title: Control group

city: Nanjing

first: Teng

last: Jiang

state: Jiangsu

address: No.140 Hanzhong Road

department: Neurology

institute: Nanjing Medical University

description: Sample B1

data_processing:
Illumina Hiseq2000 used for basecalling.
The 49nt sequence tags will go through the data cleaning analysis first, which includes getting rid of the low quality tags, 5' adaptor contaminants from the 50nt tags, to get credible clean tags.
The length distribution of the clean tags and common and specific sequences between samples will be summarised.
Map the small RNA tags to genome by SOAP to analyze their expression and distribution on the genome. The parameter is soap -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap.
Genome_build: hg 19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample

source_name: Rat hippocampus

extract_protocol:
Total RNA isolation was carried out using the mirVana™ miRNA Isolation Kit (Ambion, Austin, TX, US). The quality and quantity of RNA are assessed on the Agilent Bioanalyzer.
Biotinylated cRNA were prepared with the Ambion MessageAmp kit according to the instructions provided by the manufacturer.

treatment_protocol: TLE rats were subjected to amygdala stimulation (stimulating the lateral nucleus of the right amygdala for 20 min), whereas control rats were subjected to sham stimulation. Total RNA were extracted at 2 months after amygdala stimulation

value: 3 months

value: Hippocampus


title: TLE group

status: Public on Feb 09 2017

type: SRA

country: China

description: Sample A1

library_source: transcriptomic

molecule: total RNA

organism: Rattus norvegicus

tag: strain

value: Sprague-Dawley

tag: age

tag: tissue


title: D-KO Rep2

city: Torino

first: Ugo

last: Ala

address: Via Nizza 52

department: Dept. of Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Torino

data_processing:
Sequencing reads were trimmed out of the low-quality bases with Fastx Toolkit.
Filtered sequences were mapped on mm9 genome assembly by using TopHat v2.0.8b (67)
mRNAs quantification were performed using CuffLinks v2.2.0
mRNA differential expression quantifications were performed using Cuffdiff v2.2.0
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include gene name, genomic coordinates and FPKM values and status for each sample

organism: Mus musculus

source_name: D-KO

extract_protocol:
Samples were harvested and flash frozen in liquid nitrogen. Total RNA was extracted using RNeasy Mini Kit (QIAGEN).  RNA quality was checked by using the Bioanalyzer instrument.
Libraries were prepared from total RNA using TruSeq RNA Sample Preparation v2 according to the Illumina's protocol and sequenced

value: Cerebellum

tag: developmental stage

value: post natal day 4

tag: genotype/variation


title: CitK-KO Rep2

source_name: CitK-KO


title: CTRL Rep3

source_name: CTRL


title: CitK-KO Rep1


title: CTRL Rep2


title: RNA-26-08_1

city: Seoul

first: Abu Musa Md Talimur

last: Reza

address: 604, Animal Science Building

department: Stem Cell and Regenerative Biology

country: South Korea

institute: Konkuk University

description: smRNA

data_processing:
Illumina RTA (Real Time Analysis. v1.18) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt 1.9.dev3.
To estimate expression levels, the smRNA-Seq reads were mapped to the pre-miRNA and mature miRNA sequence of Homo sapiens using bowtie 1.1.1.
The pre-miRNA and mature miRNA sequence of Homo sapiens (hg19) were downloaded from miRBase (release 21). The read counts of mature miRNA were calculated from mapping results.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count for each samples.

organism: Homo sapiens

source_name: Exosomes

growth_protocol: Human adipose mesenchymal stem cells (hAMSCs) were cultured in a complete α-MEM medium

extract_protocol:
Exosomes were isolated using Exoquick-TC kit (SBI, USA) and the exosomal-miRNA was isolated using SeraMir Exosomal miRNA isolation kit (SBI, USA)
Libraries were constructed from smRNA using the TruSeq Small RNA Library Prep Kit following  manufacturer's protocols.

treatment_protocol: At 6,7&8 passage, 2×10^6 cells were seeded and incubated overnight. On the next day, cells were fed with new medium for another 48 h and the result medium was collected as conditioned medium (CM).

tag: primary source

value: Conditioned medium

tag: cell type

value: Adipose Mesenchymal Stem Cells

tag: cell passages


title: Cancer Patient 52

city: Fribourg

first: Rüegg

last: Curzio

address: Albert-Gockel 1

department: Département de Médecine 3

country: Switzerland

institute: Université de Fribourg

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.2.1, Martin 2011), and filtered for low complexity with Prinseq (v. 0.20.3, Schmieder and Edwards 2011).
Reads were aligned against Homo sapiens.GRCh38.76 genome using TopHat2 (v. 2.0.9, Kim et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.5.4p3, Anders et al. 2014) using Homo sapiens.GRCh38.76 gene annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

source_name: metastatic breast cancer patient

extract_protocol:
Qiagen RNeasy Plus Mini Kit was used following manufacturer's instructions
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA protocol

treatment_protocol: CD11b+ cells were isolated from 8ml total blood within 24h after venous puncture using Miltenyi MACS separation magnetic beads, and cells were lysed in Qiagen RLT buffer.

tag: diagnosis

value: metastatic breast cancer

value: CD11b+ myelomonocytic cells


title: Healthy Patient 05

source_name: healthy donor

value: healthy


title: Cancer Patient 51


title: Healthy Patient 03


title: Healthy Patient 10


title: Healthy Patient 12


title: Cancer Patient 37


title: UMSCC103

city: BUFFALO

first: SATRAJIT

last: SINHA

address: 701 ELLICOTT STREET

country: USA

institute: SUNY AT BUFFALO

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using the Tophat algorithm v2.0.7 with parameters -G -p 8 and default settings  [Trapnell C, et al. (2012) Nat Protoc Mar 1;7(3):562-78.]
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using the Cufflinks algorithm (v2.1.1). [Trapnell C, et al. (2012) Nat Protoc Mar 1;7(3):562-78.]
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values

source_name: Human cell-line

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: UMSCC29


title: SCC4


title: MRS16

city: Ilan

first: Jyh-Yih

last: Chen

address: 23-10, Dahuen Rd., Jiaushi, Ilan

country: Taiwan

institute: Academia Sinica

description: Building Transcriptome Assembly

data_processing:
Illumina Casava software used for basecalling.
Remove reads with adaptors, reads in which unknown bases are more than 10%, and   low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read).
Reads are assembled using Trinity{Grabherr MG, 2011}. The longest assembled sequences are called contigs.  Then the reads are mapped back to contigs; with paired-end reads it is able to detect contigs from the same transcript as well as the distances between these contigs. Finally, get sequences without Ns and cannot be extended on either end. Such sequences are defined as Unigenes. If there are several samples from the same species, TGICL{Pertea, 2003} is used to assemble all the unigenes from different samples to form a single set of non-redundant unigenes.  After clustering, the unigenes will be divided to two class. One is clusters, which the prefix is CL. And the other is singletons, which the prefix is Unigene or Pre.  Unigene sequences are aligned with @blastdb using blastx (evalue<0.00001). Sequence orientations are determined according to the best hit in the database. If results from different databases conflict with each other, we choose one according to this priority: @blastdb. Orientation and CDS of sequences have no hit in blast are pridicted using ESTScan{Iseli, 1999}. Original transcript sequences(5'->3') are provided if we can determine their orientations. Others sequences are provided as the assembler outputs.
Clean reads were mapped to MRS16 transcriptome assembly using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads)
Applying statistical algorithm from Chepelev et al., Genome Research 7(10):986-95 to identify differentially expressed genes between two samples.
Genome_build: De novo Epinephelus coioides transcriptome assembly MRS-16
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

organism: Epinephelus coioides

source_name: larvae (30-days-old)

growth_protocol: The Epinephelus coioides larvae were kept in a 2 tonne FRP tank feed Artemia salina prior to bacterial infection. V. alginolyticus was cultured on TSA (NaCl 1.5%) plates in a 28℃ incubator for 16 hours. Single colony of V. alginolyticus were subsequently incubated in TSB (NaCl 1.5%) media in a 28℃ incubator for a further 16 hours. Vibrio was detected by spreading the culture onto thiosulfate-citrate-bile salt-sucrose agar (TCBS) plates, and incubating the plates at 28℃ for 16 hours. V. alginolyticus formed yellow colony.

extract_protocol:
Epinephelus coioides larvae (30-days-old)  were homogeneous  whole tissue , RNA was extracted using Trizol reagent, then used RNA zol extracted again to improve quality.  RNeasy Mini Kit (Cat. No. 74106) was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNA  is enriched by using the oligo(dT) magnetic beads. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments.

treatment_protocol: At 30-days-old, the whole bodies of Epinephelus coioides larvae with an average body length of about 1.6±0.2 cm were injected with 20 μl (1.3 × 106 colony-forming units (CFU)/ml) of V. alginolyticus in Tryptic soy broth (NaCl 1.5%).

tag: infection

value: non-infected

value: whole larva


title: B4_1

description: Expression Analysis

value: Vibrio infected


title: SCC351


title: SCC71


title: root, replicate B, heat

city: Poznań

first: Zofia

last: Szweykowska-Kulińska

address: Umultowska 89

department: Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

description:
RNA was Dnase treated
NCBI_res_root_deseq_full.xlsx, NCBI_res_root_deseq_fdr_05.xlsx
krH1h_1
krH1h_2

data_processing:
Clean reads were mapped to the reference barley genome (EnsemblPlants, http://plants.ensembl.org/Hordeum_vulgare/Info/Index, version: 082214v1) using TopHat2 software.
Numbers of reads for each gene mapped to the reference genome were counted using HT-Seq software. The script was run for each fastq file for every biological replicate from every condition.
All the results were gathered in tables – one table per one comparison (e.g. a table with 2 biological replicates from roots treated with high temperature and 2 replicates from control roots).
These tables were then fed in DeSeq – R package suitable for analysis of differential gene expression based on the negative binomial distribution.
Obtained results from DeSeq were exported to spreadsheets for further analysis (full results and results with p-adjusted lower than 0.05).
Genome_build: Hordeum vulgare, version: 082214v1

organism: Hordeum vulgare

source_name: root tissue

growth_protocol: Spring barley plants, cv. Rolap, were grown in a Conviron environmental chamber (Conviron, Winnipeg, Manitoba, Canada) with a 16 h day/8 h night photoperiod.

extract_protocol:
RNA isolation was carried out using a mixture containing a 38% v/v phenol solution saturated with 0.1 M sodium acetate , supplemented with 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate, 5% v/v glycerol, 0.5% sodium lauroylsarcosine, and 5 mM EDTA. To remove polysaccharides, the Ambion Plant RNA Isolation Aid (Thermo Fisher Scientific) was added, supernatant containing RNA was purified using a Direct-zol RNA MiniPrep kit according to the manufacturer’s protocol (ZYMO RESEARCH, The Epigenetics Company, USA). RNA was Dnase treated then phenol/chloroform purified.
Oligo (dT) were used to isolate mRNA. Strand-specific RNA libraries were performed at BGI TECH SOLUTIONS (HONGKONG) CO., LIMITED

treatment_protocol: Two-week-old plants at the three-leaf stage (code 13 of Zadoks system; Zadoks et al., 1974) were subjected to heat treatment at 35.5 ºC. Control plants were grown at a constant temperature of 22 °C. Plants were collected after 1 h of heat stress.

tag: temperature

value: 2-week-old barley

tag: genotype

value: cultivar Rolap


title: MRS17

description: Expression Analysis


title: root, replicate A, heat

description:
RNA was Dnase treated
NCBI_res_root_deseq_full.xlsx, NCBI_res_root_deseq_fdr_05.xlsx
rootH1hA_1
rootH1hA_2


title: 48 hours DLX3

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were mapped to hg19 using tophat/2.0.8/bowtie-2.1.0
RPKM values were calculated with Partek 6.6
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes RPKM values

source_name: SCC13_cells_48 hours DLX3

growth_protocol: SCC13 cells cultured in DMEM/F12 + Glutamax Media (Gibco) supplemented with 10% Fetal Bovine Serum and swiched to 1% Fetal Bovine Serum at time of infection

extract_protocol:
Trizol extraction of total RNA from skin was performed according to the manufacturer's instructions.
RNA fragmentation and cDNA library preparation was performed according to the NEB Next and Ovation SP Ultralow Library System protocol. 2nM cDNA library were analyzed by Illumina HiSeq 2500.

