title: root_10uM_PO4_B1

city: Irapuato

first: Ruairidh

last: Sawers

state: Guanajuato

address: Km 9.6 Lib. N. Car. Irapuato-Leon

country: Mexico

institute: LANGEBIO-CINVESTAV

data_processing:
Basecalls were analysed with Casava 1.8.2 (Illumina, Inc., CA, USA).
Sequenced reads were mapped to the transcripts file of the B73 maize genome, version 284_6a from Phytozome 10, using bowtie2 version 2.2.4 with the parameters --very-sensitive and -a.
Individual SAM output files were used as input for the eXpress software (http://bio.math.berkeley.edu/eXpress/index.html), version 1.5.1, using default parameters.
Genome_build: 6a (Phytozome 10)
Supplementary_files_format_and_content: txt, tab delimited, eXpress output files

source_name: root

growth_protocol: Maize plants, inbred line B73, were grown for 21 days in a tube-based system supplied with Hoagland solution (Hoagland and Broyer 1936) containing the standard 1000 uM (+P) or a modified 10 uM (-P) concentration of KH2PO4. The concentration of potassium was maintained constant by addition of KCl as required.

extract_protocol:
Tissue was frozen and ground in liquid nitrogen. Total RNA was isolated using the PureLink RNA Mini Kit (Ambionby Life Technologies, CA, USA).
Up to 4ug of total RNA was fragmented, converted to cDNA and enriched by PCR according to the Illumina TruSeq RNA SamplePrep v2 protocol (Illumina, Inc., CA, USA) The libraries were confirmed in agarose gels and quantified using the microplate based PicoGreen® dsDNA quantification assay (Molecular Probes Inc., OR, USA) and Agilent Bioanalyzer system. Illumina’s barcodes were used to pool 10 samples per lane. The pools were quantitated by qPCR, using the Library Quantification kit (Kapa Biosystems, Inc., MA, USA) with the CFX Connect Real-Time PCR Detection System (Bio-rad, CA, USA) and sequenced by the Illumina HiSeq 2500 system using a TruSeq SBS sequencing kit version 3.

tag: line

tag: organ

value: root

value: whole root system

tag: treatment

value: 10 uM soil phosphate

value: 21 days


title: leaf_10uM_PO4_B1

status: Public on Feb 09 2017

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Zea mays

source_name: leaf

value: leaf

value: 10 cm of the second and third fully expanded leaves

tag: age


title: root_10uM_PO4_B2


title: leaf_1000uM_PO4_B1

value: 1000 uM soil phosphate


title: leaf_10uM_PO4_B2


title: leaf_1000uM_PO4_B2


title: root_1000uM_PO4_B2


title: root_1000uM_PO4_B1


title: scribRES+Tet Exp3 Rep1

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
fastq file processed by filering out low quality reads (<Q20) and llow quality bases (<Q20) with sickle. Adaptors were removed with cutadapt 1.0.
RNA-seq data have been aligned to C.familaris genome using TopHat 2.0.6
RPKMs were generated using custom scripts
Genome_build: C.familiaris 3.1
Supplementary_files_format_and_content: RPKMs in tsv format

organism: Canis lupus familiaris

source_name: MDCK-II cells

growth_protocol: MDCK-II scribKD cells were plated at 1,300,000 cells/10 cm plate. The cells were cultured in 10 ml DMEM + 10% tetracycline-free FBS.

extract_protocol:
67 hours after plating, RNA was harvested using Trizol reagent
Libraries were prepared from 1 µg RNA using TrueSeq RNA sample preparation V2 kit according to the manufacturers instructions

treatment_protocol: Where specified, 10 µg/ml tetracycline (Tet) was added at the time of plating. Medium +/- Tet was changed one day after plating

tag: cell type

value: Madin-Darby Canine Kidney Epithelial Cells

tag: phenotype/variation

value: resistant to cell competition (scribRES+Tet)


title: scribKD+Tet Exp2 Rep2

value: scribble knock-down (scribKD+Tet)


title: scribRES+Tet Exp3 Rep2


title: scribKD+Tet Exp1 Rep2


title: GC_AvrB_rep3

city: Verona

first: Andrea

last: Minio

address: Via dell'Artigliere 8

department: Applied Biotechnologies

country: Italy

institute: Università di Verona

data_processing:
Bcl conversion and demultiplexing were carried out using CASAVA pipeline v1.8.2 (Illumina).
Alignment with TopHat v2.0.12 (running Bowtie2 ver.2.2.4) in very sensitive mode
Read counts and differntial expression was performed with Cufflinks ver.2.2.0
Genome_build: Arabidopsis thaliana TAIR10 reference genome (ftp://ftp.arabidopsis.org/home/tair/)
Supplementary_files_format_and_content: tab-delimited text files include counts each sample

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Plants were grown in a growth chamber with a short day cycle of white light (~100 µE), 24°C/22°C day/night temperature and 70% relative humidity.

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific). Total RNA was purified using the TURBO DNA-free™ Kit (Thermo Fisher Scientific) and first-strand cDNA was synthesized using SuperScript™ II reverse transcriptase (Thermo Fisher Scientific). The cDNA was used for real-time RT-PCR analysis or samples were processed for library preparation.
RNA-Seq libraries were prepared starting from 2.5 μg of total RNA using the TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions (Illumina Inc., San Diego, California, USA).

treatment_protocol: Pseudomonas syringae pv. tomato DC3000 (Pst) and Pst DC3000 carrying the avirulence gene AvrB (PstAvrB) were grown overnight at 28°C in King’s B medium containing the appropriate antibiotics (50 mg/L rifampicin, 50 mg/L kanamycin). Bacteria were pelleted, washed three times with 10 mM MgCl2, resuspended, and diluted in 10 mM MgCl2 to the desired concentration (generally 107 cfu/mL, but 5 × 105 cfu/mL for bacterial growth assays). The bacterial solutions were inﬁltrated from the abaxial side into leaves using a 1-mL syringe without a needle. Control (mock) inoculations were carried out with 10 mM MgCl2.

tag: tissue

value: local treated leaves

value: PstAvrB 107cfu/mL

tag: genotype

value: guanylate cyclase-expressing line


title: scribKD+Tet Exp2 Rep1


title: GC_AvrB_rep2


title: GC_AvrB_rep1


title: pooled_RNA

city: Wuhan

first: Wang

last: Min

address: No.1,Shizishan Street

country: China

institute: Huazhong Agricultural University

data_processing:
Illumina base-calling Software 1.7 use for basecalling
Clean reads were obtained after removing reads of low quality, adaptors or reads with >5% unknown nucleotides. The reference sequences were obtained by de novo assembling the pooled-1_RNA and pooled-2_RNA raw files using Trinity software.
Reads alignment software was SOAPaligner/soap2 2.20. The read counts were normalized as RPKM (reads per kilobase per million mapped reads) values in regard of the differing library sizes and the length of the transcripts.Differentially expressed genes (DEGs) from different samples were identified using the R package. The criteria applied to determine significant DEGs included a false discovery rate (FDR) smaller than 10−3 and log2-fold change be equal or greater than 1. In pooled_RNA.txt, we have used the algorithm of FPKM (fragments per kilobase of exon per million fragments mapped) to calculate the estimate the gene expression level, because we did this based on the pair-end read.
genome build: Sequences in the pooled-Unigene.fa provided in processed data file files were used for read alignment.
processed data files format and content: The processed data file of pooled-Unigene.fa is in FASTA format with sequence ID and sequence size, this data was used as reference sequence and obtained by de novo assembly. The processed data file of pooled_RNA.txt is in tab-delimited text file include reference sequence ID,length and annotation. The processed data files of 0h_RNA.map.txt, 6h_RNA.map.txt,24h_RNA.map.txt and 72h_RNA.map.txt were also in tab-delimited text files includ RPKM values for each samples.

organism: Citrus trifoliata

source_name: whole plant

growth_protocol: grown under field conditions

extract_protocol:
Total RNA was extracted with RNAiso Plus (TaKaRa, Dalian, China) according to the manufacturer's instructions.
The cDNA library was constructed using mRNA-Seq assay according to the instructions. In brief, poly(A) mRNA was enriched from 20 μg of total RNA using oligo(dT) magnetic beads, and cut into short fragments (200-700 bp) with fragmentation buffer. The short mRNA fragments were synthesized into double-strand cDNA using random hexamer primers, and purified with QiaQuick PCR Purification Kit (Qiagen, CA, USA). Then cDNA was washed with EB buffer for end repairing and poly(A) addition. Illumina paired-end sequencing adapters were then ligated to the ends of the 3’-adenylated cDNA fragments. Agarose gel electrophoresis was carried out so as to select fragments with suitable size that was enriched by PCR amplification to construct the cDNA library. The library was sequenced by BGI (Shenzhen, China) on Illumina HiSeqTM 2000 platform for 5 gigabase in-depth sequencing.

treatment_protocol: Three-month-old trifoliate orange (Poncirus trifoliata (L.) Raf.) seedlings were collected from an experimental nursery at Huazhong Agricultural University. After a full wash, the plants were incubated in glass beakers filled with tap water and kept for 5 d at 25°C in a growth chamber. In order to enrich stress-responsive genes, the seedlings were treated with different stresses, including cold, salt, and drought. For cold treatment, the plants were placed at 4°C; the leaves were harvested at indicated time points (0, 6, 24, and 72 h). Salinity treatment was applied by placing the seedlings in 200 mM NaCl solution for same time schedule as cold. For drought treatment, the seedlings were placed on filter papers and dehydrated at ambient environment; the whole plants were sampled at 0, 0.5, 3, and 6 h.  These tissues were immediately frozen in liquid nitrogen after sampling and stored at -80 °C until use for further analysis.

value: root, stem, leaf

tag: developmental stage

value: Three-month-old trifoliate orange seedlings

tag: stress

value: cold, salt, drought


title: IFC rep1

city: zhengzhou

first: hongping

last: li

institute: Henan Agricultural University

source_name: maize ovary

growth_protocol: Zea mays L. (maize) inbred Yu-A474 plants were grown at a research farm of Henan Agricultural University, Henan Province, China (34º53´N, 113 º35´E, 94 m altitude) under non-stress conditions during June-October 2014.

extract_protocol:
The ovaries were isolated by removing the glumes, lemma, and palea and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Under non-stress conditions.

