control 3


title: 4moC57CS0


title: BV2_siTet2_LPS-3


title: BV2_siTet2_Ctrl-3


title: 4moRAGEnull2


title: 4moC57WT3


title: 4moC57WT2


title: BV2_siTet2_Ctrl-2


title: 7dayC57CS3


title: 7dayC57CS2


title: BV2_siScr_LPS-3

value: siScr


title: 7dayC57CS1


title: BV2_siScr_LPS-2


title: 7dayRAGEnull0


title: 7dayC57WT0


title: 7dayC57WT2


title: 7dayC57WT1


title: BV2_siScr_Ctrl-3


title: BV2_siScr_Ctrl-2


title: Lphn2-homo KO rep3

first: Choon-Soo

last: Lee

address: 28 Yongon-Dong, Jongno-gu

institute: Seoul National University Hospital

description:
Lphn2-homo KO
45_5

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Lphn2-homo KO embryo

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Lphn2 KO

value: whole embryo

tag: developmental stage

value: embryonic day 9.5


title: Col0_Dex2

value: 12 days post germination

value: seedlings with 4 open true leaves


title: Lphn2-homo KO rep1

description:
Lphn2-homo KO
45_2


title: BV2_siScr_Ctrl-1


title: BV2_siTet2_Ctrl-1


title: Lphn2-homo KO rep2

description:
Lphn2-homo KO
45_3


title: WT rep3

description:
wild type
45_8

source_name: wild type embryo

value: wild type


title: WT rep2

description:
wild type
45_7


title: Col0_Dex1

value: WT


title: 4moC57WT1


title: WT rep1

description:
wild type
32_5


title: 4moC57WT0


title: LN-LECs 100ngmL VEGFC-stimulated 72h D

city: Chicago

first: Shann

middle: S

last: Yu

state: IL

address: 5640 S Ellis Ave, Eckhardt Research Center

department: PME-Immunoengineering Center

institute: University of Chicago

description:
LEC_VC100.4
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).

data_processing:
FastQC (Babraham Bioinformatics, Cambridge, UK) - Sequence quality and contamination check
Read mapping and counting with HTSStation platform, which uses Bowtie2 algorithm.
Differential expression analysis (pairwise between 3 conditions) performed using Bioconductor Limma.R package
Adjusted p-values calculated with Benjamini-Hochberg multiple testing adjustment
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: .TXT files containing raw counts and rpkms wer generated following read mapping and read counting via the HTSStation platform, which is an integrated modular platform using the Bowtie2 algorithm to map reads to a reference mouse genome and the (Bioconductor) Limma.R package to perform differential expression statistical analyses. The Limma.R package also generates adjusted p-values values via one-way ANOVA for pairwise comparisons between the three different experimental groups tested, adjusting for the false-discovery rate using the Benjamini-Hochberg method (EMC_limma_3x5.xlsx). All data from the three files were then integrated into a single Excel file to enable rapid viewing of all results (LNLECs_RNASeq_72hVEGFCStim.xlsx).

source_name: LN-LECs 100ngmL VEGFC-stimulated 72h

growth_protocol: LECs were maintained in MEMα medium (Gibco # 22561) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 µg/mL streptomycin, with change of media every 2-3d.

extract_protocol:
The Qiagen RNeasy mini Plus kit was used for mRNA isolation from 3d-stimulated LECs, according to manufacturer's instructions.
After submission of mRNA to the EPFL Gene Expression Core Facility for library preparation and sequencing, their standard protocol for library prep involves poly-A selection and RT-PCR for selection of mRNA, and finally, library preparation using the Illumina TruSeq Stranded mRNA Prep Kit (used according to manufacturer’s protocols).

treatment_protocol: Media was supplemented with indicated concentration of murine VEGF-C (purified recombinant, expressed in HEK-293E), and incubated for 3 d. Daily visual check was performed, and aliquots of media were obtained for ELISAs/Luminexes.

tag: gender

value: female

tag: cell type

value: Lymphatic endothelial cells (Pdpn+ CD31+ CD45-) derived from pooled axillary, brachial, cervical, inguinal, and popliteal lymph nodes of C57Bl/6 mice

tag: stimulated with

value: 100 ng/mL VEGF-C for 72hrs


title: LN-LECs 100ngmL VEGFC-stimulated 72h A

description:
LEC_VC100.1
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).

tag: strain


title: BV2_siScr_LPS-1

tag: genotype


title: LN-LECs 10ngmL VEGFC-stimulated 72h D

description:
LEC_VC10.4
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).

source_name: LN-LECs 10ngmL VEGFC-stimulated 72h

value: 10 ng/mL VEGF-C for 72hrs


title: LN-LECs 10ngmL VEGFC-stimulated 72h E

description:
LEC_VC10.5
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).


title: LN-LECs 10ngmL VEGFC-stimulated 72h C

description:
LEC_VC10.3
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).


