title: Marmoset_21_infected_day3_lesion_2_run_1

source_name: Lung, animal 21, day 3, lesion 2


title: F104_1

status: Public on Jun 10 2014

type: SRA

city: Bar Harbor

first: Steven

middle: C

last: Munger

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

library_source: transcriptomic

data_processing:
Basecalls were performed with CASAVA version 1.8.0
Fragmented fastq files from CASAVA were concatenated together, and then reads that did not pass quality filtering were removed with fastq_illumina_filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/)
Read Alignment - Individualized transcriptomes (isoform sequences) derived from the genome fasta file and corresponding gene annotation gtf files were used to construct Bowtie-compatible indexes with the rsem-prepare-reference command in RSEM software (Li and Dewey, 2010; RSEM version 1.2.1). For inbred genomes (CAST, NCBIM37), each Ensembl transcript identifier corresponds to a single sequence. The Bowtie aligner (version 0.12.8) was used to align reads to transcript sequences. Alignments with up to three mismatches (-v 3) across the 100bp read were considered valid, but only the best “strata” of alignments were reported. For a given read, the best stratum is the alignment(s) with the least mismatches.
Transcript Abundance Quantitation - Estimates of isoform and gene-level abundance were obtained with RSEM (Li and Dewey 2010). Bowtie alignment files in .bam format were input into the rsem-calculate-expression command. Based on the library fragment size distributions observed on the Agilent Bioanalyzer, fragment length mean was specified as 280bp with a standard deviation of 50bp (RSEM parameters --fragment-length-mean 280 –fragment-length-sd 50). For reads with multiple valid isoform alignments, RSEM implements an expectation-maximization (EM) algorithm that assigns all or a proportion of each multimapping read to one or more isoforms based on the number of uniquely-aligning reads to those transcripts. RSEM estimates isoform expression (counts), and gene-level counts are calculated as the sum of the corresponding isoforms.
Normalization - For each sample, RSEM count estimates were normalized to the upper quartile value (after trimming zeros).
Genome_build: Mouse NCBIM37/mm9. Individualized diploid DO genomes were based on NCBIM37 coordinates.
Supplementary_files_format_and_content: All processed data files are tab-deliminited txt files. Each file contains a data matrix with rows representing Ensembl gene id's and columns representing samples. Only genes with non-zero values in ≥85% of samples were included in the final analysis.

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol:
Male and female Diversity Outbred mice (J:DO Stock# 009376) were obtained from The Jackson Laboratory (Bar Harbor, ME). Animals were received at 3 weeks of age, housed at The Jackson Laboratory, and given free access to either standard rodent chow containing 6% fat by weight (LabDiet 5K52, LabDiet, Scott Distributing, Hudson, NH) or high-fat chow containing 22% fat by weight (TD.08811, Harlan Laboratories, Madison, WI) from wean age throughout the study. Animals were phenotyped for multiple metabolic and hematological parameters as described in Svenson et al. (2012), and then sacrificed at 26 weeks of age. Liver samples were collected from each animal and stored in RNAlater® solution (Life Technologies) at -80°C.
Male mice from each of the eight DO founder strains (n= 16 for each strain, n= 128 total) were obtained from The Jackson Laboratory. Mice were received at ~3 weeks of age, housed at the University of Wisconsin Madison, and beginning at 4 weeks of age given free access to either a control diet containing 17% kcal fat (TD.8010) or a high-fat, high-sucrose diet containing 45% kcal from fat and 34% (by weight) sucrose (TD.08811). Both diets were from standard rodent chow containing 6% fat by weight (LabDiet 5K52, LabDiet, Scott Distributing, Hudson, NH) or high-fat chow containing 22% fat by weight (TD.08811, Harlan Laboratories, Madison, WI) from wean age throughout the study. With the exception of NZO mice, animals were sacrificed at 26 weeks of age, and liver samples were collected, snap frozen, and shipped on dry ice to The Jackson Laboratory for RNA-seq analysis. Due to a high level of lethality of NZO mice that were maintained on the high-fat/high-sucrose diet, all NZO mice were sacrificed at 20 weeks of age.

extract_protocol:
Livers were dissected and stored in RNAlater at -80C (DO samples), or snap frozen and stored on dry ice (founder strain samples). Total RNA was isolated using the Trizol Plus RNA extraction kit (Life Technologies) with on-column DNase digestion.
Following the Illumina TruSeq standard protocol, indexed mRNA-seq libraries were generated from 1μg total RNA followed by QC and quantitation on the Agilent Bioanalyzer and the Kapa Biosystems qPCR library quantitation method.

tag: sample id

tag: strain

value: Diversity Outbred heterogeneous stock

tag: age (weeks)

tag: genotyped sex

value: Female

tag: diet

value: Standard Chow

tag: block

tag: flowcell

tag: lane

tag: barcode

value: AGTCAA

tag: tissue

value: liver


title: F116_1

value: CTTGTA


title: Marmoset_21_infected_day3_lesion_1_run_1

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

data_processing:
Reads were aligned to the Marmoset reference genome using the gapped aligner software STAR and Ht-seq (Callithrix_jacchus.C_jacchus3.2.1.74), MERS genome (GenBank accession no. K02013).
Genome_build: Callithrix jacchus-3.2, MERS-virus (GenBank JX869059)
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each animal using Htseq and the GTF provided from ENSEMBL (Callithrix_jacchus.C_jacchus3.2.1.74).

organism: Callithrix jacchus

source_name: Lung, animal 21, day 3, lesion 1

extract_protocol:
We started with 250ul Trizol homogenate from lung and used the Qiagen miRNA kit to extract the RNA.
For Total RNA-seq analysis, approximately 2.5 ug micrograms of total RNA from each sample was submitted. In brief, ribosomal RNAs (rRNAs) were depleted using the RiboZero Human/Mouse/Rat Isolation Kit . The 50 nt single-end sequencing was done using an Illumina MiSeq™.
Libraries were TruSeq Stranded Total RNA and clustering was Illumina version 2 MiSeq reagents.