treatment_protocol: SCC13 cells were infected with Adeno-GFP or Adeno-DLX3 (Vector Biolabs- PFU of 10^10) at an MOI of 50. Cells were collected for RNA extraction after 18, 24, 36, and 48 hours post-infection.

value: Epidermal squamous cell carcinoma


title: 36 hours DLX3

source_name: SCC13_cells_36 hours DLX3


title: root, replicate B, control

description:
RNA was Dnase treated
NCBI_res_root_deseq_full.xlsx, NCBI_res_root_deseq_fdr_05.xlsx
krK1h_1
krK1h_2


title: 48 hours GFP

source_name: SCC13_cells_48 hours GFP


title: Cancer Patient 66


title: 36 hours GFP

source_name: SCC13_cells_36 hours GFP


title: RNA-26-08_3

description: smRNA


title: shoot, replicate C, heat

description:
RNA was Dnase treated
NCBI_res_K_H_deseq_full.xlsx, NCBI_res_K_H_deseq_fdr_05.xlsx
H1hC1_1
H1hC1_2

source_name: shoot tissue


title: CTRL Rep1


title: shoot, replicate B, heat

description:
RNA was Dnase treated
NCBI_res_K_H_deseq_full.xlsx, NCBI_res_K_H_deseq_fdr_05.xlsx
H1hB1_1
H1hB1_2


title: 24 hours GFP

source_name: SCC13_cells_24 hours GFP


title: 18 hours DLX3

source_name: SCC13_cells_18 hours DLX3


title: shoot, replicate A, heat

description:
RNA was Dnase treated
NCBI_res_K_H_deseq_full.xlsx, NCBI_res_K_H_deseq_fdr_05.xlsx
H1hA1_1
H1hA1_2


title: SCC15


title: shoot, replicate A, control

description:
RNA was Dnase treated
NCBI_res_K_H_deseq_full.xlsx, NCBI_res_K_H_deseq_fdr_05.xlsx
K1hA1_1
K1hA1_2


title: shoot, replicate B, control

description:
RNA was Dnase treated
NCBI_res_K_H_deseq_full.xlsx, NCBI_res_K_H_deseq_fdr_05.xlsx
K1hB1_1
K1hB1_2


title: 18 hours GFP

source_name: SCC13_cells_18 hours GFP


title: TIME_KSHV_3

status: Public on Feb 08 2017

city: Seattle

first: Terri

last: DiMaio

state: WA

address: 750 Republican St.

department: Microbiology

institute: University of Washington

data_processing: align reads, using TopHat v2.08b ( http://tophat.cbcb.umd.edu/ ) along with Bowtie 1.0.0 ( http://bowtie-bio.sourceforge.net/index.shtml ), using Ensembl's GRCh37 release 70 as the reference genome.

source_name: dermal microvasculature

extract_protocol:
RNA was isolated using the RNA isolation kit by Macherey-Nagel. Samples were cleaned and concentrated, where necessary, using Zymogen kit
RNA-seq libraries were generated using Illumina TruSeq RNA Sample Prep Kit v2 following the manufactures protocol.

value: hTert-immortalized microvascular endothelial cells

tag: passage

value: KSHV


title: TIME_KSHV_2


title: TIME_Mock_3

value: mock


title: ABA

city: Hangzhou

first: Wangshu

last: Mou

state: Zhejiang

address: Yuhangtang Road 866

department: College of Bio-engineering and Food Science

institute: Zhejiang University

data_processing:
Tophat version 2.0.9 was unsed to align the qualified reads to S. lycopersicum genome
The mapped reads were assembled by cufflinks version 2.1.1
Cumerge was applied to comerge all transcripts of the three samples to generate unique transcripts
Cuffdiff reestimates the abundance of the transcripts and concurrently test for different expression.
Supplementary_files_format_and_content: S1: The genes and transcripts generated in tomato transcriptome
Supplementary_files_format_and_content: S4: The genes expressed in CK, ABA and NDGA treated samples
Supplementary_files_format_and_content: S5: GO enrichment analysis of DEGs in response to exogenous ABA
Supplementary_files_format_and_content: S6: GO enrichment analysis of DEGs in response to exogenous NDGA
Supplementary_files_format_and_content: S7: KEGG pathway enrichment analysis of DEGs in response to exogenous ABA
Supplementary_files_format_and_content: S8: KEGG pathway enrichment analysis of DEGs in response to exogenous NDGA
Supplementary_files_format_and_content: S9: Genes related to carotenoid biosynthesis
Supplementary_files_format_and_content: S10: Genes realted to chorophyll biosynthesis
Supplementary_files_format_and_content: S11: Genes related to chorophyll degradation
Supplementary_files_format_and_content: S12: Genes related to flavonoid biosynthesis
Supplementary_files_format_and_content: S13: Genes related to reactive oxygen species (ROS) scavenging system
Supplementary_files_format_and_content: S14: Genes related to photosynthesis pathway

organism: Solanum lycopersicum var. cerasiforme

source_name: tomato fruit

extract_protocol:
Total RNA samples were prepared using the Total RNA Purication Kit, TRK1001 (LC Science, Houston, TX), treated with RNase-free DNaseI following the manufacturer's procedure to remove contaminated genomic DNA. The quantity and purity of total RNA were analysed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA).Equal quantities of high-quantity RNA of each sample were blended for cDNA library construction.
The poly (A) messgener RNA was isolated from the total RNA samples with oligo (dT) attached magnetic beads (Invitrogen). The mRNA was frangmented into short pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to the first-strand cDNAs by random hexamer primers. Then the second-strand cDNAs were synthesized to construct the final cDNA library according to the instruction of mRNA-Seq sample preparation kit (Illumina, San Diego, USA) and the paired-end cDNA with a length of 300 bp (±50 bp). After that, the cDNA libraries were sequenced on the Illumina HiSeqTM 2000 platform at the LC-BIO (Hangzhou, China) following the manufacturer’s recommendations.

treatment_protocol: For each group, 25 μL each of ABA (10 mM), NDGA (1 mM) solutions and control (distilled water) was injected into the fruits with the same depth from the pedicle by microsyringe, respectively

tag: time point

value: postharvest

value: pericarp

tag: treatment

value: ABA


title: TIME_KSHV_1


title: TIME_Mock_2


title: TIME_Mock_1


title: msc2_H5

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description:
Single cell transcriptome from input mesenchymal stem cells
processed data file: data.cast.log2.liverbud

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.

source_name: MSC

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

tag: cell type or stage

value: Mesenchymal stem cell 2


title: msc2_H3


title: msc2_H7


title: msc2_H11


title: msc2_H10


title: msc2_G8


title: msc2_G6


title: msc2_G7


title: shoot, replicate C, control

description:
RNA was Dnase treated
NCBI_res_K_H_deseq_full.xlsx, NCBI_res_K_H_deseq_fdr_05.xlsx
K1hC1_1
K1hC1_2


title: msc2_G5


title: NDGA

value: NDGA


title: CK

value: water


title: D1_S_rep2

city: Beijing

first: hongyan

last: sun

address: Poultry genetic group, College of Animal Science and Technology, China Agricultural Univeristy, Yuanmingyuan West Rd. No. 2, Haidian District, Beijing, China

institute: Iowa State University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to gallus gallus 4 whole genome using TopHat software (version 2.0.9) and Bowtie (2.1.0).
The HTseq package (version 0.5.4p3) in Python was used to calculate the number of aligned reads per exon through Ensembl annotation of the chicken genome. The number of read counts per gene was identified in the output file by Ensembl gene ID.
Qlucore Omics Explorer (v3.0) was used to perform principle component analysis (PCA). The detected genes (count number > 1) from the 24 samples were log2 transformed and subjected to normalization (mean = 0 and variance = 1). Bioconductor package EdgeR (version 3.0.8) developed in R software (version 2.15.3) was used to identify the differentially expressed (DE) genes.
Genome_build: gallus gallus 4
Supplementary_files_format_and_content: tab-delimited text files include read number for each genes for each Sample.

organism: Gallus gallus

source_name: bone marrow_susceptible_1dpi

extract_protocol:
RNA samples were isolated using the Ambion MagMax-96 Kit (AM1839) (Applied Biosystems, Foster City, CA) and immediately stored at -80C. All extraction procedures were performed according to manufacturer’s recommendations. A NanoDrop ND-1000 UV-vis Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) was used to quantify the RNA. In addition, the quality of RNA was tested using the Agilent 2100 Bioanalyser (Agilent Technologies). The RNA Integrity Number (RIN) was greater than 9.0 for all the RNA samples applied to construct the cDNA libraries.
The initial total RNA was converted into a cDNA sequencing library through the Illumina TruSeq® RNA Sample Preparation v2 Kit following manufacturer’s instructions (Protocol: #15026495, May 2012). First, 0.1 g - 4 g total RNA was purified using Poly-T oligo-attached magnetic beads to obtain the mRNA fragments. Next, the first-strand cDNA was synthesized from the mRNA fragments. Finally, second-strand cDNA synthesis, end repair, 3’ end adenylation, and adapter ligation were performed and PCR amplification was conducted. The cDNA libraries were validated and quantified using a Qubit® Quantitation Platform and an HS dsDNA kit (Invitrogen, Paisley, UK). Twenty-four cDNA libraries were generated from the twenty-four samples, in terms one cDNA library for one sample. One of the each of the six treatments was pooled into one lane to sequence. Thus, four lanes were used to sequence the twenty-four cDNA libraries through the Illumina® HiSeq 2000 at the Iowa State University (ISU) DNA facility.

tag: strain

value: Commercial broiler

value: bone marrow

value: four weeks

tag: gender

value: male

tag: phenotype

value: susceptible


title: 24 hours DLX3

source_name: SCC13_cells_24 hours DLX3


title: msc2_H9


title: msc2_G1


title: msc2_G4


title: msc2_H8


title: msc2_H6


title: msc2_G10


title: msc2_G11


title: msc2_F8


title: root, replicate A, control

description:
RNA was Dnase treated
NCBI_res_root_deseq_full.xlsx, NCBI_res_root_deseq_fdr_05.xlsx
rootK1hA_1
rootK1hA_2

tag: age

value: 2-week-old barley


title: msc2_G12


title: msc2_H4


title: msc2_F6


title: msc2_F5


title: msc2_F4


title: msc2_G9


title: msc2_F1


title: msc2_F7


title: msc2_F3


title: msc2_E9


title: msc2_F11


title: msc2_E7


title: msc2_E5


title: msc2_F12


title: msc2_F10


title: msc2_E6


title: msc2_G2


title: msc2_E4


title: msc2_E1


title: msc2_D9


title: msc2_D8


title: msc2_D4


title: msc2_E11


title: msc2_D7


title: msc2_D6


title: msc2_D2


title: msc2_D1


title: msc2_D3


title: msc2_D12


title: msc2_D11


title: msc2_C8


title: msc2_C9


title: msc2_C6


title: msc2_C7


title: msc2_C5


title: msc2_C4


title: msc2_F9


title: msc2_C3


title: msc2_E3


title: msc2_C11


title: msc2_B6


title: msc2_C10


title: msc2_B7


title: msc2_B5


title: msc2_B1


title: msc2_B4


title: msc2_B3


title: msc2_B10


title: msc2_A8


title: msc2_D10


title: msc2_B12


title: msc2_A3


title: msc2_A1


title: msc2_A2


title: msc2_A7


title: msc2_C1


title: msc2_B11


title: msc2_A4


title: msc2_A11


title: msc2_A10


title: msc1_G6

value: Mesenchymal stem cell 1


title: msc1_G5


title: msc1_G7


title: msc1_H4


title: msc1_G2


title: msc2_C2


title: msc1_G11


title: msc2_A12


title: msc1_F5


title: msc1_F2


title: msc1_E5


title: msc1_F4


title: msc1_C7


title: msc1_H8


title: msc1_D4


title: msc1_D5


title: msc1_C6


title: msc1_B9


title: msc1_A3


title: msc1_A5


title: msc1_B10


title: msc1_B4


title: msc1_C5


title: mh2_H3

description:
Single cell transcriptome from 2-D hepatocyte lineage
processed data file: data.cast.log2.lineage