title: LN-LECs 10ngmL VEGFC-stimulated 72h B

description:
LEC_VC10.2
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).


title: LN-LECs 10ngmL VEGFC-stimulated 72h A

description:
LEC_VC10.1
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).


title: LN-LECs unstimulated 72h D

description:
LEC_VC0.4
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).

source_name: LN-LECs unstimulated 72h

value: none (unstimulated control)


title: LN-LECs unstimulated 72h C

description:
LEC_VC0.3
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).


title: LN-LECs unstimulated 72h E

description:
LEC_VC0.5
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).


title: LN-LECs unstimulated 72h A

description:
LEC_VC0.1
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).


title: Mock 0hr_1

city: Pohang

first: Gi-Cheon

middle: careful

state: Hyoja-dong Namgu

address: POSTECH, postech biotech center Rm 430, Hyoja-dong Namgu, pohang

institute: IBS

data_processing:
QC/adapter sequence trimming for raw FASTQ sequences  Raw read quality evaluation by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc ) with default options.  Adapter sequence trimming by CutAdapt (https://pypi.python.org/pypi/cutadapt)
Mapping on mouse reference genome  By TopHat2 (http://tophat.cbcb.umd.edu) and bowtie2 (http://bowtie-bio.sourceforge.net)
Expression and DEG analysis  Expression analysis by CuffLinks (http://cufflinks.cbcb.umd.edu) with default options[4].  DEG analysis by CuffDiff (http://cufflinks.cbcb.umd.edu) with significance thresholds as FDR<0.05, p<0.001, and p<0.01. Scatter plot and volcano plot by in-house R scripts. Unsupervised clustering by in-house R scripts
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts generated by CuffLinks

source_name: SP-DC

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Ribospin II RNA purification kit (GeneAll, Korea)
TruSeq Stranded mRNA Sample Preparation Protocol (Illumina)

value: splenic dendritic cell

tag: agent

value: Mock

tag: time


title: CSGG 4hr_3

value: CSGG


title: Mock 4hr_2


title: CSGG 8hr_5


title: Mock 8hr_4


title: LN-LECs 100ngmL VEGFC-stimulated 72h C

description:
LEC_VC100.3
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).


title: LN-LECs 100ngmL VEGFC-stimulated 72h B

description:
LEC_VC100.2
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).


title: chicken mock-infection

city: University Park

first: Suresh

middle: Varma

last: Kuchipudi

state: PA

address: Animal Diagnostic Laboratory, Wiley Lane

department: Veterinary and Biomedical Sciences

institute: The Pennsylvania State University

data_processing:
Illumina HiSeq 2000 used for high-throughput sequencing of cDNA library
Read quality check parameters such as base quality score distribution, sequence quality score distribution, average base content per read, GC distribution in the reads, PCR amplification issues, over-represented sequences, biasing of kmers, and read-length distribution were analysed from the obtained FASTQ file. Based on quality of sequence reads, trimming was done to retain only high quality sequences for further analysis. In addition, the low-quality sequence reads were excluded from the analysis.
From the trimmed paired-end reads, contaminating sequences were removed, including non-polyA tailed RNAs, mitochondrial genome sequences, ribosomal RNAs, transfer RNAs, adapter sequences and others. The contamination removal step was performed for chicken samples using the help of Bowtie 2 (version 2.2.2), in-house Perl scripts and Picard tools (version 1.115).  No contamination removal step was performed for Japanese quail samples as the transfer RNA and ribosomal RNA sequences were not available for Japanese quail.
The gene expression estimation was performed using cufflinks program.
The differential gene expression analysis was performed using cuffdiff program of cufflink package with default settings
Genome_build: Galgal4
Supplementary_files_format_and_content: tab-delimited files show FPKM values of control and virus-infected samples

organism: Gallus gallus

source_name: spleen

extract_protocol:
TRIzol followed by DNase treatment.  Quality and quantity were determined by Agilent 2100 Bioanallyzer per manufacturer's instructions.  Ribosomal RNA contamination was evaluated by RNA 6000 Pico Chip kit (Agilent, USA) using an Agilent 2100 BioAnalyzer.  Ribosomal RNA was depleted using a RiboMinus Transcriptome Isolation kit (Agilent, USA).
RNA was subjected to fragmentation to obtain approximately 200 bp length fragments, which were reverse transcribed into double-stranded cDNA. The cDNA was treated to generate blunt ends, then adapter sequences were ligated to both ends of the cDNA. High-throughput sequencing of the cDNA library was carried out on an Illumina HiSeq 2000 platform (Illumina, USA)

treatment_protocol: Three-week old chickens or Japanese quails were infected with 10^7 EID50 of LaSota or 2K3 strains of NDV by the oculo-nasal route. Mock-infected animals received phosphate buffered saline.  Animals were euthanized 24 hour following infection.