tag: developmental state

value: before pollination

value: ovary

value: IFC mutant


title: t0

city: Minneapolis

first: Kristi

middle: L

last: Frank

state: MN

address: 420 Delaware St SE, MMC196

department: Dept. of Microbiology

country: USA

institute: University of Minnesota

description:
Sample 1: r1t0
Sample 3: r2t0
RNA treated with Dnase to remove contaminating DNA and MICROBExpress to deplete bacterial rRNA

data_processing:
Base call files were generated with Illumina Real Time Analysis software.
Primary analysis and de-multiplexing were performed with CASAVA (version 1.8.2, Illumina) to generate FASTQ files for each sample.
All data analysis was carried out using the Galaxy server maintained by the Minnesota Supercomputing Institute at the University of Minnesota.  De-multiplexed FASTQ files were assessed for quality, prepared for trimming, and trimmed using FastQC, FASTQ Groomer, and FASTQ Trimmer, respectively
The trimmed paired end reads in separate files were joined with FASTQ interlacer and further processed in FASTQ de-interlacer.
The left and right de-interlaced files for each sequenced sample were aligned using Bowtie for Illumina, and the resulting SAM output files were sorted with SortSAM.
Transcript abundance for each sample was carried out with Cufflinks using the OG1RF genome for reference annotation.
The Cufflinks assemblies of the biological replicates for each time point were merged with Cuffmerge
Cuffcompare and Cuffdiff were then used to analyze the Cuffmerge output files for statically significant differences in gene expression between the subdermal chamber inocula and 4 hours post-inoculation samples
Genome_build: ASM17257v2 (CP002621)
Supplementary_files_format_and_content: Tab-delimited .txt file with FPKM values, fold-change, and statistical analysis results

organism: Enterococcus faecalis

source_name: input inoculum

growth_protocol: E. faecalis OG1RF(pCF10) was inoculated into 10-25 ml BH medium and incubated for ~15-16 hours, then diluted 1:5 into 25-50 ml of fresh BH medium and incubated for 2 more hours.  Bacteria were harvested by centrifugation for 15-20 min at 6000 rpm in a Beckman JA-17 rotor at 4°C.  Pellets were resuspended to an optical density at a wavelength of 600 nm of ~1.7-1.8 in KPBS.  Aliquots of the prepared inoculum were  processed in RNAprotect Bacteria Reagent.

extract_protocol:
Frozen pellets were thawed, resuspended in 0.4 ml of RNase-free TE containing 50 mg/ml lysozyme and 1000 U/ml mutanolysin, homogenized using a hand-held motorized homogenizer with RNase-free pellet pestles (Fisher Scientific, Pittsburgh, PA), and incubated for 10 min at 37°C.  Each sample was then split in half and extracted in duplicate with the RNeasy Mini Kit (Qiagen Inc.) according to the manufacturer’s instructions with an added homogenization step using the QIAshredder (Qiagen Inc.) immediately after the addition of Buffer RLT.  RNA was eluted from each column with two 30 μl volumes of RNase-free water, and total RNA from duplicate extractions of each sample were pooled together.  All OG1RF(pCF10) RNA eluates obtained from a single rabbit were further pooled.Contaminating DNA was removed using a TURBO DNA-free kit (Ambion, Austin, TX) following the rigorous protocol as directed by the manufacturer. DNase-treated RNA was ethanol precipitated in the presence of a glycogen carrier and resuspended in RNase-free TE.  RNA harvested from rabbits was first treated with MICROBEnrich (Ambion) followed by MICROBExpress (Ambion), according to the manufacturer’s instructions, to deplete eukaryotic RNA and bacterial rRNA, respectively.  RNA from the infection inoculum was treated with MICROBExpress only.
Library creation and sequencing were performed by the University of Minnesota Genomics Center.  Indexed libraries were created using the TruSeq RNA Sample Preparation Kit v2 (Illumina, Inc., San Diego, CA) according to the manufacturer’s instructions.  Indexed libraries were size selected to 320 bp +/- 5% using a LabChip XT instrument (Perkin Elmer, Waltham, MA).  Prepared libraries were hybridized to paired end flow cells, clonally amplified on an Illumina cBot, and sequenced using Illumina SBS chemistry in a 100 bp paired end run on an Illumina HiSeq 2000 instrument.

treatment_protocol: Two ml of serous fluid were aspirated from the subdermal chamber and were replaced with 2 ml of prepared inoculum. At 4 hours post-inoculation, 25-28 ml of aspirate was collected, immediately added to twice the volume of RNAprotect Bacteria Reagent, and processed according to the manufacturer's directions.  Cells were condensed into twelve pellets.

tag: strain

tag: growth medium

value: trypsinized beef heart dialysate

tag: biological replicates

value: 1 and 2


title: scribKD+Tet Exp1 Rep1


title: GC_mock_rep3

value: MgCl2 10mM


title: GC_mock_rep2


title: GC_mock_rep1


title: scribKD-Tet Exp2 Rep2

value: wild-type scribble expression (scribKD-Tet)


title: WT_AvrB_rep3

value: wild-type


title: scribKD-Tet Exp1 Rep2 re-sequenced

value: Madin-Darby Canine Kidney Epithelial Cells


title: scribKD-Tet Exp1 Rep2


title: WT_mock_rep3


title: WT_AvrB_rep1


title: WT_mock_rep2


title: scribRES+Tet Exp2 Rep2

value: resistant to cell competition (scribRES+Tet)


title: IFC rep2


title: WT_mock_rep1


title: WT_AvrB_rep2


title: scribRES+Tet Exp2 Rep1


title: scribKD-Tet Exp2 Rep1


title: Taipei309_seedling

city: Guangzhou

first: Munan

last: Xie

state: Guangdong

address: No.135 Xin Gangxi Road, Haizhu District,

department: School of life sciences

institute: Sun Yat-sen University

description: small RNAs

data_processing:
For all small rna libraries, after (1) trim three prime adaptor and (2) filter out low quality or adaptor contaminated reads, we retain only short trimmed reads of sizes from 19 to 30 nt.
The retained reads were search against the Rfam database using the SOAP software, the reads mapped to structural RNAs [rRNA, tRNA, small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA)] with more than 2 mismatches were removed, reads corresponding to repeats/transposons were also discarded by performing searches against the repeat database (http://www.girinst.org/server/RepBase/).
The remaining reads that corresponded to the precursor of all known rice miRNAs from miRBase ( Release 14, http://www.mirbase.org/index.shtml) were used to estimate the expression level of each rice miRNA
Reads counts were calculated by the the read number of each gene or region by total mapped read number in each library.
For transcriptome libraries, all the reads were mapped to the reference genome of rice (Oryza sativa L. ssp. japonica cv. Nipponbare) using Bowtie software package. Reads which could be mapped equally well to multiple locations without mismatch or with up to 2 mismatches were assigned to one position at random and were retained for further analyses as described previously[29]. The reads count for each gene or genomic region ,which according to the tige6.0 gff3 file, were recovered
Genome_build: Oryza sativa
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each miRNAs or mRNAs

organism: Oryza sativa Japonica Group

growth_protocol: The uniformly germinated seeds were transferred into Yoshida nutrient solution and grown under a 16-hour light (28°C) /8-hour dark (25°C) photoperiod for 1 week

extract_protocol:
Total RNAs were extracted by using TRIzol Reagent (Invitrogen). For grains, the husks of the seeds were removed before RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 1 week

value: seedling

tag: subspecies


title: Nipponbare_seedling

description: small RNAs

value: Nipponbare


title: Taipei309_seed

description: small RNAs

value: seed


title: Nipponbare_seed

description: small RNAs


title: Heukgyeong_seedling

description: small RNAs

value: Heukgyeong


title: LI4-816

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

data_processing:
Sequence reads were analyzed using CLCBio Genomic workbench software 7.0 (CLC Bio, Aarhus, Denmark).
Quality control analysis was performed using the NGS quality control tool. A hierarchical clustering of the samples was also performed. All samples passed the quality control
Sequence paired-end reads (76bp) were assembled against the annotated Sscrofa10.2 reference genome using the genome, annotated genes and mRNA tracks
Data was normalized by calculating the reads per kilo base per million mapped reads’ (RPKM) for each gene
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: Processed data file includes normalized expression values (RPKM) for all genes in all 24 samples

organism: Sus scrofa

source_name: purebred male newborns 4 month-old

growth_protocol: All tissues were collected within 15 min postmortem, snap-frozen in liquid nitrogen, and then stored at -80° C until processing.

extract_protocol:
Total RNA was extracted from 50-100mg samples of muscle using the RiboPure TM of High Quality total RNA kit (Ambion, Austin, TX, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-100 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The quality of the RNA was evaluated using the RNA Integrity Number (RIN) value from the Agilent 2100 Bioanalyzer device (Agilent technologies, Santa Clara, CA, USA). The RIN values ranged from 7.8 to 9.8
Sequencing libraries were made using the mRNA-Seq sample preparation kit (Illumina Inc., Cat. # RS-100-0801) according to manufacturer’s protocol. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp on a on a HiSeq2000 sequence analyzer (Illumina, Inc). Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files.

treatment_protocol: 50-100 mg samples of each tissue were ground in liquid nitrogen with mortar and pestle.

value: pure Iberian

tag: Sex

value: male

value: four months

value: Longissimus dorsi muscle


title: LI4-909


title: Xb

city: Fuzhou

first: Chen

last: Lisong

address: Shangdian street NO.15

institute: Fujian Agriculture and Forestry University

description: 5-mm-long Citrus sinensis root apices were excised from the seedlings

data_processing:
Basecalls performed
Get rid of some contaminant reads from the fq file and get the final clean reads.
The clear reads were mapped to Citrus clementina genome (JGI version 0.9, http://www.phytozome.org/clementine.php, 35976 sequences) using SOAP, only perfectly mapped sequences were retained and analyzed further. rRNAs, tRNAs, snRNAs and snoRNAs were removed from the sRNAs sequences through BLASTn search using NCBI Genebank database (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi/) and Rfam (10.1) database (http://www.sanger.ac.uk/resources/databases/rfam.html) (e = 0.01). The remaining sequences were aligned with known plant miRNAs from miRBase 18 (http://www.mirbase.org/).
Reads that were not annotated were used to predict novel miRNAs using a prediction software Mireap (http://sourceforge.net/projects/mireap/), which was developed by the BGI
Genome_build: citrus clementina genome v0.9 (JGI)
Supplementary_files_format_and_content: txt files with cleaned reads; At series level, supplementary files include counts associated with specific miRNAs and stastical analysis to identify differentially expressed miRNAs.

organism: Citrus sinensis

source_name: boron-sufficient roots

growth_protocol: 5-week-old seedlings of ‘Xuegan’ [Citrus sinensis (L.) Osbeck] were transplanted into 6 L pots containing fine river sand. Ten weeks after transplanting, each pot was supplied every other day with B-deficient (0 μM H3BO3) or -sufficient (10 μM H3BO3, control) nutrient solution for 15 weeks. There were 10 replications per B treatment with 2 pots in a completely randomized design.