source_name: iPSC line TkDA3-4

value: Mature hepatocyte-like 2


title: mh2_H12


title: mh2_G9


title: mh2_H11


title: mh2_G8


title: mh2_G7


title: mh2_H1


title: mh2_G3


title: mh2_G2


title: mh2_G6


title: mh2_G1


title: msc1_E6


title: mh2_G12


title: msc1_D2


title: mh2_G10


title: mh2_F9


title: mh2_F6


title: mh2_F4


title: mh2_F8


title: mh2_F12


title: msc1_C4


title: mh2_F2


title: msc1_A12


title: mh2_E6


title: mh2_E7


title: mh2_F10


title: mh2_D8


title: mh2_E10


title: mh2_D3


title: mh2_D1


title: mh2_C9


title: mh2_D4


title: mh2_E11


title: mh2_C6


title: mh2_C2


title: mh2_D2


title: mh2_C1


title: mh2_C5


title: mh2_B4


title: mh2_B11


title: mh2_B12


title: mh2_B1


title: mh2_B2


title: mh2_A7


title: mh2_A9


title: mh2_A4


title: mh2_A12


title: mh2_A3


title: mh2_A11


title: mh1_H9

value: Mature hepatocyte-like 1


title: mh1_H8


title: mh1_H4


title: mh1_H11


title: mh1_H2


title: mh1_H7


title: mh1_F5


title: mh1_H12


title: mh1_G1


title: mh1_F8


title: mh1_H3


title: mh1_F4


title: mh1_F1


title: mh2_H5


title: mh1_E5


title: mh1_F11


title: mh1_D7


title: mh1_E11


title: mh1_E2


title: mh1_E1


title: mh1_D3


title: mh1_D2


title: mh1_D11


title: mh1_B9


title: mh1_C9


title: mh1_B4


title: mh1_G6


title: mh1_F3


title: mh1_B12


title: mh1_A5


title: mh1_A2


title: lb6_E1

description:
Single cell transcriptome from dissociated liver bud
processed data file: data.cast.log2.liverbud

source_name: liver bud

value: Liver bud 6


title: mh1_A7


title: lb6_D2


title: lb6_F4


title: lb6_E5


title: lb6_B6


title: lb6_H6


title: lb6_D11


title: lb6_C9


title: lb5_G6

value: Liver bud 5


title: lb5_H11


title: lb5_H10


title: lb6_A8


title: mh1_B8


title: lb5_G2


title: lb5_F9


title: lb5_F6


title: lb5_G1


title: lb5_F5


title: lb6_H5


title: lb5_G11


title: lb5_F2


title: mh1_C11


title: lb5_F1


title: lb5_E9


title: lb5_F12


title: lb5_E10


title: lb5_E8


title: lb5_D9


title: lb5_H2


title: lb5_D12


title: lb5_D8


title: lb6_D3


title: lb5_D10


title: lb5_C5


title: lb5_B8


title: mh2_C7


title: lb5_C4


title: lb5_C1


title: lb5_C11


title: lb5_B9


title: lb5_D5


title: lb5_B3


title: lb5_A7


title: lb5_A5


title: lb5_A6


title: lb5_B7


title: lb5_B11


title: lb5_A3


title: lb5_E11


title: lb5_A11


title: lb5_D4


title: lb4_H9

value: Liver bud 4


title: lb5_A10


title: lb4_H10


title: lb4_G7


title: lb4_H2


title: lb4_G5


title: lb4_G8


title: lb4_G6


title: lb4_G2


title: lb4_G4


title: lb4_F8


title: lb4_F2


title: lb4_G1


title: lb4_F4


title: lb4_F3


title: lb3_H7

value: Liver bud 3


title: lb4_F1


title: lb3_G9


title: lb3_H10


title: lb3_H9


title: lb3_G4


title: lb3_G2


title: lb3_G5


title: lb3_G1


title: lb3_G10


title: lb3_F10


title: lb3_G8


title: lb3_E9


title: lb3_E3


title: lb3_E5


title: lb3_D2


title: lb3_D3


title: lb3_D7


title: lb5_A4


title: lb3_D11


title: lb3_C9


title: lb3_B7


title: lb3_A5


title: lb2_H6

value: Liver bud 2


title: lb3_B12


title: lb2_H3


title: lb2_H5


title: lb2_H12


title: lb2_H10


title: lb3_A6


title: lb2_H11


title: lb2_G9


title: lb2_G3


title: lb2_G4


title: lb2_G12


title: lb2_G10


title: lb2_G1


title: lb3_E10


title: lb3_D4


title: lb2_F7


title: lb2_F8


title: lb2_F9


title: lb2_F3


title: lb2_F1


title: lb2_F6


title: lb2_F12


title: lb3_B1


title: lb2_E8


title: lb2_F10


title: lb2_E3


title: lb2_E4


title: lb2_E2


title: lb2_E1


title: lb2_E11


title: lb2_E10


title: lb2_D9


title: lb2_E12


title: lb2_D6


title: lb2_D12


title: lb2_D11


title: lb2_D10


title: lb2_C9


title: lb2_C8


title: lb2_C12


title: lb2_F11


title: lb2_B5


title: lb2_B8


title: lb2_E7


title: lb2_B3


title: lb2_B6


title: lb2_B1


title: lb2_B2


title: lb2_D8


title: lb2_G8


title: lb2_B11


title: lb2_A6


title: lb2_A7


title: lb2_D3


title: lb2_A4


title: lb1_H8

value: Liver bud 1


title: lb2_A10


title: lb1_H3


title: lb1_H2


title: lb2_C1


title: lb1_G3


title: mh1_E6


title: lb1_G5


title: lb1_G8


title: lb1_G2


title: lb2_B7


title: lb1_H1


title: lb1_F5


title: lb2_D7


title: lb1_E7


title: lb2_B12


title: lb1_D10


title: lb1_D1


title: lb1_C8


title: lb1_C2


title: lb1_C11


title: lb1_B10


title: lb1_B12


title: lb1_A9


title: lb1_A4


title: lb1_B5


title: ipsc_H9

value: iPSC line


title: lb1_A1


title: ipsc_H8


title: ipsc_H4


title: lb1_F6


title: ipsc_H12


title: ipsc_H11


title: ipsc_H1


title: ipsc_H10


title: ipsc_G8


title: ipsc_H2


title: ipsc_G3


title: ipsc_G4


title: ipsc_G5


title: ipsc_G7


title: lb1_B6


title: ipsc_G12


title: ipsc_F7


title: ipsc_F9


title: ipsc_F5


title: ipsc_H7


title: ipsc_F8


title: lb1_A6


title: ipsc_F3


title: ipsc_F10


title: ipsc_G9


title: ipsc_F11


title: ipsc_F1


title: ipsc_E8


title: ipsc_G2


title: ipsc_E2


title: ipsc_E3


title: ipsc_E7


title: ipsc_E1


title: ipsc_E11


title: ipsc_E10


title: ipsc_E5


title: ipsc_F2


title: ipsc_D3


title: ipsc_D9


title: ipsc_D12


title: ipsc_D11


title: ipsc_G11


title: ipsc_D7


title: ipsc_D5


title: ipsc_D4


title: ipsc_C8


title: ipsc_C7


title: ipsc_E12


title: lb1_D9


title: ipsc_C6


title: ipsc_C5


title: ipsc_C3


title: ipsc_C12


title: ipsc_C2


title: ipsc_C11


title: ipsc_C4


title: ipsc_D2


title: 5-6-L-P15-M-Liver_LSBS

city: Columbus

first: Matt

last: Cannon

state: OH

address: 700 Children's Dr.

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

description: processed data file: percentMethFinal.txt.gz

library_source: genomic

data_processing:
Library strategy: Locus specific bisulfite Sequencing
We analyzed RRBS and locus specific bisulfite sequencing data by aligning fastq files to the mouse genome (mm9) using Bismark (v0.7.6) with bowtie2
We then combined replicates for each sample and summarized methylation data using the Bismark methylation_extractor.
We counted methylated and unmethylated CpGs at each genomic locus using perl scripts and imported the data into R for statistical analysis.
To remove uninformative CpG loci from RRBS data, we omitted any CpGs where greater than 10% of samples had coverage less than 10X. We then removed any CpGs that were unmethylated (<10%) in all samples of all ages. These CpGs are not informative for our study as they do not change between ages and introduce bias into the data because they are primarily located in CpG dense areas.
For locus specific data, we removed any data points with less than 100X coverage and any CpG where greater than 10% of samples had missing data.
Using R, we calculated the percent methylation at each locus for each sample and compared values between groups using a students t-test.
We derived false discovery rates (FDR) from t-test p-values using the qvalue package for R.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: The first two columns are the Chromosome and base location of each CpG, and the following columns correspond to each sample. The values are the percent methylation for that CpG in that sample.

molecule: genomic DNA

source_name: Liver

growth_protocol: Mice were maintained under standard conditions

extract_protocol:
DNA was extracted using a Qiagen all-prep DNA/RNA kit
RRBS libraries were constructed using the Truseq DNA LT kit, with a bisulfite treatment after adapter ligation. For locus specific bisulfite sequencing, we bisulfite treated DNA and PCR amplified regions of interest using primers with a 5' tail. A second PCR recognizing the 5' tail added barcode and adapter sequences.

tag: developmental stage

tag: tissue

value: Liver


title: WT_XR-seq_exp1

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mah. Universite Cad No 27

department: Faculty of Natural Sciences and Engineering

country: Turkey

institute: Sabanci University

data_processing:
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: NC_000913.2

organism: Escherichia coli

growth_protocol: Nonselective LB medium at 37o.

extract_protocol:
HIRT lysis procedure.
Hu et al. 2015 Genes Dev 29(9):948-960 procedure.

treatment_protocol: Irradiation at an OD600 of 0.8 with 120 J/m2 UVC at room temperature. Chilled after 5 minutes.