tag: species

value: chicken

tag: infection status

value: mock

value: spleen

value: 3 weeks


title: chicken LaSota

value: LaSota


title: chicken 2K3


title: Input

city: Houaton

first: Rainer

middle: B

last: Lanz

state: TX

address: One Baylor Plaza

department: Molecular and Cellular biology

institute: Baylor College of Medicine

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the mouse genome (mm9) using the BWA algorithm (default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm9
Supplementary_files_format_and_content: The bed file has two 'components' (two UCSC tracks). The first 'batch' shows the track summit only, hence the coordinates are the same. The second 'batch' shows the four column description of the ChIP binding sites. A search for "track name=" will show the start of the two 'batches'.

source_name: whole uterus

growth_protocol: standard chow

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina NextSeq 500.

treatment_protocol: wild type female mated with vasectomized males. Uteri harvest at day 4.5 of pseudopregnancy. Serum progesterone levels used to confirm stage of pregnancy.

value: 8 weeks

value: day 4.5 of pseudopregnancy

value: uterus

tag: chip antibody


title: FOXO1_ChIPseq


title: Acetyl-H3_ChIPSeq, TPA-treated HL-60 cells

first: Kee-Beom

address: Heusokdong

institute: Chung-Ang University

data_processing:
Basecalls performed using MACS version 1.4.2
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: Peripheral blood leukocytes

extract_protocol:
HL-60 cells were cultured for 48 h in the presence of 32 nM TPA or DMSO control as indicated and cross-linked by the addition of 1/10 volume of freshly-prepared formaldehyde cross-linking buffer (11% formaldehyde, 10 mM HEPES-KOH [pH 7.6], 100mM NaCl, 1 mM EDTA, 0.5 mM EGTA) to cell culture dishes and incubated for 10 min at room temperature. Glycine was added to a final concentration of 125 mM and cells were incubated for 5 min at room temperature. The samples were sonicated and the sonicated lysates were subjected to immunoprecipitation using the indicated antibodies and protein A/G Agarosebeads. Precipitates were washed and DNA was extracted.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

tag: cell line

value: HL-60 promyelocytic leukemia cells

value: TPA

tag: antibody

value: Acetyl-H3 (abcam, catalog# ab 47915, lot# GR-64225-3)


title: PolII_ChIPSeq, TPA-treated HL-60 cells

value: PolII (santacruz, catalog# sc-899x, lot# H1012)


title: PolII_ChIPSeq, DMSO-treated HL-60 cells

value: DMSO


title: LN-LECs unstimulated 72h B

description:
LEC_VC0.2
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).

value: female

value: Lymphatic endothelial cells (Pdpn+ CD31+ CD45-) derived from pooled axillary, brachial, cervical, inguinal, and popliteal lymph nodes of C57Bl/6 mice

value: none (unstimulated control)


title: LN-LECs 100ngmL VEGFC-stimulated 72h E

description:
LEC_VC100.5
RNA isolated from LECs with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).

value: 100 ng/mL VEGF-C for 72hrs


title: Control-P2

description: processed data file: EoE_GERDvsControl_Proximal_AllGenes.txt

data_processing:
Fastq data files aligned to human Hg19 genome with Bowtie short read aligner version 0.12.7
Bowtie aligned sam files were parsed into binary point data files and differentially expressed genes identified using the RNASeq application from USeq software version 7.8.
RNASeq application calculates fraction of reads that are exonic, intronic and intergenic and makes normalized read data tracks (RPKM) from the point data for visualization in the Integrated Genome Browser.
RNASeq application runs MultipleReplicaDefinedRegionScanSeqs (MRDRSS) for calculating differential expression using Anders DESeq negative binomial statistics and Benjamini and Hochberg mulitple testing correction.
Disease specific unannotated (novel) RNAs were identified using Cufflinks and Cuffcompare software and differential expression calcuated using MRDRSS application.
Genome_build: Human Hg19
Supplementary_files_format_and_content: text files with individual sample RPKM values, fold change and false discovery rate

source_name: control_proximal esophagus

extract_protocol:
TriZol
Illumina TruSeq RNA sample prep kit using barcodes for mulitplexing

value: male

tag: disease

value: control esophagus, no disease

value: Esophageal biopsies

tag: location

value: proximal esophagus


title: Control-D2

description: processed data file: EoE_GERDvsControl_Distal_AllGenes.txt

source_name: control_distal esophagus

tag: tissue

value: distal esophagus


title: Control-D1


title: GERD-D2

source_name: GERD_distal esophagus

value: gastroesophageal reflux disease


title: Control-P1


title: Control-P3


title: GERD-D1


title: GERD-D3


title: Control-D3


title: GERD-P3

source_name: GERD_proximal esophagus


title: Acetyl-H3_ChIPSeq, DMSO-treated HL-60 cells


title: EoE-D2

source_name: EoE_distal esophagus

value: eosinophilic esophagitis


title: GERD-P1


title: EoE-P3

source_name: EoE_proximal esophagus


title: EoE-P2


title: GERD-P2


title: EoE-P1


title: DHA_hypothalamus_rep1 [RRBS]

