title: METSIM833

tag: age

tag: tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: log10 total cholesterol (mmol/l)

tag: log10 ldl cholesterol (mmol/l)

tag: log10 hdl cholesterol (mmol/l)

tag: log10 total triglycerides (mmol/l)

tag: log10 serum apoa1 (g/l)

tag: log10 serum apob (g/l)

tag: log10 urinary albumin excretion rate (ug/min)


title: KO macrophages (S1056 to S1075) #10

status: Public on Mar 31 2013

type: SRA

city: Dresden

first: Tina

last: Schumann

address: Fetscherstraße 74

department: Medical Faculty "Carl Gustav Carus"

country: Germany

institute: Institute of Immunology

library_source: transcriptomic

data_processing:
pBWA version 0.5.9-r32-MPI-patch2 against mm9
Reads per exon were computed using bedtools version 2.11, summarized per gene based on Ensembl Gene 61 annotation.
The raw counts (absolute number of reads) were normalized with the DESeq R package (v.1.8.1) and sample to sample correlation (Pearson's correlation coefficient) was computed based on the normalized counts.
Genome_build: mm9 (UCSC)
Supplementary_files_format_and_content: tab delimited file with sample size normalized counts per gene (rows) and sample (columns)

molecule: total RNA

organism: Mus musculus

source_name: mouse peritoneal macrophages

extract_protocol:
Cells were lysed immediately in µMACS™ mRNA Isolation Kit lysis buffer and cleaned with with LysateClear Columns (Miltenyi Biotec). mRNA was enriched using Oligo(dT) beads.
Poly-dT-enrichment, DNAse treatment, chemical fragmentation, ss-Synthesis, strand specific library prep according to: Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Jul 20. doi:10.1093/nar/gkp596

tag: strain

tag: age

value: 17 weeks

tag: Sex

value: female

tag: genotype

value: SAMHD1 KO

tag: cell type

value: peritoneal macrophages


title: KO macrophages (S1056 to S1075) #9

value: 19 weeks


title: KO macrophages (S1056 to S1075) #8


title: METSIM520

status: Public on Apr 01 2013

city: Los Angeles

first: Mete

last: Civelek

state: CA

address: 675 Charles E. Young Dr. S. MRL 3220

department: Medicine

country: USA

institute: University of California Los Angeles

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.
The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 –k.  Novoalign software trims the adapter sequences while aligning.
We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.
To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA

organism: Homo sapiens

source_name: adipose tissue

extract_protocol:
Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturer’s instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.
Small RNA libraries were prepared using  the Illumina  TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501)

treatment_protocol: We analyzed samples from 200 male human subjects that are part of the METSIM (METabolic Syndrome In Men) study. The population-based cross-sectional METSIM study included 10,197 men, aged from 45 to 73 years, who were randomly selected from the population register of the Kuopio town in eastern Finland (population 95,000). Every participant had a 1-day outpatient visit to the Clinical Research Unit at the University of Kuopio, including an interview on the history of previous diseases and current drug treatment and an evaluation of glucose tolerance and cardiovascular risk factors. After 12 hours of fasting, a 2-h oral 75-g glucose tolerance test was performed and the blood samples were drawn at 0, 30 and 120 min. Plasma glucose was measured by enzymatic hexokinase photometric assay (Konelab Systems reagents; Thermo Fischer Scientific, Vantaa, Finland). Insulin was determined by immunoassay (ADVIA Centaur Insulin IRI no. 02230141; Siemens Medical Solutions Diagnostics, Tarrytown, NY). Height and weight were measured to the nearest 0.5 cm and 0.1 kg, respectively. Waist (at the midpoint between the lateral iliac crest and lowest rib) and hip circumference (at the level of the trochanter major) were measured to the nearest 0.5 cm. Body composition was determined by bioelectrical impedance (RJL Systems) in subjects in the supine position after a 12-hour fast.

tag: tissue

value: adipose tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 serum bilirubin (umol/l)

tag: log10 serum alanine aminotransfrase (u/l)

tag: log10 creatinine (umol/l)


title: KO macrophages (S1056 to S1075) #6

tag: strain

tag: age

value: 20 weeks

tag: Sex

value: male

tag: genotype

tag: cell type


title: Surface_fish_eye

city: Beijing

first: Fanwei

last: Meng

address: 1 Beichen West Road,Chaoyang District

department: State Key Laboratory of Biomembrane and Membrane Biotechnology

country: China

institute: Institue of Zoology, Chinese Academy of Sciences

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 de novo assembled or mapped to de novo assembled transcriptome using bowtie v0.12.2 with parameters -v 3 -k 1 -e 100 -a  --best
Reads Per Kilobase of exon per Megabase of library size (RPKM (Reads Per Kilobase of exon per Million mapped sequence reads) were calculated using a protocol from Mortazavi et al., Nat Methods , 2008. In short, we merged the number of reads of surface fish and cavefish that mapped to the same unigene of either our Sinocyclocheilus transcriptome or the zebrafish unigene database, and converted mapped read numbers to RPKM values.
Genome_build: de novo assembled Sinocyclocheilus transcriptome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Sinocyclocheilus angustiporus

source_name: eye

extract_protocol: Total RNA was isolated using a TRIzol reagent (Invitrogen) from whole eye and brain of adult surface and cave species respectively. Two individuals were used in each species. Oligo(dT) selection was performed by using MicroPoly(A) PuristTM (Ambion) according to the manufacturer's protocol. Superscript III First-Strand Synthesis System (Invitrogen) was used to create first-strand cDNA. The second-strand cDNA was synthesized using random primers and Klenow exo- polymerase (Epicentre). cDNA was sheared to short fragments with Biorupter® Sonicator, and then the fragments were connected with sequencing adapters. After size selection, suitable fragments were used as templates for PCR amplification. Finally, four libraries (200 – 400 bp insert) were sequenced using Illumina sequencer GA-II paired-end 80-nt or HiSeq 2000 paired-ed 100-nt (Illumina Inc., San Diego, CA, USA).

tag: tissue

value: eye

value: adult

tag: sample type

value: surface fish


title: KO macrophages (S1056 to S1075) #4

value: 21 weeks


title: KO macrophages (S1056 to S1075) #2


title: KO macrophages (S1056 to S1075) #1


title: WT macrophages (S1056 to S1075) #10

value: wild type


title: WT macrophages (S1056 to S1075) #8


title: KO macrophages (S1056 to S1075) #3


title: WT macrophages (S1056 to S1075) #7


title: WT macrophages (S1056 to S1075) #6


title: WT macrophages (S1056 to S1075) #9


title: WT macrophages (S1056 to S1075) #4


title: WT macrophages (S1056 to S1075) #5


title: WT macrophages (S1056 to S1075) #2


title: WT macrophages (S1056 to S1075) #3


title: WT macrophages (S1056 to S1075) #1

value: 24 weeks


title: Histone Input 1

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description: ChIP-seq

library_source: genomic

data_processing:
All ChIP-seq and Dnase-seqexperiments were aligned against hg19 using bowtie  with the -m 1 option
All RNA-seq experiments were aligned against hg19 using tophat  with the standard parameters and using Ensembl GRCH37 version 65 as a reference transcript database
FPKM for all RNA-seq experiments were performed using cufflinks  and cuffdiff using the -T option (for time series) and using Ensembl GRCh37 version 65 as a reference transcript annotation (no novel assembly)
Genome_build: hg19
Supplementary_files_format_and_content: The processed FPKM file is  CSV file with each row a different Ensembl gene that has the FPKM at each of the 4 time points
Supplementary_files_format_and_content: The BED files for the ChIP-seq and Dnase I samples are all the aligned, non-filtered reads

molecule: genomic DNA

source_name: Primary Human Umbilical Vein Endothelial Cells

growth_protocol: Primary HUVEC purchased from Lonza within 3-6 passages were grown in EGM2 medium (Lonza) up to 80%-90% confluence

extract_protocol: Illumina multiplex library protocol modified to use 2 rather than 3 primers; DHS-seq protocol using modified, indexed primers.

treatment_protocol: HUVEC cells cultured in full EGM2 medium were changed to EBM2 medium (Lonza) with 0.5% FBS overnight. VEGFa (50ug/ml, R&D Systems) was added the next day and samples were collected at 0, 1, 4, and 12 hours

tag: passages

tag: treatment

value: VEGF

tag: time


title: p300 Input

description: ChIP-seq

value: Primary Human Umbilical Vein Endothelial Cells


title: ETS1 Hour 12

description: ChIP-seq

tag: chip antibody

tag: chip antibody manufactuer

value: Santa Cruz

tag: chip antibody catalog #


title: ETS1 Input

description: ChIP-seq


title: Histone Input 2

description: ChIP-seq


title: ETS1 Hour 4

description: ChIP-seq


title: KO macrophages (S1056 to S1075) #7


title: ETS1 Hour 1

description: ChIP-seq


title: DHS Hour 4 Rep 2

description: Dnase-seq


title: DHS Hour 0 Rep 2

description: Dnase-seq


title: DHS Hour 12 Rep 2

description: Dnase-seq


title: KO macrophages (S1056 to S1075) #5


title: DHS Hour 4 Rep 1

description: Dnase-seq


title: ETS Hour 0

description: ChIP-seq


title: DHS Hour 1 Rep 2

description: Dnase-seq


title: DHS Hour 12 Rep 1

description: Dnase-seq


title: RNA-seq Hour 1

description: RNA-seq


title: DHS Hour 0 Rep 1

description: Dnase-seq


title: RNA-seq Hour 0

description: RNA-seq


title: RNA-seq Hour 4

description: RNA-seq


title: RNA-seq Hour 12

description: RNA-seq


title: p300 Hour 4 Rep 2

description: ChIP-seq


title: DHS Hour 1 Rep 1

description: Dnase-seq


title: p300 Hour 12 Rep 1

description: ChIP-seq


title: p300 Hour 0 Rep 2

description: ChIP-seq


title: METSIM951

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 total cholesterol (mmol/l)

tag: log10 ldl cholesterol (mmol/l)

tag: log10 hdl cholesterol (mmol/l)

tag: log10 total triglycerides (mmol/l)

tag: log10 serum apoa1 (g/l)

tag: log10 serum apob (g/l)

tag: log10 urinary albumin excretion rate (ug/min)


title: p300 Hour 1 Rep 2

description: ChIP-seq

tag: cell type

tag: passages

tag: treatment

tag: time

tag: chip antibody

tag: chip antibody manufactuer

tag: chip antibody catalog #


title: p300 Hour 4 Rep 1

description: ChIP-seq


title: p300 Hour 0 Rep 1

description: ChIP-seq


title: p300 Hour 1 Rep 1

description: ChIP-seq


title: H3K27ac Hour 12

description: ChIP-seq

value: Abcam


title: H3K27ac Hour 1

description: ChIP-seq


title: H3K27ac Hour 4

description: ChIP-seq


title: H3K27ac Hour 0

description: ChIP-seq


title: WT Pbx1 Input

city: Madrid

first: Daniel

last: Mateos San Martín

address: Melchor Fernández Almagro 3

department: DBDC

country: Spain

institute: Fundación CNIC

data_processing:
read mapping with BWA software
peak calling with PICS algorithm
Genome_build: mm9
Supplementary_files_format_and_content: bed file format representing PICS peak calling and score

source_name: E11.5 Embryo Trunk

extract_protocol: E11.5 embryonic trunks were dissected, disgregated and the resulting single cell suspension subjected to cross-linking, sonication and immunoprecipitation. Libraries were constructed with Illumina kit.