value: lung

tag: animal number

tag: treatment

value: Middle East respiratory syndrome coronavirus (MERS-CoV) infection

tag: day of infection

tag: lesion number

tag: technical replicate


title: F103_1

value: GTTTCG


title: F102_1

value: ACAGTG


title: Marmoset_20_infected_day3_lesion_1_run_2

source_name: Lung, animal 20, day 3, lesion 1


title: Marmoset_20_infected_day3_lesion_2_run_2

source_name: Lung, animal 20, day 3, lesion 2


title: Marmoset_20_infected_day3_lesion_1_run_1


title: F101_1


title: F100_1

value: High Fat

value: CCGTCC


title: Marmoset_19_infected_day3_lesion_2_run_2

source_name: Lung, animal 19, day 3, lesion 2


title: Marmoset_19_infected_day3_lesion_1_run_2

source_name: Lung, animal 19, day 3, lesion 1


title: Marmoset_20_infected_day3_lesion_2_run_1


title: Marmoset_19_infected_day3_lesion_1_run_1


title: Marmoset_19_infected_day3_lesion_2_run_1


title: Anisomycin replicate 1B

city: Berkeley

first: Liana

middle: F

last: Lareau

state: CA

address: Barker Hall 424

department: California Institute for Quantitative Biosciences

institute: University of California, Berkeley

description: anisomycin_1A and anisomycin_1B are technical replicates from the same culture.

data_processing:
library strategy: Ribo-Seq (ribosome profiling)
Cloning linker sequences were trimmed from Illumina reads. Trimmed sequences were aligned to S. cerevisiae ribosomal and noncoding RNA sequences using bowtie v. 0.12.7 or v. 1.0.0 to remove rRNA reads. The non-rRNA reads were aligned to the S. cerevisiae genome as a first pass to remove any reads that mapped to multiple locations. Reads that passed this filter were then aligned to the S. cerevisiae transcriptome with bowtie, allowing two mismatches and only reporting alignments of reads that mapped uniquely in the transcriptome (bowtie -v 2 -m 1 -a --norc --best –strata). A list of read counts and read lengths per nucleotide position in the transcriptome, based on the 5’ end of the mapped read, was generated.
The counts of small and large footprints from ribosomes with each codon positioned in the inferred A site were generated from the list of reads at each nucleotide position. The large footprints were defined as 28 nt reads with the 5’ end 15 nt upstream of the codon at position i, and 29 nt reads with the 5’ end 16 nt upstream of i. Small footprints included 20 nt and 21 nt reads with the 5’ end 15 nt upstream of i and 21 nt and 22 nt reads with the 5’ end 16 nt upstream of i. For each gene, the analysis included codons 51 through the second codon before the stop codon, to avoid the region at the beginning of genes from which ribosomes have been depleted by runoff elongation during harvest. Genes with fewer than 10 footprints in total were excluded, as were any non-unique 20mer regions within genes.
Genome_build: sacCer2
Supplementary_files_format_and_content: A percodon.txt file for each sample provides the count of small and large ribosome footprints at each codon, starting at the 51st codon of each gene. Files include gene symbol, codon position, codon sequence, and count of small and large ribosome footprints with that position in the inferred A site. Genes with fewer than 10 footprints are excluded.

organism: Saccharomyces cerevisiae

source_name: Anisomycin

growth_protocol: Yeast were innoculated from an overnight culture into 500mL of YEPD media then grown at 30C from a starting OD of 0.2 to a final OD of ~0.6.

extract_protocol:
Cells were harvested by filtration then frozen in liquid N2 and pulverized using a Retsch mixer mill. Lysis buffer was added to cell powder and lysates were clarified by centrifugation. RNAse I was added to cell lysate. After RNAse digestion, lysate was sedimented in a linear 10%-50% sucrose gradient at 35000rpm for 3 hours. Gradients were fractionated and the monosome peak fraction was collected. RNA was purified using a miRNeasy Mini kit from Qiagen.
RNA was size selected using 18 and 34 nt size markers then treated to remove the 3’ phosphate and ligated to the Universal miRNA cloning linker from New England Biolabs. Ligated fragments were reverse transcribed using a primer complementary to the cloning linker which introduced sequencing adapters. RNA template was removed and cDNA was circularized using CircLigase ssDNA ligase from Epicentre. Ribosomal RNAs were removed by hybridization to subtraction oligos. Libraries were amplified with PCR. Libraries were then sequenced on an Illumina Genome Analyzer 2 or an Illumina HiSeq 2000.

treatment_protocol: Anisomycin was added to mid-log cells at 100 µg/mL and cells were allowed to grow for an additional 30 minutes prior to harvest. Anisomycin was also present at 100 µg/mL in the lysis buffer.

value: anisomycin


title: Untreated replicate 2

source_name: Untreated

treatment_protocol: untreated

value: untreated


title: Cycloheximide replicate 1

source_name: Cycloheximide

treatment_protocol: Cycloheximide was added to cells prior to harvest at 100 µg/mL and was also present at 100 µg/mL in the lysis buffer.