city: Los Angeles

first: Xia

last: Yang

state: CA

address: 610 Charles E. Young Dr. East

institute: UCLA

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Bisulfite-converted reads were aligned to aligned to rat genome (UCSC assembly 5.0) using using the bisulfite aligner BS Seeker2, which utilizes the short read aligner Bowtie. As bisulfite treatment converted unmethylated cytosines (Cs) to thymines (Ts), we estimated the methylation level at each covered cytosine by methylation percentage which was calculated as NC/(NC + NT), where NC is the number of methylated reads and NT is the number of unmethylated reads
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files including the methylation level of cytosines in CpG, CHH and CHG context. The 8 fields in the files are (1) chromosome, (2) nucleotide on Watson (+) strand, (3) position, (4) context (CG/CHG/CHH), (5) dinucleotide-context (CA/CC/CG/CT), (6) methylation-level = #_of_C / (#_of_C + #_of_T)., (7) #_of_C (methylated C, the count of reads showing C here), (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)

organism: Rattus norvegicus

extract_protocol:
Geome DNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of DNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Qubit RNA assay (Life Technologies, NY, USA) and gel electrophoresis
Reduced representation bisulfite sequencing (RRBS) libraries were constructed as described previously with some modifications (Chen, P.Y. et al. Physiol Genomics 45, 565-576). Briefly, about 1,000 ng genomic DNA was digested with the MspI enzyme. Digested DNA was then purified, end-repaired, and adenylated, followed by ligation to Illumina TruSeq barcode adapters (Illumina Inc, CA, USA). Fragments of 150-300 bp in size were selected, bisulfite-treated, and sequenced using an Illumina Hiseq 2500 System (Illumina Inc, CA, USA).

treatment_protocol: Rats were fed with fructose and/or DHA for 6 weeks

value: Sprague Dawley

tag: fed with

value: DHA for 6 wks

value: hypothalamus


title: DHA_hypothalamus_rep4 [RRBS]


title: DHA_hippocampus_rep3 [RRBS]

value: hippocampus


title: DHA_hypothalamus_rep2 [RRBS]


title: DHA_hippocampus_rep1 [RRBS]


title: EoE-D1


title: DHA_hippocampus_rep2 [RRBS]


title: DHA_hippocampus_rep4 [RRBS]


title: DHA_hypothalamus_rep3 [RRBS]


title: DO8-3

city: Qingdao

first: Lina

last: Sun

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of Sciences

description: mRNA

data_processing:
The original image data was transferred into sequence data by base calling (using CASAVA version 1.5+), (defined as ‘raw reads’) and saved as fastq files that include the detailed reads sequences and the reads quality information.
To obtain clean reads, it is necessary to remove the dirty raw reads prior to data analysis. This process encompasses the following procedures: (1) remove reads with adaptors; (2) remove reads in which unknown bases are greater than 10%; (3) remove low-quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read).
A comparison of “clean reads” by SOAPaligner/soap2 (parameters:-m 0 -x 1000 -s 28 -l 32 -v 2 -r 2) was carried out using the reference databases from large-scale transcriptome profiling.
Genome_build: Not provided.
Supplementary_files_format_and_content: *.gene.FPKM.xls: Excel files include FPKM values.

organism: Apostichopus japonicus

source_name: Apostichopus japonicus respiratory tree, DO8

extract_protocol:
According to the instructions provided by the manufacturer of the RNase-free DNase (Qiagen Inc., Hilden, Germany), an RNeasy mini kit including DNase treatment was used to isolate total RNA from nine samples (three replicates in each group) of the respiratory tree from the three different groups (DO2, DO4, and DO8).
The RNA samples from three individuals per replicate were pooled in equal amounts for library construction. Libraries were prepared from the nine RNA pools by Beijing Genomics Institute, Shenzhen, China (BGI-Shenzhen). Strict quality control (QC) was applied in each experimental step to obtain highly reliable sequencing data. Magnetic beads with poly-T-oligos attached were used to isolate poly(A) mRNA. The target RNA was then purified. The target RNA was fragmented into short sequences, reverse-transcribed into single-strand cDNA using the N6 random primer (Promega, Madison, WI, USA), and synthesized into double-stranded cDNA (dscDNA) with DNA polymerase I and RNase H (Promega, Madison, WI, USA). Next, the end of the dscDNA was repaired and ligated with a sequencing adapter. The ligation product was amplified using specific primers. The PCR product was denatured by heating and the single strand DNA was cyclized using splint oligo and DNA ligase. Finally, high-throughput sequencing was performed with the prepared cDNA libraries using the BGISEQ-500 RS platform at BGI-Shenzhen.