tag: genotype/variation

value: Wild-type


title: ipsc_C10


title: ipsc_B8


title: 3-5-L-P20-M-Liver_LSBS


title: ipsc_B9


title: 5-4-L-P10-M-Liver_LSBS


title: ipsc_B6


title: ipsc_B7


title: 2-5-L-P15-M-Liver_LSBS


title: ipsc_D10


title: 20-17-L-E18.5-M-Liver_LSBS


title: ipsc_B5


title: 10-44-L-E18.5-M-Liver_LSBS


title: ipsc_C9


title: ipsc_B4


title: ipsc_B3


title: wk9-14_LSBS


title: ipsc_B2


title: wk9-211_LSBS


title: ipsc_B12


title: ipsc_B1


title: wk9-100_LSBS


title: ipsc_B11


title: wk9-101_LSBS


title: wk9-134_LSBS


title: P5_Liv_5_LSBS


title: P5_Liv_3_LSBS


title: ipsc_A7


title: P5_Liv_2_LSBS


title: ipsc_A8


title: P5_Liv_4_LSBS


title: ipsc_A9


title: ipsc_B10


title: ipsc_A5


title: P5_Liv_1_LSBS


title: ipsc_A2


title: ipsc_A4


title: ipsc_A3


title: P20_Liv_5_LSBS


title: P20_Liv_4_LSBS


title: P20_Liv_2_LSBS


title: ipsc_A12


title: P15_Liv_4_LSBS


title: ipsc_A11


title: P15_Liv_3_LSBS


title: ipsc_A10


title: P20_Liv_1_LSBS


title: P15_Liv_2_LSBS


title: P15_Liv_1_LSBS


title: ih1_H7

value: Immature hepatocyte-like 1


title: ih1_H5


title: ih1_H4


title: P10_Liv_4_LSBS


title: ih1_H3


title: ih1_H8


title: ih1_H1


title: ih1_H11


title: P10_Liv_2_LSBS


title: P10_Liv_3_LSBS


title: ih1_H10


title: lb1_A12


title: ih1_G9


title: ih1_G8


title: P10_Liv_1_LSBS


title: P1_Liv_4_LSBS


title: P1_Liv_3_LSBS


title: ih1_G7


title: E18_Liv_6_LSBS


title: P1_Liv_1_LSBS


title: P10_Liv_5_LSBS


title: ih1_G3


title: ih1_G6


title: ih1_G12


title: E18_Liv_15_LSBS


title: E18_Liv_14_LSBS


title: ih1_G11


title: E18_Liv_1_LSBS


title: P20_Liv_3_LSBS


title: ih1_G1


title: ih1_F8


title: 2-3-L-P5-F-Liver

description:
Sequencing of specific loci after bisulfite conversion of genomic DNA
processed data file(s): LocusSpecificSummary.txt.gz

data_processing:
library strategy: locus specific bisulfite sequencing
We analyzed RRBS and locus specific bisulfite sequencing data by aligning fastq files to the mouse genome (mm9) using Bismark (v0.7.6) with bowtie2
We then combined replicates for each sample and summarized methylation data using the Bismark methylation_extractor.
We counted methylated and unmethylated CpGs at each genomic locus using perl scripts and imported the data into R for statistical analysis.
To remove uninformative CpG loci from RRBS data, we omitted any CpGs where greater than 10% of samples had coverage less than 10X. We then removed any CpGs that were unmethylated (<10%) in all samples of all ages. These CpGs are not informative for our study as they do not change between ages and introduce bias into the data because they are primarily located in CpG dense areas.
For locus specific data, we removed any data points with less than 100X coverage and any CpG where greater than 10% of samples had missing data.
Using R, we calculated the percent methylation at each locus for each sample and compared values between groups using a student’s t-test.
We derived false discovery rates (FDR) from t-test p-values using the qvalue package for R.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: For RrbsSummary files, the columns are: chromosome, base, change in percent between ages, pvalue and qvalue. For LocusSpecificSummary.txt.gz, the columns are: locus   chromosome, CpG identifier, age, sex, percentMethylation for that sample, pvalueOfChangeWithAge and qvalue

value: liver


title: 4-2-L-P5-F-Liver


title: 5-7-L-P20-M-Liver


title: ih1_F7


title: 5-3-L-P5-F-Liver


title: 3-2-L-P5-M-Liver


title: ih1_F6


title: 4-5-L-P20-M-Liver


title: P1_Liv_5_LSBS


title: 3-5-L-P20-M-Liver


title: ih1_F5


title: ih1_F4


title: ih1_F2


title: 2-7-L-P20-F-Liver


title: 2-6-L-P20-F-Liver


title: ih1_F12


title: 5-6-L-P15-M-Liver


title: ih1_G10


title: ih1_F9


title: P1_Liv_2_LSBS


title: 5-5-L-P15-F-Liver


title: 5-4-L-P10-M-Liver


title: ih1_F11


title: ih1_F10


title: ih1_G4


title: lb2_C11


title: ih1_E8


title: ih1_E9


title: 4-3-L-P10-F-Liver


title: 4-1-L-P1-M-Liver


title: ih1_F1


title: 3-1-L-P1-M-Liver


title: 1-1-L-P1-M-Liver


title: ipsc_H3


title: 4-9-L-mo6-M-Liver


title: 4-4-L-P15-F-Liver


title: 4-7-L-mo6-F-Liver


title: 4-13-L-mo6-M-Liver


title: 1-9-L-mo6-M-Liver


title: ih1_E2


title: ih1_E3


title: ih1_E6


title: ih1_E10


title: ih1_D9


title: ih1_E11


title: ih1_E12


title: 2-11-L-mo6-F-Liver


title: ih1_E1


title: ih1_E5


title: ih1_E7


title: 6-11-L-E18.5-M-Liver


title: ih1_D8


title: 3-3-L-P10-F-Liver


title: ih1_D7


title: 5-1-L-P1-F-Liver


title: 20-17-L-E18.5-M-Liver


title: ih1_D2


title: ih1_D1


title: ih1_D12


title: 2-4-L-P10-F-Liver


title: ih1_D6


title: ih1_D11


title: 6-10-L-E18.5-F-Liver


title: 2-1-L-P1-F-Liver


title: ih1_C9


title: 7-39-L-E18.5-F-Liver


title: ih1_D5


title: ih1_C5


title: ih1_C8


title: ih1_C12


title: ih1_C10


title: ih1_C4


title: ih1_C7


title: ih1_C11


title: ih1_D10


title: ih1_C2


title: ih1_C1


title: ih1_B2


title: ih1_B7


title: ih1_B4


title: ih1_B11


title: ih1_A9


title: ih1_B6


title: ih1_A5


title: ih1_A8


title: ih1_A6


title: ih1_B10


title: 10-44-L-E18.5-M-Liver


title: ih1_A4


title: ih1_C3


title: ih1_A12


title: ih1_B5


title: ih1_A11


title: he2_E8

value: Hepatic endoderm 2


title: he2_E9


title: ih1_A3


title: he2_E5


title: he2_E7


title: he2_E2


title: he2_E1


title: he2_E6


title: he2_D9


title: he2_D8


title: he2_D6


title: he2_D4


title: he2_D3


title: he2_D2


title: he2_D12


title: he2_D1


title: he2_D10


title: he2_C9


title: ih1_A7


title: ih1_A10


title: he2_C8


title: he2_C6


title: he2_C7


title: he2_C5


title: he2_C3


title: he2_C2


title: he2_C11


title: he2_C12


title: he2_C1


title: 12347_RSC

city: Nijmegen

first: Clyde

last: Francks

address: Wundtlaan 1

department: Language & Genetics

country: Netherlands

institute: Max Planck Institute for Psycholinguistics

description: individual 12347: right spinal cord

data_processing:
Illumina Hiseq 2000 direct base-call/ CASAVA 1.7(?)
alignment: SOAPaligner/SOAP2.21
Tophat (v2.08) and Cufflink (v2.0.2) were used to refine alignments, and produce counts/rpkm data
Genome_build: hg19
Supplementary_files_format_and_content: For each library, tab-delimited text files contain: GeneID, Uniq_reads_num, gene_length,percentage_gene_coverage,rpkm.

source_name: spinal cord

growth_protocol: The embryos resulted from voluntary chemical abortions

extract_protocol:
The spinal cord (SC) and the hindbrain (HB) were dissected out and separated from each other, after which they were also separated into left and right halves down the midline. Thirty mg of tissue was homogenised using a Precellys 24 bead mill homogeniser  using ceramic 1.4mm beads for soft tissue homogenising  with 600ul of RTL plus Buffer with 10µl/ml of β-Mercaptoethanol and 5µl/ml of reagent DX (Qiagen). RNA and DNA was extracted from the tissue using a QIAcube  using an AllPrep DNA/RNA Mini Kit  following the manufacturer’s recommended protocol. RNA quality was assessed using an Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols (BGI)

tag: carnegie stage

tag: Sex

value: female

value: spinal cord

tag: tissue side

value: right


title: he2_D5


title: ih1_B8


title: he2_C10


title: he2_D7


title: 12347_LSC

description: individual 12347: left spinal cord

value: left


title: he2_D11


title: he2_B9


title: he2_B7


title: he2_B6


title: 12347_LHB

description: individual 12347: left hindbrain

source_name: hindbrain

value: hindbrain


title: 12341_RSC

description: individual 12341: right spinal cord

value: male


title: he2_B8


title: he2_B4


title: 12341_LSC

description: individual 12341: left spinal cord


title: he2_B3


title: he2_C4


title: 12341_LHB

description: individual 12341: left hindbrain


title: 12307_RSC

description: individual 12307: right spinal cord


title: he2_E4


title: 12341_RHB

description: individual 12341: right hindbrain


title: he2_B11


title: he2_B10


title: he2_A9


title: 12347_RHB

description: individual 12347: right hindbrain


title: 12307_LSC

description: individual 12307: left spinal cord


title: 12307_RHB

description: individual 12307: right hindbrain


title: he2_A7


title: he2_A6


title: 12307_LHB

description: individual 12307: left hindbrain


title: 12301_RHB

description: individual 12301: right hindbrain


title: he2_A8


title: 12301_LSC

description: individual 12301: left spinal cord


title: 12301_RSC

description: individual 12301: right spinal cord


title: he2_A5


title: 12301_LHB

description: individual 12301: left hindbrain


title: ih1_A2


title: he2_A4


title: 12292_RSC

description: individual 12292: right spinal cord


title: he2_A3


title: 12292_LSC

description: individual 12292: left spinal cord


title: 12292_LHB

description: individual 12292: left hindbrain


title: he2_A2


title: 12292_RHB

description: individual 12292: right hindbrain


title: he2_B12


title: 12285_RSC

description: individual 12285: right spinal cord


title: he2_A12


title: he2_A1


title: he2_A10


title: he1_H8

value: Hepatic endoderm 1


title: 12285_RHB

description: individual 12285: right hindbrain


title: 12285_LSC

description: individual 12285: left spinal cord


title: he1_H6


title: he1_H4


title: 12255_RSC

description: individual 12255: right spinal cord


title: he1_H3


title: 12255_LSC

description: individual 12255: left spinal cord


title: 12255_LHB

description: individual 12255: left hindbrain


title: 12254_RSC

description: individual 12254: right spinal cord


title: he1_H2


title: he1_H1


title: he1_H12


title: 12254_RHB

description: individual 12254: right hindbrain


title: he1_H11


title: 12254_LHB

description: individual 12254: left hindbrain


title: 12254_LSC

description: individual 12254: left spinal cord


title: he1_G6


title: he1_G3


title: 12232_RHB

description: individual 12232: right hindbrain


title: he2_A11


title: 12232_RSC

description: individual 12232: right spinal cord


title: 12232_LSC

description: individual 12232: left spinal cord


title: he1_G11


title: 12232_LHB

description: individual 12232: left hindbrain


title: he1_H5


title: 11993_RSC

description: individual 11993: right spinal cord


title: he1_G12


title: he1_F7


title: he1_F6


title: 11993_RHB

description: individual 11993: right hindbrain


title: 12255_RHB

description: individual 12255: right hindbrain


title: 12285_LHB

description: individual 12285: left hindbrain


title: 11993_LSC

description: individual 11993: left spinal cord


title: 11985_RHB

description: individual 11985: right hindbrain


title: he1_F3


title: 11985_RSC

description: individual 11985: right spinal cord


title: he1_F2


title: 11985_LSC

description: individual 11985: left spinal cord


title: 11985_LHB

description: individual 11985: left hindbrain


title: he1_F9


title: he1_F12


title: he1_F11


title: 11978_RSC

description: individual 11978: right spinal cord


title: 11978_LHB

description: individual 11978: left hindbrain


title: 11978_LSC

description: individual 11978: left spinal cord


title: he1_E2


title: he1_E6


title: he1_E12


title: 11978_RHB

description: individual 11978: right hindbrain


title: he1_F5


title: he1_E1


title: 11963_RHB

description: individual 11963: right hindbrain


title: he1_E11


title: 11963_RSC

description: individual 11963: right spinal cord


title: 11993_LHB

description: individual 11993: left hindbrain


title: he1_D9


title: he1_F4


title: 11963_LHB

description: individual 11963: left hindbrain


title: he1_F1


title: he1_D8


title: 11962_RSC

description: individual 11962: right spinal cord


title: he1_D6


title: 11954_RHB

description: individual 11954: right hindbrain


title: he1_D5


title: 11962_LSC

description: individual 11962: left spinal cord


title: he1_E8


title: 11954_LHB

description: individual 11954: left hindbrain


title: 11905_RHB

description: individual 11905: right hindbrain


title: 11903_RHB

description: individual 11903: right hindbrain


title: 11905_LHB

description: individual 11905: left hindbrain


title: 11963_LSC

description: individual 11963: left spinal cord


title: 11903_RSC

description: individual 11903: right spinal cord


title: he1_D12


title: he1_C2


title: he1_C11


title: 11903_LHB

description: individual 11903: left hindbrain


title: 11898_RHB

description: individual 11898: right hindbrain


title: 11898_LSC

description: individual 11898: left spinal cord


title: he1_C8


title: he1_C6


title: he1_C10


title: he1_C7


title: 11903_LSC

description: individual 11903: left spinal cord


title: he1_B8


title: he1_C4


title: he1_B5


title: he1_B4


title: RJ2_H3K4me3_Input_Rep1

city: Montpellier cedex 5

first: Julie

middle: A. J.