tag: strain

tag: tissue

value: embryo trunk

tag: developmental stage

value: embryonic day 11.5


title: WT Prep Input


title: WT Meis Input


title: WT Prep ChIP

value: Prep1/2 (N15 Santa Cruz)


title: p300 Hour 12 Rep 2

description: ChIP-seq


title: Fungal_mycelia_T24

city: rockville

first: suchitra

last: pakala

state: maryland

address: 9704 medical center dr

institute: JCVI

description: polyA RNA from Aspergillus fumigatus at T24

data_processing:
Raw sequence data generated by GA II were processed, filtered and normalized using the Illumina pipeline (www.illumina.com) to generate raw sequence reads files. All reads were then filtered and aligned to the annotataed Aspergillus fumigatus AF293 genome to calculate gene expression values in gene in RPKM (Reads Per Kilobase exon Model per million mapped reads) units using CLC Bio Genomic Workbench with default parameters: minimum length fraction (0.9, minimum similarity fraction (0.8), maximum number of hits per read (10).
Processed data file build: Aspergillus fumigatus AF293 genome build 2.1.

molecule: polyA RNA

organism: Aspergillus fumigatus

source_name: Mycelia

growth_protocol: 2x10(7) conidia/ml were inoculated into 400 ml of liquid glucose minimal medium (LGMM). Cultures were incubated for 6h at 37°C with 300 rpm. For t=0 normoxia conditions the germlings were harvested by pouring them over a filter paper in a Buechner funnel and snap frozen immediately in liquid nitrogen. For the hypoxia time points the germlings were collected by centrifugation (8 min at 3000 rpm). For the 12h time point all germlings were pelleted and resuspended in 50 ml of LGMM and transferred to 150ml of LGMM preconditioned in hypoxia (INVIVO2 400 Hypoxia Chamber, Ruskinn, 1% O2, 5% CO2, 94% N2). The cultures were then incubated for 12h in hypoxia (37°C at 150 rpm). For the 24h and 36h time point the 400ml starting culture was split into 2 200 ml fractions. The 2 fractions were each pelleted and resuspended in 50 ml of LGMM and transferred to 150ml of LGMM preconditioned in hypoxia as above. The cultures were then incubated for 24h and 36h in hypoxia (37°C at 150 rpm).

extract_protocol: Each total RNA sample (20-50ug) was treated with DNase and enriched for mRNA using oligo (dT) tags.  Samples of poly (A) RNA (0.2- 1ug) were fragmented into smaller pieces (200-500 bp) and used to synthesize cDNA. Library construction was performed according to the Illumina protocol (www.illumina.com)

treatment_protocol: The liquid cultures were pored over a filter paper in a Buechner funnel and snap frozen immediately in liquid nitrogen. Tissue was stored at -80°C and lyophilized at the same time after all samples were collected. Total RNA extraction was then done simultaneously with all time points using RNeasy spin columns (Qiagen RNA kit).

tag: stress

value: hypoxia

value: 24 hr


title: Fungal_mycelia_T0

description: polyA RNA from Aspergillus fumigatus at T0

value: normoxia

value: 0 hr


title: WT Pbx1 ChIP


title: Fungal_mycelia_T36

description: polyA RNA from Aspergillus fumigatus at T36

value: 36 hr


title: WT Meis ChIP


title: Meis KO RNAseq 1600

data_processing:
mapping and transcription estimation with RSEM
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadsheets containing all Ensembl v63 genes with expression data and fold change between WT and mutants

source_name: E11.5 Embryo

extract_protocol: total RNA was purified from whole E11.5 mouse embryos (Prep1 hypomorphic, Meis1 KO and wt control littermates of each). mRNA was purified and the library for Illumina chromatin sequencing prepared according to the Illumina recommendations. mRNA samples were sequenced using the single-end 68bp protocol. Reads (~7M per sample) were mapped and transcript expression estimated using RSEM.

value: whole embryo

tag: genotype/variation

value: Meis KO


title: Prep Hypo RNAseq

description: ExpressedGenes_Counts_HypoPrepvsWT_ann.xlsx

value: Prep Hypo


title: Prep1 WT RNAseq

value: wild type


title: Meis WT RNAseq 1599


title: Meis WT RNAseq 1603


title: Meis WT RNAseq M8


title: Meis KO RNAseq 1601


title: Fungal_mycelia_T12

description: polyA RNA from Aspergillus fumigatus at T12

value: 12 hr


title: V5-TopoIIa etoposide BrgWT

status: Public on Mar 30 2013

city: West Lafayette

first: Emily

last: Dykhuizen

state: IN

address: 201 S. University

department: medicinal chemistry and molecular pharmacology

institute: Purdue University

description: ethanol treatment

data_processing:
Mapped reads with Bowtie (version 0.12.8)
Called peaks with MACS (version 1.4.2)
Genome_build: mm9
Supplementary_files_format_and_content: bed format, peaks

source_name: V5-TopoIIa etoposide BrgWT

growth_protocol: ES cells derived from Brg1f/f-actinCreER mice were maintained on a layer of mouse embryonic feeders. The cell line was infected with V5-tagged human Topoisomerase 0Iia and the endogenouse mouse Topoisomerase Iia was knocked down.

extract_protocol:
Lysates were clarified from sonicated cells and TopoIIa-DNA covalent complexes were isolated with antibody.
The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3'A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was ampliﬁed using the adaptor primers for 17 cycles and the fragments around 300 bp isolated from agarose gel. The puriﬁed DNA was used directly for cluster generation and sequencing analysis using the Solexa 1G Genome Analyzer following manufacturer protocols.

treatment_protocol: Cells were plated on gelatin with tamoxifen or ethanol for 24 hours, and then in ES cell media for 48 hours. Cells were treated with etoposide (100 micromolar) for 10 minutes before lysing.

tag: cell line

value: Brgf/f-CreER infected with V5-hTopoIIa and sh mTopoIIa

value: Embryonic Stem Cells

value: wild-type

value: anti V5 (Invitrogen)


title: AEST_pectin

status: Public on Mar 29 2013

city: Seoul

first: Jaejoon

last: Jung

address: Anam-dong 5 Ga

country: South Korea

institute: Korea University

description: RNA isolated from pectin-utilizing A. aestuarii cells

data_processing:
Base-calling: CASAVA v1.6
Alignment: CLC Genomics Workbench 4.5
Generation of normalized abundance measurement: CLC Genomics Workbench 4.5
Genome_build: Alishewanella jeotgali (AHTH01000000), A. aestuarii (ALAB01000000), A. agri (AKKU01000000)
Supplementary_files_format_and_content: txt

organism: Alishewanella aestuarii

source_name: Alishewanella aestuarii grown on pectin

extract_protocol: Total RNA was isolated from 5 ml of stationary cells, using the RNeasy Mini kit (QIAGEN, USA), according to the manufacturer’s instructions. The RNA was subjected to a subtractive Hyb-based rRNA removal process using the MICROBExpress Bacterial mRNA Enrichment Kit (Ambion). RNA sequencing was performed using the Illumina Genome Analyzer IIx to generate single-ended 36-bp reads.

tag: genotype

value: Wild type

value: Apple Pectin


title: short_capRNA__1_tech

city: Cambridge

first: Thomas

middle: A

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: single-end

data_processing:
Reads were aligned to the reference sequence using bwa-0.5.9 then sorted and indexed using samtools
Short-cap reads with quality scores >=10 were extracted, split by strand, and the numbe of tag 5' ends aligning at a given site were counted
Pairs of long-cap reads with quality scores >= 10 were extracted.
Genome_build: WS220/ce10
Supplementary_files_format_and_content: bigWig files of of cap start positions for short-cap libraries bigBed files of read-pair mappings for long-cap libraries

molecule: nuclear RNA

organism: Caenorhabditis elegans

source_name: mixed embryos

growth_protocol: Worms were grown in liquid culture and two million adults bleached to obtain mixed staged embryos as previously described (Stiernagle, 2006). Nuclei were isolated from embryos using the method of Ooi et al (Ooi et al., 2010). Nuclei were further purified by centrifugation through a 1.8M sucrose cushion in 10 mM Tris pH 7.5, 10 mM MgCl2. RNA was extracted from the purified nuclei using Tripure (Roche).

extract_protocol: To prepare short capRNA-seq libraries, we followed the published method by Nechaev et al (Nechaev et al., 2010) with minor modification.  In brief, total nuclear RNA (20 to 25 ug) was run on a polyacrylamide gel and a size range of 20 to 100 nt extracted.  To enrich for capped RNA, the purified short nuclear RNA was incubated with 5’ to 3’ RNA nuclease, Terminator (Epicentre), to deplete non-capped RNA.  The enriched short capped RNA was cloned and PCRed using Illumina short RNA-seq adapters according to the manual instruction.  To construct long capRNA-seq libraries, total nuclear RNA was incubated with DNAse I (Ambion) to remove genomic DNA contamination followed by Qiagen Mini-Elute columns (cut-off size >200 nt RNAs).  These cleaned-up “long” nuclear RNAs were treated with Terminator nuclease to enrich for capped RNA.  Strand specific long capRNA libraries were made using the dUTP replacement method (Levin et al., 2010, Sultan et al., 2012) and Illumina paired end adapters.