value: cycloheximide


title: Marmoset_22_infected_day6_lesion_1_run_2

source_name: Lung, animal 22, day 6, lesion 1


title: Anisomycin replicate 1A


title: Untreated replicate 1


title: prg-1_L1_small RNA

status: Public on Jun 09 2014

city: Beijing

first: Jiajia

last: Wang

address: 1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Removed the low quality sequence and adaptor using the independent development of software by BGI
Removed the sequence smaller than 18nt
Removed the sequence containing polyA
Achieved clean datasets from BGI, length-reads-sequence
Clean small RNAs aligned to the ce10 genome with no mismatach by using Bowtie-0.12.8
genome build: ce10

organism: Caenorhabditis elegans

source_name: prg-1 L1, whole worms

growth_protocol: Animals were grown at 20˚C with feeding on OP50

extract_protocol:
Total RNA was extracted from each of the six different developmental stages using the Trizol protocol. Small RNAs were size-selected by gel electrophoresis, and used poly(A) to extract L1-L4 mRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole worm

tag: genotype

value: prg-1 mutant


title: prg-1_L2_small RNA

source_name: prg-1 L2, whole worms


title: prg-1_L3_small RNA

source_name: prg-1 L3, whole worms


title: prg-1_L4_small RNA

source_name: prg-1 L4, whole worms


title: prg-1_Young adult_small RNA

source_name: prg-1 young adult, whole worms


title: prg-1_Embryo_small RNA

source_name: prg-1 Embryo, whole worms


title: prg-1_L4_mRNA

data_processing:
Reads were aligned to the ce10 genome assembly using TopHat v2.0.8
For each sample, FPKM was computed by Cufflinks v2.1.1
Genome_build: ce10
Supplementary_files_format_and_content: gene_fpkm

molecule: polyA RNA


title: prg-1_L3_mRNA


title: prg-1_L2_mRNA


title: prg-1_L1_mRNA


title: RNA-seq of LV sh-Gm6871 transduced mES cells - Replicate 1

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

description:
See also Castro-Diaz et al., 2014 for details regarding cell growth protocol and analysis of this data for L1 expression
Processed data file: mES_CTRLvsGmKD_allreps_L1_rpkm.txt
Processed data file: mES_CTRLvsGmKD_allreps_refseq_rpkm.txt
mES_Gm6871-KD_Rep1

data_processing:
Raw reads were mapped to the human genome (hg19), transcriptome (refseq) and a list of full-length L1( obtained from UCSC genome browser) using Bowtie 0.12.5
Chip-seq: peaks were called using MACS
RNA-seq: RPKN computed for all genes and full-length L1 elements. For L1 elements, the total number of reads mapped on the transcriptome were used for the normalization
mm9, UCSC mouse Repeatmasker and hg19, UCSC human Repeatmasker
Genome_build: hg19, mm9
Supplementary_files_format_and_content: text files contain RPKM values for all genes and full-length L1 elements for each sample
Supplementary_files_format_and_content: bedfiles contain the results of the peakcalled using MACS

source_name: Embryonic stem cells (ES3)

extract_protocol:
cytoplasmic RNA was extracted (with MN RNA extraction kit and on column DNAse treatment). The quality was assessed on a bioanalyzer, analyzed by RT-qPCR with positive and negative controls, selected for polyA+ RNA and  sequenced.
Libraries were prepared according to Illumina's instructions

tag: cell line

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: LV sh-Gm6871 transduced

tag: time point

value: 4 days after LV-sh transduction


title: RNA-seq of LV sh-empty transduced mES cells - Replicate 1

description:
See also Castro-Diaz et al., 2014 for details regarding cell growth protocol and analysis of this data for L1 expression
Processed data file: mES_CTRLvsGmKD_allreps_L1_rpkm.txt
Processed data file: mES_CTRLvsGmKD_allreps_refseq_rpkm.txt
mES_control_Rep1

tag: strain

value: LV sh-empty transduced


title: RNA-seq of LV sh-Gm6871 transduced mES cells - Replicate 2

description:
See also Castro-Diaz et al., 2014 for details regarding cell growth protocol and analysis of this data for L1 expression
Processed data file: mES_CTRLvsGmKD_allreps_L1_rpkm.txt
Processed data file: mES_CTRLvsGmKD_allreps_refseq_rpkm.txt
mES_Gm6871-KD_Rep2


title: RNA-seq of LV sh-empty transduced mES cells - Replicate 2

description:
See also Castro-Diaz et al., 2014 for details regarding cell growth protocol and analysis of this data for L1 expression
Processed data file: mES_CTRLvsGmKD_allreps_L1_rpkm.txt
Processed data file: mES_CTRLvsGmKD_allreps_refseq_rpkm.txt
mES_control_Rep2


title: Total input of mES KAP1 ChIP-seq

description:
See also Castro-Diaz et al., 2014 for details regarding cell growth protocol and analysis of this data
mES_KAP1_Ti

library_source: genomic

molecule: genomic DNA

source_name: Embryonic stem cells (J1)

extract_protocol:
ES cell samples (WT) were washed 2x (in PBS + 2% FCS), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde), quenched with glycine (at 125mM on ice), washed 3x (PBS) and pelleted at 10e7 cells per ependorf. Pellets were lysed, resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to glass 12x12mm tubes (Covaris: 520081) and sonicated (Covaris settings: 20% duty cycle, intensity 5, 200cyles/ burst, 30 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification on a Bioanalyzer (Agilent 2100 machine).
Libraries were prepared according to Illumina's instructions

value: WT

tag: chip antibody

value: none (input)


title: Total Input of Gm6871-HA ChIP

description:
See also Castro-Diaz et al., 2014 for details regarding cell growth protocol and analysis of this data
mES_Gm6871-HA_Ti

extract_protocol:
ES cell samples (ES3 cells overexpressing an HA-tagged Gm6871 expression vector) were washed 2x (in PBS + 2% FCS), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde), quenched with glycine (at 125mM on ice), washed 3x (PBS) and pelleted at 10e7 cells per ependorf. Pellets were lysed, resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to glass 12x12mm tubes (Covaris: 520081) and sonicated (Covaris settings: 20% duty cycle, PIP 140, 200cyles/ burst, 30 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification on a Bioanalyzer (Agilent 2100 machine).
Libraries were prepared according to Illumina's instructions

value: overexpressing HA-tagged Gm6871

value: 2 days after doxycycline induction of Gm6871-HA expression vector expression.