extract_protocol:
About 0.1 g mixed frozen B-sufficient and -deficient roots from five replictations were used to extract RNA. Total RNA was extracted from frozen roots using TRIzol reagent (Invitrogen, Carlsbad, CA)
Small RNA samples were sequenced by Beijing Genomics Institute (BGI) (Shenzhen, Guangdong, China) using the high throughput pyrosequencing technology developed by Illumina. Two sRNA libraries were constructed, sRNAs were isolated from the total RNA by size fractionation with 15% Tris-borate-EDTA urea polyacrylamide gel (TBU). Then the sRNAs were ligated with 5' and 3' adaptor by T4 RNA ligase after being dephosphorylatd by alkaline phosphatase. The adaptor-ligated sRNAs were transcribed to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen). Thereafter, the single-stranded cDNA was used as templates for double-stranded synthesis by PCR amplification using the primer designed according to the adapter sequence. The obtained PCR products were sequenced on a Solexa sequencer (Illumina) at the Beijing Genomics Institute (BGI), Shenzhen, China.

treatment_protocol: Xa(B-deficient ,0 μM H3BO3),Xb(B-sufficient ,10 μM H3BO3)

tag: cultivar

value: Xuegan

value: seedlings

value: root apices


title: LI4-907


title: Xa

source_name: boron-deficiect roots


title: LI4-903


title: muscle-mixure

city: Beijing

first: Zhonglin

last: Tang

address: No. 2 Yuanmingyuan West Road, Beijing, 100193, P.R.China,

department: Institute of Animal Science

institute: Chinese Academy of Agricultural Sciences

data_processing:
Adaptors in the total RNA-seq reads were firstly trimmed by custom scripts.
Processed reads from each sample were aligned to the reference genome of Sus scrofa (version 10.2, downloaded from ENSEMBL) by using TopHat (version 1.3.2). Parameters were set for strand-specific mapping (--library-type ‘fr-second strand’ for SMART protocol and 'fr-first strand' for dUTP protocol).
Mapped reads from each sample were assembled into transcripts independently by using Cufflinks,also with the assistance of known annotations.Putative transcripts were retrieved with the parameter '--min-frags-per-transfrag 3'.
assembled transcripts from each sample were merged into a consensus transcriptome by using Cuffmerge
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: multiple muscle tissues

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).  Genomic DNA was removed by DNase I (Qiagen, Beijing, China). The quantity and quality of the RNA were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, California, USA). Ribosomal RNA was depleted using Ribo-Zero Magnetic kit (Epicentre, Madison, WI ). The mixed libraries were constructed by mixing equal quantities of each RNA sample. Strand-specific libraries for the paired-end sequencing were prepared using SMART or dUTP protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: multiple breeds

value: multiple time points

value: longissimus dorsi


title: LI4-905


title: tissue-mixure

source_name: multiple tissues

value: multiple tissues


title: scribKD-Tet Exp1 Rep1

value: Madin-Darby Canine Kidney Epithelial Cells

value: wild-type scribble expression (scribKD-Tet)


title: LC4-708

source_name: crossbred male newborn 4 month-old

value: crossbred Iberian x Duroc


title: LC4-758


title: LC4-732


title: LC4-702


title: LC4-748


title: LI4-889


title: LI1-323

source_name: purebred male newborns at birth

value: postnatal day 1


title: LI1-345


title: LI1-431


title: LC4-714


title: LI1-503


title: Heukgyeong_seed

description: small RNAs

value: 1 week

value: seed


title: LC1-429

source_name: crossbred male newborn at birth


title: LC1-426


title: LI1-504

value: pure Iberian


title: LC1-427

value: male


title: LC1-402


title: LC1-412


title: ovary

source_name: ovary, postnatal 240 days

value: Guizhou mini-pigs

value: postnatal 240 days

value: ovary


title: kindey

source_name: kindey, postnatal 240 days

value: kindey


title: muscle_D0

source_name: longissimus dorsi, postnatal 0 days

value: postnatal 0 days


title: muscle_D240

source_name: longissimus dorsi, postnatal 240 days


title: adipose

source_name: adipose, postnatal 240 days

value: adipose


title: spleen

source_name: spleen, postnatal 240 days

value: spleen


title: lung

source_name: lung, postnatal 240 days

value: lung


title: liver

source_name: liver, postnatal 240 days

value: liver


title: testis

source_name: testis, postnatal 240 days

value: testis


title: Rathuwee_seedling

description: small RNAs

organism: Oryza sativa Indica Group

value: seedling

value: Rathuwee


title: Guangluai4_seedling

description: small RNAs


title: KDM105_seed

description: small RNAs


title: muscle_D30

source_name: longissimus dorsi, postnatal 30 days

value: postnatal 30 days

value: longissimus dorsi


title: heart

source_name: heart, postnatal 240 days

value: heart


title: Rathuwee_seed

description: small RNAs

value: 1 week

value: seed


title: Guangluai4_seed

description: small RNAs


title: HR10_SCC_R1

city: Houston

first: Kenneth

last: Tsai

state: TX

address: 2130 West Holcombe Blvd , LSP9.4218

department: Dermatology & Translational Molecular Pathology

institute: University of Texas MD Anderson Cancer Center

data_processing:
Illumina small RNA adapter sequences were trimmed from the reads, and reads of length below 10nt or ending in homopolymers of length 9 nt or above were discarded.
Total usable number of reads for each sample was calculated.
The reads were mapped to the miRBase reference using BLAST; the abundance of each expressed microRNA was quantified as a fraction of the usable reads, and expressed as parts per million.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text format, containing quantile normalized microRNA abundance

organism: Mus musculus

source_name: cutaneous squamous cell carcinoma (cuSCC)

extract_protocol:
RNA was extracted from tissues by homogenizing in TRIZOL reagent and purified using Purelink Kits (Invitrogen).
Libraries were prepared in accordance with standard protocols for the Illumina HiSeq platform.

value: skin


title: HR10_CHR_R1

source_name: nonlesional, chronically UV-exposed skin (NS)


title: HR10_PAP_R1

source_name: papilloma

value: papilloma


title: HR9_PAP_R1


title: HR9_SCC_R1

value: cutaneous squamous cell carcinoma (cuSCC)


title: LC1-425

value: crossbred Iberian x Duroc

value: male

value: postnatal day 1

value: Longissimus dorsi muscle


title: HR9_CHR_R1

value: nonlesional, chronically UV-exposed skin (NS)


title: HR8_SCC_R1


title: HR8_CHR_R1


title: HR8_PAP_R1


title: HR7_PAP_R1


title: HR7_SCC_R1


title: HR7_CHR_R1


title: HR3_PAP_R1


title: HR3_SCC_R1


title: LI1-330

value: pure Iberian


title: HR2_SCC_R1


title: HR2_PAP_R1


title: HR2_CHR_R1


title: 12-AK

data_processing:
Illumina small RNA adapter sequences were trimmed from the reads, and reads of length below 10nt or ending in homopolymers of length 9 nt or above were discarded.
Total usable number of reads for each sample was calculated.
The reads were mapped to the miRBase reference using BLAST; the abundance of each expressed microRNA was quantified as a fraction of the usable reads, and expressed as parts per million.
Genome_build: hg19
Supplementary_files_format_and_content: TAB-delimited text format, containing quantile normalized microRNA abundance

organism: Homo sapiens

source_name: actinic keratosis (AK)

value: actinic keratosis (AK)


title: 12-SCC


title: KDM105_seedling

description: small RNAs

value: seedling


title: 10-SCC


title: 10-AK


title: 8-SCC


title: 8-NS


title: 8-AK


title: 6-AK


title: 10-NS


title: 5-SCC


title: 5-AK


title: 5-NS


title: 4-SCC2


title: 6-NS


title: 4-NS


title: HR3_CHR_R1


title: 4-AK2


title: 3-AK


title: 3-NS


title: 2-NS


title: 2-SCC


title: 1-NS


title: 1-AK


title: PBER

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

description: microRNA

data_processing:
Sequenced reads were processed and aligned to the UCSC reference human genome using miRDeep2 software by default setting
To calculate gene expression intensity, read counts of each miRNA were normalized into corresponding transcripts per million(TPM): actual miRNA count×1,000,000/total count of clean reads.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: peripheral blood (PB) CD34+ cells treatment

extract_protocol:
Total RNA was extracted from HESC, ESER, FLER and PBER cells using TRIzol® Reagent (Invitrogen, Carlsbad, CA) per manufacturer’s instruction
cDNA library was constructed using Small RNA Sample Preparation Kit (Illumina)

value: PBER (adult stage)

value: peripheral blood (PB) CD34+-derived erythroid cells


title: FLER

description: microRNA

source_name: fetal liver cells

value: FLER (fetal stage)

value: fetal liver cells


title: 6-SCC


title: HESC

description: microRNA

source_name: H1 cell line

value: Undifferentiated HESC


title: ESER

description: microRNA

source_name: H1 cell line treatment

value: ESER (embryonic stage)

value: ES-derived erythroid cells


title: Lyko12-3

city: Göttingen

first: Jörg

last: Wilting

address: Kreuzbergring 36

department: Anatomy and Cell Biology

country: Germany

institute: University Medical School Göttingen

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
Candidate genes were filtered to a minimum of 2x fold change and FDR-corrected pvalue<0.05. For functional analysis gene ontology enrichment was tested accounting for gene length via R-package goseq.
Genome_build: Human NCBI genome built
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample; normalised text file and raw data txt files

source_name: normal lymphatic collector from woman

extract_protocol:
Total RNA was isolated from LECs and BECs using peqGOLD Tri-Fast (PeqLab, Erlangen, Germany) according to the manufacturer’s instructions. Lymphatic collector samples of six female donors (age between 44 and 61 years) were isolated from surrounding connective tissue and snap-frozen in liquid nitrogen. The tissue was finely ground in liquid nitrogen using pestle and mortar, and immediately taken up in Tri-Fast reagent (PeqLab). Subsequently total RNA was prepared according to the manufacturer’s instructions.
Library preparation for RNA-Seq was performed using the TruSeq™ RNA Sample Prep Kit v2 (Illumina, Cat. N°RS-122-2002) starting from 1000 ng of total RNA.
cDNA libraries were amplified and sequenced by use of cBot and HiSeq2000 from Illumina (SR; 1x50 bp; ~25-40 million reads per sample). Sequence images were transformed with Illumina software BaseCaller to bcl files, which were de-multiplexed to fastq files with CASAVA v1.8.2.

value: normal lymphatic collector


title: Lyko13-1


title: Lyko13-2


title: Lyko12-1


title: Lyko4-1


title: Lyko5-1


title: Lyko4-2


title: 4-SCC

value: skin

value: cutaneous squamous cell carcinoma (cuSCC)


title: 4-AK


title: Lyko1


title: LEC9A

source_name: dermal juvenile lymph-vascular endothelial cells from foreskin


title: LEC1

source_name: dermal juvenile lymph-vascular endothelial cells from lymphangioma


title: 2-AK


title: LEC2

value: dermal juvenile lymph-vascular endothelial cells


title: 3-SCC


title: UNSWCD_infected2

city: Sydney

first: Nandan

middle: P

last: Deshpande

state: NSW

address: Kensington Campus

department: School of Biotechnology and Biological Sciences

country: Australia

institute: Systems Biology Initiative

data_processing:
DynamicTrim.pl + LengthSort.pl
Mapped trimmed read to hg19 using tophat/2.0.4
Used htseq-count to get count values for individual samples
Genome_build: hg19
Supplementary_files_format_and_content: Combined counts file.