value: mixed embryos

value: N2 (wild-type)


title: E15.5 WT BioRep1 Lane005

city: OMAHA

first: You

last: Li

state: NE

address: Emile St

department: Department of Genetics, Cell Biology and Anatomy

institute: University of Nebraska Medical Center

description: T2 G3

data_processing:
fastq quality control:fastQC v0.10.1
alignment: TopHat v1.4.1
transcriptome assembly, transcripts quantification and tests for differentially expression: Cufflinks v1.3.0
visualizing the output from Cufflinks: CummeRbund v1.2.0
Genome_build: mm9, NCBI build 37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Palate

extract_protocol:
Palates were removed from fetuses as duplicates at E14.5, E15.5, and E16,5 and stored in RNALater until extraction; and RNA was harvested from tissues using RNeasy Kit (Qiagen, CA) and evaluated the RNA for purity and concentration by NanoDrop (Wilmington, DE). RNA integrity numbers (RIN) were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Libraries were prepared using the Illumina mRNA-Seq Sample Preparation Kit (San Diego, CA) according to the manufacturer’s instructions. Briefly, poly(A) + RNA was recovered from 1 µg of total RNA using two rounds of isolation with oligo-dT-coated Sera-Mag magnetic beads. The recovered poly (A) + RNA was then chemically fragmented. RNA fragments were converted to cDNA using SuperScript II and random primers. The second strands were synthesized using RNaseH and DNA Pol I. The ends of the cDNA were repaired using T4 DNA polymerase, T4 polynucleotide kinase, and Klenow DNA polymerase. A single adenosine was added to the 3’ end using Klenow fragment (3’ to 5’ exo minus). Adaptors were attached to both ends of the cDNA using T4 DNA ligase. RNA fragments were extracted from a 2% low range ultra agarose sizing gel. The fragments were amplified by 15 cycles of PCR using Phusion DNA polymerase. Libraries were validated with Agilent Bioanalyzer (Palo Alto, CA).

value: Palatal shelves

tag: age

value: Embryonic day 15.5

value: TGF-beta3 +/+


title: E15.5 WT BioRep1 Lane003

description: T2 G3


title: E15.5 WT BioRep2 Lane005

description: T2 G3


title: E15.5 TGFβ3-KO BioRep2 Lane005

description: T2 G1

value: TGF-beta3 -/-


title: E15.5 WT BioRep2 Lane003

description: T2 G3


title: E15.5 TGFβ3-HT BioRep1 Lane005

description: T2 G2

value: Embryonic day 14.5

value: TGF-beta3 +/-


title: E15.5 TGFβ3-HT BioRep1 Lane003

description: T2 G2


title: E15.5 TGFβ3-HT BioRep2 Lane003

description: T2 G2


title: E15.5 TGFβ3-KO BioRep2 Lane003

description: T2 G1


title: V5-TopoIIa etoposide BrgKO

description: tamoxifen treatment

source_name: V5-TopoIIa etoposide BrgKO


title: input BrgWT

description: ethanol treatment

source_name: input BrgWT


title: E15.5 TGFβ3-KO BioRep1 Lane003

description: T2 G1


title: Meis KO RNAseq M1

value: whole embryo

value: embryonic day 11.5

value: Meis KO


title: E15.5 TGFβ3-KO BioRep1 Lane005

description: T2 G1


title: E14.5 WT BioRep2 Lane002

description: T1 G3


title: Input

city: Munich

first: Anne

last: Dueck

state: Bavaria

address: Biedersteiner Str.29

department: Institute of Pharmacology and Toxicology

institute: TUM

description: small RNA sequencing data

data_processing:
sequenced on a GA-IIx, 38 sequencing cycles
Basecalls performed using SCS.2.6, CASAVA version 1.6
Barcode splitting and adapter trimming was performed using custom scripts.
Reads were mapped to H. sapiens genome assembly using megablast software.
Genome_build: GRCh37

source_name: HeLa cells

growth_protocol: HeLa cells were grown in suspension in Joklik's medium

extract_protocol:
Cells were harvested, lysed and cleared by centrifugation. After immunoprecipitation, beads were washed several times and the RNA was recovered by Proteinase K digestion and phenol/chloroform extraction
Libraries were constructed according to Illumina's small RNA cloning kit v1.5 using the following adapters:  5′adapter 5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′; 3′adapter 5′-Phospho-T-4nt-Barcode-CGTATGCCGTCTTCTGCTTG-(C7amino)-3′. Used barcodes: Ago1=ACTA; Ago2=GTAA; Ago3=TACA; Ago4=ATGA; Control=GAGA; Input=CATA.

tag: antibodies

tag: barcode srna cloning

value: CATA

value: HeLa


title: input BrgKO

description: tamoxifen treatment

source_name: input BrgKO

value: Brgf/f-CreER infected with V5-hTopoIIa and sh mTopoIIa

tag: cell type

value: Embryonic Stem Cells


title: E14.5 TGFβ3-HT BioRep2 Lane002

description: T1 G2


title: E14.5 TGFβ3-HT BioRep1 Lane002

description: T1 G2


title: E14.5 TGFβ3-HT BioRep2 Lane001

description: T1 G2


title: E14.5 WT BioRep1 Lane001

description: T1 G3


title: E14.5 WT BioRep2 Lane001

description: T1 G3


title: E14.5 TGFβ3-KO BioRep1 Lane002

description: T1 G1


title: E14.5 WT BioRep1 Lane002

description: T1 G3


title: E14.5 TGFβ3-KO BioRep1 Lane001

description: T1 G1


title: E14.5 TGFβ3-HT BioRep1 Lane001

description: T1 G2


title: E15.5 TGFβ3-HT BioRep2 Lane005

description: T2 G2


title: Ago4 IP

description: small RNA sequencing data

value: monoclonal antibody against endogenous human Argonaute4, clone 6C10 (Petri et al., 2011)

value: ATGA


title: Ago3 IP

description: small RNA sequencing data

value: monoclonal antibody against endogenous human Argonaute3, clone 5A3 Weinmann et al., 2009)

value: TACA


title: Ago2 IP

description: small RNA sequencing data

value: monoclonal antibody against endogenous human Argonaute2, clone 11A9 (Ruedel et al., 2008)

value: GTAA


title: Ago1 IP

description: small RNA sequencing data

value: monoclonal antibody against endogenous human Argonaute1, clone 4B8 (Beitzinger et al., 2007)

value: ACTA


title: M_MAC_Donor2

city: Frederick

first: Xiaojun

last: Hu

state: MD

address: 1050 Boyles St.

department: CSP

institute: SAIC_Frederick, INc

data_processing:
Basecalls performed using RTA 1.8.70.0
The raw reads were trimmed against Illumina adapters, and rRNA, primers, mitochondria contaminations, and filtered by minimum length 15, maximum length 32 and phred-score 20 using fastq-mcf (code.google.com/p/ea-utils/wiki/FastqMcf). Then the reads were collapsed to tags by our own perl script. Tags containing 1 read were treated as machine error and removed. The clean tags were mapped to the hg19 build of the human genome (UCSC Genome Browser) and human mature miRNA (miRbase v19) using novoalign (http://www.novocraft.com/) with 2 mismatches.
Qualified tags were inputted into the publicly available miRNA discovery program, miRDeep to identify novel miRNAs
Reads counts were calculated using our own scripts from novoalign mapping result, and then were normalized by DESeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized value for each Sample ...

source_name: CD14+ monocytes

growth_protocol: CD14+ monocytes were isolated from healthy donor peripheral blood enriched leukopacks (Blood Bank, National Institute of Health, Bethesda, MD, USA) using MACS CD14 MicroBeads (Miltenyi Biotec, Auburn, CA, USA). Monocytes were differentiated into macrophages using 25 ng/ml M-CSF (R&D Systems, Minneapolis, MN, USA) (M-Mac) or a combination of M-CSF and 100 ng/ml IL-27 (R&D Systems) (I-Mac). Initially the monocytes were in Macrophage serum free media (Invitrogen, Carlsbad, CA, USA) which was replaced after three days with DMEM (Invitrogen) with 10% FBS (HyClone Laboratories, Logan, UT, USA), 25 mM HEPES (Quality Biology, Gaithersburg, MD, USA) and 5 µg/ml Gentamicin (Invitrogen) containing the same concentration of IL-27. Cells were incubated at 37°C in a 5% CO2 incubator for a total 7 days.

extract_protocol:
Total RNA was extracted using the Qiagen miRNeasy kit (Qiagen, Hilden, Germany). Prior to RNA sequencing, samples from Donor 1 and 2 were subjected to analysis by the Agilent Bioanalyzer RNA Nano chip (Agilent Technologies, Santa Clara, CA, USA) to confirm RNA purity and quality (all four samples had a RNA integrity number of 10).
Four microRNA libraries were prepared using Illumina TruSeq Small RNA Sample Preparation protocol according to the manufacturer’s instructions. Briefly, the specifically modified RNA 3’ adaptor, which has a high affinity for Dicer cleavage products, and 5’ adaptor were aligned to the gel purified small RNA, followed by reverse transcription and library enrichment by PCR amplification. The size, purity, and concentration of the final cDNA library were validated using an Agilent Bioanalyzer 2100. Samples were sequenced on GAIIx with 36 cycles using Illumina TruSeq v3 chemistry.

value: macrophage

tag: treatments

value: M-CSF

tag: donor


title: METSIM1764

value: adipose tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 serum bilirubin (umol/l)

tag: log10 serum alanine aminotransfrase (u/l)

tag: log10 creatinine (umol/l)

tag: log10 total cholesterol (mmol/l)

tag: log10 ldl cholesterol (mmol/l)

tag: log10 hdl cholesterol (mmol/l)

tag: log10 total triglycerides (mmol/l)

tag: log10 serum apoa1 (g/l)

tag: log10 serum apob (g/l)

tag: log10 urinary albumin excretion rate (ug/min)


title: I_MAC_Donor2

tag: cell type

tag: treatments

value: M-CSF + IL27

tag: donor


title: I_MAC_Donor1


title: E14.5 TGFβ3-KO BioRep2 Lane001

description: T1 G1

tag: strain

tag: tissue

value: Palatal shelves

tag: age

value: Embryonic day 14.5

tag: genotype

value: TGF-beta3 -/-


title: E14.5 TGFβ3-KO BioRep2 Lane002

description: T1 G1


title: AJE_pectin

description: RNA isolated from pectin-utilizing A. jeotgali cells

organism: Alishewanella jeotgali

source_name: Alishewanella jeotgali grown on pectin

value: Wild type

tag: treatment

value: Apple Pectin


title: M_MAC_Donor1


title: CG_93.2

status: Public on Mar 28 2013

city: Toronto

first: Stephen

last: Wright

state: Ontario

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

country: Canada

institute: University of Toronto

description: C. grandiflora grown from wild-collected seed from Mikro Papingo, Greece

data_processing:
Illumina flourescence data was processed through the illumina analysis Pipeline for basecalling and quality assignment
For flowerbud samples, illumina fastq quality scores were converted to PHRED+33, leaf samples were retained at the PHRED+64 format
Reads were aligned to the Capsella reference genome using bowtie. The initial release JGI Maker gene models were used to assign expresion using the tophat-cufflinks pipeline including the data normalization option to generate expression FPKM: fragments per Kilobase of exon per million reads.
Genome_build: Capsella Rubella v1 (also listed as 183), http://www.phytozome.org/dataUsagePolicy.php?org=Org_Crubella
Supplementary_files_format_and_content: TAB delimitted single sample FPKM expression reads, gene models are descibed here ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Crubella/annotation/Crubella_183_gene.gff3.gz