title: Gm6871-HA ChIP-seq in  mES cells

description:
See also Castro-Diaz et al., 2014 for details regarding cell growth protocol and analysis of this data
mES_Gm6871-HA_ChIP

extract_protocol:
ES cell samples (ES3 cells overexpressing an HA-tagged Gm6871 expression vector) were washed 2x (in PBS + 2% FCS), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde), quenched with glycine (at 125mM on ice), washed 3x (PBS) and pelleted at 10e7 cells per ependorf. Pellets were lysed, resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to glass 12x12mm tubes (Covaris: 520081) and sonicated (Covaris settings: 5% duty cycle, PIP 140, 200cyles/ burst, 20 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification on a Bioanalyzer (Agilent 2100 machine).
Libraries were prepared according to Illumina's instructions

value: Mouse anti-HA antibody (Covance, catalog# MMS-101P)


title: KAP1 ChIP-seq in WT mES cells

description:
See also Castro-Diaz et al., 2014 for details regarding cell growth protocol and analysis of this data
mES_KAP1_ChIP

value: Custom rabbit anti-KAP1 antibody, 5ug per IP


title: 75Ep 21C

city: Bodø

first: Jorge

middle: M. O.

last: Fernandes

address: Stoverveien 65E

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: University of Nordland

data_processing:
Raw color reads were pre-processed using CLC Genomics Workbench 4.9
Low quality reads and adapter sequences were removed using CLC Genomics Workbench 4.9
Reads not matching to miRNAs in ncRNA database were removed using BLAST
Conserved miRNAs were identified using miRBase 18.0
Species-specific miRNAs were identified using Pleurinectiformes and Solea EST database from NCBI followed by RNA secondary structure predition tool in CLC Genomics Workbench 4.9
Expression patterns were determined using hierarchical clustering with Euclidean distance and complete linkage algorithms implemented in the MeV online server
Genome_build: miRBase 18.0
Supplementary_files_format_and_content: Expression of 320 conserved miRNAs across 8 samples (log2)

organism: Solea senegalensis

source_name: Whole embryos

growth_protocol: Eggs obtained by natural spawning of captive broodstock fish

extract_protocol:
Embryos and larvae were killed by over-anaesthesia with MS222, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent and mirVana miRNA isolation kit
RNA libraries were prepared for sequencing using standard protocols using SOLiD total RNA-seq kit with SOLiD 3 barcode primers

treatment_protocol: Embryos were incubated at two different temperatures, 15 °C or 21 °C

tag: developmental stage

value: 75% epiboly stage

tag: incubation temperature


title: 20S 15C

value: 20 somite stage


title: 20S 21C


title: 75Ep 15C


title: Met 15C

source_name: Whole larvae

value: Metamorphosis climax


title: 18.WT.t40

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Basecalls performed using CASAVA version 1.8.2
GRO-seq reads were aligned to the hg19 genome assembly using BWA v0.5.9 with the following configurations: -l 36, -n 3
BAM files representing the same sample were merged and reads mapping to Ensembl rRNAs or to regions blacklisted for mappability by the Encode project were removed.
Further analysis was conducted using Bioconductor.  Reads were extended to 250bp and each sample was normalised to a read depth of 20 million.  A subset of the protein coding human Ensembl transcriptome was created by filtering for transcripts >=30kb.  The largest transcript was selected per gene, resulting in a list of  8529.  Bp level coverage of the region 2kb upstream to 120kb downstream of each transcript's TSS was calculated for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing mean normalized read depth across selected protein coding Ensembl transcripts.  Covers the region -2kb upstream to +120kb downstream of the TSS.

organism: Homo sapiens

source_name: HEK293T-rex cells, 18.WT.t40

growth_protocol: Constitutively KD cells were grown in presence of Doxycycline to induce physiological level of an shRNA resistant full length version of RECQL5, or in the absence of Doxycycline to shut off the expression of the protein for 4 days.

extract_protocol:
Transcription competent nuclei were prepared using the Nuclei Isolation Kit (Sigma) according to manufacturers' recommendations and Run-On was performed as previously described (Core et al., 2008)
Strand specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 100mM of DRB to stop transcription, after a double wash with PBS, cells were released in fresh medium and 10', 25' and 40' after release cells were processed for Run-On experiments.

tag: cell line clone

tag: recql5 status

value: wild-type

value: Doxycycline 40 min


title: Hatch 15C

value: Newly-hatched larvae


title: Met 21C


title: 18.WT.t0

source_name: HEK293T-rex cells, 18.WT.t0

value: Doxycycline 0 min


title: 18.WT.t10

source_name: HEK293T-rex cells, 18.WT.t10

value: Doxycycline 10 min


title: 18.KD.t40

source_name: HEK293T-rex cells, 18.KD.t40

value: knock-down


title: 18.KD.t10

source_name: HEK293T-rex cells, 18.KD.t10


title: 18.KD.t0

source_name: HEK293T-rex cells, 18.KD.t0


title: 15.WT.t25

source_name: HEK293T-rex cells, 15.WT.t25

value: Doxycycline 25 min


title: 15.WT.t10

source_name: HEK293T-rex cells, 15.WT.t10


title: 15.KD.t40

source_name: HEK293T-rex cells, 15.KD.t40


title: 15.WT.t40

source_name: HEK293T-rex cells, 15.WT.t40


title: 18.WT.t25

source_name: HEK293T-rex cells, 18.WT.t25


title: 15.KD.t25

source_name: HEK293T-rex cells, 15.KD.t25


title: 15.KD.t10

source_name: HEK293T-rex cells, 15.KD.t10


title: 18.KD.t25

source_name: HEK293T-rex cells, 18.KD.t25


title: RNA-seq of LV sh-DNMTs transduced hES cells

description:
See also Castro-Diaz et al., 2014 for details regarding cell growth protocol and analysis of this data for L1 expression
Processed data file: hES_CTRLvsTKD_refseq_rpkm.txt
Processed data file: hES_CTRLvsTKD_L1_rpkm.txt
hES_DNMTs-TKD