growth_protocol: Caco-2 cells were grown in Minimal Essential Media, supplemented with 10% v/v Fetal Bovine Serum, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 2.25 mg l-1 sodium bicarbonate and 100 μg ml-1 penicillin and streptomycin

extract_protocol:
RNA extraction was performed using the Isolate II RNA Extraction Mini Kit (Bioline)
Illumina TruSeq RNA Sample Prep Kit (version 3) according to manufacturer's instructions, with 2 µg of total RNA being used per sample.

treatment_protocol: Infection with C. concisus UNSWCD

tag: cell line

value: C. concisus UNSWCD infection


title: Lyko26


title: UNSWCD_infected3

tag: treatment


title: UNSWCD_infected1


title: YJ  mRNAseq

first: shaofang

last: Li

state: Beijing

address: No 50, ZhanghuaLu, HAIDIAN

department: Beijing Vegetable Research Center

institute: Beijing Academy of Agriculture and Forestry Science

data_processing:
For mRNAseq, the reads were mapped to the TAIR10 genome using TopHat, and in-house R scripts were employed to calculate the normalized reads of every nucleotide.
For mRNAseq, The Wiggle format files with normalized read densities for each nucleotide. The normalized reads were calculated as RPM(reads per million).
Genome_build: TAIR10

molecule: polyA RNA

source_name: polyA+ RNA from ten-day-old YJ seedlings

growth_protocol: Plants were grown with 16hr of light

extract_protocol:
The total RNA was extracted with trizol, and treated with Dnase I to clean up the genomic DNA contamination.
The mRNAseq libraries were build using True-seq mRNA sample preparation kit (Illumina).

tag: line

value: YJ

tag: age

value: 10 days


title: YJ Bsseq rep2

library_source: genomic

data_processing:
The raw reads that passed the Illumina quality control steps were retained, and duplicated reads were removed prior to mapping. For BSseq, the reads were mapped to the TAIR10 genome using BS Seeker, and in-house R and Perl scripts were employed to convert the BS Seeker-aligned reads to the methylation level of every cytosine.
For BSseq, the Wiggle files contain the methylation level for each nucleotide that are calculated as the methylated number of cytosine divided by total number of cytosine.
Genome_build: TAIR10

molecule: genomic DNA

source_name: bisulfite converted DNA from ten-day-old YJ seedlings

extract_protocol:
Genomic DNA was extracted using the DNeasy Plant Mini Kit.
To generate the whole-genome bisulfite sequencing (BS-seq) libraries, genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen). One microgram of genomic DNA was sonicated into fragments 100 to 300 bp in length using a Diagenode Bioruptor. The sonicated DNA fragments were purified using the PureLink PCR Purification Kit (Invitrogen). End repair was performed using the End-It™ DNA End-Repair Kit (Epicenter) followed by purification of the Agencourt AMPure XP-PCR Purification system. 3’-end adenylation was performed at 37°C for 30 min using dATP and Klenow Fragment (3’"5’ exo-) (New England Biolabs), followed by purification using the Agencourt AMPure XP-PCR Purification system. The purified DNA was ligated with methylated adapters from the TruSeq DNA Sample Preparation Kit (Illumina). The ligation products were purified with AMPure XP beads twice. Less than 400 ng ligated product was used for bisulfite conversion using the MethylCode Kit (Invitrogen) according to the manufacturer’s guidelines, except for the addition of 12 μg carrier RNA (Qiagen) to the conversion product before column purification. The final conversion product was amplified using Pfu Cx Turbo (Agilent) under the following PCR conditions: 2 min at 95°C; 9 cycles of 15 s at 98°C, 30 s at 60°C and 4 min at 72°C; and 10 min at 72°C. The PCR product was purified using AMPure XP beads prior to a 101-cycle sequencing run (single end) on an Illumina HiSeq 2000.


title: Lyko12-2

tag: cell type


title: YJ suvh1 Bsseq rep2

source_name: bisulfite converted DNA from ten-day-old YJ suvh1 seedlings

value: YJ suvh1

tag: tissue


title: Lyko5-2


title: BAA_untreated3

treatment_protocol: control

value: control


title: UNSWCD_Untreated2


title: UNSWCD_Untreated3


title: YJ Bsseq rep1

value: seedling


title: BAA_untreated1


title: BAA_infected3

treatment_protocol: Infection with C. concisus BAA

value: C. concisus BAA infection


title: BAA_untreated2


title: YJ suvh1 mRNAseq

source_name: polyA+ RNA from ten-day-old YJ suvh1 seedlings


title: 12-SCC

data_processing:
The mRNA-seq paired-end reads were aligned to the human reference genome, GRCh37/hg19, using the MOSAIK alignment software. The overlaps between aligned reads and annotated genomic features, such as genes/exons were counted using HTSeq software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes HTSeq counts

source_name: skin

value: cuSCC


title: BEC

source_name: dermal juvenile blood-vascular endothelial cells from foreskin


title: BAA_infected2


title: 12-AK

value: actinic keratosis (AK)


title: 10-SCC


title: BAA_infected1


title: 10-AK


title: 8-SCC


title: 8-NS

value: nonlesional,chronically UV-exposed skin (NS)


title: 8-AK


title: YJ suvh1 Bsseq rep1


title: 10-NS


title: 6-AK


title: 4-SCC2


title: 5-AK


title: 5-NS


title: UNSWCD_Untreated1


title: 5-SCC


title: 6-SCC


title: 6-NS


title: 4-AK


title: 4-SCC


title: 4-AK2


title: 4-NS


title: 2-SCC


title: 3-AK


title: 2-AK


title: PT supplemented group [before PT_3]

city: Daegu

first: Ri

last: Ryu

address: 80 Daehak-ro

department: Food Science and Nutrition

country: South Korea

institute: Kyungpook National 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 with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using TopHat 1.3.3, which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks 2.0.2 software in default options.
The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for "PT" sample.

source_name: before_PT_ PBMCs

growth_protocol: Fifty subjects with mild metabolic syndrome were enrolled in this study. Subjects excluded were pregnant women, type 1 diabetic, those treated with insulin and any drugs for the control of blood glucose, blood lipids and body weight and those using functional food products, since they may affect the results of the this study. This was performed in accordance with the Declaration of Helsinki, and all subjects provide written informed consent prior to participating in this study.

extract_protocol:
Total RNA was extracted from the peripheral blood mononuclear cells (PBMCs) using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.
Libraries were constructed from mRNA using the Illumina TruSeq RNA Sample Prep Kit following  manufacturer's protocols.

treatment_protocol: All subjects were randomly divided into two nutritional intervention groups: placebo (n=25) and PT (n=25). Subjects consumed either six capsules containing starch (3 g per day; placebo group), PT (2 g per day) in the morning, afternoon and evening daily for 12 weeks.

tag: subject status

value: mild metabolic syndrome

tag: subject id

tag: nutritional intervention group

value: pterocarpan-rich extract soybean leaf (PT)

tag: time point

value: before PT-supplemented

value: pheripheral mononuclear cells


title: PT supplemented group [before PT_8]


title: 3-SCC

value: skin


title: MDABrM_consh_rep1

city: Philadelphia

first: Qing

last: Chen

state: PA

address: 3601 Spruce Street, Room 442

institute: The Wistar Institute

description: TRAP RNA

data_processing:
Samples were barcoded
run on a Hiseq 2000 platform in a 50bp/50bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).
An average of 50 million paired reads were generated per sample.
The data were analyzed using the TopHat2-HTSeq-DESeq2 pipeline as previously described.
Genome_build: hg19
Supplementary_files_format_and_content: counts file in txt  format

growth_protocol: MDA231-BrM2 cells  were cultured in DMEM with 10% fetal bovine serum (FBS) and 2 mM L-Glutamine.

extract_protocol:
Cocultured MDA231-BrM2 TRAP cells and astrocytes were lysed. Anti-GFP antibody coated sepharose beads (GE Healthcare) were used for immunoprecipitation. Polysome-associated RNA was purified with RNAqeuous micro kit.
TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions

treatment_protocol: Astrocytes and cancer cells were cocultured at ratio of 1:1 for 24 h.

value: breast cancer cell line

tag: metastatic derivative

value: brain

tag: coculture


title: MDABrM_consh_Astro_rep1

description: TRAP RNA

value: with Astrocytes


title: MDABrM_consh_Astro_rep2

description: TRAP RNA


title: MDABrM_consh_rep2

description: TRAP RNA


title: MDABrM_Cx43sh2_Astro_rep2

description: TRAP RNA


title: MDABrM_Cx43sh1_Astro_rep2

description: TRAP RNA


title: MDABrM_Cx43sh2_Astro_rep1

description: TRAP RNA


title: MDABrM_Cx43sh1_Astro_rep1

description: TRAP RNA


title: 1-AK


title: 3-NS


title: PT supplemented group [before PT_4]


title: Drosophila heph2 mutant

city: Boulder

first: Ravinder

last: Singh

state: CO

address: UCB 347

department: MCD Biology

institute: Univ Colorado

data_processing:
TopHat 2.0.4 alignment using r5.44 flybase annotation
Cufflinks 2.0.0 cuffdiff for gene differential expression and quantification
DAVID v6.7 for gene ontology analysis
Genome_build: flybase r5.44
Supplementary_files_format_and_content: Cufflinks differential expression

organism: Drosophila melanogaster

source_name: Adult flies

extract_protocol:
trizol poly-A purified,
standard Illumina TruSeq

value: whole adult flie

value: male

tag: genotype/variation

value: heph2 mutant


title: Control

value: control


title: 94948

description: Sentinel lymph node from breast cancer patients with metastatic sentinel lymph node but without metastatic Non-sentinel lymph nodes

data_processing:
Sequenced reads were processed and aligned to the UCSC reference human genome using software Tophat by default setting
Aligned result were fed to software Cufflinks to assemble transcripts and estimate their abundances.
To calculate gene expression intensity, reads counts were normalized to the number of fragments per kilobase of transcript per million mapped reads (FPKM) according to the gene length and total mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: breast tumor

extract_protocol:
According to the indicating line drawn by pathologist on the reverse side of each slices, the metastatic tumor in SLN were scraped into a 1.5 ml RNase-free tube and then sent for RNA extraction with RNeasy FFPE kit (Qiagen, Germany) following manufacturer’s instructions.
Libraries of mRNA converted from total RNA were constructed using the Illumina ®TruSeq™ RNA Sample Preparation Kit (USA) according to the manufacturer’s instructions.