organism: Capsella grandiflora

source_name: leaf tissue

growth_protocol: Standardized greenhouse conditions

extract_protocol:
Qiagen Rneasy Plant Mini kit, standard protocol
Standard Illumina paired-end mRNA seq

value: leaf tissue

tag: developmental stage

value: maturing leaves


title: long_capRNA_1

description: paired-end

value: mixed embryos

value: N2 (wild-type)


title: Background_ChIPSeq

city: Durham

first: Karen

middle: Elizabeth

last: Hayden

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and policy

institute: Duke University

description: Chromatin IP against  Normal Mouse IgG

data_processing:
HuRef_CENPA.fastq converted to nonredundant 50mer kmer library (50 bp window, 1bp slide)
HuRef_Background.fastq converted to nonredundant 50mer kmer library (50 bp window, 1bp slide)
hg19 alpha satellite sequences converted to nonredundant 50mer kmer library (50 bp window, 1bp slide), base position indexed
Calculated log transformed ratio of HuRef_CENPA.fastq 50-mers relative to HuRef_Background.fastq 50-mers
Enriched 50-mers (>=2-fold) are referenced to hg19 using 50-mers, with base position indexed
Genome_build: hg19/GRCh37
processed data files format and content: wiggle format (*.wig), for all chromosome assemblies

source_name: HuRef Cell line

growth_protocol: HuRef Lymphoblast cells were cultured in Eagle’s minimum essential medium with 2mM L-glutamine and Earle’s BSS adjusted to contain 1.5 g/L sodium bicarbonate, 0.1mM non-essential amino acids, and 1.0mM sodium pyruvate, 90%; fetal bovine serum, 10%.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody (monoclonal antibody designed for human CENP-A.  Stressgen; KAM-CC006).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: HuRef

value: Lymphoblast

tag: chip antibody

value: Normal Mouse IgG; Upstate (cat#12-371)


title: short_capRNA_1

description: single-end


title: AGRI_pectin

description: RNA isolated from pectin-utilizing A. agri cells

organism: Alishewanella agri

source_name: Alishewanella agri grown on pectin


title: CG_AxE

description: C. grandiflora F1 from cross between two C. grandiflora from Corfu, Greece


title: short_capRNA_2

description: single-end


title: CG_85.33

description: C. grandiflora grown from wild-collected seed from Koutselio, Greece


title: CG_5a

description: C. grandiflora grown from wild-collected seed from Troumpeta, Greece


title: CENPA_ChIPSeq

description: Chromatin IP against CENP-A

value: hCENPA; Stressgen (KAM-CC006)


title: AJE_succinate

description: Reference for other samples derived from pectin-utilizing cells

source_name: Alishewanella jeotgali grown on succinate

value: Succinate


title: CG_86.8

description: C. grandiflora grown from wild-collected seed from Kalenzi, Greece


title: CG_103.17

description: C. grandiflora grown from wild-collected seed from Pili, Greece


title: CG_91.2

description: C. grandiflora grown from wild-collected seed from Ano Pedina, Greece


title: CG_94.12


title: CG_95.15


title: CG_83.17

description: C .grandiflora grown from wild-collected seeds from Mesolongion, Greece


title: S1_Cr1Gr1

description: C. rubella from Samos, Greece (inbred in the greenhouse since 2002)

organism: Capsella rubella

source_name: floral tissue

value: floral tissue

value: mixed floral bud


title: Control IP

description: small RNA sequencing data

tag: antibodies

value: monoclonal antibody against RmC, rat protein (complement system)

tag: barcode srna cloning

value: GAGA

value: HeLa


title: S1_Cr81.02

description: C. rubella from Megalopoli, Greece


title: S1_Cg103.02


title: S1_CgAxF


title: S1_Cr34.11

description: Samples grown from seed gathered in San Luca, Italy


title: S1_Cr75.2

description: C. rubella from Kalavrita, Greece


title: S1_Cg88.23

description: C. grandiflora grown from wild-collected seed from Monodendri, Greece


title: S1_Cg85.9

description: C. grandiflora grown from wild-collected seed from Metsovo, Greece


title: long_capRNA_2

description: paired-end


title: Wild Louisiana N. crassa isolate JW96

city: Berkeley

first: Charles

middle: Robert

last: Hall

address: 341 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

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 FGSC 2489 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods. 2008.  The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the transcript and by the size of the library.
Genome_build: V10
Supplementary_files_format_and_content: tab-delimited text file including gene specific RPKM values for each Sample

organism: Neurospora crassa

source_name: Mycelia

extract_protocol:
mycelia were harvested, flash frozen on liquid nitrogen, 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

tag: source

value: mycelia

value: 16 hours


title: Wild Louisiana N. crassa isolate JW75


title: peripheral blood from sample 2, remission

city: Zhangzhou

first: AYang

last: Wu

address: 59, Shengli Road

institute: Zhangzhou municipal hospital of Fujian province

data_processing: We used TopHat 1.3.3 software to align the sequence reads to reference genome (GRCh37.5). Then we used the cufflinks program of Cufflinks 1.3.0 to call the expression values (FPKM, Fragments Per Kilobase of exon model per Million mapped fragments) of mapped human genes and detect differentially expressed genes.

source_name: peripheral blood, remission

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit. The RNA extraction is Trizol.Briefly, 10 ug of each total RNA sample was used for polyA mRNA selection using streptavidin-coated magnetic beads, followed by thermal mRNA fragmentation. The fragmented mRNA was subjected to cDNA synthesis using reverse transcriptase (Super- Script II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase) and 3-'A' add process (Klenow exo- fragment), was finally ligated to Illumina Truseq adaptors. Size selection was performed using a 2% agarose gel, generating cDNA libraries ranging in size 380 bp. Finally, the libraries were enriched using 15 cycles of PCR and purified by the QIAquick PCR purification kit (Qiagen). The enriched libraries were diluted with Elution Buffer to a final concentration of 10 nM. Each library was run at a concentration of 11 pM on one Genome Analyzer (GAII) lane using 115 bp sequencing. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: peripheral blood

tag: disease

tag: Stage

value: remission


title: Wild Louisiana N. crassa isolate JW70


title: Wild Louisiana N. crassa isolate JW76


title: Wild Louisiana N. crassa isolate JW7


title: Wild Louisiana N. crassa isolate JW60


title: Wild Louisiana N. crassa isolate JW66


title: Wild Louisiana N. crassa isolate JW27


title: peripheral blood from sample 1, primary tumor

source_name: peripheral blood, primary tumor

value: primary tumor


title: Wild Louisiana N. crassa isolate JW262


title: Wild Louisiana N. crassa isolate JW59


title: Wild Louisiana N. crassa isolate JW260


title: Wild Louisiana N. crassa isolate JW258


title: Wild Louisiana N. crassa isolate JW256


title: Wild Louisiana N. crassa isolate JW250


title: Wild Louisiana N. crassa isolate JW254


title: Wild Louisiana N. crassa isolate JW246


title: Wild Louisiana N. crassa isolate JW245


title: Wild Louisiana N. crassa isolate JW248


title: Wild Louisiana N. crassa isolate JW240


title: Wild Louisiana N. crassa isolate JW238


title: Wild Louisiana N. crassa isolate JW24


title: Wild Louisiana N. crassa isolate JW234


title: Wild Louisiana N. crassa isolate JW230


title: Wild Louisiana N. crassa isolate JW224


title: Wild Louisiana N. crassa isolate JW228


title: Wild Louisiana N. crassa isolate JW233


title: Wild Louisiana N. crassa isolate JW261


title: Wild Louisiana N. crassa isolate JW220


title: Wild Louisiana N. crassa isolate JW210


title: Wild Louisiana N. crassa isolate JW5


title: Wild Louisiana N. crassa isolate JW222


title: Wild Louisiana N. crassa isolate JW216


title: Wild Louisiana N. crassa isolate JW252


title: Wild Louisiana N. crassa isolate JW9


title: Wild Louisiana N. crassa isolate JW204


title: Wild Louisiana N. crassa isolate JW202


title: Wild Louisiana N. crassa isolate JW200


title: Wild Louisiana N. crassa isolate JW199


title: Wild Louisiana N. crassa isolate JW206


title: Wild Louisiana N. crassa isolate JW266


title: Wild Louisiana N. crassa isolate JW242


title: Wild Louisiana N. crassa isolate JW187


title: Wild Louisiana N. crassa isolate JW20


title: Wild Louisiana N. crassa isolate JW188


title: Wild Louisiana N. crassa isolate JW190


title: Wild Louisiana N. crassa isolate JW184


title: Wild Louisiana N. crassa isolate JW182


title: Wild Louisiana N. crassa isolate JW22


title: Wild Louisiana N. crassa isolate JW180


title: Wild Louisiana N. crassa isolate JW209


title: Wild Louisiana N. crassa isolate JW179


title: Wild Louisiana N. crassa isolate JW176


title: Wild Louisiana N. crassa isolate JW178


title: Wild Louisiana N. crassa isolate JW172


title: Wild Louisiana N. crassa isolate JW218


title: Wild Louisiana N. crassa isolate JW174


title: Wild Louisiana N. crassa isolate JW168


title: Wild Louisiana N. crassa isolate JW169


title: Wild Louisiana N. crassa isolate JW167


title: Wild Louisiana N. crassa isolate JW164


title: Wild Louisiana N. crassa isolate JW160


title: Wild Louisiana N. crassa isolate JW171


title: Wild Louisiana N. crassa isolate JW161


title: Wild Louisiana N. crassa isolate JW196


title: Wild Louisiana N. crassa isolate JW16


title: Wild Louisiana N. crassa isolate JW156


title: Wild Louisiana N. crassa isolate JW148


title: Wild Louisiana N. crassa isolate D119


title: Wild Louisiana N. crassa isolate D143


title: Wild Louisiana N. crassa isolate D118


title: Wild Louisiana N. crassa isolate D117


title: Wild Louisiana N. crassa isolate JW18


title: Wild Louisiana N. crassa isolate D114


title: Wild Louisiana N. crassa isolate 847


title: Wild Louisiana N. crassa isolate D111


title: Wild Louisiana N. crassa isolate D110


title: Wild Louisiana N. crassa isolate D112


title: Wild Louisiana N. crassa isolate 4498


title: Wild Louisiana N. crassa isolate 4497


title: Wild Louisiana N. crassa isolate 4500


title: Wild Louisiana N. crassa isolate 4494


title: Wild Louisiana N. crassa isolate 4489


title: Wild Louisiana N. crassa isolate 4487


title: Wild Louisiana N. crassa isolate 4496


title: Wild Louisiana N. crassa isolate JW193


title: Wild Louisiana N. crassa isolate JW159


title: Wild Louisiana N. crassa isolate JW162


title: Wild Louisiana N. crassa isolate 4471


title: Wild Louisiana N. crassa isolate 4472


title: Wild Louisiana N. crassa isolate 4479


title: Wild Louisiana N. crassa isolate 4483


title: Wild Louisiana N. crassa isolate 4476


title: placenta RNA rep2

city: Davis

first: Janine

last: LaSalle

address: Medical Microbiology and Immunology

institute: UC Davis

data_processing:
Sequencing index was in first 4 bases of sequencing read.  For raw fastq files, first four bases were removed and separate fastq files were made for each indexed replicate.
Reads were mapped to the hg18 version of the genome using TopHat (version 1).  Parameters:  --library-type fr-unstranded –GTF –butterfly-search –no-novel-juncs --prefilter-multihits
Cufflinks was used to assemble the mapped reads into transcripts, omitting reads that did not align to known transcripts.  Parameters:  --library-type fr-unstranded – GTF –frag-bias-correct –multi-read-correct –frag-len-mean 390 –compatible-hits-norm
Genome_build: hg18
Supplementary_files_format_and_content: fpkm_tracking file from Cufflinks

source_name: placenta

extract_protocol: RNA was extracted using the NuGEN Ovation RNA-Seq System.  Indexed adapters were added using the NuGEN Encore NGS Library System I.