treatment_protocol: One group of sea cucumbers was maintained as the control group with high DO water (DO8) at around 8 mg/L, whereas the other two groups were kept in sea water with nitrogen aeration where the DO concentration gradually decreased to approximately 4 mg/L DO (DO4) and 2 mg/L DO (DO2), which is defined as hypoxia, and they were maintained for 3 days.

value: Respiratory tree

tag: condition

value: Dissolved oxygen 8 mg/L


title: bin M1

city: Barcelona

first: Riddhiman

last: Dhar

state: Barcelona

address: C/ Dr. Aiguader, 88

department: EMBL-CRG Systems Biology Program

country: Spain

institute: Centre for Genomic Regulation

data_processing:
Base calling was performed with bcl2fastq2 v2.17.1.14
bowtie2 --local -x Ref_cdna -1 *_read1.fastq.gz -2 *_read2.fastq.gz --no-head --no-sq -S *.sam
Custom code to count uniquely and concordantly mapping read pairs from SAM files
Normalization using RUVg method in R package RUVSeq using ERCC Spike-ins as control
Diffrentially expressed genes were identified using R package DESeq2
Genome_build: R64-1-1 Saccharomyces cerevisiae reference cDNA sequence (Ensembl)
Supplementary_files_format_and_content: raw count of uniquely and concordantly mapping read pairs

source_name: yeast cells

growth_protocol: Cells were grown in SCD medium for 24 hours at 30°C, then diluted 1:50 into fresh SCD medium and grown for 20 hours. Then diluted again to fresh SCD medium and grown for 4 hours.

extract_protocol:
Total RNA was isolated using MasterPure yeast RNA isolation kit (Epicentre) following manufacturer’s protocol.
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocol
RNA-seq, performed in Illumina HiSeq 2500 using TruSeq v4 chemistry

treatment_protocol: Cells were washed twice with PBS, then were re-suspended in PBS. TMRE was added to a final conc. of 100nM from a 10mM stock dissolved in DMSO. Cells were incubated at 30°C for 30 minutes, were washed twice with PBS and were sorted by cell sorter (BD Aria II SORP cell sorter) into four bins (HI,M1,M2, and LO).


title: bin LO


title: DO8-1

description: mRNA


title: bin HI


title: DO2-3

description: mRNA

source_name: Apostichopus japonicus respiratory tree, DO2

value: Dissolved oxygen 2 mg/L (hypoxia)


title: DO4-1

description: mRNA

source_name: Apostichopus japonicus respiratory tree, DO4

value: Dissolved oxygen 4 mg/L


title: DO4-2

description: mRNA


title: DO4-3

description: mRNA


title: DO8-2

description: mRNA


title: DO2-2

description: mRNA


title: DO2-1

description: mRNA


title: HIV_24h_r

city: Basel

first: Monica

last: Golumbeanu

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

data_processing:
Illumina adapter sequences were removed from RNA-Seq reads using Cutadapt v1.7.1. Afterwards, the reads were filtered using Prinseq-lite, which removed their poly-A and low-quality (quality score less than 6) boundaries and kept for further analysis only the reads longer than 30 nucleotides, with a mean quality score larger than 20. The FastQC software was used for quality assessment of the datasets.
Sequencing reads that passed quality filtering were aligned using STAR v2.5 to the GRCh37 Human Genome Assembly concatenated to the HIVeGFP/VSV-G HIV genome sequence.
The number of reads aligned to each gene was retrieved at each time point with HTSeq-count v0.5.3 with option –inverse, using the Ensembl genome annotations for human and HIV.
The read counts per gene were normalized using the median-of-ratios method introduced with the DESeq tool.
Genome_build: hg19
Supplementary_files_format_and_content: tables (tab delimited txt files) with the raw numbers of counted reads for each gene and condition, and with the corresponding normalized read counts

growth_protocol: SupT1 cells (lymphoblastic T cell line) were cultured in RPMI 1640 medium depleted for K and R amino acids, with 10% (v/v) heat-inactivated fetal bovine serum (FBS) (Invitrogen). Isotope-labeled amino acids (13C6-L-lysine, 13C615N4-L-arginine; Cambridge Isotope Laboratories (CIL), Andover, MA) were included in the heavy (H) SILAC medium at 100 mg/l, while normal Arginine and Lysine were used in the light (L) SILAC medium. Heavy or light SILAC labeling was achieved by culturing the cells in the two media (H and L) for a minimum of 2 weeks to allow for at least 5 cell divisions. K and R heavy isotope incorporation and cell viability were checked. H-labeled cells were Mock infected, while the L-labeled cells were infected with an HIVeGFP/VSV-G virus at 3 μg/10^6 cells, in presence of 5 μg/ml polybrene and followed by a 30-minute spinoculation at 1500g. A 60% infection success rate was obtained at 24h, which signed a quasi-universal invection (i.e., 93% GFP+ at 36h).