last: Clement

address: 141, rue de la Cardonille

department: IGH

country: France

institute: CNRS

description:
processed data file:
CHIP_H3K4me3_Specific_RJ2_peaks.bed
CHIP_H3K4me3_Commons_peaks.bed

data_processing:
Base-calling was performed  using CASAVA
ChIPseq reads were aligned to the mm9 genome using Bowtie (H3K4me3), Bowtie2 (PRDM9, H3K36me3) or BWA and its modified algorithm proposed in Khil et al., 2012  (DMC1)
Reads that were unmapped, multi-mapped, unpaired, duplicated were filtered out in each experiment, unpaired reads were removed for paired-end experiments, and reads that  mapped with more than 1 mismatch were removed in all but DMC1 ChIPseq experiments.
Peaks were called using MACS1.3.7 (H3K4me3) or MACS2 (PRDM9, DMC1, H3K36me3)
IDR method was used to deal with replicates for PRDM9 and DMC1 peaks
Genome_build: mm9
Supplementary_files_format_and_content: bedfiles represent peaks called from MACS1.3.7 or MACS2 for all but H3K36me3 ChIPseq experiments ; bigwig were built from merged replicates after alignment step for H3K36me3 ChIPseq experiment

extract_protocol:
Cell suspension was prepared by filtering homogenized tissue, then lysed.Lysates were sonicated and chromatin complexes were isolated with appropriate antibody.
Standard library construction was performed with the Illumina Trueseq protocol (Illumina, IP-202-9001DOC). For DMC1 ChIP an additional step of kinetic enrichment was performed as described in Khil et al. 2012.
ChIP-seq for all but DMC1 CHIPseq experiment ; SSDS method described in Khil et al. 2012 for DMC1 ChIPseq

treatment_protocol: Antibodies against PRDM9 were homemade (anti-PRDM9 BdM). They were raised by immunizing two rabbits with recombinant full-length PRDM9Cst protein fused to 6x HIS at the N-terminus. PRDM9 polyclonal serum was then affinity-purified by incubation with PRDM9Dom2 recombinant protein immobilized on a nitrocellulose membrane.

tag: tissue/cells

value: elutriated testis cells (pachytene)

value: adult

tag: chip antibody

value: anti-H3K4me3 (Abcam, ab8580)


title: he1_C3


title: he1_D10


title: RJ2_H3K4me3_ChIPseq_Rep1


title: he1_B6


title: 11898_RSC

description: individual 11898: right spinal cord


title: B6_H3K4me3_Input_Rep1

description:
processed data file:
CHIP_H3K4me3_Specific_B6_peaks.bed
CHIP_H3K4me3_Commons_peaks.bed


title: he1_B3


title: he1_C5


title: 11898_LHB

description: individual 11898: left hindbrain


title: B6_H3K4me3_ChIPseq_Rep1


title: he1_B2


title: he1_B10


title: he1_B11


title: he1_A3


title: he1_A4


title: he1_A7


title: ec_H9

description:
Single cell transcriptome from input endothelial cells
processed data file: data.cast.log2.liverbud

source_name: HUVEC

value: Endothelial cells


title: ec_H7


title: he1_A10


title: he1_A9


title: ec_H8


title: ec_H5


title: ec_H6


title: ec_H3


title: he1_A12


title: VR2 LDMa (LPA derived macrophages)

city: Bhubaneswar

first: Vivek

last: Rai

state: Orissa

address: Nalco Square

country: India

institute: Institute of Life Sciences

data_processing:
Read QC, Trim filter and get clean reads
Map reads to mouse reference genome using CLC bio Genomic Workbench VER-9.0
Get the read count matrix for each gene and estimate differential gene expression
Analysed data of differential expression using Kal's z-test, filter differentially expressed genes based on FDR p value
Biological interepretation
Genome_build: Mus musculus mm9
Supplementary_files_format_and_content: Excel sheets listing differentially expressed genes

source_name: bone marrow

extract_protocol:
Monocytes were isolated from bone marrow of C57BL/6 mice and differentiated in presence of LPA. RNA was isolated using Trizol reagent. Illumina NEBNext® Ultra™ RNA Library Prep Kit (Catalog: E7530L) with 1ug of total RNA was used for sequencing library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 6 weeks

tag: genotype

value: Wild type


title: WT_9771

city: New York City

first: Lin

last: Tian

state: New York

address: Mortimer B. Zuckerman Research Center, 417 East 68th Street

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description: CD4+ T cell competent background

data_processing:
Illumina Nextseq 500 automatically used bcl2fastq2 (version 2.17) for basecalling. FASTQ files were downloaded from BaseSpace.
RNA-seq NGS reads were mapped using STAR RNA-seq aligner (version 2.4.1d) and quantified using RSEM (version 1.2.28).
Average insert sizes were calculated for each sample. Consistent with Bioanalyzer electrophoresis plot, one sample (CD4KO_9768) was shown to be an outlier and was removed before proceeding to downstream analysis. An outlier is defined as a number that is more than 1.5 times the inter-quartile range away from either the lower or upper quartiles. Speciﬁcally, if a number is less than Q1 - 1.5×IQR or greater than Q3 + 1.5×IQR, then it is an outlier.
DEseq2 R package was used to normalize the gene expression matrix.
Genome_build: GRCm38.83
Supplementary_files_format_and_content: 20 RSEM read quantification files for 20 samples (containing Transcript Per Million (TPM) and Fragments Per Kilobase of transcript per Million (FPKM) information); VN.Rdata file contains the sample annotation table and gene expression matrix tables with mouse gene symbols or ortholog human gene symbols as row names.

source_name: Purified tumor-associated CD31+ endothelial cells

growth_protocol: 0.5 million E0771 tumor cells were injected into the mammary fat pad of C57BL/6J mice with different immunodeficient backgrounds. Tumor growth was monitored every two days, and tumors were resected when tumor volume reached 500mm3.

extract_protocol:
The tumors were dissociated into single cell suspensions using the mouse Tumor Dissociation Kit, and endothelial cells were enriched with CD31 microbeads (both from Miltenyi). The isolated cells were subjected to flow cytometry activated cell sorting to further purify tumor-associated CD31+ endothelial cells. The cells were sorted directly into TRIzol LS (Thermo Fisher), and RNA was extracted as per manufacturer's instructions. Double-strand cDNA (dsDNA) were synthesized using Multiple Annealing based RNA-seq approach (MATQ). Illumina Nextera XT DNA Sample Prep Kit was used with 1 ng of dsDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Nextera Illumina protocols

tag: tumor cell line

tag: end timepoint

value: Tumor size reach 500mm3.

tag: mouse stain

tag: genetic background

value: WT


title: WT_9748

description: CD4+ T cell competent background


title: WT_9772

description: CD4+ T cell competent background


title: WT_9749

description: CD4+ T cell competent background


title: ec_H12

tag: cell type or stage


title: ec_G9


title: VR1 Mo (Monocytes)

tag: strain


title: ec_H10


title: Tie2Cre_H2Abf_9583

description: CD4+ T cell deficient background

value: Tie2Cre;H2Ab fl/fl


title: Tie2Cre_H2Abf_9589

description: CD4+ T cell deficient background


title: ec_G7


title: ec_H4


title: ec_G8


title: Tie2Cre_H2Abf_9582

description: CD4+ T cell deficient background


title: ec_G6


title: ec_G1


title: ec_G2


title: Tie2Cre_9504

description: CD4+ T cell competent background


title: Tie2Cre_H2Abf_9576

description: CD4+ T cell deficient background


title: Tie2Cre_9501

description: CD4+ T cell competent background


title: TCRKO_9766

description: CD4+ T cell deficient background

value: TCRKO


title: TCRKO_9767

description: CD4+ T cell deficient background


title: ec_G10


title: Tie2Cre_9502

description: CD4+ T cell competent background


title: ec_F6


title: ec_F7


title: ec_F3


title: CD8KO_9753

description: CD4+ T cell competent background


title: CD4KO_9769

description: CD4+ T cell deficient background


title: ec_F5


title: ec_E8


title: Id1tg/tg thymus ILC2 rep 2

city: Oklahoma City

first: Xiao-Hong

state: OK

address: 825 NE 13th street

institute: Oklahoma Medical Research Foundation

description: Homozygous Id1 transgenic mice exhibit a complete block in T cell development and dramatic augmentation in ILC2 production in the thymus, which leads to accumulation of ILC2s throughout the body.

data_processing:
Base-calling was processed using the Illumina Pipeline software v.1.7.
Sequencing reads were aligned to the Mus musculus genome reference (mm9) using Star ver. 2.4.0h.
Gene-level read counts were determined using HTSeq ver. 0.5.3p9 with the Ensembl Mus musculus NCBIM37 (release 67) annotation.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include transcript read counts for each sample.

source_name: Thymus

growth_protocol: The mice are maintained on regular diet.

extract_protocol:
Total RNA was purified from ILC2 cells of Id1 transgenic thymus and MLN as well as from MLN ILC2s cultured. Approximately 300,000 cells were used in the preparation of each sample.
RNA libraries were prepared using the Illumina Truseq Stranded mRNA library prep kits according to standard Illumina protocols.

treatment_protocol: Sorted MLN ILC2s were cultured in 10 ng/ml each of IL-7, IL-25 and IL-33 for one week.  The cells were harvested for RNA-seq along with untreated cells.

tag: cell type

value: Thymus

value: Id1 transgenic mice, which express Id1 off the proximal promoter of the lck gene, were originally generated on the FVB/N background and backcrossed to C57BL/J for at least 10 generations.  Homozygous transgenic mice were used in the analyses.


title: ec_G12


title: ec_F11


title: CD4KO_9768

description: CD4+ T cell deficient background


title: ec_E7


title: CD8KO_9752

description: CD4+ T cell competent background


title: ec_E9


title: Id1tg/tg thymus ILC2 rep 1


title: Id1tg/tg MLN ILC2 rep 2

source_name: Mesenteric lymph nodes (MLN)

value: Mesenteric lymph nodes (MLN)


title: Id1tg/tg MLN ILC2 rep 1


title: ec_E4


title: TCRKO_9765

description: CD4+ T cell deficient background


title: ec_F9


title: ec_F12


title: ec_E2


title: ec_E3


title: Id1tg/tg MLN ILC2 cultured rep 2


title: CD4KO_9770

description: CD4+ T cell deficient background


title: ec_E1


title: Id1tg/tg MLN ILC2 cultured rep 1


title: ec_E11


title: ec_F4


title: CD8KO_9751

description: CD4+ T cell competent background


title: WT_sample_27

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

state: CA

address: 9500 Gilman Drive

institute: HHMI/UCSD

description: RNA-seq, 50bp reads

data_processing:
The sequencing reads were aligned to the mouse genome mm8 by using Bowtie (Langmead et al., 2009)
The aligned sequencing reads were counted over gene exons by using HOMER (http://homer.salk.edu/homer/) that computed the RPKM values.
The differentially expressed genes between KO and WT samples were statistically defined by a two-tailed, two-sample T-test between the replicates (p-value < 0.05).
The heatmaps of differential expressed genes were displayed by using R packages “pheatmap” and “gplots” (heatmap.2() function).
Genome_build: mm8
Supplementary_files_format_and_content: RPKM values of RefSeq genes in mm8 as computed by HOMER (http://homer.salk.edu/homer/)

source_name: WT, B cells

growth_protocol: Conditional Gps2flox/flox mice were generated by inGenious Targeting Laboratory. Homozygous Gps2flox/flox mice were then used for crossing with heterozygous 129sv CD19-cre mice (Rickert et al., 1997) (Jackson Laboratories). The CD19 promoter specifically directs expression at the earliest stages and throughout B-lymphocyte development and differentiation (Rickert et al., 1997). Splenic B cells were isolated from single cells suspension of total splenocytes prepared according to standard protocols (DeFuria et al., 2013). B cell purification was achieved by magnetic depletion using the MACS Pan B cells Isolation Kit (Miltenyi Biotech). Purity of the B cells populations was verified by flow cytometric analysis with CD19 and CD3 labeling.