value: placenta from full-term pregnancy

tag: Sex

value: male


title: Wild Louisiana N. crassa isolate 4470


title: Wild Louisiana N. crassa isolate JW10


title: placenta 3 - MethylC-seq

data_processing:
Reads were aligned to the genome using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment. BS Seeker parameters: -e 85 -m 3 -a adapter2.
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage. Methylation data for both DNA strands were combined. Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates. Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%
Genome_build: hg18
Supplementary_files_format_and_content: BED file with the name field giving the % methylation at that CpG site

extract_protocol:
Tissue DNA was purified using Qiagen's Puregene kit.
The genomic DNA was sonicated to ~300 bp and methylated Illumina adapters were ligated to the ends. 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions. The library was then amplified using 2.5 U PfuTurboCx Hotstart DNA Polymerase (Stratagene) for 14 cycles using Illumina's standard amplification protocol.


title: Wild Louisiana N. crassa isolate 4469


title: placenta RNA rep1


title: Wild Louisiana N. crassa isolate 4468


title: placenta 1 (technical replicate 2) - MethylC-seq

data_processing:
Reads were aligned to the genome using BS Seeker.
100 bp reads were trimmed at the 3' end to 75 bp for BS Seeker alignment.  BS Seeker parameters:  -e 75 -m 2.
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage. Methylation data for both DNA strands were combined. Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates. Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%
Genome_build: hg18
Supplementary_files_format_and_content: BED file with the name field giving the % methylation at that CpG site

source_name: placenta from full-term pregnancy

extract_protocol: Tissue DNA was purified using Qiagen's Puregene kit.  The genomic DNA was sonicated to ~300 bp and methylated Illumina adapters were ligated to the ends.  500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions.  The library was then amplified using 2.5 U PfuTurboCx Hotstart DNA Polymerase (Stratagene) for 14 cycles using Illumina's standard amplification protocol.


title: Wild Louisiana N. crassa isolate 4463


title: placenta 2 - MethylC-seq


title: Wild Louisiana N. crassa isolate D113


title: placenta 1 (technical replicate 1) - MethylC-seq

data_processing:
Reads were aligned to the genome using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment.  BS Seeker parameters:  -e 85 -m 3 -a adapter2.
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage. Methylation data for both DNA strands were combined. Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates. Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%
Genome_build: hg18
Supplementary_files_format_and_content: BED file with the name field giving the % methylation at that CpG site


title: Wild Louisiana N. crassa isolate 4465


title: Er_0_bud

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Methylated cytosine calls were made using the pipeline described in Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. 2009. Nature
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab separated file of methylated cytosine positions

organism: Arabidopsis thaliana

source_name: mixed stage inflorescence

extract_protocol:
DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations.
Approximately one to three micrograms of genomic DNA was sonicated to ~100 bp using the Covaris S2 System using the following parameters: cycle number = 6, duty cycle = 20%, intensity = 5, cycles/burst = 200 and time = 60 seconds. Sonicated DNA was purified using Qiagen DNeasy minielute columns (Qiagen). Each sequencing library was constructed similar to genomic DNA libraries except the ligation was performed with methylated adapters provided by Illumina. Ligation products were purified with AMPure XP beads (Beckman) at a ratio of 1.8X of beads to sample. Up to 450 ng of ligated DNA was bisulfite treated using the MethylCode Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines and then PCR amplified using Pfu Cx Turbo (Agilent, Santa Clara, CA) using the following PCR conditions (2 minutes at 95C, 4 cycles of 15 seconds at 98C, 30 seconds at 60C, 4 minutes at 72C and 10 minutes at 72C).

tag: cultivar

value: mixed stage inflorescence

tag: ecotype id


title: Wild Louisiana N. crassa isolate 4459


title: Wild Louisiana N. crassa isolate 4457


title: Er_0

source_name: leaf

value: leaf


title: Wild Louisiana N. crassa isolate 4455


title: Wild Louisiana N. crassa isolate 4452


title: Wild Louisiana N. crassa isolate D116


title: Wild Louisiana N. crassa isolate 4453


title: Wild Louisiana N. crassa isolate 4451


title: Gl_GS_RNAseq

city: Stockholm

first: Oscar

last: Franzen

address: Berzelius väg 35

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
Paired-end reads were aligned with bwa.
FPKM values were computed using cufflinks.
Genome_build: See GiardiaDB.org for reference genomes.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

organism: Giardia duodenalis

source_name: Trophozoites

extract_protocol: Poly(A) selection was performed using the Poly(A) purist MAG system. The purified mRNA from was treated with Turbo DNA-free kit. Sequencing libraries were prepared using ScriptSeq™ mRNA-Seq library Preparation Kit.

value: GS (B)

tag: passage

value: in vitro adapted


title: Gl_AS175P33_RNAseq

tag: strain

value: passage 33


title: Gl_AS175P4_RNAseq

value: passage 4


title: Wild Louisiana N. crassa isolate 4486


title: Gl_P15_RNAseq


title: Wild Louisiana N. crassa isolate 4448


title: Wild Louisiana N. crassa isolate 4449


title: Gl_WB_RNAseq

value: WB (A)


title: Rome-1

data_processing:
Bioscope version 1.3 was used to align .csfasta and .qual files to SNP-substituted reference genomes for each accession using default parameters which allows up to 10 locations per sequenced read.
Cufflinks version 1.1 was used to quantify gene expression values using the following parameters: -F 0 –b –N –library-type fr-secondstrand –G TAIR10.gtf.
Genome_build: TAIR10
Supplementary_files_format_and_content: Expression values for all genes in the TAIR10 reference annotation as defined by Cufflinks version 1.1

extract_protocol:
RNA was isolated using the Qiagen Plant RNeasy kit (Qiagen) following the manufacturer’s instructions.
RNA-Seq libraries were prepared according to the described methods in Li, L. et al. Linking photoreceptor excitation to changes in plant architecture. Genes Dev 26, 785-790 (2012).

tag: tissue


title: Wild Louisiana N. crassa isolate 2489

tag: age


title: Wild Louisiana N. crassa isolate 1693


title: pbx2/4-MO; prdm1-/- rep3

city: Seattle

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
Reads were aligned by tophat 1.4
gene counts are collected using Bioconductor Rsamtools package. Reads mapped to M locations are counted as 1/M at each occurrence.
differentential gene expression detection was performed by edgeR.
Genome_build: Zv9 release 63
Supplementary_files_format_and_content: GSE45532_gene.counts.csv: Read counts extracted by Bioconductor packages for each ENSEMBL genes.  Reads that mapped to M locations are counted as 1/M for each occurrence. The columns are: gene name, ENSEMBL ID, and read counts for all samples.
Supplementary_files_format_and_content: GSE45532_double.genes.csv:  Differential expressed genes between Double knockout pbx2/4-MO;prdm1-/- vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name, ENSEMBL gene.id, edgeR pvalue, edgeR log fold change.
Supplementary_files_format_and_content: GSE45532_pbx.genes.csv: Differential expressed genes between pbx2/4-MO vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name, ENSEMBL gene.id, edgeR pvalue, edgeR log fold change.
Supplementary_files_format_and_content: GSE45532_prdm.genes.csv: Differential expressed genes between prom1-/- vs. control.  Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff.  The columns are gene name, ENSEMBL gene.id, edgeR pvalue, edgeR log fold change.

organism: Danio rerio

source_name: embryos

extract_protocol:
Total RNA from individual embryos was isolated using the RNAqueous Micro Kit (Ambion). Samples were genotyped, pooled, then further cleaned and concentrated using the RNeasy MinElute Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embryos were injected with pbx2/4 morpholinos or control morpholinos at the 1 cell stage.

value: 10 somites

value: AB

tag: genotype

value: pbx2/4-MO; prdm1-/-


title: pbx2/4-MO; prdm1-/- rep2


title: Ra-0


title: pbx2/4-MO rep3

value: pbx2/4-MO; prdm1+/+


title: pbx2/4-MO; prdm1-/- rep1


title: Rennes-1


title: pbx2/4-MO rep1


title: pbx2/4-MO rep2


title: La-0


title: Lan-0


title: Lp2-2


title: Benk_1


title: prdm1-/- rep3

value: control-MO; prdm1-/-


title: Bch_1


title: prdm1-/- rep2


title: control rep3

value: control-MO; prdm1+/+


title: prdm1-/- rep1


title: Baa_1


title: Ba_1


title: control rep2


title: control rep1


title: NK cells - MethylC-seq

data_processing:
Reads were aligned to the genome using BS Seeker.
76 bp reads were processed with BS Seeker parameters -e 75 -m 2.
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage. Methylation data for both DNA strands were combined. Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates. Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%
Genome_build: hg18
Supplementary_files_format_and_content: BED file with the name field giving the % methylation at that CpG site

source_name: NK cells (adolescent male)

value: NK cells


title: Appt_1


title: Rooster Wild Type Adult small RNA

status: Public on Mar 27 2013

city: Worcester

first: Christian

last: Roy

state: Massachusetts

address: 364 Plantation St

institute: Umass Med

description: small RNA

data_processing:
genome build: gg3
Small RNA sequence analysis was as described (Li et al., 2009)
Supplementary_files_format_and_content: BED file containing annotations of piRNA-producing genes and csv file containing rpkm values available on Series record

organism: Gallus gallus

source_name: testes

extract_protocol: Small RNA libraries were constructed and sequenced as described (Ghildiyal et al., 2008; Seitz et al., 2008) except that 18–35 nt RNA was isolated and 2S rRNA depletion omitted.