source_name: Embryonic stem cells (H1)

value: embryonic stem cells

value: LV sh-DNMTs transduced

value: Cells at passage 69 (p69)


title: 15.KD.t0

source_name: HEK293T-rex cells, 15.KD.t0


title: Hatch 21C

source_name: Whole larvae


title: 15.WT.t0

source_name: HEK293T-rex cells, 15.WT.t0


title: RNA-seq of LV sh-empty transduced hES cells

description:
See also Castro-Diaz et al., 2014 for details regarding cell growth protocol and analysis of this data for L1 expression
Processed data file: hES_CTRLvsTKD_refseq_rpkm.txt
Processed data file: hES_CTRLvsTKD_L1_rpkm.txt
hES_control

value: LV sh-empty transduced


title: delNS1-2_M0.1_18h_26

city: Baltimore

first: David

middle: A

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

description: H. sapiens + hRSV deletion mutant

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Human GRCh37 whole genome reference using TopHat v1.4.0 and/or human respiratory syncytial virus (hRSV, AF035006) reference using Bowtie v0.12.9
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: H. sapiens(GRCh37)
Genome_build: hRSV(AF035006)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: hRSV NS1 deletion mutant infected 18hr MOI 0.1

growth_protocol: A549 cells infected with hRSV

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

treatment_protocol: cells collected by trypsinization; immediately put in Ambion reagent; stored at -80

value: A549 (human lung epithelial cells)


title: RNAPolII.Doxy0.0

description: Processed data file: RNAPolII.Doxy0.0_peaks.txt

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie 0.12.7 with default parameters appart from the “--best” option.
BAM files representing the same sample were merged and reads mapping to regions blacklisted for mappability by the Encode project were removed.
Peaks were called against an IgG control using MACS v1.4.2 with the following settings: --gsize (hs), --tsize (36), --mfold (8,30), --pvalue (0.00001)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files detailing the peaks called by MACS (see supplementary files linked to Series record)

source_name: HEK293 cells, RNAPolII.Doxy0.0

growth_protocol: HEK293 cells were infected with lentiviral supernatant carrying shRNA specific for RECQL5 or CTRL shRNA. Once KD efficiency was assessed by Western Blot, cells were processed for RNA Pol II. ChIP-Seq. HEK293T-rex cells were transfected with the pcDNA4/TO-RECQL5 plasmid, carrying a full length version of RCQL5 under a Doxycycline inducible promoter. Once the doses of Doxycycline for the overexpression where assessed by Western Blot the samples were processed for RNA Pol II ChIP-Seq.

extract_protocol:
Cells were cross-linked with formaldehyde 1% final. Nuclei were extracted in low salt conditions and burst in high salt before shearing the DNA to reduce the size to 300-400 bp and performing ChIP with an RNA Pol II specific antibody.
DNA libraries were prepared according to Illumina's instructions and run on a GAIIX sequencer

value: RNA polymerase II

value: Doxycyline 0.0 ng/ml


title: Sp early stationary phase (ES) RNA-Seq

city: Taipei

first: Daryi

address: 128 Academia Road Sec. 2, Nankang Taipei 115 Taiwan

department: Biodiversity Research Center

country: Taiwan

institute: Academia Sinica

description:
Sp early stationary phase (ES) RNA-Seq
Sp_ES1

data_processing:
Bowtie (Trapnell et al., 2009) and TopHat (Pachter et al.,2009) were used to map the paired-end reads to the genome with default parameters.
To determine the complete transcriptional landscape, we designed a method to detect all the transcripts. The read depth (i.e., the number of reads at a given position) was used to define a transcript unit and the transcript boundaries were manually annotated. For the computational detection of each transcript unit, we iterated the following four-step process. (i) We selected a position with the highest read depth as the starting point. We also used the criteria that for any position to be considered in this analysis, it should have a read depth greater than or equal to five. (ii) We extended the boundary in both directions (upstream and down stream) by one base pair until the mean read depth of the transcript was at least four times higher than the read depth of the neighboring position. (iii) The boundary of this transcript was reassigned to include the reads that contained the position at which the mean read depth satisfied the criteria in step (ii). (iv) The region that was already assigned as a transcript was flagged and excluded from the following cycles.
BPKM (bases per kilo-base of gene model per million mapped bases) was calculated (Yang et. al., 2011) for each annotated transcripts for different samples and used as a measure of expression level.
Genome_build: For Saccharomyces cerevisiae BY4741:  Saccharomyces Genome Database (SGD), Saccharomyces cerevisiae S288C reference genome Release 64-1-1 (last modified: 03-Feb-2011).
Genome_build: For Saccharomyces paradoxus a-CC154:  Saccharomyces paradoxus CBS432, Liti et al. (2009) Population genomics of domestic and wild yeasts. Nature 458: 337–341.
Supplementary_files_format_and_content: tab-delimited text files include BPKM values for each sample

organism: Saccharomyces paradoxus

source_name: Yeast S. paradoxus strain a-CC154

growth_protocol: Cultures were grown in YPED medium (1.5% yeast extract, 1% peptone, 2% dextrose, 2 g/L SC Amino Acid mix, 100 mg/L adenine, 100 mg/L tryptophan, 100 mg/L uracil) at 30°C. The cells were harvested at mid-log phase with the OD600 values being 0.802 (S. cerevisiae) and 0.827 (S. paradoxus). For early stationary phase, the cells were taken two hours after the glucose levels reached zero, for which glucose levels were monitored hourly using Glucose (HK) assay kit (Sigma-Aldrich, MO, USA). OD600 values for early stationary phase were 2.22 (S. cerevisiae) and 2.217 (S. paradoxus). The samples were collected by harvesting 12 ml of mid-log and early-stationary cultures and were quenched by adding to 20 ml pre-chilled liquid methanol at a final concentration of 60%, which was later removed by centrifugation, washed in RNase-free water and stored these overnight at -80°C.