extract_protocol:
Total RNA was prepared with RNeasy® plus Mini Kit (Qiagen) according to the manufacturer’s protocol.  For RNA-seq experiments, the RNA quality was assessed on the Agilent 2100 Bioanalyzer (BUMC Microarray Core).
cDNA libraries were prepared either with the NEBNext Ultra Directional Library Preparation Kit for Illumina or with the Illumina TruSeq Stranded total RNA Sample Prep Kit with rRNA depletion by RiboZero Gold and then sequenced on a HiSeq2500 (single strand, 50bp reads).

value: wildtype

value: B cells


title: WT_sample_12

description: RNA-seq, 50bp reads


title: ec_E10


title: KO_sample_g84

description: RNA-seq, 50bp reads

source_name: KO, B cells


title: ec_D9


title: KO_sample_26

description: RNA-seq, 50bp reads


title: ec_E6


title: ec_D8


title: KO_sample_13

description: RNA-seq, 50bp reads


title: ec_D7


title: ec_D6


title: 9wk_210

description: Reduced Representation Bisulfite Sequencing (RRBS)

data_processing:
We analyzed RRBS and locus specific bisulfite sequencing data by aligning fastq files to the mouse genome (mm9) using Bismark (v0.7.6) with bowtie2
We then combined replicates for each sample and summarized methylation data using the Bismark methylation_extractor.
We counted methylated and unmethylated CpGs at each genomic locus using perl scripts and imported the data into R for statistical analysis.
To remove uninformative CpG loci from RRBS data, we omitted any CpGs where greater than 10% of samples had coverage less than 10X. We then removed any CpGs that were unmethylated (<10%) in all samples of all ages. These CpGs are not informative for our study as they do not change between ages and introduce bias into the data because they are primarily located in CpG dense areas.
For locus specific data, we removed any data points with less than 100X coverage and any CpG where greater than 10% of samples had missing data.
Using R, we calculated the percent methylation at each locus for each sample and compared values between groups using a student’s t-test.
We derived false discovery rates (FDR) from t-test p-values using the qvalue package for R.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: For RRBS data files, the columns are: chromosome, base,

tag: age

value: 9 weeks

value: liver


title: WT_sample_g84

description: RNA-seq, 50bp reads


title: 9wk_133


title: ec_D4


title: ec_D10


title: ec_D1


title: 9wk_13


title: P5_Mus_2_RRBS

description: processed data file: ThreeTissueMuscleFiltered.txt.gz

data_processing:
We analyzed RRBS and locus specific bisulfite sequencing data by aligning fastq files to the mouse genome (mm9) using Bismark (v0.7.6) with bowtie2
We then combined replicates for each sample and summarized methylation data using the Bismark methylation_extractor.
We counted methylated and unmethylated CpGs at each genomic locus using perl scripts and imported the data into R for statistical analysis.
To remove uninformative CpG loci from RRBS data, we omitted any CpGs where greater than 10% of samples had coverage less than 10X. We then removed any CpGs that were unmethylated (<10%) in all samples of all ages. These CpGs are not informative for our study as they do not change between ages and introduce bias into the data because they are primarily located in CpG dense areas.
For locus specific data, we removed any data points with less than 100X coverage and any CpG where greater than 10% of samples had missing data.
Using R, we calculated the percent methylation at each locus for each sample and compared values between groups using a students t-test.
We derived false discovery rates (FDR) from t-test p-values using the qvalue package for R.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: The first two columns are the Chromosome and base location of each CpG, and the following columns correspond to each sample. The values are the percent methylation for that CpG in that sample.

source_name: Muscle

tag: developmental stage

value: Muscle


title: P20_Mus_2_RRBS

tag: tissue


title: ec_D2


title: ec_C7


title: P5_Mus_4_RRBS


title: P5_Mus_3_RRBS


title: ec_D12


title: ec_C9


title: P20_Mus_3_RRBS


title: ec_C6


title: ec_C8


title: P20_Mus_5_RRBS


title: ec_C5


title: P1_Mus_4_RRBS


title: P1_Mus_5_RRBS


title: P1_Mus_3_RRBS


title: P20_Mus_1_RRBS


title: ec_C1


title: ec_C12


title: P1_Mus_1_RRBS


title: P1_Mus_2_RRBS


title: P15_Mus_4_RRBS


title: ec_C11


title: ec_C10


title: P15_Mus_3_RRBS


title: ec_B9


title: P15_Mus_2_RRBS


title: P15_Mus_1_RRBS


title: ec_B6


title: ec_B2


title: ec_B1


title: P10_Mus_3_RRBS


title: P10_Mus_5_RRBS


title: P10_Mus_4_RRBS


title: E18_Mus_9_RRBS


title: ec_C4


title: E18_Mus_1_RRBS


title: ec_B3


title: E18_Mus_15_RRBS


title: ec_B12


title: ec_A7


title: ec_B10


title: E18_Mus_14_RRBS


title: P10_Mus_1_RRBS


title: ec_A8


title: P5_Liv_5_RRBS

description: processed data file: ThreeTissueLiverFiltered.txt.gz

value: Liver


title: ec_A6


title: ec_A5


title: P5_Liv_4_RRBS


title: P5_Liv_3_RRBS


title: ec_A4


title: ec_B5


title: ec_A3


title: P20_Liv_5_RRBS


title: P20_Liv_4_RRBS


title: P5_Liv_1_RRBS


title: ec_B11


title: ec_A11


title: P20_Liv_2_RRBS


title: ec_A1


title: P1_Liv_3_RRBS


title: P20_Liv_1_RRBS


title: ec_A10


title: P1_Liv_5_RRBS


title: ec_A12


title: de_H4

value: Definitive endoderm 1


title: de_H5


title: de_H6


title: P20_Liv_3_RRBS


title: P1_Liv_2_RRBS


title: P15_Liv_1_RRBS


title: P15_Liv_2_RRBS


title: de_H10


title: de_H12


title: de_G9


title: P10_Liv_2_RRBS


title: P10_Liv_1_RRBS


title: E18_Liv_6_RRBS


title: de_G7


title: de_G6


title: de_G4


title: de_H9


title: de_G1


title: de_H7


title: E18_Liv_14_RRBS


title: P15_Liv_4_RRBS


title: de_G11


title: E18_Liv_15_RRBS


title: P5_Ht_5_RRBS

description: processed data file: ThreeTissueHeartFiltered.txt.gz

source_name: Heart

value: Heart


title: P1_Liv_1_RRBS


title: de_G12


title: P5_Ht_3_RRBS


title: de_F9


title: P5_Ht_2_RRBS


title: de_F8


title: P20_Ht_5_RRBS


title: P5_Ht_1_RRBS


title: de_F4


title: de_F7


title: P10_Liv_4_RRBS


title: de_F3


title: P20_Ht_4_RRBS


title: de_F2


title: P20_Ht_3_RRBS


title: P20_Ht_2_RRBS


title: de_F1


title: P20_Ht_1_RRBS


title: E18_Liv_1_RRBS


title: de_G10


title: P1_Ht_5_RRBS


title: de_F12


title: de_F11


title: P1_Ht_4_RRBS


title: de_F10


title: P1_Ht_2_RRBS


title: de_E6


title: P1_Ht_3_RRBS


title: de_E8


title: P15_Ht_5_RRBS


title: P15_Ht_4_RRBS


title: de_E3


title: de_E4


title: P15_Ht_3_RRBS


title: P15_Ht_2_RRBS


title: de_E2


title: de_E12


title: Act_HPV_3

city: Zurich

first: Maria

last: Antsiferova

state: Schweiz

address: HPL F16.1, Otto-Stern-Weg 7

institute: ETH Zurich

description: rRNA depleted stranded

data_processing:
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends (four bases from read start and read end), and filtering reads with low quality (phred quality <20) using Trimmomatic
Sequence alignment and isoform expression quantification of the resulting high-quality reads to the Mus musculus reference genome (build GRCm38) was performed with the RSEM algorithm (version 1.2.18) with the option for estimation of the read start position distribution turned on.
To detect differentially expressed genes we applied the count based negative binomial model implemented in the software package edgeR (version: 3.10.2), in which the normalization factor was calculated by the trimmed mean of M values (TMM) method.
The gene-wise dispersions were estimated by conditional maximum likelihood, and an empirical Bayes procedure was used to shrink the dispersions towards a consensus value
Differential expression was assessed using an exact test adapted for over-dispersed data. Genes showing altered expression with adjusted (Benjamini and Hochberg method) p-value (false discovery rate, FDR) < 0.05 were considered as differentially expressed.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel spreadsheet file with the results of EdgeR comparison of different genotypes (log2Ratio, fdr), normalized counts, and FPKM values for each sample.

source_name: macrophages

extract_protocol:
Total RNA was isolated immediately after sorting using the RNeasy Micro Kit (Qiagen, Hilden, Germany) and stored at -80°C.
After ribosomal RNA depletion using the Ribo-Zero Magnetic Kit (Epicentre/Illumina, Madison, WI) and a modified Protocol For Truly Low Input Total RNA Samples (Clontech, Mountain View, CA), the SMARTer Stranded RNA-Seq Kit (Clontech) was used according to the manufacturer`s instructions. The quality of amplified libraries was validated using a TapeStation (Agilent). Concentrations of labeled fragments were measured using absolute quantification qPCR with primers specific to Illumina sequencing adapters. The libraries were then sequenced on an Illumina Hiseq 2500 v3. Approximately 20 million reads were generated per sample.

treatment_protocol: Dorsal and ventral parts of the mouse ears were separated, minced with scissors, and digested with 0.25 mg/ml Liberase TL (Roche) in DMEM for 1 h at 37°C. Following digestion, the cell suspension was filtered through a 70  µm nylon strainer, centrifuged at 300g at 4°C for 10 min, and resuspended in FACS buffer. Ear skin macrophages were enriched by FACS sorting of CD45+F4/80+CD11b+ cells from the non-cancerous ear skin of 12-15 week- old mice. For each replicate, ear skin from 3-6 mice per genotype was pooled. CD3 and CD140 were used as additional negative markers. Dead cells were excluded by Sytox Green staining. Cells (50-200 x 10^3 per sample) were sorted into cold empty Eppendorf tubes and centrifuged for total RNA extraction.