tag: tumor stage

value: NSLN negative


title: 86923

description: Sentinel lymph node from breast cancer patients with metastatic sentinel lymph node and metastatic Non-sentinel lymph nodes

value: NSLN positive


title: 76948


title: 67161


title: MAZ, ChIPseq, T778 cells

city: Freiburg

first: Henriette

last: Franz

address: Alberstr: 17

department: Anatomy and Cellbiology

institute: University Freiburg

data_processing:
peak finding algorithm MACS 2
All peaks with FDR greater than 2 % were excluded from further analysis
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are wiggle (wig) and bed files. The wig files include the read data mapped to the hg19 genome. The bed files contain the peaks that were obtained when normalizing the reads of the LSD1 ChIP-Seq to the Input.

source_name: T778 cells

growth_protocol: Human T778 liposarcoma cells were maintained in RPMI medium supplemented with 10 % FBS and glutamine.

extract_protocol:
Metzger, E., et al. Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation. Nat Cell Biol 10, 53-60 (2008).
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the hg19 reference genome using bowtie 2
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).

tag: differentiation stage

value: Liposarcoma cells

tag: genotype

value: Control

tag: passages

tag: chip antibody

value: MAZ


title: T778 cells RNAi Control, biological replicate 1

data_processing:
We aligned these reads to the hg19 build of the human genome using TopHat version 2
The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR and DESeq version 1.8.3.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file are text files that include the overall read count for a specific transcript (indicated by the NM accession number)

growth_protocol: Human T778 liposarcoma  cells were maintained in RPMI medium supplemented with 10 % FBS and glutamine.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).

treatment_protocol: Knockdown was performed using transfection with Fugene HD with pRTS_Puro_miSPIN1 or pRTS_Puro_milacZ according to the manufaturer's instructions. Cells were selected with 1µg/ml puromycin for 5 days. Then the miRNA was induced by addition of 0.5µg/ml doxycycline. The cells were harvested 2d after induction.

value: Liposarcoma Cells

value: RNAi Control


title: T778 cells RNAi Control, biological replicate 2


title: T778 cells RNAi LSD1, biological replicate 1

value: RNAi SPIN1


title: 84816


title: SPIN1, ChIPseq, T778 cells, biological replicate 1

data_processing:
peak finding algorithm MACS 1.41
All peaks with FDR greater than 2 % were excluded from further analysis
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are wiggle (wig) and bed files. The wig files include the read data mapped to the hg19 genome. The bed files contain the peaks that were obtained when normalizing the reads of the LSD1 ChIP-Seq to the Input.


title: T778 cells RNAi LSD1, biological replicate 2


title: Input, T778 cells, biological replicate 2


title: Input, T778 cells, biological replicate 1


title: Input, T778 cells


title: A549-P-2

data_processing:
Sequenced reads were mapped to hg19 whole genome using tophat version 2.0.3
Cufflinks version 2.0.2 was used to calculate the normalized gene expression level
Genome_build: hg19
Supplementary_files_format_and_content: one tab-delimited text file include RPKM values for four Samples

extract_protocol:
Total RNA was isolated using TRIZOL® Reagent.
Using the Illumina mRNA-Seq library preparation kit, the cDNA library was constructed according to the manufacturer’s instructions. Transcriptome sequencing was then conducted using Illumina Hiseq 2000 Genome Analyzer platform in pair-ended manner with the read length of 100-bp.

tag: strain

value: lung

value: non-small cell lung cancer

tag: abraxane sensitivity

value: sensitive


title: A549-P-1


title: A549-P-100


title: A549/Abr-100

value: resistant


title: H3K4me3, ChIPseq, T778 cells, biological replicate 1

value: H3K4me3 ( Abcam, ab8580)


title: A549/Abr


title: 2-NS

value: nonlesional,chronically UV-exposed skin (NS)

value: skin


title: T778 cells RNAi Control, biological replicate 3


title: Sample 7_mRNA_old

city: Elk Grove

first: joseph

middle: M

last: dhahbi

state: ca

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

data_processing:
Paired-end sequencing reads aligned to Drosophila reference genome dm6 (NCBI genome/47) with Tophat v2 using the default parameters.
Cufflinks package used to assemble transcripts and measure relative abundance in FPKM.
Differential expression was examined using the Cuffcompare and Cuffdiff in the Cufflinks package.
Genome_build: Drosophila dm6 (NCBI genome/47)
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample. This is a differential expression file generated by cuffdiff comparing mRNA levels in body tisuues between young and old flies.

source_name: Old

growth_protocol: Young (2 days old) and old (25 days old) males flies were anesthetized and used to collect samples of hemolymph and body tissues.

extract_protocol:
Total RNA, including small RNA, was extracted from body tissues using miRNeasy kit (Qiagen).
RNA libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420S).  Illumina HiSeq2000 was used to sequence the libraries (50bp, paired-end)

tag: tissue type

value: Body tissue

tag: age

value: 25 days

tag: Sex

value: male


title: Sample 9_mRNA_old


title: Sample 8_mRNA_old


title: Sample 12_mRNA_old


title: Sample 10_mRNA_old


title: Sample 6_mRNA_old


title: Sample 11_mRNA_old


title: Sample 4_mRNA_young

source_name: young

value: 2 days


title: Sample 1_mRNA_young


title: Sample 2_mRNA_young


title: nab-GAL4, UAS-prosperoRNAi, UAS-dicer2 BP

city: Marseille

first: Cedric

last: Maurange

address: Parc Scientifique de Luminy, case 907

country: France

institute: CNRS / Aix-Marseille University

description: BP

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software and Real-Time Analysis component from Illumina
Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer).
A splice junction mapper, TopHat2 (2.0.9 with bowtie 2.1.0), was used to align RNA-seq reads to Drosophila melanogaster genome (dm3) with a set of gene model annotations (downloaded from UCSC on March 6, 2013). Final read alignments having more than 3 mismatches were discarded.
Counting was performed with HTSeq-count 0.5.3p9 (union mode). The data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene.
Differentially expressed genes were identified using the Bioconductor package DESeq (v1.2.5). Genes with less than 15 reads (cumulating all the analysed samples) were filtered and thus removed from the analysis. Data were normalized using the DESeq normalization method. Genes with adjusted p-value less than 5% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.
Genome_build: dm3 (UCSC)
Supplementary_files_format_and_content: Tab-separated text files. First column is the gene identifier (Gene symbol|Entrez gene ID), the following columns are normalized abundance measurements for each sample.

source_name: late L3 ventral nerve cord (VNC)

growth_protocol: Crosses were grown 7 days at 18°C and then switched at 29°C. Wandering L3 VNCs were dissected 3 days after the 29°C switch

extract_protocol:
Wandering L3 VNCs were dissected in cold PBS 3 days after the 29°C switch, during 30-minute dissection rounds. Dissected VNCs were put in 500μL cold Lysis Buffer (RA1 from the Total RNA Isolation kit, Macherey Nagel) supplemented with 50 μL glass beads (diameter 0.75-1mm, Roth, A554.1) and frozen in liquid nitrogen at the end of the dissection round. Sample tubes were then stored at -80°C up to RNA extraction. Triplicates were made for each condition with brain numbers as follows (1) n=79, n=57, n=65; (2) n= 70, n=58, n=78; (3) n=51, n=60, n=82. For the RNA extraction, dissected brains stored in liquid nitrogen were thawed on ice. 10 μL TCEP were added to each tube following by 40s vortex. RNA extraction was then performed following the Total RNA Isolation NucleoSpin RNA XS protocol (Macherey Nagel). RNA quality and quantity was checked by running samples on an Experion RNA HighSens Chip (Biorad, 700-7105) and send to the Montpellier Genomix platforme for RNA sequencing.
RNA-Seq libraries were prepared with the 'TruSeq Stranded RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.
Stranded RNA-seq

tag: tissue

value: VNC containing tumorigenic neuroblasts

tag: developmental stage

value: Late L3

tag: treatment

value: nab-GAL4, UAS-prosperoRNAi, UAS-dicer2


title: nab-GAL4, UAS-prosperoRNAi, UAS-dicer2, UAS-chinmoRNAi CPC

description: CPC

value: VNC containing tumorigenic neuroblasts with decreased Chinmo


title: nab-GAL4, UAS-prosperoRNAi, UAS-dicer2, UAS-chinmoRNAi APC

description: APC


title: nab-GAL4, UAS-prosperoRNAi, UAS-dicer2, UAS-chinmoRNAi BPC

description: BPC


title: nab-GAL4, UAS-prosperoRNAi, UAS-dicer2 AP

description: AP


title: nab-GAL4, UAS-prosperoRNAi, UAS-dicer2, UAS-chinmoFL CPCC

description: CPCC

value: VNC containing tumorigenic neuroblasts over-expressing Chinmo


title: juvenile skin melanocytes, patient's code C032

city: Tartu

first: Paula

last: Reemann

address: Ravila 19

department: Institute of Biomedicine and Translational Medicine, Department of Physiology

country: Estonia

institute: University of Tartu

description: barcode info: #BC016   c032Mc

data_processing:
Lifescope software
F3 forward reads were trimmed to 45 bp and F5 reverse reads were trimmed to 25 bp
All color-spaced reads were aligned to human reference genome (Ensembl, release 73) using TopHat v2.1.0 [Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, et al. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36.] that used Bowtie version 1.0.0 [Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.].
RPKM (reads per kilobase of transcript per million mapped reads) values for gene expression levels were calculated with Cufflinks v2.0.2 [Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 12:R22.] and raw counts were retrieved with HTSeq version 0.5.3p9 (http://www-huber.embl.de/users/anders/HTSeq/) using gene annotations of protein coding genes downloaded from Ensembl (release 73).
Differential expression was estimated on raw counts with edgeR [Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140.].
Genome_build: Homo_sapiens GRCh37, ensembl release 73
Supplementary_files_format_and_content: Tab-delimited text files contains the ensembl gene counts calculated with HTSeq
Supplementary_files_format_and_content: Output files from Cufflinks are given in tab delimited and general transfer format (GTF)