value: testes

value: Adult

value: White Leghorn of the Cornell Special C strain

value: wild-type


title: Amel_Worker_brain3

city: Duesseldorf

first: Christina

last: Schulte

address: Universitaetssrasse 1

department: Evolutionary Genetics

institute: Heinrich-Heine-Universitaet

data_processing:
Sequencing was performed using CASAVA version 1.8.2 on Illumina HiSeq2500 instrument
Reads that passed Illumina pipeline quality filtering criteria (those output to LaneX_X_fastq files) were mapped to a reference genome
Mapping was then performed using Tophat v.2.0.8 (Trapnell et al., 2012), with Bowtie v2.1.0 (Langmead et al., 2010), and samtools 0.1.18 (Li et al., 2009), and parameters “  A reference annotation (ref_Amel_4.5_top_level) was supplied in gtf format with the -G option.
The reference sequence for mapping was the Assembly v.4.5 from ncbi (ftp://ftp.ncbi.nih.gov/genomes/Apis_mellifera/Assembled_chromosomes/seq/)
BAM files were used to generate FPKM values using Cufflinks version 2.0.2 (Trapnell et al,. 2012)
Genome_build: Amel_4.5
Supplementary_files_format_and_content: FPKM values for the mapped and assembled reads

organism: Apis mellifera carnica

source_name: Brain

growth_protocol: Wildtype drone, worker and queen honeybee pupae were collected out of a feral colony in pupal stage 4-5. Brains were disected, frozen in liquid nitrogen and stored at 80°C until RNA isolation.

extract_protocol: Total RNA was isolated from single brains using Trizol method. 50 µl Trizol were added to a single brain and the tissue was pestled. After incubation for 5 min at room temperature 10 µl chloroform were added. The solution was mixed for 30 sec and centrifuged for 15 min on 13,000 rpm. The upper phase was transferred into a new tube and 20 µl isopropanol were added and mixed. The solution was incubated for 10 min at room temperature and then centrifuged for 10 min at 13,000 rpm and 4°C. The pellet was dired for 5 min at room temperature and then diluted in 10 µl RNAse free water.

value: Pupa (stage 4-5)

value: Female

value: Brain


title: Amel_Drone_brain3

value: Male


title: Amel_Drone_brain1


title: Amel_Drone_brain2


title: Wild Louisiana N. crassa isolate 4450

value: mycelia

value: 16 hours


title: Mouse Wild Type 6 weeks dpp Oxidized small RNA

description: Oxidized small RNA

data_processing:
genome build: mm9
Small RNA sequence analysis was as described (Li et al., 2009)
Supplementary_files_format_and_content: BED file containing annotations of piRNA-producing genes and csv file containing rpkm values available on Series record


title: Amel_Worker_brain1


title: Amel_Worker_brain2


title: Mouse Wild Type 20.5 dpp Oxidized small RNA

description: Oxidized small RNA


title: Mouse Wild Type 17.5 dpp Oxidized small RNA

description: Oxidized small RNA


title: Mouse Miwi Heterozygous 14.5 dpp Oxidized small RNA

description: Oxidized small RNA

value: mixed 129X1/SvJ x C57BL/6J

value: Miwi-Het


title: Mouse Miwi Heterozygous 17.5 dpp Oxidized small RNA

description: Oxidized small RNA


title: Mouse A-Myb Mutant 14.5 dpp Oxidized small RNA

description: Oxidized small RNA

value: A-Myb-Mut


title: Mouse A-Myb Mutant 17.5 dpp Oxidized small RNA

description: Oxidized small RNA


title: Mouse Spo11 Heterozygous 14.5 dpp small RNA

description: small RNA


title: Mouse Spo11 Mutant 14.5 dpp small RNA

description: small RNA


title: Mouse Miwi Mutant 17.5 dpp small RNA

description: small RNA

value: Miwi-Mut


title: Mouse A-Myb Heterozygous 14.5 dpp Oxidized small RNA

description: Oxidized small RNA

value: A-Myb-Het


title: Mouse A-Myb Heterozygous 17.5 dpp Oxidized small RNA

description: Oxidized small RNA


title: Mouse Wild Type 6 weeks dpp small RNA

description: small RNA


title: Mouse Wild Type 20.5 dpp small RNA

description: small RNA


title: Mouse Wild Type 17.5 dpp small RNA

description: small RNA


title: Mouse Wild Type 12.5 dpp Oxidized small RNA

description: Oxidized small RNA


title: kidney - MethylC-seq

source_name: kidney (4 year-old male)

value: kidney

value: male


title: Mouse Wild Type 10.5 dpp Oxidized small RNA

description: Oxidized small RNA

value: testes


title: Mouse Wild Type 14.5 dpp Oxidized small RNA

description: Oxidized small RNA


title: cerebellum - MethylC-seq

source_name: cerebellum (8 year-old male)

value: cerebellum


title: Mouse Wild Type 10.5 dpp small RNA

description: small RNA


title: Mouse A-Myb Mutant 17.5 dpp small RNA

description: small RNA


title: Mouse Miwi Mutant 17.5 dpp Oxidized small RNA

description: Oxidized small RNA


title: Mouse Miwi Heterozygous 17.5 dpp small RNA

description: small RNA


title: Mouse Miwi Mutant 14.5 dpp small RNA

description: small RNA


title: Mouse Miwi Heterozygous 14.5 dpp small RNA

description: small RNA


title: Mouse A-Myb Mutant 14.5 dpp small RNA

description: small RNA


title: Mouse A-Myb Heterozygous 14.5 dpp small RNA

description: small RNA


title: Mouse Miwi Mutant 14.5 dpp Oxidized small RNA

description: Oxidized small RNA


title: Mouse A-Myb Heterozygous 17.5 dpp small RNA

description: small RNA


title: Mouse Wild Type 12.5 dpp small RNA

description: small RNA


title: Wild Type Adult PAS

description: library strategy: PAS-Seq

data_processing:
PAS library was analyzed as follows: We first removed adaptors and performed quality control using Flexbar 2.2 (http://sourceforge.net/projects/theflexibleadap) with the parameters “-at 3 -ao 10 --min-readlength 30 --max-uncalled 70 --phred-pre-trim 10.” For reads beginning with GGG including (NGG, NNG or GNG) and ending with three or more adenosines, we removed the first three nucleotides and mapped the remaining sequence with and without the tailing adenosines to the mouse genome using TopHat 2.0.4. We retained only those reads that could be mapped to the genome without the trailing adenosine residues. Genome-mapping reads containing trailing adenosines were regarded as potentially originating from internal priming and thus discarded. The 3′ end of the mapped, retained read was reported as the site of cleavage and polyadenylation.
Genome_build: mm9
Supplementary_files_format_and_content: BED

growth_protocol: Mice were maintained and used according to the guidelines of the Institutional Animal Care and Use Committee of the University of Massachusetts Medical School.

extract_protocol: PAS-seq libraries (Table S1) were prepared essentially as described (Shepard et al., 2011) and sequenced using a HiSeq 2000 (100 nt read length).

value: Adult


title: Wild Type 10.5 dpp CAGE

data_processing:
CAGE libraries were analyzed as follows: After removing adaptor sequences and checking read quality using Flexbar 2.2 with the parameters of “-at 3 -ao 10 --min-readlength 20 --max-uncalled 70 --phred-pre-trim 10”, we retained only reads beginning with NG or GG (the last two nucleotides on the 5′ adaptor). We then removed the first two nucleotides and mapped the sequences to the mouse genome using TopHat 2.0.4. All unique 5′ ends of the mapped positions were considered as CAGE-tag starting sites and grouped into tag clusters using a distance-based method in which the maximal distance between two neighboring tags was required to be <20 bp. The peak position of a tag cluster was then reported as the transcription start site.
Genome_build: mm9
Supplementary_files_format_and_content: BED

extract_protocol: CAGE (cap analysis of gene expression) was as described (Yang et al., 2011)

value: wild-type


title: Wild Type Adult CAGE


title: Mouse Wild Type 14.5 dpp small RNA

description: small RNA


title: Rooster Wild Type Adult Oxidized small RNA

description: Oxidized small RNA

value: White Leghorn of the Cornell Special C strain


title: VS8

status: Public on Mar 26 2013

city: Lanzhou

first: Zhipeng

last: Liu

address: No. 768, Jiayuguan west road

institute: College of Pastoral Agricultural Science and Technology, Lanzhou University

data_processing: To get the clean reads, removing the dirty raw reads is needed before data analysis. Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment. Raw reads of every sample can't be less than requirement of the contract. In addition, statistical analysis is conducted to summarize the number of clean reads that align to the reference genome, which provides the general information of the project.

organism: Vicia sativa

source_name: Roots

growth_protocol: Plants were grown in a greenhouse under a 16-hr light/8-hr dark cycle at 22°C at Lanzhou University, Lanzhou, China.

extract_protocol: After extracting the total RNA from the eight organs, mRNA is enriched by using the oligo(dT) magnetic beads. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000 (BGI Shenzhen).

value: Lanjian 3

value: Roots

tag: development stage

value: 2-week-old seedlings


title: VS7

source_name: Leaves

value: Leaves


title: VS6

source_name: Carpels

value: Carpels

value: Floral stage 12 of approximately 45 days plants


title: VS5

source_name: Stamens

value: Stamens


title: VS4

source_name: Ventral petals

value: Ventral petals


title: Alate queen

city: Atlanta

first: Brendan

last: Hunt

state: GA

address: 310 Ferst Dr

department: School of Biology

institute: Georgia Institute of Technology

description: Approximately equal masses of genomic DNA were pooled from five individual alate queens

data_processing:
Each of our sequenced libraries underwent basic quality control by Beijing Genomics Institute and passed the FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) quality control metrics of ‘per base sequence quality’, ‘per sequence quality scores’, ‘per base N content’, ‘sequence length distribution’, and ‘overrepresented sequences’ upon receipt.
We used the program Bismark to align raw sequencing reads to the reference genome (gnF).  We first mapped our paired end 90 base reads using the ‘paired end’ option in Bismark, which implemented Bowtie2.  We then took the reads that failed to map during the first alignment and reran the forward reads using the ‘directional’ option in Bismark, specifying that reads can only align in the forward direction.  We did not map ‘reverse’ reads that failed to map with the ‘paired end’ option because these reads could not be treated as directional (when we attempted to map non-mapping ‘reverse’ reads non-directionally, this resulted in limited mis-mapping that incorrectly gave the appearance of non-CG methylation).
Aligned reads were processed using SAMtools to remove duplicate reads with the ‘rmdup’ function and to generate files in ‘pileup’ format, which was subsequently parsed using custom perl scripts to obtain methylated and unmethylated read counts on a nucleotide-specific basis.  Given the symmetrical nature of CpG dinucleotides, reads from each strand ('watson' and 'crick') were merged.
Genome_build: gnF
Supplementary_files_format_and_content: tab-delimited text file includes unconverted (base 'C') and converted (base 'T') read counts for each library, for each CpG dinucleotide in the genome covered by at least one read

organism: Solenopsis invicta

source_name: whole bodies

extract_protocol: DNA was extracted using standard phenol-chloroform extractions.  Bisulfite conversion and sequencing was performed by Beijing Genomics Institute (Shenzhen, China).  Unmethylated enterobacteria phage lambda  DNA (GenBank accession: J02459.1) was added to each genomic DNA sample as a control for bisulfite conversion efficiency.  Each sample was then fragmented by sonication.  Illumina (San Diego, CA, USA) methylated paired end sequencing adaptors were ligated to 3’-dA overhangs following DNA-end repair.  Bisulfite treatment was performed using the ZYMO EZ DNA Methylation-Gold kit (Zymo Research Corporation, Irvine, CA, USA).  Bisulfite-treated Illumina libraries were then desalted, size selected, subject to PCR amplification, and size selected once again prior to sequencing.  Obtained sequencing reads were paired end with a length of 2 x 90 nucleotides.