value: 12-16 weeks

value: ear skin

tag: cell type/source

value: FACS-sorted F4/80+CD11b+CD45+ cells


title: Act_HPV_2

description: rRNA depleted stranded


title: P15_Ht_1_RRBS


title: Act_HPV_1

description: rRNA depleted stranded


title: de_E10


title: de_E11


title: Act_wt_3

description: rRNA depleted stranded


title: de_D8


title: Act_wt_2

description: rRNA depleted stranded


title: ec_A2

value: Endothelial cells


title: de_D6


title: de_D7


title: Act_wt_1

description: rRNA depleted stranded


title: de_D5


title: wt_HPV_2

description: rRNA depleted stranded


title: de_D4


title: wt_HPV_3

description: rRNA depleted stranded


title: de_E5


title: de_D3


title: wt_wt_3

description: rRNA depleted stranded

value: wt/wt


title: de_E1


title: wt_HPV_1

description: rRNA depleted stranded


title: de_D11


title: de_D2


title: de_D12


title: de_C9


title: de_C7


title: de_C6


title: de_C5


title: de_C1


title: wt_wt_2

description: rRNA depleted stranded


title: de_C10


title: de_B9


title: de_C12


title: Cardiac mesoderm, Foxa2- 2

city: New York

first: Andrew

last: Sharp

state: NY

address: 1470 Madison Av

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.8 software used for basecalling
RNA-seq reads were aligned to the mm10 genome assembly using STAR 2.5.0a_alpha aligner with parameters --outSAMtype BAM   SortedByCoordinate, --outSAMstrandField intronMotif, --outSAMattributes All
Removed duplicates using Picard MarkDuplicates 1.112(1930) with parameters REMOVE_DUPLICATES=true , ASSUME_SORTED=true, VALIDATION_STRINGENCY=SILENT, CREATE_INDEX=true
Counted the raw reads using HTSeq 0.6.0
Performed differential expression analysis using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: read.counts.txt are htseq-count files.

source_name: Foxa2-hCD4 tagged mES cells

growth_protocol: SF-ES + PD, Lif, CHIR

extract_protocol:
Ambion RNAqueous Micro kit
Illumina TruSeq V2

value: Cardiac mesoderm, Foxa2-

tag: differentiation protocol

value: mESC directed differentiation to cardiomyocytes


title: Flk1+ high 2

value: Flk1+ high


title: Endoderm 1

value: Endoderm

value: mESC directed differentiation to endoderm


title: Cardiac mesoderm, Foxa2+ 2

value: Cardiac mesoderm, Foxa2+


title: Cardiac mesoderm, Foxa2+ 1


title: de_B8


title: Cardiac mesoderm, Foxa2- 1


title: Endoderm 2


title: Cardiac mesoderm, Foxa2+ 3


title: 9wk_211

description:
Reduced Representation Bisulfite Sequencing (RRBS)
processed data file(s): RrbsSummaryP1-9wk.txt.gz

data_processing:
We analyzed RRBS and locus specific bisulfite sequencing data by aligning fastq files to the mouse genome (mm9) using Bismark (v0.7.6) with bowtie2
We then combined replicates for each sample and summarized methylation data using the Bismark methylation_extractor.
We counted methylated and unmethylated CpGs at each genomic locus using perl scripts and imported the data into R for statistical analysis.
To remove uninformative CpG loci from RRBS data, we omitted any CpGs where greater than 10% of samples had coverage less than 10X. We then removed any CpGs that were unmethylated (<10%) in all samples of all ages. These CpGs are not informative for our study as they do not change between ages and introduce bias into the data because they are primarily located in CpG dense areas.
For locus specific data, we removed any data points with less than 100X coverage and any CpG where greater than 10% of samples had missing data.
Using R, we calculated the percent methylation at each locus for each sample and compared values between groups using a student’s t-test.
We derived false discovery rates (FDR) from t-test p-values using the qvalue package for R.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: For RrbsSummary files, the columns are: chromosome, base, change in percent between ages, pvalue and qvalue. For LocusSpecificSummary.txt.gz, the columns are: locus   chromosome, CpG identifier, age, sex, percentMethylation for that sample, pvalueOfChangeWithAge and qvalue

value: 9 weeks


title: de_B7


title: wt_wt_1

description: rRNA depleted stranded


title: Flk1+ high 1


title: 9wk_14

value: liver


title: de_B3


title: de_B2


title: Cardiac mesoderm, Foxa2- 3


title: 9wk_134


title: de_C4


title: de_B1


title: de_B11


title: de_A8


title: 9wk_100


title: 6MoP1_35

description:
Reduced Representation Bisulfite Sequencing (RRBS)
processed data file(s): RrbsSummaryE18-P1.txt.gz,RrbsSummaryP1-9wk.txt.gz


title: 6MoP1_31


title: de_A2


title: 6MoP1_32


title: de_A7


title: 6MoP1_22


title: 6MoP1_25


title: de_A3


title: HL60_DREAM

city: Philadelphia

first: Takahiro

last: Sato

state: PA

address: 3307 North Broad Street

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

data_processing:
Library strategy: DREAM
Illumina HiSeq2500 paired end sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to hg19 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*Xma/(c*Xma+Sma)), where c=2.342 was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), MethReads (observed number of reads corresponding to methylated CpG, Xma), UnmethReads (observed number of reads corresponding to unmethylated CpG, Sma), RawMethylation (unadjusted methylation value), AdjMethylation (methylation value adjusted based on the spiked in standards).

source_name: HL60 cell line

growth_protocol: HL60 cell line was cultured in IMDM medium with 20% FBS

extract_protocol:
phenol-chloroform
Five micrograms of genomic DNA spiked with 500 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

tag: cell line

value: acute promyelocytic leukemia

value: Peripheral blood leukocytes were obtained by leukopheresis from a 36-year-old Caucasian female with acute promyelocytic leukemia

tag: Sex

value: female


title: 6MoP1_27


title: 6MoP1_34


title: DAC_Depsi-3

description: Each sample was run on two separate lanes on the HiSeq2500 generating two fastq files. The two files were merged for final analysis.

data_processing:
Illumina HiSeq2500 single end sequencing
tophat2 --sensitive alignment of the reads in two fastq files from each sample to hg19, generating one BAM file per sample
ht-seq-count  with default settings to generate counts of each gene
edgeR to generate RPKM and fold change of each condition compared to control, only keep genes with at least one read in one of the samples
export fold change of each inhibitor vs. control into a text file, then import all the fold changes into one excel file
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format. The first 30 columns are the RPKMs of the individual samples. The following columns are the fold change and FDR of the triplicates of each condition compared against the triplicates of control samples

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen)
Strand-specific RNA libraries were generated from 1μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina)

treatment_protocol: Cells were treated daily with 100nM decitabine (5-aza-CdR, Sigma), 10uM S2101 (Millipore), 1uM UNC0638 (Sigma), and 1uM GSK343 (Sigma) for 96 hours, or 20nM depsipeptide (Romidepsin, Sigma) was added for 24 hours


title: de_B4

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.

source_name: iPSC line TkDA3-4

value: Definitive endoderm 1


title: de_A5


title: de_A10


title: 9wk_15


title: DAC_GSK343-3


title: 6MoP1_15


title: Depsi-3


title: E18-5_41L

description:
Reduced Representation Bisulfite Sequencing (RRBS)
processed data file(s): RrbsSummaryE18-P1.txt.gz


title: GSK343-3


title: E18-5_37L


title: 9wk_101


title: 9wk_102


title: de_A11


title: E18-5_17L


title: 6MoP1_24


title: UNC0638-3


title: DAC_UNC0638-3


title: S2101-3


title: DAC_S2101-3


title: E18-5_11L


title: F3L_F3

first: Yicun

last: Chen

address: Fuchun Street

department: Institute of Subtropical Forestry

institute: Chinese Academy of Forestry

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then assembly use Trinity
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Trinity assembly
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ;Trinity assembly result

organism: Vernicia fordii

source_name: V. fordii_F. oxysporum_late stage_root

growth_protocol: V. fordii and V. montana plantlets with two or three leaves and approximately 30 cm in height were used. All plantlet were kept under growth chamber conditions at 26℃ with 16-h light/8-h dark photoperiod.

extract_protocol:
Total RNA was extracted from the plant roots and root-stem transition region using the EASYspin plant RNA mini kit (Aidlab, Beijing, China) QIAGEN RNeasy plant mini kit (QIAGEN, Valencia, CA). RNA integrity was confirmed using the UV-Vis Spectrophotometer Q5000 (Quawell, USA). All RNA samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers (RIN) ≥8.0. mRNA was purified from 30 µg of total RNA using Sera-mag Magnetic Oligo(dT) Beads (Illumina) and fragmented into small pieces using divalent cations under elevated temperature.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Before inoculation, the plantlet was sterilized in a solution containing 75% ethanol for 1 min, and 0.5% sodium hypochlorite for 3 min, and then 90% ethanol for 30 sec, and followed by rinsing three times in sterile water. For inoculation, a spore concentration of 1×10^6 spores per mL, diluted with sterile distilled water, was used to inoculate the plants. Before inoculations, the plants were carefully removed from the soil, and the roots were rinsed with sterile water and then dipped for 30 min into the fungal inoculum. The plants were sampled at 2-15 dpi (days post inoculation). The root, peel and leaves were cut and immediately frozen in liquid nitrogen and stored at -80℃ until retrieved for RNA preparation.

value: seedling; root

tag: infected with

value: Fusarium oxysporum

tag: pathogen infection stage

value: 3; late stage


title: F3I1_F3


title: E18-5_44L

source_name: Liver


title: Cntrl-3


title: DAC_Depsi-2


title: DAC-3


title: F2L_F2

source_name: V. fordii_F. oxysporum_middle stage_root

value: 2; middle stage


title: Depsi-2


title: F2I1_F2


title: F1H_F1

source_name: V. fordii_F. oxysporum_early stage_root

value: 1; early stage


title: F2H_F2


title: F1I1_F1


title: F1L_F1


title: F0L_F0

source_name: V. fordii_no pathogen infection_root

value: 0; no pathogen infection


title: S2101-2


title: Cntrl-2


title: GSK343-2


title: UNC0638-2


title: F0H_F0


title: DAC_S2101-2


title: DAC-2


title: DAC_Depsi-1


title: Depsi-1


title: DAC_GSK343-2


title: F0I1_F0


title: DAC_S2101-1


title: UNC0638-1


title: S2101-1


title: DAC_GSK343-1


title: DAC_UNC0638-2


title: F3H_F3


title: DAC-1


title: DAC_UNC0638-1


title: GSK343-1


title: Cntrl-1


title: V9M_JQ1_24hr RNA Seq

city: Cleveland Heights

first: Peter

last: Scacheri

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

data_processing:
Adapter and quality trimming of both ChIP-Seq and RNA-Seq reads was done using FASTX Toolkit 0.0.13. Reads below 25bp in length or reads with Phred quality scores below 20 were discarded
ChIP-seq reads were aligned to hg19 with Bowtie2 version 2.0.6, using default parameters. RNA-Seq reads were aligned to hg19 using TopHat v1.3.2
Potential PCR duplicates were removed from aligned ChIP Seq reads files
ChIP-Seq peaks were called using MACS v1.4. Cufflinks v1.3.0, run with genomic bias correction, was used to calculate transcript abundancies in the RNA-Seq data.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq WIG tracks were generated with MACS v.14. The WIG signal was divided by mean WIG signal for each sample, and the WIGs were converted to bigWIGs

molecule: polyA RNA

source_name: CRC cell line

growth_protocol: CRC cell lines were grown in MEM media supplemented as previously described, except for COLO205 cells which were grown in RPMI-1640 supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 1% penicillin/streptomycin.