source_name: juvenile skin melanocytes

extract_protocol: ribodepleted whole transcriptome

value: Melanocytes

tag: patient

value: cell culture


title: juvenile skin keratinocytes, patient's code C030

description: barcode info: #BC014   c030Kc

source_name: juvenile skin keratinocytes

value: Keratinocytes


title: juvenile skin keratinocytes, patient's code C025

description: barcode info: #BC013   c025Kc


title: juvenile skin fibroblasts, patient's code C025

description: barcode info: #BC016   c025Fb

source_name: juvenile skin fibroblasts

value: Fibroblasts


title: nab-GAL4, UAS-prosperoRNAi, UAS-dicer2, UAS-chinmoFL BPCC

description: BPCC


title: juvenile skin keratinocytes, patient's code C024

description: barcode info: #BC013   c024Kc


title: juvenile skin biopsy, patient's code C014

description: barcode info: #BC015   c014 whole skin

source_name: juvenile skin biopsy

value: Whole skin

value: biopsy material


title: nab-GAL4, UAS-prosperoRNAi, UAS-dicer2, UAS-chinmoFL APCC

description: APCC


title: Ads_Flox5_lung3m

city: Logroño

first: Jose

middle: Garcia

last: pichel

state: La Rioja

address: Piqueras 98

department: Oncology

institute: FUNDACIÓN RIOJA SALUD - CIBIR

data_processing:
Illumina base-calling was performed off-line with OLB v1.9.4
Sequenced reads were trimmed for adaptor sequence with Cutadapt and then mapped to mus musculus.GRCm38_71 whole genome using tophat v2.0.6.
Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) were calculated using SeqSolve (Integromics). This analysis uses Cufflinks in order to quantify gene expression.
Genome_build: mus musculus.GRCm38_71 (Ensembl)
Supplementary_files_format_and_content: FPKM_tracking format including FPKM values for each Sample

source_name: Lung

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

value: C57BL/6 (enriched)

value: lung

value: Igf1rfl/fl (normal/control)


title: Sample 5_mRNA_old

value: Body tissue

value: 25 days


title: juvenile skin melanocytes, patient's code C022

description: barcode info: #BC012   c022Mc


title: Ads_Flox3_lung3m


title: juvenile skin melanocytes, patient's code C026

description: barcode info: #BC011   c026Mc


title: 7B1 mutant - rep 2

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

institute: University of Oxford

description:
S. Lycopersicum cv. Rutgers
Processed data file: SLycopersicum_GeneExpressionLevels_allGenes.xlsx
Processed data file: SLycopersicum_GeneExpressionLevels_DEG.xlsx

data_processing:
All reads containing unassigned nucleotides were discarded.
The matching to the genome (v2.5, Sly) was done full length, with 2 mismatches allowed.
The gene expression was calculated as indicated in Mortazavi et al. 2008.
The differential expression analysis was conducted using NoiSeq.
Genome_build: SL2.50
Supplementary_files_format_and_content: SLycopersicum_GeneExpressionLevels_allGenes.xlsx: Excel file includes raw counts and normalized expression values (RPKMs) of all genes.
Supplementary_files_format_and_content: SLycopersicum_GeneExpressionLevels_DEG.xls: Excel file includes normalized expression values (FPKMs) of the differentially expressed genes. The "log2" column indicates the log2 of the ratio between the normalized expression levels for wild type and mutant; the "Pr" is the corrected p-value under the NoiSeq model.

organism: Solanum lycopersicum

source_name: anther, 7B1 mutant

growth_protocol: The 7B-1 mutant and wild type (cv. Rutgers) tomatoes were grown in a growth chamber set for long day condition (16/8 h light/dark). Flower buds of different sizes, smaller, equal and larger than 4-5 mm were collected from WT and 7B-1 flowers and the stamens were dissected under a microscope.

extract_protocol:
Total RNA was extracted using RNeasy plant miniRNA extraction kit (Qiagen) from 7B-1 and WT anthers of different sizes and pooled separately in equimolar ratio.
Two mRNA libraries were constructed using the TruSeq mRNA Sample Preparation Kit from Illumina (Illumina, San Diego, CA, USA).

tag: cultivar

value: Rutgers

value: 7B1 mutant

value: anther


title: Ads_Flox3_lung4m


title: Sample 3_mRNA_young

value: 2 days

value: male


title: Ads_Flox2_lung3m


title: juvenile skin fibroblasts, patient's code C026

description: barcode info: #BC009   c026Fb


title: nab-GAL4, UAS-prosperoRNAi, UAS-dicer2 CP

description: CP

value: VNC containing tumorigenic neuroblasts

value: Late L3

value: nab-GAL4, UAS-prosperoRNAi, UAS-dicer2


title: juvenile skin melanocytes, patient's code C002

description: barcode info: #BC010   c002Mc

value: Melanocytes

value: cell culture


title: Ads_Flox1_lung3m


title: WT - rep1

source_name: anther, wild type

value: wild type


title: 7B1 mutant - rep 1


title: juvenile skin biopsy, patient's code C011

description: barcode info: #BC014   c011 whole skin

value: Whole skin

value: biopsy material


title: juvenile skin keratinocytes, patient's code C032

description: barcode info: #BC015   c032Kc

value: Keratinocytes


title: RAG1-/-Sgo1-/+ (L4)

city: Oklahoma City

first: Hiroshi

middle: Y

last: Yamada

state: Oklahoma

department: Medicine

institute: OUHSC

data_processing:
Genesifter software was used for base-calling and alignment.
BWA Paired-End (GATKv3) pipeline was used to align with Mus musculus (build 37.2) genome. Pairwise and Cluster analyses were done using Genesifter software and differential gene lists were exported as tab delimited files.
Pairwise settings were as follows: normalize to mapped reads, statistical analysis using EdgeR differential genes narrowed to 2 fold min for final analysis, data correct using Benjamini Hochberg method.
Pairwise analysis was done using RPKMs and determination of fold significance using EdgeR with a significance value (p value) cutoff of 0.05. Then fold cutoff was set to 2.0-fold for identifying differentially expressed genes and for subsequent pathway analysis.
Genome_build: Mus musculus build 37.2 (MGSCv37)
Supplementary_files_format_and_content: [.txt] RPKMs and differentially expressed genes

source_name: RAG1-/-Sgo1-/+, lung

growth_protocol: all mice were maintained to 12 months of age

extract_protocol:
Total RNA was extracted from normal-looking lung tissues using Trizol reagent.
Libraries were prepared according to Illumina's instructions accompanying the RNA TruSeq V2 Library construction kit.   Libraries were sequenced on the Illumina MiSeq following the manufacturer's protocols.

treatment_protocol: No experimental treatment was applied

value: normal-looking lung


title: RAG1-/-Sgo1-/+ (L5)


title: RAG1-/-Sgo1-/+ (L6)


title: WT - rep2


title: RAG1-/- (L1)

source_name: RAG1-/-, lung


title: HeLa WT 72hr

first: Stephen

last: Taylor

institute: CBRG

data_processing:
x100 bp reads were produced with the Illumina Hi-seq sequencer.
After quality and adaptor trimming, an average of ~115 million reads were generated for each sample of which there was a single replicate.
Reads were trimmed using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned with TopHat version 1.1.4.
Reads were aligned to the GRCh37/hg19 human reference genome build and quantified by Cufflinks as RPKM (reads per kilobase million).

source_name: Untreated WT HeLa cells cultured for 72h

growth_protocol: HeLa cells were cultured at the concentration of 100,000 cells per ml in 1.5ml complete Minimum Essential Medium per well of a 12-well plate for 48h or 72h.

extract_protocol:
RNA was extracted from frozen cell pellets using the Ambion miRvana RNA isolation kit.
Sequencing library was made by following standard protocol: http://www.illumina.com/documents/products/technotes/technote-truseq-rna-access.pdf. Superscript III reverse transcriptase (Life Technologies) and Illumina’s TruSeq Stranded Total RNA Sample Prep Kit (Illumina) were used for making the cDNA library.

tag: cell type

value: Human cervical cancer cells (HeLa)


title: RAG1-/- (L2)

tag: genotype/variation


title: Rathuwee_mRNA_seedling_1

city: Guangzhou

first: Munan

last: Xie

address: No.135 Xin Gangxi Road, Haizhu District,

institute: Sun Yat-sen University

description: mRNAs

data_processing:
For all small rna libraries, after (1) trim three prime adaptor and (2) filter out low quality or adaptor contaminated reads, we retain only short trimmed reads of sizes from 19 to 30 nt.
The retained reads were search against the Rfam database using the SOAP software, the reads mapped to structural RNAs [rRNA, tRNA, small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA)] with more than 2 mismatches were removed, reads corresponding to repeats/transposons were also discarded by performing searches against the repeat database (http://www.girinst.org/server/RepBase/).
The remaining reads that corresponded to the precursor of all known rice miRNAs from miRBase ( Release 14, http://www.mirbase.org/index.shtml) were used to estimate the expression level of each rice miRNA
Reads counts were calculated by the the read number of each gene or region by total mapped read number in each library.
For transcriptome libraries, all the reads were mapped to the reference genome of rice (Oryza sativa L. ssp. japonica cv. Nipponbare) using Bowtie software package. Reads which could be mapped equally well to multiple locations without mismatch or with up to 2 mismatches were assigned to one position at random and were retained for further analyses as described previously[29]. The reads count for each gene or genomic region ,which according to the tige6.0 gff3 file, were recovered
Genome_build: Oryza sativa
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each miRNAs or mRNAs

extract_protocol:
Total RNAs were extracted by using TRIzol Reagent (Invitrogen). For grains, the husks of the seeds were removed before RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 1 week

value: seedling

tag: subspecies

value: Rathuwee


title: RAG1-/- (L3)


title: HeLa WT + GFP 72hr

source_name: GFP-transduced HeLa cells cultured for 72h


title: Guangluai4_mRNA_seedling_1

description: mRNAs


title: KDM105_mRNA_seedling_1

description: mRNAs


title: HeLa WT + IDO 72hr

source_name: IDO1-transduced HeLa cells cultured for 72h


title: HeLa WT + IDO 48hr

source_name: IDO1-transduced HeLa cells cultured for 48h


title: HeLa WT + IFN 48hr

source_name: WT HeLa cells treated with 1000 U/ml IFN gamma and cultured for 48h


title: Wild_type2

city: College Park

middle: Adrian

last: Carrillo

state: MD

address: 1413 Animal Sciences Center

department: Department of Animal and Avian Sciences

institute: University of Maryland

data_processing:
Sequencing analyses in the Solexa 1G Genome Analyzer (Illumina)
Alignment with Bowtie
The peak-calling step was applied individually for each sample using Model Based Analysis of ChIP-Seq (MACS)
Identification of the Differentially Methylated Regions (DMRs) was accomplished implementing the DiffBind R package.It computes differentially bound sites using affinity data. The set of peaks identified by MACS and the bam files containing aligned reads for each sample, was the input for DiffBind. The program creates a matrix with the consensus peaks; for this case it was obtained with a “minimum overlap” of 3, determined by the number of replications in the experiment.  After creating a contrast between conditions (transgenic vs wild), DiffBind runs an edgeR analysis, which is an empirical Bayes method. For normalization, the default method TMM (Trimmed Mean of M-values) that subtracts the controls reads and considers the effective library size (reads in peaks), was applied.  The threshold utilized was 0.1, for False Discovery Rate (FDR).
For the genomic annotation of the DMRs, the software ChIPpeakAnno was used. ChIPpeakAnno provides information about the overlaps, relative position and distances for the inquired feature.
Genome_build: mm10
Supplementary_files_format_and_content: peak calling from MACS: bed
Supplementary_files_format_and_content: DiffBind R Package: Suppl_Table2_DMRs.txt
Supplementary_files_format_and_content: ChIPpeakAnno: Anno_TSS.txt

growth_protocol: Grossly, we found no apparent developmental defects in the transgenic animals. The animals lived normally and were able to breed. To determine the impact of ΔDNMT3B4-del in lungs of the animals, we examined the lungs from 43 Tg(SPC-DNMTΔ3B/DG) mice with age ranging from 12 to 16 months and 20 age matched wild-type mice.