extract_protocol:
Cell samples were stored in RNALater at the time of collection. Total RNA extraction was performed using Illustra RNAspin mini isolation kit (GE Healthcare) and further processed for mRNA-Seq library preparation (TruSeq RNA sample prep kit, Illumina – that starts with capture of polyA-containing transcripts), followed by cluster generation (TruSeq single-end cluster generation kit, Illumina) and high-throughput sequencing on Illumina HiSeq2000 at the Genomics Technology Facility, University of Lausanne.
Total RNA extraction was performed using Illustra RNAspin mini isolation kit (GE Healthcare) and further processed for mRNA-Seq library preparation (TruSeq RNA sample prep kit, Illumina – that starts with capture of polyA-containing transcripts), followed by cluster generation (TruSeq single-end cluster generation kit, Illumina) and high-throughput sequencing on Illumina HiSeq2000 at the Genomics Technology Facility, University of Lausanne.
Illumina TruSeq: 100 NT, single end (RNA-Seq)

treatment_protocol: Cells were either mock infected or infected with an HIVeGFP/VSV-G virus at 3 μg/10^6 cells, in presence of 5 μg/ml polybrene, by spinoculation at 1500g for 30 minutes. Cells were then washed and further cultured in respective corresponding SILAC culture media. At different time points, cells were colletected for total RNA extraction (for transcriptome analysis by RNASeq) and cell lysis (for proteome analysis).

value: Sup T1 CD4+ T Cells

tag: infection

value: HIV

tag: time (after infection)


title: HIV_12h

tag: cell type


title: HIV_24h


title: HIV_18h


title: HIV_30h


title: HIV_6h


title: Mock_30h

value: Mock


title: Mock_24h_r


title: Mock_18h


title: bin M2

tag: strain


title: Mock_24h


title: Mock_6h


title: hibernating liver DGE

city: Guangzhou

first: Lihong

last: Yuan

state: Guangdong

address: 105 Xin-gang Xi road

institute: Guangdong Entomological Institute

description:
MY-GZ
Solexa Digital Gene Expression (DGE) sequencing

data_processing:
Total 17,792 genes were annotated based on the current 1.7 × coverage genome of microbat (Myotis lucifugus) and used as reference genes (Hubbard et al. 2002). According to the Solexa tags preparation, the 3' most CATG sites within 3 Kb of 3' UTR for each reference gene were identified by in-house Perl script and used to construct the reference tag dataset. After removing the adapter contaminants and the low quality tags (containing Ns), the clean Solexa tags of each library were mapped onto the gene reference tag dataset separately by SOAP (Li et al. 2008). Only perfect matches were considered, and no mismatches were allowed. For genes that have multi-tags were found in Solexa tags, only the 3' most expressed tags were taken into account as the gene expression value. Whereas, for tags that mapped onto different genes, the mean value of tag number was used as the expression level for each gene.
Genome_build: Myoluc2.0, INSDC Assembly GCA_000147115.1, Sep 2010
Supplementary_files_format_and_content: text file containing tag sequence and its expression value

organism: Myotis pilosus

source_name: Liver

extract_protocol:
Tissues of Myotis ricketti in hibernating and aroused states, which were collected and stored at -80C, were used for RNA extraction and library preparation.
Solexa Digital Gene Expression (DGE) sequencing

tag: developmental stage

value: adult

tag: state

value: hibernation

value: liver


title: aroused liver DGE

description:
DZ-GZ
Solexa Digital Gene Expression (DGE) sequencing

value: aroused state


title: flag-RIP-flag-SRSF3

city: Kunming

first: Baowei

last: Jiao

state: Yunnan

address: 32 Jiaochang Donglu Kunming

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
RIP-Seq reads were aligned to the h19 genome assembly using hisat2 version 2.0.5 with the following configurations: --no-unal --dta  --dta-cufflinks --score-min  L,0,-0.2  --no-mixed  --no-discordant  --no-unal  --known-splicesite-infile
expression value were calculated using stringtie version 1.3.0 with the following configurations: -a 6
RIP enrichment  were called using ASPeak.pl version 2.0.0 with default setting
RNA-seq: Reads were aligned to the h19 genome assembly using STAR_2.5.2a_modified; expression value were calculated using Version 1.4.6-p5 with the following configurations: -T 5 -a $gtf2 -t exon
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: RIP against flag in MDA-MB231 overexpressed flag-SRSF3

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: breast cancer cell line


title: input-flag-SRSF3

source_name: input RNA in MDA-MB231 overexpressed flag-SRSF3


title: RIP-flag-TDP43

source_name: RIP against flag in MDA-MB231 overexpressed flag-TDP43


title: control_miRNA seq

city: Wuhan

first: Hao

last: Zhang

state: Hubei

address: Nanhu Road 7#

department: Institute of Animal Husbandry and Veterinary Sciences

institute: Hubei Academy of Agricultural Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
After removing the adaptors, low quality tags and contaminants reads, the clean reads were aligned with the duck genome
The expressions of miRNAs were normalized by Fragments per Kilobase of Transcript per Million Fragments Mapped (FPKM)
Genome_build: BGI_duck_1.0
Supplementary_files_format_and_content: The processed data columns are annotated as:  CC.tpm  CT.tpm is the "The expressions of miRNAs were normalized by Fragments per Kilobase of Transcript per Million Fragments Mapped   (FPKM)".  The processed data columns are annotated as: CC.readcount    CT.readcount  were unnormalized.