extract_protocol:
Total RNA was isolated with Yeast RNA Purification Kit (MasterPure™ Epicentre). Genomic DNA contamination was removed with Turbo DNase (Ambion) followed by phenol chloroform extraction. The cDNA libraries for RNA samples were constructed using TruSeq RNA Sample Preparation Kits v2 based on the guide (Illumina, Cat. No RS-122-2001). PolyA-containing mRNA was purified using 50 μl RNA Purification Beads for each sample.
The strand-specific cDNA library was constructed by dUTP second-strand method (Parkhomchuk et. al., 2009). The purified RNA fragments were reverse-transcribed into first-strand cDNA using SuperScript II Reverse Transcriptase (Invitrogen, Cat. No 18064-014) and random primers (Illumina, Cat. No. RS-122-2001). The first strand cDNA/RNA hybrid was precipitated with ethanol and ammonium acetate. The second-strand cDNA synthesis was performed in a 80 μl reaction volume using NEBNext® mRNA Second Strand Synthesis Module (NEB, NEB # E611lL) and dNTP/dUTP mix (Fermentas , Cat. No. R0251, dTTP→dUTP ) at 16°C for 2.5 hours. The DNA fragments were purified by QIAquick PCR Purification Kit (Qiagen, Cat. No 28106) and treated with T4 DNA polymerase, E. coli DNA polymerase I Klenow fragment and T4 Polynucleotide Kinase in a 30 μl reaction using the buffer and the enzyme in the kit (Illumina, Cat. No RS-122-2001) at 37°C for 30 min. The blunt phosphorylated DNA fragments were purified by the MinElute PCR Purification Kit (Qiagen, Cat. No 28006) and treated with Klenow fragment of DNA polymerase lacking exonuclease activity in the presence of dATP to add an adenine overhang to the 3’ ends of each strand in a 30 μl reaction using the kit (Illumina, Cat. No. RS-122-2001) at 37°C for 30 min. Adapters required for sequencing on the Illumina platform were added to DNA fragments by ligation in a 37.5 μl reaction using the kit (Illumina, Cat. No. RS-122-2001). The ligation products were purified by the MinElute PCR Purification Kit (Qiagen, Cat. No 28604) and eluted the ligation products in the size range from 350 to 450 bp from the gel. These products were precipitated and resuspended in 21 μl TrueSeq Resuspension Buffer using QIAquick Gel extraction Kit (Qiagen, Cat. No 28704) and treated with USER™ Enzyme mixture (Uracil-Specific Excision Reagent, NEB, Cat. No M5505L) to degrade the dUTP in the coding strand (second strand). The adapter-modified DNA fragments were amplified by the kit (Illumina, Cat. No. RS-122-2001). The amplified products were purified by Agencourt AMPure XP (Beckman, Cat. No A63881) and collected in 30 μl Resuspension Buffer (Qiagen, Cat. No 28604). After quantification by Quant-iT dsDNA HS Assay Kit (Invitrogen, Cat. No Q32851) and KAPA QPCR Library Quantification Kit (KAPABiosystem. Cat. No kk4822), calculation of molar concentration and quality examination by Expersion DNA 1K Analysis Kit (Bio-Rad Cat. No 700-7107), this DNA library was prepared for sequencing.

treatment_protocol: For heat shock culture, 12 ml of mid-log culture was harvested by centrifugation. Cells were re-suspended in 10 ml of 42°C pre-warmed YPD medium and put in a 42°C water bath for 15 minutes and quenched by adding to 20 ml liquid pre-chilled methanol, which was later removed by centrifugation, washed in RNase-free water and stored these overnight at -80°C.

tag: growth phase

value: early stationary phase


title: Sp mid-log phase (ML) RNA-Seq

description:
Sp mid-log phase (ML) RNA-Seq
Sp_ML1

value: mid-log phase


title: Sp heat shock treatment (HS) RNA-Seq

description:
Sp heat shock treatment (HS) RNA-Seq
Sp_HS1

value: heat shock


title: IgG.control

description:
Control used in peak calling
Processed data file: RNAPolII.Doxy0.0_peaks.txt
Processed data file: RNAPolII.Doxy1.0_peaks.txt

source_name: HEK293 cells, IgG.control

value: Non-specific IgG control


title: delNS1-2_M0.1_18h_25

description: H. sapiens + hRSV deletion mutant


title: RSV_M0.1_18h_23

description: H. sapiens + hRSV

source_name: hRSV infected 18hr MOI 0.1


title: delNS1-2_M3_18h_22

description: H. sapiens + hRSV deletion mutant

source_name: hRSV NS1 deletion mutant infected 18hr MOI 3


title: RNAPolII.shRECQL5-7

description: Processed data file: RNAPolII.shRECQL5-7_peaks.txt

source_name: HEK293 cells, RNAPolII.shRECQL5-7

value: RECQL5 shRNA 7


title: IgG.shRECQL5-7

description:
Control used in peak calling
Processed data file: RNAPolII.shRECQL5-7_peaks.txt