extract_protocol:
Genomic DNA from three samples of each group was extracted using the Wizard Genomic DNA purification kit (Promega, A1120)
MethylCap kit (Diagenode, C02020010) was employed for the acquisition of methylated DNA

treatment_protocol: Microinjection of the transgene into pro-nuclei of fertilized eggs gave rise to total 30 live pups, 6 of them carried SPC/Δ3B4DG transgene with 4 of them achieved germ-line transmission. These founder lines were named as: Tg(SPC-DNMTΔ3B/DG)1lm, Tg(SPC-DNMTΔ3B/DG)3lm, Tg(SPC-DNMTΔ3B/DG)25lm and Tg(SPC-DNMTΔ3B/DG)27lm according to MGI-Guidelines for Nomenclature of Gene, Genetic Markers, Alleles, and Mutations in Mouse and Rat: http://www.informatics.jax.org/mgihome/nomen/gene.shtml.

value: Wild type

value: 12-16 months

value: lung


title: Wild_type3


title: HeLa WT 48hr

source_name: Untreated WT HeLa cells cultured for 48h


title: Wild_type1


title: HeLa WT + GFP 48hr

source_name: GFP-transduced HeLa cells cultured for 48h


title: Transgenic3


title: Transgenic2

value: SPC-DNMTdeltaB/DG


title: Transgenic1


title: bursa_D5_S_rep4

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

extract_protocol:
RNA samples were isolated using the Ambion MagMax-96 Kit (AM1839) (Applied Biosystems, Foster City, CA) and immediately stored at -80 . 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.

value: Commercial broiler

value: bursa

value: four weeks

tag: gender

value: male

tag: days post infection

tag: pathogen

value: Avian Pathogenic Escherichia coli O1

tag: phenotype

value: susceptible


title: HeLa WT + IFN 72hr

source_name: WT HeLa cells treated with 1000 U/ml IFN gamma and cultured for 72h


title: bursa_D1_S_rep2

tag: strain


title: bursa_D5_S_rep1


title: bursa_D5_R_rep4

value: resistant


title: bursa_D1_S_rep4


title: bursa_D1_S_rep1


title: bursa_D5_R_rep2


title: bursa_D5_S_rep3


title: bursa_D1_R_rep3


title: bursa_D5_R_rep1


title: bursa_D1_R_rep4


title: bursa_D1_S_rep3


title: bursa_D1_R_rep2


title: bursa_D5_NC_rep2

value: none (mock-challenged)


title: bursa_D5_NC_rep3


title: bursa_D5_S_rep2


title: bursa_D1_R_rep1


title: bursa_D5_R_rep3


title: bursa_D1_NC rep2

source_name: bursa_D1_NC rep2


title: thymus_5_dpi_susceptible_APEC_rep4

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.

value: thymus

tag: days post-infection


title: bursa_D1_NC rep3

source_name: bursa_D1_NC rep3


title: thymus_5_dpi_susceptible_APEC_rep3


title: thymus_1_dpi_susceptible_APEC_rep4


title: thymus_5_dpi_susceptible_APEC_rep2


title: bursa_D5_NC_rep1


title: thymus_1_dpi_susceptible_APEC_rep3


title: thymus_5_dpi_susceptible_APEC_rep1


title: thymus_1_dpi_susceptible_APEC_rep1


title: thymus_5_dpi_resistant_APEC_rep3


title: thymus_5_dpi_resistant_APEC_rep4


title: thymus_1_dpi_resistant_APEC_rep4


title: thymus_1_dpi_resistant_APEC_rep2


title: thymus_1_dpi_resistant_APEC_rep1


title: thymus_1_dpi_resistant_APEC_rep3


title: thymus_5_dpi_negative_control_rep4


title: thymus_5_dpi_resistant_APEC_rep1


title: thymus_5_dpi_negative_control_rep1


title: thymus_1_dpi_negative_control_rep4

description: D1_NC rep4


title: Taipei309_mRNA_seedling_1

description: mRNAs


title: thymus_1_dpi_negative_control_rep2

description: D1_NC rep2


title: thymus_1_dpi_negative_control_rep3

description: D1_NC rep3


title: bursa_D1_NC rep1

source_name: bursa_D1_NC rep1


title: thymus_5_dpi_negative_control_rep2


title: thymus_1_dpi_negative_control_rep1

description: D1_NC rep1


title: thymus_1_dpi_susceptible_APEC_rep2


title: Heukgyeong_mRNA_seedling_1

description: mRNAs

value: Heukgyeong


title: D5_S_rep4

source_name: bone marrow_susceptible_5dpi

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.

value: bone marrow


title: D5_S_rep3


title: L30-3 (egg-laying)

city: Zheng

first: HONG

last: LI

address: 95 Wenhua Road, Jinshui District

institute: Henan Agriculture University

data_processing:
The adaptor sequences and low-quality reads including those unknown bases N, sequences smaller than 18nt and bases quality less than 10 were eliminated by using Fastx (fastx_toolkit-0.0.13.2).
The clean reads from each sample was aligned to the latest Sanger miRBase database 20.0 (http://www.mirbase.org/)
The miRCat tool in sRNA Toolkit software package was used to predict novel miRNA.
Genome_build: Gallus gallus4.0
Supplementary_files_format_and_content: Text files include miRNAs TPM values for each Sample

source_name: Liver

extract_protocol:
All the chickens were raised in cages under the same environment with ad libitum water and food. Healthy individuals were randomly sampled and then slaughtered at juvenile of 20 weeks (20w group) and egg-laying stages of 30 weeks (30w group). The liver tissue was immediately collected, snap-frozen in liquid nitrogen, and stored under -80°C. The small RNA used for sequencing was extracted with mirVana™ miRNA Isolation Kit (Austin TX, US) according to the manufacturer’s instruction. The quality and quantity of the total RNA were assessed by the Agilent 2100
Briefly, 3’ and 5’ RNA adapters were ligated to the total RNA with T4 RNA ligase, successively. Subsequently, the ligated RNAs were subjected to reverse-transcriped PCR to synthesis cDNA, and then the cDNA was amplified by PCR. The amplification products with appropriate length were purified from agarose gel to construct sequence libraries, and then were sequenced with a single-read 1×36 nt multiplex procedure on an Illumina HiSeq 2500 following the manufacturer’s instruction (Illumina).

tag: breed

value: Lushi

value: 30 weeks

value: female

value: liver


title: D5_S_rep1

city: Beijing

tag: age


title: L30-1 (egg-laying)

tag: Sex


title: L30-2 (egg-laying)

tag: tissue


title: D5_S_rep2


title: D1_S_rep4

source_name: bone marrow_susceptible_1dpi


title: thymus_5_dpi_resistant_APEC_rep2


title: L20-3 (juvenile)

value: 20 weeks


title: D1_S_rep3


title: thymus_5_dpi_negative_control_rep3


title: L20-1 (juvenile)


title: input DNA

city: Sai Kung

first: Yukinori

last: Hirano

address: Clear water bay

department: LIFS

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
Basecalls and alignment on dm 3 were performed using Lifescope with default configurations
The read with lower mapping quality than 8 was eliminated.
The peaks were called by comparing ChIP DNA with input DNA, using PICS on Strand NGS with a default setting except for the following parameters; for PICS, 120 bp as an average fragment length, 10 bp as a minimum distance between forward and reverse reads, 200 bp as a minimum distance between forward and reverse reads, 100 bp as a window width, with 5% false discovery rate.
The peaks were called by comparing ChIP DNA with input DNA, using ERD on Strand NGS, 2 as an enrichment factor, 100 bp as a window size, 10 bp as a window slide size, 100 bp as a minimum region size.
Overlapping peaks called by PICS and ERD were determined as peaks.
When trained flies and naïve flies were compared, the read counts in the individual peaks were statistically analyzed as follows. First, the centers of the H3K9Ac and H4K16Ac peaks were first extracted and then used to create neighboring 400 bp windows. The mapped reads were counted in these 400 bp windows for each biological replicate of ChIP-seq analysis. The counted read numbers in individual regions were normalized by elav for H3K9Ac ChIP-seq, and gapdh2 for H4K16Ac ChIP. The normalized read numbers in individual windows obtained from the spaced trained flies and the naïve flies were analyzed by Student’s t test (p < 0.05). Standard deviations of the normalized read numbers in individual windows from 3 replicates of naïve flies were 0.07 in H3K9Ac-ChIP-seq and 0.10 in H4K16Ac-ChIP-seq. Significantly increased peaks showing a more than 1.2-fold increase (>2SD) were determined as sites with an increase in H3K9Ac or H4K16Ac.
Genome_build: dm3 (BDGP R5)
Supplementary_files_format_and_content: txt files were generated using Strand NGS; FDR determined by PICS and fold increase determined by ERD were shown. Increase in histone acetylation was determined using three replicates of each naïve and trained flies, and the mean, SD and p value by student t test were shown.
Supplementary_files_format_and_content: all peak H3K9Ac.txt [txt showing all H3K9 peaks from 3 replicates of spaced trained samples (determined by overlaps between PICS and ERD)]
Supplementary_files_format_and_content: all peak H4K16Ac.txt [txt showing all H4K16 peaks from 3 replicates of spaced trained samples (determined by overlaps between PICS and ERD)]
Supplementary_files_format_and_content: H3K9Ac increased sites.txt [txt showing statistically increased sites in H3K9Ac based on three replicates]
Supplementary_files_format_and_content: H4K16Ac increased sites.txt [txt showing statistically increased sites in H4K16Ac based on three replicates]
Supplementary_files_format_and_content: CREB sites.txt [txt showing CREB binding sites (determined by overlaps between PICS and ERD)]
Supplementary_files_format_and_content: CRTC sites.txt [txt showing CRTC binding sites (determined by overlaps between PICS and ERD)]

source_name: mushroom body

growth_protocol: Flies were raised under a 12 h:12 h, light:dark cycle, at 23℃ and 60% humidity.