organism: Anas platyrhynchos

source_name: duodenum

growth_protocol: The experiment was carried out using one-day-old female Jingjiang ducks. 20 ducks were divided into two groups and placed under natural conditions of light and  temperature.

extract_protocol:
Total RNA of each sample was extracted with Trizol (Invitrogen, USA). Using a Novex 15% TBE-Urea gel, 20–30-nt long RNA fragments were isolated and purified from 10 μg of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control group ducks and transported group ducks were placed in the newborn poulty carry cases.  The transported group were placed in the transport vehicle and transported 8 hours, and the transport took place on ordinary roads and bumpy roads at speeds between 40 and 70 km/hr.Ducks in control group has not been transported.

tag: stain

value: Jingjiang duck

value: normal duodenum

tag: treated

value: control group has not been transported.


title: transported_miRNA seq

value: duodenum mucosa damage caused by transportation stress

value: placed in the transport vehicle and transported 8 hours


title: input-flag-TDP43

source_name: input RNA of MDA-MB231 overexpressed flag-TDP43


title: sh-TDP43_+_sh-SRSF3_rep1

source_name: total RNA from MDA-MB231 treated with sh-TDP43 ＆sh-SRSF3


title: sh-TDP43_+_sh-SRSF3_rep2


title: sh-TDP43_rep2

source_name: total RNA from MDA-MB231 treated with sh-TDP43


title: sh-TDP43_rep1


title: sh-SRSF3_rep2

source_name: total RNA from MDA-MB231 treated with sh-SRSF3


title: sh-SRSF3_rep1


title: sh-control_rep2

source_name: total RNA from MDA-MB231 treated with sh-control


title: hibernation adipose DGE

description: Solexa Digital Gene Expression (DGE) sequencing

data_processing: Total 17,792 genes were annotated based on the current 1.7 Ã coverage genome of microbat (Myotis lucifugus) and used as reference genes (Hubbard et al. 2002). According to the Solexa tags preparation, the 3â most CATG sites within 3 Kb of 3â UTR for each reference gene were identified by in-house Perl script and used to construct the reference tag dataset. After removing the adapter contaminants and the low quality tags (containing Ns), the clean Solexa tags of each library were mapped onto the gene reference tag dataset separately by SOAP (Li et al. 2008). Only perfect matches were considered, and no mismatches were allowed. For genes that have multi-tags were found in Solexa tags, only the 3â most expressed tags were taken into account as the gene expression value. Whereas, for tags that mapped onto different genes, the mean value of tag number was used as the expression level for each gene.

source_name: adipose tissue

extract_protocol: According to the manufacturerâs instruction, total RNA was isolated from bat brain and adipose tissues of hibernating and active states by the RNAiso kit (TakaRa). Five microgram total RNA of each was incubated with oligo-dT beads to capture the polyadenlyated RNA fraction, and double strand cDNA were synthesized while the RNA was bound to the beads. Then cDNA fragments were digested with NlaIII to bring a CATG site at the most 3â end, and ligated with the GEX adapter 1 which contains MmeI restriction site. After digested with MmeI, 21 nt fragments (contains a 17 nt tag) were extracted by dephosphorylation and phenol, and ligated with the GEX adapter 2 which contains the sequencing primers. Subsequently, the PCR was performed with two primers that anneal to the ends of the GEX adapter 2 to selectively enrich the cDNA tags. Finally, the Illumina Cluster Station and Solexa Genome Analyzer II were programmed for subsequent cDNA tags sequencing and the quantitative expression level of the unique transcripts was demonstrated by the number of times the sequence was detected.

treatment_protocol: Tissues of Myotis ricketti in hibernating and aroused states, which were collected and stored at -80 ÂºC, were used for RNA extraction and library preparation.

value: adipose


title: aroused adipose DGE


title: hibernation brain DGE

source_name: whole brain

value: brain


title: sh-control_rep1


title: aroused brain DGE


title: Mock_12h


title: sample S12 tumor tissue_rna

city: Hangzhou

first: Yimin

last: Zhu

state: Zhejiang

address: Yuhangtang Road

institute: Zhejiang university

description: processed data file: S12T-VS-S12N.GeneDiffExp.txt

data_processing:
The following data processing including gene expression level and differentially expressed genes were statistically analyzed by the method of Audic andClaverie3. The gene expression level was calculated by using RPKM (Reads Per kb per Million reads). If there was more than one transcript for one gene, the longest one was used to calculate its expression level and coverage. The RPKM values can be directly used for comparing the difference of gene expression among samples. The significantly differentially expressed genes (DEG) were determined at a threshold false discovery rate (FDR) ≤0.05 and the absolute value of log2Ratio ≥ 0.585.
genome build: hg19
processed data files format and content: text file with RPKM and statistics

source_name: colonrectal

extract_protocol:
RNA extraction protocol not provided.
The total RNA samples were first treated with DNase I to degrade any possible DNA contamination. Then the mRNA was enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments (about 200 bp). The first strand of cDNA was synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition was then performed. Finally, sequencing adaptors were ligated to the fragments. The fragments were enriched by PCR amplification. During the QC step, Agilent2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System were used to qualify and quantify of the sample library. The library products were ready for sequencing via Illumina HiSeq2000.