source_name: HEK293 cells, IgG.shRECQL5-7


title: delNS1-2_M3_18h_21

description: H. sapiens + hRSV deletion mutant


title: IgG.shRECQL5-5

description:
Control used in peak calling
Processed data file: RNAPolII.shRECQL5-5_peaks.txt

source_name: HEK293 cells, IgG.shRECQL5-5

value: RECQL5 shRNA 5


title: RNAPolII.shRECQL5-5

description: Processed data file: RNAPolII.shRECQL5-5_peaks.txt

source_name: HEK293 cells, RNAPolII.shRECQL5-5


title: RSV_M3_18h_19

description: H. sapiens + hRSV

source_name: hRSV infected 18hr MOI 3


title: mock_0h_02

description: H. sapiens

source_name: 0 hr mock infected


title: IgG.shCTRL

description:
Control used in peak calling
Processed data file: RNAPolII.shCTRL_peaks.txt

source_name: HEK293 cells, IgG.shCTRL

value: control shRNA


title: RSV_M3_18h_20

description: H. sapiens + hRSV


title: Sc heat shock treatment (HS) RNA-Seq

description:
Sc heat shock treatment (HS) RNA-Seq
Sc_HS1

source_name: Yeast S. cerevisiae strain BY4741


title: Sc early stationary phase (ES) RNA-Seq

description:
Sc early stationary phase (ES) RNA-Seq
Sc_ES1


title: ChIP Input, replicate 2

status: Public on Jun 08 2014

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
small RNA-seq, CAP-seq and GRO-seq libraries: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0), fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings, after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini), reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3, release 5) and BigWig files and 1kb bin overlaps were generated with Samtools v 0.1.16 and BedTools v2.16.1
RNA-seq libraries: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0), reads were trimmed to high-quality bases 6-46. For RPKM calculations, files containing 2nd reads were reverse complemented and combined with the 1st reads and then aligned to the genome with bowtie v0.12.7 to D. mel. genome (dm3, release 5). For visualization, paired-end reads were aligned using GSNAP (version 2013-05-09) and BigWig files and 1kb bin overlaps were generated with Samtools v 0.1.16 and BedTools v2.16.1.
ChIP-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0). Reads were trimmed to bases 2-50, N-containing reads and reads smaller than 20nt were discarded. Reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3, release 5) and BigWig files and 1kb bin overlaps were generated with Samtools v 0.1.16 and BedTools v2.16.1.
Genome_build: Drosophila melanogaster dm3, release 5; GCA_000001215.2
Supplementary_files_format_and_content: tab-delimited file containing the annotations and processed read counts for all 1kb bins genome-wide.

organism: Drosophila melanogaster

source_name: ChIP Input

growth_protocol: Flies were kept at strandard conditions at 25º C.

extract_protocol:
ChIP-seq was performed according to Lee et al, Nat Protoc, 2006
ChIP-seq libraries were generated using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) and the Kapa HiFi Library Amp Real-Time Kit (Peqlab) for amplification.

value: 4-6 days old adult

tag: Sex

value: female

tag: tissue

value: ovary

tag: germline knock-down

value: control


title: mock_0h_01

description: H. sapiens


title: ChIP Input, replicate 1


title: H3K4me2 ChIP from control germline knock-down ovaries, replicate 1

value: Anti-dimethyl-Histone H3 (Lys4)

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: H3K4me2 ChIP from control germline knock-down ovaries, replicate 2


title: Sc mid-log phase (ML) RNA-Seq

description:
Sc mid-log phase (ML) RNA-Seq
Sc_ML1


title: RNA Polymerase II ChIP from rhino germline knock-down ovaries

value: rhino

value: Anti-RNA polymerase II CTD repeat YSPTSPS [8WG16] antibody

value: Abcam


title: RSV_M0.1_18h_24

description: H. sapiens + hRSV

value: A549 (human lung epithelial cells)


title: H3K9me3 ChIP from piwi germline knock-down ovaries, replicate 2

value: piwi

value: Histone H3K9me3 antibody (pAb)

value: Active Motif


title: H3K9me3 ChIP from rhino germline knock-down ovaries, replicate 2


title: H3K9me3 ChIP from control germline knock-down ovaries, replicate 2


title: H3K9me3 ChIP from piwi germline knock-down ovaries, replicate 1


title: Cutoff ChIP from cutoff germline knock-down ovaries

value: cutoff

value: custom-made rabbit polyclonal antibody


title: H3K9me3 ChIP from rhino germline knock-down ovaries, replicate 1


title: H3K9me3 ChIP from control germline knock-down ovaries, replicate 1


title: Cutoff ChIP from control germline knock-down ovaries


title: Deadlock ChIP from control germline knock-down ovaries


title: Deadlock ChIP from deadlock germline knock-down ovaries

value: deadlock


title: Rhino ChIP from piwi germline knock-down ovaries, replicate 2


title: Rhino ChIP from piwi germline knock-down ovaries, replicate 1


title: RNAPolII.Doxy1.0

description: Processed data file: RNAPolII.Doxy1.0_peaks.txt

source_name: HEK293 cells, RNAPolII.Doxy1.0

tag: cell line

value: RNA polymerase II

tag: treatment

value: Doxycyline 1.0 ng/ml (to induce overexpression of RECQL5)


title: Rhino ChIP from cutoff germline knock-down ovaries

value: 4-6 days old adult

value: female


title: Rhino ChIP from rhino germline knock-down ovaries

value: ovary


title: RNAPolII.shCTRL

description: Processed data file: RNAPolII.shCTRL_peaks.txt

source_name: HEK293 cells, RNAPolII.shCTRL

value: control shRNA


title: Rhino ChIP from control germline knock-down ovaries, replicate 1

value: control


title: Rhino ChIP from control germline knock-down ovaries, replicate 2


title: nascent RNA from global nuclear run on (GRO) in rhino germline knock-down ovaries