tag: developmental stage

value: adult

tag: morph

value: Alate queen

tag: gender

value: female


title: Male (haploid)

description: Approximately equal masses of genomic DNA were pooled from five individual haploid males

value: Male (haploid)

value: male


title: Worker

description: Approximately equal masses of genomic DNA were pooled from three DNA extractions from multiple workers (> 10 individuals with total masses of 32 mg, 25 mg, and 21 mg used for each DNA extraction)

value: Worker


title: VS1

source_name: Sepals

value: Sepals


title: VS3

source_name: Lateral petals

value: Lateral petals


title: VS2

source_name: Dorsal petals

value: Dorsal petals


title: 727R mbovis 24h

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

data_processing:
Cluster generation and sequencing of the pooled RNA-seq library was carried out on an Illumina® Cluster Station and Illumina® Genome Analyzer IIx sequencer according to the manufacturer’s instructions (Illumina). The pooled library was sequenced as single-end read 84-mers using Illumina® version 4.0 sequencing kits and the standard Illumina® Genome Analyzer IIx pipeline. The Illumina® Sequencing Control Software version 2.9 and Real Time Analysis version 1.9 software packages were used for real-time tracking of the sequencing run, real-time image processing, the generation of base intensity values and base calling.
Sequence reads obtained from seven lanes of the Illumina flow cell were deconvoluted into 14 individual libraries (Raw data files) using the unique indexed barcoded adapters. A Perl script was used to screen adapter artefacts, removing any reads containing a full-length match to the 33 nucleotide Illumina® adapter sequence, allowing up to four mismatches. Read quality was then assessed using FastQC software [version 0.9] (www.bioinformatics.bbsrc.ac.uk/projects/fastqc), revealing low Phred scores at the 3' end of sequence reads. Consequently, nine nucleotides were trimmed from the 3' ends of all sequence reads using the FASTX Toolkit [version 0.0.13] (http://hannonlab.cshl.edu/fastx_toolkit) generating usable reads of 69 nucleotides.
Deconvoluted quality-checked sequence reads were aligned to the B. taurus reference genome (Btau 4.0.63 genome release) with the TopHat splice junction mapper [version 1.3.0], which aligns reads using the Bowtie aligner (version 0.12.7). The Bowtie alignment procedure was configured for strand-specific libraries and to filter only unique hits to the reference genome sequence.
To obtain raw counts per transcript, HTSeq package [version 0.5.3p1] (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) was used on alignment files in BAM format. HTSeq-count was used with option overlap resolution mode set to intersection non-empty. Counts of uniquely-mapped reads were obtained for all bovine Ensembl genes and transcripts, with separate counts obtained for sense (Processed sense data files) and antisense (Processed antisense data files) DNA strands.
Once raw counts were obtained from HTseq-count, analysis of differential expression was performed in the R statistical programming environment using the edgeR (version 2.2.5) Bioconductor package and lattice [version 0.19-30] (http://lattice.r-forge.r-project.org). First, quality checks were performed by plotting the density of counts per feature (a feature being a gene or transcript generated respectively from the sense or antisense strand) for each sample and also by generating a multidimensional scaling plot of the RNA-seq data. The edgeR software package was used to determine differential expression using the paired-sample statistical test. Filtering of lowly expressed features was performed by retaining only features with at least one count per million in three or more libraries. A normalisation factor was calculated using the default trimmed mean of M values (TMM) method, and the dispersion parameter for each feature was estimated as the Cox-Reid common dispersion method in the edgeR package. Differential expression was evaluated by fitting a negative binomial generalized linear model for each feature and then adjusting the P-value for multiple testing using the Benjamini-Hochberg correction with a false discovery rate (FDR) of 0.05.
Genome_build: Bos taurus reference genome version 4.0.63
Supplementary_files_format_and_content: Tab-delimited text files include raw count values per genes

organism: Bos taurus

source_name: Monocyte-derived macrophages

growth_protocol: Seven age-matched (three-year old) Holstein-Friesian females were used. All animals were maintained under uniform housing conditions and nutritional regimens at the UCD Lyons Research Farm (Newcastle, County Kildare, Ireland). The animals were selected from an experimental herd without a recent history of bovine tuberculosis infection. This was confirmed using the single intradermal tuberculin test (SICTT) and the BoviGAM® IFN-g enzyme linked immunosorbent assay (ELISA; Prionics AG, Schlieren-Zurich, Switzerland) with all animals testing negative. These cattle also tested negative for Brucella abortus, M. avium subsp. paratuberculosis, Salmonella typhimurium, bovine herpesvirus 1 and bovine viral diarrhoea (BVD) virus. For monocyte isolation, 300 ml of whole blood was collected in acid citrate dextrose buffer (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) in sterile bottles. Blood was layered onto Accuspin™ tubes containing Histopaque® 1077 (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and following density gradient centrifugation, peripheral blood mononuclear cells (PBMC) were collected. Contaminating red blood cells (RBC) were removed following resuspension and subsequent incubation of the PBMC in RBC lysis buffer (10mM KHCO3, 150mM NH4Cl, 0.1mM EDTA pH 8.0) for 5 minutes at room temperature. After incubation, PBMC were washed twice with phosphate-buffered saline (PBS) before resuspending cells in phosphate-buffered saline (PBS) containing 1% bovine serum albumin (BSA, Sigma-Aldrich Ireland Ltd., Dublin, Ireland). Monocytes were then isolated using the MACS® protocol and a human anti-CD14 antibody (Miltenyi Biotec Ltd., Surrey, UK), which has been shown to be cross-reactive with bovine monocytes. All procedures were carried out according to the manufacturers’ instructions. The identity and purity of monocytes was confirmed by flow cytometry using an anti-CD14 FITC labelled antibody. Purified monocytes were seeded at 1 × 106/ml in 24-well tissue culture plates in RPMI 1640 medium (Invitrogen Ltd., Paisley, UK) containing 15% heat inactivated foetal calf serum (FCS; Sigma-Aldrich Ireland Ltd., Dublin, Ireland), 1% non-essential amino acids (NEAA; Sigma-Aldrich Ireland Ltd., Dublin, Ireland), gentamicin (5 µg/ml; Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and incubated at 37°C, 5% CO2. Following 24 hours incubation (day one) the media was replaced with 1ml fresh antibiotic-containing media to remove any non-adhered cells. On day three, media was replaced with 1 ml antibiotic-free culture media (RPMI 1640 medium containing 15% heat inactivated FCS and 1% NEAA only). To ensure that the same number of MDM were subjected to different treatments between experiments, cells were dissociated on day five using a non-enzymatic cell dissociation solution (Sigma-Aldrich Ireland Ltd., Dublin, Ireland), counted and then re-seeded at 2 × 105 cells/well in 24-well tissue culture plates (Sarstedt, County Wexford, Ireland) using antibiotic-free culture media. By day eight, 80-100% confluent monolayers of MDM were generated that displayed the characteristic macrophage morphology as confirmed by Giemsa staining (data not shown). Day eight MDM were used for the in vitro challenge experiments with M. bovis.