extract_protocol:
Heads were collected and homogenized in crosslinking buffer. The nuclei were dissolved in extraction buffer, sonicated to dissociate the individual nuclei, and precipitated with ANTI-FLAG M2 Affinity Gel. The precipitates were rinsed 4 times in extraction buffer, with 5 min nutation at 4℃ between washes, and subjected to ChIP analysis. The purified mushroom body nuclei were sonicated, resulting in fragmentation of DNA ranging from 100 bp to 500 bp. The extracts were centrifuged to remove insoluble materials including the M2 Affinity Gel, and the supernatants were used for immunoprecipitation with specific antibodies.
The ChIP DNA samples prepared were used to prepare a library for SOLiD5500, according to the manufacturer’s instructions.

treatment_protocol: Flies were subjected to spaced trained in which an odor is paired with electrical shocks.

tag: chip antibody

value: naïve


title: Nipponbare_mRNA_seedling_1

description: mRNAs

value: 1 week

value: seedling

value: Nipponbare


title: CRTC_ChIPSeq

description: CRTC sites.txt

value: anti-CRTC (lab made antibodies)

tag: treatment

value: spaced trained 1d


title: D1_S_rep1

value: Commercial broiler

value: four weeks

value: male

value: susceptible


title: D5_R_rep2

source_name: bone marrow_resistant_5dpi

value: resistant


title: D5_R_rep4

value: bone marrow


title: D5_R_rep3


title: CREB_ChIPSeq

description: CREB sites.txt

value: anti-CREB (lab made antibodies)


title: 94812

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

data_processing:
Sequenced reads were processed and aligned to the UCSC reference human genome using software Tophat by default setting
Aligned result were fed to software Cufflinks to assemble transcripts and estimate their abundances.
To calculate gene expression intensity, reads counts were normalized to the number of fragments per kilobase of transcript per million mapped reads (FPKM) according to the gene length and total mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: breast tumor

extract_protocol:
According to the indicating line drawn by pathologist on the reverse side of each slices, the metastatic tumor in SLN were scraped into a 1.5 ml RNase-free tube and then sent for RNA extraction with RNeasy FFPE kit (Qiagen, Germany) following manufacturer’s instructions.
Libraries of mRNA converted from total RNA were constructed using the Illumina ®TruSeq™ RNA Sample Preparation Kit (USA) according to the manufacturer’s instructions.

tag: tumor stage

value: NSLN positive


title: D1_R_rep4

source_name: bone marrow_resistant_1dpi


title: D5_R_rep1


title: D1_R_rep3


title: D1_R_rep2


title: D1_R_rep1


title: D5_NC_rep2

description: mock-challenged

source_name: bone marrow_negative_control_5dpi


title: L20-2 (juvenile)

value: Lushi

value: female


title: D1_NC rep3

description: mock-challenged

source_name: bone marrow_negative_control_1dpi


title: RatID_10_TH_TRM_mRNA

city: Kuopio

first: Anssi

last: Lipponen

address: Neulaniementie 2

department: A. I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Base calling were performed with OLBv1.8 software.
Reads were aligned to the rat genome (Rnor_5.0) using Spliced Transcripts Alignment to a Reference (STAR) (version 2.3.0e_r291).
Differentially expressing genes were identified with DEseq2 R-package (R version 3.1.0).
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: Tab-delimited raw count matrices

organism: Rattus norvegicus

source_name: Ipslateral thalamus, TBI

growth_protocol: Adult male Sprague-Dawley (Harlan, Netherlands) weight 330-371g at a time of traumatic brain injury were housed in a controlled enviroment (21-23 °C, 12h dark/light cycle, 50-60% relative humidity) with drinking and feeding ad libitum.

extract_protocol:
Tissue was collected at 3 months after TBI. For tissue collection rats were anesthetized with isoflurane and decapitated. The brain was removed from skull, flushed with 0.9% cold sodium chloride, and two 2-mm-thick coronal slices (between -2.2 to -6.2 from the bregma) were cut with a slicing matrix. Perilesional cortex, thalamus, and dentate gyrus (including CA3c-b) were dissected under the magnifying glass on top of the light table.  Samples were stored at -80oC until RNA extraction.
Total RNA extraction were done by using the DNaesy Blood & Tissue kit (Qiagen #69504), followed by DNase digestion. RNA quality was verified on the Shimadzu MultiNA capillary electrophoresis system (Shimadzu). Poly-A mRNA was isolated with Dynabead Oligo(dT) enrichment (Invitrogen). Sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina® (New England Biolabs). Libraries were quantified on MultiNA system and sequenced at a concentration of 13 pM on the Genome Analyzer IIx (Illumina Inc, CA, USA) using the TruSeq version 5 cluster kit (cBot) and SBS kit (36 cycles).

treatment_protocol: The induction of TBI was done according the lateral fluid precussion (LFP) described by McIntosh et al. (1989) and Kharatishvili  et al. (2006). Animals were anesthezied with an intraperitoneal (i.p.) injection of a solution (6 ml/kg) containing sodium pentobarbital (58 mg/kg), chloral hydrate (60 mg/kg), magnesium sulphate (127.2 mg/kg), propylene glycol (42.8%) and absolute ethanol (11.6%) and placed in a Kopf stereotactic frame (David Kopf Instruments, Tujunga, CA, USA). The skull was exposed with a midline skin incision followed by extraction of the periosteum. The left temporal muscle was detached from the lateral ridge and then a circular craniectomy (diameter 5mm) was performed over the left parietal lobe midway between lambda and bregma keeping the dura mater intact. The edges of craniectomy were sealed with a modified LuerLock cap that was filled with saline while the calvaria was covered with dental acrylate (Selectaplus CN, Dentsply DeTrey GmbH, Dreieich, Germany). Lateral FPI was induced 90 min after the administration of anaesthesia by connecting the rat to a fluid-precussion device (AmScien Instruments, Richmond, VA, USA) via a female Luer-Lock fitting. In this study the main of the impact was 3.32 +/- 0.01 atm. Control animals received anaesthesia and all surgical procedures but without lateral FPI.

value: Sprague-Dawley

value: Male

value: ipslateral thalamus

value: TBI


title: D1_NC rep4

description: mock-challenged


title: RatID_9_TH_TRM_mRNA


title: RatID_8_TH_TRM_mRNA


title: D5_NC_rep1

description: mock-challenged


title: D1_NC rep2

description: mock-challenged


title: RatID_7_TH_TRM_mRNA


title: RatID_5_TH_SHM_mRNA

source_name: Ipslateral thalamus, sham operated

value: sham operated


title: RatID_6_TH_TRM_mRNA


title: D1_NC rep1

description: mock-challenged


title: RatID_2_TH_SHM_mRNA


title: RatID_3_TH_SHM_mRNA


title: RatID_1_TH_SHM_mRNA


title: D5_NC_rep4

description: mock-challenged


title: Control-3_RNA-Seq

city: Atlanta

first: Guangping

last: Chen

state: GA

address: 1639 Pierce Drive

department: Renal Division

institute: Emory University

description:
Ot3048
rat STZ-induced diabetic animal model

data_processing:
RNA-seq reads were aligned to the rn4 genome assembly using STAR version 2.3.1t.
Uniquely mapped reads were used to calculate the numbers of reads per gene.
Differential gene expression analysis is performed using R/Bioconductor package DESeq version 1.16.0.
Genome_build: rn4
Supplementary_files_format_and_content: A tab-delimited text file include raw counts for all Samples

source_name: Control-3, kidney inner medulla

extract_protocol:
[Tissue collection] The terminal half of the IM (IM tip) was dissected from kidney and used for RNA preparation.
[RNA preparation] The total RNA from rat IM tip was extracted using Trizol Reagent (Invitrogen). The RNA samples were purified using an RNeasy Mini Kit (Qiagen). Quantification and purity assessment of the RNA samples were determined on a NanoDrop Spectrophotometer (Nano-Drop Technologies).  RNA quality was assessed with an Agilent Bioanalyzer 2100.
[cDNA preparation] Equal amounts of purified mRNA was transcripted to cDNA using a SMARTer PCR cDNA Synthesis Kit (Clontech Cat#634925).
The cDNAs (Ctrl n=3, STZ n=3) for high-throughput sequencing were fragmented by DNase I and ligated to Illumina adapters.
These adapter-ligated cDNA fragments were amplified and sequenced on the Illumina HiSeq2000 sequencer.

treatment_protocol: Male Sprague-Dawley rats, 3 months (~150 g), were purchased from Charles River Laboratories. Rats were injected with STZ (62.5 mg/kg body weight prepared fresh in 0.1 M citrate buffer, pH 4.0) or vehicle into the tail vein. Diabetes was confirmed by measuring blood glucose (One Touch Profile Diabetes Tracking Kit) 24 h after STZ injection.  At 15 d after injection, rats were sacrificed by decapitation.

value: kidney inner medulla

tag: disease state

value: control


title: Control-2_RNA-Seq

description:
Ot3047
rat STZ-induced diabetic animal model

source_name: Control-2, kidney inner medulla


title: STZ-3_RNA-Seq

description:
Ot3054
rat STZ-induced diabetic animal model

source_name: STZ-3, kidney inner medulla

value: STZ-induced diabetes


title: Control-1_RNA-Seq

description:
Ot3046
rat STZ-induced diabetic animal model

source_name: Control-1, kidney inner medulla


title: MAH6

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

data_processing:
All the reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
Paired end fastq files were mapped to refenrence genome by using Tophat 2.0.10 with default parameters.
The output mapping files from the TopHat2 alignment, along with the GTF file from ENSEMBL (http://uswest.ensembl.org/) rat gene annotation v75.30, were used in the htseq-count (http://www-huber.embl.de/users/anders/HTSeq/) to count the total number of reads mapped to each gene.
The expression level of mRNAs in each library was obtained by normalizing reads number to counts per million reads (CPM): CPM = (gene reads number / total mapped reads number per library) × 1,000,000.
Genome_build: Rn5
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample

source_name: Mesenteric arteries, IRW treated

extract_protocol:
mesenteric artery samples were frozen on liquid nitrogen, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-200-0012) 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: tissue type

value: Mesenteric arteries


title: MAH2


title: STZ-1_RNA-Seq

description:
Ot3052
rat STZ-induced diabetic animal model

source_name: STZ-1, kidney inner medulla


title: MAH5


title: STZ-2_RNA-Seq

description:
Ot3053
rat STZ-induced diabetic animal model

source_name: STZ-2, kidney inner medulla


title: D5_NC_rep3

description: mock-challenged

value: Commercial broiler

value: four weeks

value: male


title: MAH4


title: MAC4

source_name: Mesenteric arteries, vehicle control


title: MAC5


title: MAH3


title: MAH1


title: MAC1


title: MAC6


title: MAC2


title: D-KO Rep1

city: Torino

first: Ugo

last: Ala

address: Via Nizza 52

department: Dept. of Molecular Biotechnology and Health Sciences

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

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: RatID_4_TH_SHM_mRNA

tag: gender


title: P53-KO Rep3


title: D-KO Rep3


title: P53-KO Rep1


title: CitK-KO Rep3

source_name: CitK-KO


title: P53-KO Rep2