extract_protocol:
For ChIP-Seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For DNase Hypersensitivity, nuclei were isolated and treated with DNase I. For RNA-Seq samples, cells were lysed and RNA extracted with TRIzol according to the manufacturer’s protocol.
ChIP-Seq libraries were prepared with NEB reagents as previously described. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated 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 and library fragments of ~250 bp were band isolated from an agarose gel. DNase Hypersensitivity libraries were prepared as previously described.  Briefly, DNase I treated DNA was blunt-ended. DNA fragments were ligated to biotinylated linkers and digested with MmeI, producing 2 bp overhangs for ligation with a second linker or Illumina adapters. DNA was then PCR amplified and library fragments of ~86 bp were band isolated from a gel. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For RNA-Seq samples, CRC cells at ~0.5×10^6 cells/well in 6-well plates were treated with 500nM JQ1 for 0.5, 1, 6, or 24 hours, or 0 hours as a control

value: colorectal cancer cell line


title: V9M_JQ1_1hr RNA Seq


title: V9M_JQ1_0.5hr RNA Seq


title: V9M_JQ1_6hr RNA Seq


title: V703_JQ1_24hr RNA Seq


title: V703_JQ1_6hr RNA Seq


title: V9M_0hr RNA Seq


title: V703_JQ1_1hr RNA Seq


title: V703_JQ1_0.5hr RNA Seq


title: V576_JQ1_6hr RNA Seq


title: V703_0hr RNA Seq


title: V576_0hr RNA Seq


title: V576_JQ1_24hr RNA Seq


title: V576_JQ1_0.5hr RNA Seq


title: V457_JQ1_6hr RNA Seq


title: V457_JQ1_0.5hr RNA Seq


title: V457_JQ1_1hr RNA Seq


title: V410_JQ1_1hr RNA Seq


title: V457_JQ1_24hr RNA Seq


title: V576_JQ1_1hr RNA Seq


title: V410_JQ1_0.5hr RNA Seq


title: V389_JQ1_24hr RNA Seq


title: V410_0hr RNA Seq


title: V389_JQ1_1hr RNA Seq


title: V457_0hr RNA Seq


title: V389_JQ1_6hr RNA Seq


title: V389_JQ1_0.5hr RNA Seq


title: V940 input DNA


title: V868 input DNA


title: V855 input DNA


title: V429 input DNA


title: V481 input DNA


title: V411 input DNA


title: V968 input DNA


title: V784 input DNA


title: V410_JQ1_6hr RNA Seq


title: V866 input DNA


title: V5 input DNA


title: V456 input DNA


title: V410_JQ1_24hr RNA Seq


title: V1074 input DNA


title: V1106 input DNA


title: V1024 input DNA


title: V206 input DNA


title: SW480 input DNA


title: V1058 input DNA


title: COLO205 input DNA


title: V503 input DNA


title: V1009 input DNA


title: V389_0hr RNA Seq


title: C29 input DNA

source_name: Colon Crypt

value: normal colon crypt


title: C28 input DNA


title: C37 input DNA


title: CRC_7A H3K4me1 ChIP Seq

source_name: primary CRC tumor tissue

value: primary colorectal cancer tumor

tag: chip antibody

value: rabbit anti-H3K4me1 (Abcam #8895)


title: CRC_17A H3K4me1 ChIP Seq


title: V968 H3K4me1 ChIP Seq


title: V940 H3K4me1 ChIP Seq


title: Crypt5 input DNA


title: CRC_6A H3K4me1 ChIP Seq


title: V868 H3K4me1 ChIP Seq


title: HCT116 input DNA


title: Old_CR_1_6_10

city: Seoul

first: Hang-Rae

last: Kim

address: 103 Daehak-ro, Jongno-gu

department: Anatomy and Cell Biology

institute: Seoul National University College of Medicine

data_processing:
Sequences were sorted using their unique barcode, and low-quality reads (average quality score < 25 or read length < 300 bp) were removed.
Primer sequences were trimmed by pairwise alignment and the hmm-search program of the HMMER 3.0 package
Trimmed sequences were clustered to correct for sequencing error, and representative sequences were assigned to operational taxonomic units (OTUs; 97% identity)
Taxonomic identification was performed using the EzTaxon-e database (http://eztaxon-e.ezbiocloud.net/) by the highest pairwise similarity among the top five BLASTN results
Possible chimera sequences were removed using the UCHIME software. The read numbers in each sample were normalized by random subsampling, and the diversity indices were calculated using the Mothur software. A Unifrac clustering, heatmap and principal coordinate analysis were performed using CLcommunity (ChunLab). We also performed LEfSe analysis on the website http://huttenhowe.sph.harvard.edu/galaxy.
Genome_build: EzTaxon-e database (http://eztaxon-e.ezbiocloud.net)
Supplementary_files_format_and_content: tab-delimited text files include ‘microbial phylotypes classification’ for each sample; sum (number): each bacteria species sequence read number,    sum (ratio): (each bacteria species sequence read number/total bacteria species read number)*100 as a percentage from total read read number.

source_name: gut microbiota (ceca contents)

extract_protocol:
DNA was extracted using the FastDNA SPIN extraction kit (MP Biomedicals, Santa Ana, CA, USA).
PCR amplification of the V1-V3 region of bacterial 16S rRNA gene was performed using universal primers incorporating the FLX Titanium adapters and a sample barcode sequence. The forward primer (27F, bold type) was 5¢-CCT-ATC-CCC-TGT-GTG-CCT-TGG-CAG-TCT-CAG-Linker-AGA-GTT-TGA-TCC-TGG-CTC-AG-3¢, in which the sequence of the 454 adapter2 is shown underlined and the 454 key in italics. The reverse primer (536R, bold type) was 5¢-CCA-TCT-CAT-CCC-TGC-GTG-TCT-CCG-ACT-CAG-Barcode-Linker-TTA-CCC-GCG-GCT-GCT-GGC-AC-3¢, in which the 454 adapter 1 sequence is underlined and the 454 key is shown in italics. The amplified PCR products were purified, quantified and subjected to emulsion PCR using protocols developed by Roche Life Sciences (Roche, Branford, CT, USA).
Pyrosequencing was performed by ChunLab Inc. (Seoul, Korea) using a 454b GS FLX Titanium Sequencing System according to the method

treatment_protocol: To compare the overall structural changes in the gut microbiota, young and old mice were treated with vehicle, syringaresinol (SYR, 10 mg/kg or 50 mg/kg), or caloric restriction (CR).

value: 40 weeks

tag: invervention

value: 30% caloric restriction


title: Old_CR_1_6_2


title: Old_CR_1_6_6


title: Old_CR_1_6_8


title: V866 H3K4me1 ChIP Seq


title: V855 H3K4me1 ChIP Seq


title: Old_SYR50_1_5_8

value: 50 mg/kg of Syringaresinol


title: Old_CR_1_6_4


title: Old_CR_1_6_5


title: Old_SYR50_1_5_10


title: Old_SYR50_1_5_7


title: Old_SYR50_1_5_6


title: V1051 input DNA


title: CRC_23A H3K4me1 ChIP Seq


title: V8 H3K4me1 ChIP Seq


title: Old_SYR50_1_5_4


title: Old_SYR10_1_4_7

value: 10 mg/kg of Syringaresinol


title: Old_SYR10_1_4_5


title: Old_SYR50_1_5_3


title: Old_SYR10_1_4_3


title: Old_SYR10_1_4_2


title: V784 H3K4me1 ChIP Seq


title: V852 H3K4me1 ChIP Seq


title: Old_SYR10_1_4_4


title: V481 H3K4me1 ChIP Seq


title: V456 H3K4me1 ChIP Seq


title: V503 H3K4me1 ChIP Seq


title: V432 H3K4me1 ChIP Seq


title: Old_Vehicle_1_1_4

value: vehicle


title: Old_Vehicle_1_1_9


title: Old_Vehicle_1_1_6


title: Old_SYR10_1_4_1


title: Old_Vehicle_1_1_8


title: Old_Vehicle_1_1_2


title: Old_Vehicle_1_1_1


title: Young_1_7_9

value: 6 weeks

value: free


title: V411 H3K4me1 ChIP Seq


title: Young_1_7_8


title: Young_1_7_4


title: Young_1_7_6


title: V206 H3K4me1 ChIP Seq


title: V1106 H3K4me1 ChIP Seq


title: Young_1_7_3


title: 532

city: Strasbourg

first: Olivier

last: Lefebvre

address: 3 Avenue Molière

institute: Inserm

description: Tumors overexpressing mouse laminin alpha 1 chain

data_processing:
Illumina Casava1.7 software used for basecalling.
The separation of RNA sequencing reads coming from the human tumor cells and the host murine cells was performed in silico using the Xenome software (Conway et al., 2012, DOI:10.1093/bioinformatics/bts236). Each Fastq file was separated into mouse specific and human specific sequencing reads. These were subsequently aligned using Tophat2 (Kim et al., 2013) and processed using the Cufflinks (Roberts et al., 2011) pipeline to generate the final expression files
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Human and mouse specific reads were separated and use to generated comparative expression of the 2 groups at species level.  2 xls file were generated for Human and mouse reads.

organism:
Homo sapiens
Mus musculus

source_name: Subcutaneous tumor_HT29 xenograft_overexpressing_mouse laminin alpha 1 chain

growth_protocol: 4 weeks tumor growth

extract_protocol:
RNA was extracted with the Tri Reagent according to manufacturer’s instructions (Molecular Research Center Inc)
Library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “Truseq RNA sample preparation low throughput” protocol with some modifications. Briefly, mRNA was purified from 2 µg total RNA using oligo-dT magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers, then the second strand of the cDNA was synthesized using Polymerase I and RNase H. The next steps of RNA-Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit (Beckman Coulter, Fullerton, USA) with the SPRI-TE instrument (Beckman Coulter). Briefly, in this system double stranded cDNA fragments were blunted, phosphorylated and ligated to indexed adapter dimers, and fragments in the range of ~200-400 bp were size selected. The automated steps were followed by PCR amplification (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), then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation, Beverly, USA). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent, Les Ulis, France).

tag: xenograft host

value: nude mice

tag: xenograft tissue

value: human colorectal cancer


title: V1058 H3K4me1 ChIP Seq


title: OLE-06-12


title: 530


title: OLE-03-5

description: Control tumor


title: 526

description: Control tumor


title: 527

description: Control tumor


title: V1074 H3K4me1 ChIP Seq


title: V1009 H3K4me1 ChIP Seq


title: L3

city: Pisa

first: Tommaso

last: Giordani

address: via del Borghetto 80

department: Department of Agricolture, Food and Enviroment

institute: University of Pisa

data_processing:
Sequenced reads were trimmed using trimmomatic version 0.33 with the following parameters: CROP 115, HEADCROP 15,MINLEN 100
Ribosomal RNA sequences from public database NCBI were used to remove rRNA from libraries using CLC Genomic workbench (v. 8.0.3) mapping strategy.
Reads were mapped using CLC-Genomic Workbench 8.0.3 onto a Ovis aries transcriptome (Oar v. 4.0)
Gene expression level was calculated and expressed as mreads per kilobase per million reads mapped (RPKM) as described in Mortazavi et al. (2008)
Genome_build: Reference transcriptome: GCF_000298735.2_Oar_v4.0_rna.fna
Supplementary_files_format_and_content: Tab-delimited text file including RPKM values for each sample

organism: Ovis aries

source_name: milk somatic cells

growth_protocol: Three Comisana 90 days of lactation sheep were used. Starting in February 2015, each sheep was fed grass hay and a commercial concentrate for three weeks. Diet was formulated according to a nutrient requirements of an ewe weighing 65 kg and producing 1 kh of milk at 6,5% fat. Animal health was constantly monitored.

extract_protocol:
MSC were pelletted from 250 ml of fresh milk at 1100g for 10 min at 4°C. The cell pellet was washed twice in PBS, pH 7.2 with 0.5 mM EDTA and resuspended in 3 ml of Trizol Reagent (Life Technologies). RNA extraction continued following the Trizol protocol, performing all centrifugation steps at 4°C and isopropanol precipitation at -80°C for 30 min. A DNAse I (Roche) treatment was performed according to the manufacturer’s instructions, to completely remove genomic DNA contamination. Finally RNA was purified by phenol/chloroform extraction and precipitated following standard procedures.
RNA-Seq library was generated using the TruSeq RNA-Seq Sample Prep kit, according to the manufacturer protocol (Illumina Inc., San Diego, CA, USA)

treatment_protocol: The same  sheep were fed grass, hay and a concentrate containing 20 % of extruded linseed on dry matter basis for three weeks. Milk from each sheep was collected at the beginning and at the end of  the experiment.

tag: breed

value: Comisana

tag: sheep id

value: milk somatic cells


title: L2