extract_protocol:
All RNA extractions were performed in the CL3 laboratory using an RNeasy kit incorporating an on-column DNase treatment step (Qiagen Ltd., Crawley, UK) according to the manufacturer’s instructions. RNA quantity and quality was assessed using both the NanoDropTM 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and the Agilent 2100 Bioanalyzer using an RNA 6000 Nano LabChip kit (Agilent Technologies, Cork, Ireland). All samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers (RIN) greater than 8.5.
In total, 14 strand-specific RNA libraries for high-throughput sequencing were prepared (seven libraries for each treatment: M. bovis-infected and control samples) using 200 ng of total RNA. Total RNA was first heated at 65°C for 5 min to disrupt any secondary structure. Purification of poly(A) RNA was performed using a Dynabeads® mRNA DIRECTTM Micro Kit according to the manufacturer’s instructions (Invitrogen™/Life Technologies Ltd., Paisley, UK). Purified poly(A) RNA was then fragmented using 1× RNA Fragmentation Reagent (Ambion®/Life Technologies Corporation, Warrington, UK) for 5 min at 70°C and precipitated using 68 mM sodium acetate pH 5.2 (Ambion), 227 ng/μl glycogen (Ambion) and 30 μl of 100% ethanol (Sigma-Aldrich Ltd., Dublin, Ireland). Pellets were washed with 80% ethanol, air-dried for 10 min at room temperature and re-suspended in 10.5 µl DNase- and RNase-free water. Synthesis of first strand cDNA was performed by incubating fragmented RNA with 261 mM Random Hexamer Primers (Invitrogen), 1× first strand buffer (Invitrogen); 10 mM DTT (Invitrogen); 0.5 mM dNTPs; 20 U RNaseOUTTM Recombinant Ribonuclease Inhibitor; and 200 U SuperScript® II Reverse Transcriptase (Invitrogen) at 25°C for 10 min, at 42°C for 50 min, and 70°C for 15 min. First strand synthesis reaction mixtures were purified using MicroSpinTM G-50 columns according to the manufacturer’s instructions (GE Healthcare UK Ltd., Little Chalfont, Buckinghamshire, UK). Second strand cDNA synthesis, involving the incorporation of uracil, was performed by adding the first strand cDNA synthesis reaction to a second strand reaction mix consisting of 0.065× first strand buffer (Invitrogen); 1× second strand buffer (Invitrogen); a dNTP mix consisting of a final concentration of 0.3 mM dATP, dCTP, dGTP (Sigma-Aldrich) and 0.3 mM dUTP (Bioline Reagents Ltd., London, UK); 1 mM DTT (Invitrogen); 2 U RNase H (Invitrogen) and 50 U E. coli DNA Polymerase I (Invitrogen). Reactions were incubated at 16°C for 2.5 h. The double stranded cDNA was subsequently purified using a QIAquick PCR Purification kit (Qiagen) according to the manufacturer’s instructions and eluted in 30 µl of the provided elution buffer. Blunt-end repair of cDNA was performed in a 100 µl reaction containing 1× T4 DNA ligase buffer with 10 mM dATP (New England Biolabs® Inc., MA, USA), 0.4 mM of each dNTP (Invitrogen), 15 U T4 DNA polymerase (New England Biolabs), 5 U DNA Polymerase I Large [Klenow] Fragment (New England Biolabs) and 50 U T4 polynucleotide kinase (New England Biolabs). Reactions were incubated at 20°C for 30 min and the cDNA was then purified using a QIAquick PCR Purification Kit (Qiagen) according to the manufacturer’s instructions and eluted in 32 µl of the provided elution buffer. To facilitate Illumina® GA adaptor ligation, a single ‘A’ base was added to the 3' ends of the blunt-end repaired cDNA samples. 32 µl of purified phosphorylated blunt end-repaired cDNA was included in a final 50 µl reaction mixture containing: 1× Klenow fragment buffer (New England Biolabs); 0.2 mM dATP (Invitrogen), and 15 U Klenow fragment with 3'-to-5' exonuclease activity (New England Biolabs). Reactions were incubated at 37°C for 30 min, after which cDNA was purified using a QIAquick MinElute Kit (Qiagen) according to the manufacturer’s instructions and eluted in 21 µl of the provided elution buffer. Illumina® RNA-seq adaptor ligation reactions (50 µl volumes) involved incubation of 21 µl of phosphorylated blunt-ended cDNA containing a 3'-dATP overhang with 1× Quick DNA ligase buffer (New England Biolabs); 30 nM custom indexed single-read adaptors (see Samples_barcode.xlsx) and 15 U T4 DNA ligase (Invitrogen). Reaction mixes were incubated at room temperature for 15 min and purified using a QIAquick MinElute Kit according to the manufacturer’s instructions (Qiagen) and eluted in 10 µl of the provided elution buffer. Adaptor-ligated cDNA was gel-purified using 2.5% agarose gels stained with 1 μg/ml ethidium bromide (Invitrogen). Gels were electrophoresed at 100 Volts using 1× TAE buffer (Invitrogen) for 75 min at room temperature. Size fractionated bands corresponding to 200 bp (+50 bp) were excised from each sample and purified using a QIAquick Gel Extraction kit (Qiagen) according to the manufacturer’s instructions and eluted in 30 µl of elution buffer. To generate strand-specific RNA-seq libraries, the second strand of the gel-purified adapter-ligated cDNA containing uracil was digested enzymatically in 30 µl reaction volumes containing 1× Uracil-DNA Glycosylase buffer and 1 U Uracil-DNA Glycosylase (Bioline). Reactions were incubated at 37°C for 15 min followed by 94°C for 10 min. PCR enrichment amplifications (50 µl) containing 15 μl of second strand-digested, adaptor-ligated cDNA; 1× Phusion® High-Fidelity DNA polymerase buffer (New England Biolabs); 334 nM each Illumina® PCR primer (Illumina® Inc., San Diego, CA, USA); 0.4 mM each of dATP, dCTP, DGTP and dTTP (Invitrogen) and 1 U Phusion® High-Fidelity DNA polymerase (New England Biolabs). PCR amplification reactions consisted of an initial denaturation step of 98°C for 30 seconds, 18 cycles of 98°C for 10 seconds, 65°C for 30 seconds and 72°C for 30 seconds, followed by a final extension step of 72°C for 5 min. PCR products were visualised following electrophoresis on a 2% agarose gel stained with ethidium bromide (0.6 µg/ml; Invitrogen) and purified to remove PCR-generated adaptor-dimers using an Agencourt AMPure XP kit (Beckman Coulter Genomics, Danvers, MA, USA) according to the manufacturer’s instructions with final elution in 30 μl of 1× TE buffer. All RNA-seq libraries were quantified using a Qubit® Fluorometer and Qubit® double stranded DNA High Sensitivity Assay Kit (Invitrogen). RNA-seq library quality was assessed using an Agilent Bioanalyzer and Agilent High sensitivity DNA chip (Agilent) and confirmed that library insert sizes were ~200-250 bp for all individual libraries. Individual RNA-seq libraries were standardised and pooled in equimolar quantities (10 µM for each individual library). The quantity and quality of the final pooled library was assessed as described above prior to sequencing.

treatment_protocol: Culturing of M. bovis was performed in a Biosafety Containment Level 3 (CL3) laboratory and conformed to the national guidelines on the use of Hazard Group 3 infectious organisms. A clinical isolate of M. bovis, obtained from an infected Irish animal was supplied by Dr. Eamon Costello (Department of Agriculture, Fisheries and Food, Backweston, County Kildare) was used in the current study. M. bovis stocks for MDM-challenge experiments were cultured in Middlebrook 7H9 medium (DifcoTM, Becton-Dickinson, Dublin, Ireland) containing 10% (volume/volume) Middlebrook albumin-dextrose-catalase (ADC) enrichment (DifcoTM, Becton-Dickinson, Dublin, Ireland), 0.05% Tween 80 (Sigma-Aldrich, Dublin, Ireland) and 0.40% (weight/volume) sodium pyruvate (Sigma-Aldrich, Dublin, Ireland) at 37°C. For colony forming unit (cfu) counting Middlebrook 7H11 medium (DifcoTM, Becton-Dickinson, Dublin, Ireland) containing 0.40% (volume per volume) sodium pyruvate and 10% (volume/volume) Middlebrook (ADC) enrichment. Bacterial cultures were grown to mid-logarithmic phase as determined by spectrophotometric analysis prior to the challenge experiments using the purified bovine MDM. All challenge experiments including the preparation of non-challenge control samples were performed in the CL3 laboratory. MDM samples (seeded at 2 × 105 cells per well) were challenged with M. bovis (4 × 105 cells/well; based on bacterial cell counts performed using a Petroff Hausser chamber (Fisher-Scientific, Dublin, Ireland) [multiplicity of infection 2:1] and incubated at 37°C, 5% CO2 for 24 hours. For the non-challenged control samples at 24 hours, antibiotic-free culture media (RPMI 1640 medium containing 15% heat inactivated FCS and 1% NEAA only) was added to each well. After 2 hours post-challenge, the media from all 24 hours challenge experiments was replaced with 0.5 ml fresh antibiotic-free culture media per well and re-incubated at 37°C, 5% CO2 until MDM were required for harvesting. Challenged and non-challenged control MDMs were lysed and harvested using RLT/1% β-mercaptoethanol buffer (Qiagen Ltd., Crawley, UK) at the designated time points. For each treatment, MDM lysates from two culture plate wells were pooled and stored at ‑80°C until required for RNA extraction.

value: Holstein-Friesian

value: Female

value: Four years old

tag: animal id

tag: cell type

value: Monocyte-derived macrophages

tag: infection status

value: M. bovis-infected


title: 727R control 24h

value: Control uninfected


title: 721 control 24h


title: 724R mbovis 24h


title: 721 mbovis 24h


title: 716 mbovis 24h


title: 716 control 24h


title: 713 mbovis 24h


title: 713 control 24h


title: 706 control 24h


title: Rooster Input DNA ChIPSeq

data_processing:
ChIP-seq reads were aligned to the genome (mouse mm9, chicken gg3) using Bowtie version 0.12.7 (Langmead et al., 2009). Reads were mapped uniquely using the '-M 1 --best --strata' switches and one mismatch was allowed (-v 1).
ChIP peaks were identified using MACS version 1.4.1 (Zhang et al., 2008) using default arguments, input as control, and a cutoff p-value = 10-25 was used. Peaks of all p-values are supplied here.
Genome_build: Gallus_gallus-2.1
Supplementary_files_format_and_content: BED files containing called peaks (all p-values).

source_name: Testes, input

extract_protocol:
ChIP was performed as described (Chen et al., 2008) except that testes were macerated on ice and then fixed with 1.5% (w/v) formaldehyde for 20 min. Samples were then further crushed using 20 strokes with a 'B' pestle in a Dounce homogenizer (Kimble-Chase, Vineland, NJ, USA). Chromatin was sheared by sonication and immunoprecipitated using anti-A-MYB (HPA008791; Sigma, St. Louis, MO, USA), anti-H3K4me3 (ab8580; Abcam, Cambridge, MA, USA), or anti-RNA polymerase II antibody (N20, sc899, Santa Cruz Biotechnology, Santa Cruz, CA, USA); immunoglobulin G (IgG; Sigma, item 2729) served as a control.
ChIP-seq libraries were prepared following the Illumina ChIP-seq protocol and sequenced on a HiSeq 2000 (50 nt reads).

tag: breed

value: Brown Leghorn

value: testes

tag: chip antibody

value: immunoglobulin G


title: 700 mbovis 24h

tag: Sex


title: 700 control 24h


title: Rooster H3K4me3_ChIPSeq

source_name: Testes, H3K4me3_ChIP


title: 706 mbovis 24h


title: Male (diploid)

description: Approximately equal masses of genomic DNA were pooled from five individual diploid males

value: adult

value: Male (diploid)


title: Rooster A-MYB ChIPSeq

source_name: Testes, A-MYB ChIP

value: anti-A-MYB


title: T6-Spin1i-1-R mRNA-seq

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
mRNA-seq reads were uniquely mapped to the genome using Bowtie (Langmead et al., 2009) allowing two mismatches. For smRNA-seq reads, adapter sequences were trimmed first, and then were uniquely mapped to the genome using Bowtie allowing no mismatches, and reads were categorized by their lengths for analyses
Genome_build: MSU 6.1
Supplementary_files_format_and_content: Column 1 is the read sequence. Column 2 is the number of reads with the given sequence.

organism: Oryza sativa

source_name: 3wk-old leaf tissue

extract_protocol: Total RNA (10 ug) for each sample was used to purify poly-A mRNA; this mRNA was used for synthesis and amplification of cDNA. The RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit from Illumina (San Diego, CA).

treatment_protocol: RNA-seq libraries were constructed from total RNA isolated using TRIzol reagent (Invitrogen, Life Technologies, USA) from leaf tissues

value: leaf

value: Spin1 RNAi

tag: ecotype

value: Nipponbare

tag: rna subtype

value: polyA mRNA


title: T6-Pi9-R mRNA-seq


title: T6-PiZt-11-R mRNA-seq

value: PiZt 11