tag: disease state

value: tumor

value: colorectal


title: sample S12 tumor tissue_medip

data_processing:
After base calling, low-quality reads were omitted and the clean reads were aligned to the UCSC human reference genome (hg19) using SOAP2 (Version 2.21). Mismatches of no more than two bases were allowed in the alignment.
Identification of group-wise DMR and DhMR was performed by a strategy of sliding windows along the whole genome descripted in our previous research. This strategy identified DMR and DhMR between tumor and corresponding normal tissues based on the threshold with P-value < 0.05 and at least 5 CG sites.
genome build: hg19
processed data files format and content: wig format

extract_protocol:
DNA extraction protocol not provided.
Prior to immunoprecipitation, 5 μg of genomic DNA was sonicated to a mean size of 200 bp fragments, followed with end repair, <A> base addition and adaptor ligation steps according to Illumina Paired-End protocol. The libraries were sequenced using Illumina HiSeq analyzer according to the manufacturer’s instructions. After base calling, low-quality reads were omitted and the clean reads were aligned to the UCSC human reference genome (hg19) using SOAP2 (Version 2.21). Mismatches of no more than two bases were allowed in the alignment.


title: sample S12 Normal tissue_rna

value: normal


title: sample S12 tumor tissue_hmedip

data_processing:
Library strategy: MeDIP-Seq with anti-hydroxymethylcytosine antibody
After base calling, low-quality reads were omitted and the clean reads were aligned to the UCSC human reference genome (hg19) using SOAP2 (Version 2.21). Mismatches of no more than two bases were allowed in the alignment.
Identification of group-wise DMR and DhMR was performed by a strategy of sliding windows along the whole genome descripted in our previous research. This strategy identified DMR and DhMR between tumor and corresponding normal tissues based on the threshold with P-value < 0.05 and at least 5 CG sites.
genome build: hg19
processed data files format and content: wig format


title: sample S12 Normal tissue_medip


title: sample 2553763 Tumor tissue_rna

description: processed data file: 2553763T-VS-2553763N.GeneDiffExp.txt


title: sample 2551349 Tumor tissue_rna

description: processed data file: 2551349T-VS-2551349N.GeneDiffExp.txt


title: sample 2553763 Normal tissue_hmedip


title: sample 2553763 Tumor tissue_hmedip


title: sample 2553763 Normal tissue_rna


title: sample 2553763 Tumor tissue_medip


title: ICC8261 Genotype control 2

first: Nitin

address: Plenty Road

institute: RMIT University

data_processing:
Trimmomatic command line was used to remove low quality reads.
High quality filtered reads were aligned to the Chickpea referemce genome (Cicer arietinum ASM33114v1) (Varshney et al., 2013) TopHat v2.1.1
To analyse gene expression, a consensus reference-guided assembly of the transcriptome data from all samples will be generated using Cufflinks (v2.0.2) and the genes exhibiting a significant difference between treatment and control samples (at least two-fold change with P-value ≤ 0.05) considered to be differentially expressed.
To process data from high-throughput sequencing the read count was performed by HTseq python package
To analyse the gene expression of leaf tissue samples two different R programming analysis methods were used, DESeq2 (Love et al. 2014a) and EdgeR (Robinson et al. 2010). A stringent cut-off (q –value  0.001 and log2 fold change  1.0), was used for selecting differentially expressed genes.
Genome_build: ASM33114v1
Supplementary_files_format_and_content: RNAseq.gene.counts, DESeq2 and EdgeR data

source_name: Cicer arietinum L. Chickpea Leaf tissue

extract_protocol:
RNA was extracted using Qiagen Rneasy mini kit
The sequencing for leaf samples was performed by Illumina HiSeq 1000 in one lane each to generate 2×150 base pair paired-end reads

value: Shoot apical meristem stage

tag: treatment

value: well watered (WW)


title: sample 2553763 Normal tissue_medip


title: sample 2551349 Tumor tissue_medip


title: sample 2551349 Normal tissue_hmedip


title: sample 2551349 Tumor tissue_hmedip


title: sample 2551349 Normal tissue_rna


title: sample 2551349 Normal tissue_medip


title: sample 2539382 Tumor tissue_medip