data_processing:
Library strategy: GRO-Seq
small RNA-seq, CAP-seq and GRO-seq libraries: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0), fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings, after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini), reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3, release 5) and BigWig files and 1kb bin overlaps were generated with Samtools v 0.1.16 and BedTools v2.16.1
RNA-seq libraries: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0), reads were trimmed to high-quality bases 6-46. For RPKM calculations, files containing 2nd reads were reverse complemented and combined with the 1st reads and then aligned to the genome with bowtie v0.12.7 to D. mel. genome (dm3, release 5). For visualization, paired-end reads were aligned using GSNAP (version 2013-05-09) and BigWig files and 1kb bin overlaps were generated with Samtools v 0.1.16 and BedTools v2.16.1.
ChIP-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0). Reads were trimmed to bases 2-50, N-containing reads and reads smaller than 20nt were discarded. Reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3, release 5) and BigWig files and 1kb bin overlaps were generated with Samtools v 0.1.16 and BedTools v2.16.1.
Genome_build: Drosophila melanogaster dm3, release 5; GCA_000001215.2
Supplementary_files_format_and_content: tab-delimited file containing the annotations and processed read counts for all 1kb bins genome-wide.

extract_protocol:
GRO-seq was performed according to Shpiz and Kalmykova, Piwi-Interacting RNAs: Methods and Protocols, 2013 and Core et al, Science, 2008
Purified and fractionated GRO fragments were ligated with 3' and 5' linkers. 1st strand cDNA synthesis was performed using SuperScript III (Invitrogen) and the library was amplified using the Kapa HiFi Library Amp real time Kit (Peqlab) with Illumina TruSeq compatible primers.

value: rhino


title: Rhino ChIP from deadlock germline knock-down ovaries


title: 5'-capped RNA from control germline knock-down ovaries

data_processing:
Library strategy: Cap-Seq
small RNA-seq, CAP-seq and GRO-seq libraries: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0), fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings, after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini), reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3, release 5) and BigWig files and 1kb bin overlaps were generated with Samtools v 0.1.16 and BedTools v2.16.1
RNA-seq libraries: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0), reads were trimmed to high-quality bases 6-46. For RPKM calculations, files containing 2nd reads were reverse complemented and combined with the 1st reads and then aligned to the genome with bowtie v0.12.7 to D. mel. genome (dm3, release 5). For visualization, paired-end reads were aligned using GSNAP (version 2013-05-09) and BigWig files and 1kb bin overlaps were generated with Samtools v 0.1.16 and BedTools v2.16.1.
ChIP-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0). Reads were trimmed to bases 2-50, N-containing reads and reads smaller than 20nt were discarded. Reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3, release 5) and BigWig files and 1kb bin overlaps were generated with Samtools v 0.1.16 and BedTools v2.16.1.
Genome_build: Drosophila melanogaster dm3, release 5; GCA_000001215.2
Supplementary_files_format_and_content: tab-delimited file containing the annotations and processed read counts for all 1kb bins genome-wide.

extract_protocol:
Cap-seq was performed according to Nachaev et al, Science, 2010 and Gu et al, Cell, 2013
Purified Capped RNA fragments were ligated with 3' and 5' linkers. 1st strand cDNA synthesis was performed using SuperScript III (Invitrogen) and the library was amplified using the Kapa HiFi Library Amp real time Kit (Peqlab) with Illumina TruSeq compatible primers.


title: nascent RNA from global nuclear run on (GRO) in control germline knock-down ovaries


title: RNA Polymerase II ChIP from control germline knock-down ovaries

value: Anti-RNA polymerase II CTD repeat YSPTSPS [8WG16] antibody


title: ribosomal RNA depleted total RNA from deadlock germline knock-down ovaries

extract_protocol:
RNA-seq was performed according to Zhang et al, Silence, 2012
Total RNA was extracted using Trizol and depleted for ribosomal RNA (Ribo-Zero Kit, Epicentre). For 2nd strand synthesis, dUTP was added to generate stranded libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). The Kapa HiFi Library Amp Real-Time Kit (Peqlab) with Illumina TruSeq compatible primers was used to amplify the library.


title: ribosomal RNA depleted total RNA from cutoff germline knock-down ovaries


title: ribosomal RNA depleted total RNA from control germline knock-down ovaries, replicate 2


title: ribosomal RNA depleted total RNA from rhino germline knock-down ovaries


title: small RNAs from a Piwi-IP in piwi germline knock-down ovaries (=somatic piRNAs)

extract_protocol:
smallRNA cloning was performed according to Brennecke et al, Cell, 2007
small RNAs were PAGE selected and 3' and 5' linkers was ligated. 1st strand cDNA synthesis was performed using SuperScript III (Invitrogen) and the library was amplified using the Kapa HiFi Library Amp real time Kit (Peqlab) with Illumina TruSeq compatible primers.

tag: molecule subtype

value: small RNA


title: ribosomal RNA depleted total RNA from control germline knock-down ovaries, replicate 1


title: small RNAs (18-29nt) from rhino germline knock-down ovaries


title: small RNAs (18-29nt) from deadlock germline knock-down ovaries


title: small RNAs (18-29nt) from control germline knock-down ovaries


title: small RNAs (18-29nt) from cutoff germline knock-down ovaries


title: MK_C5

city: Bethesda

first: Nigel

last: Crawford

address: 50 South Drive, Room 5154

institute: Human Genome Research Institute

data_processing:
Data was processed using RTA1.8.70.0 and CASAVA 1.7.0.
Sequence reads were aligned to the mouse genome (mm9; downloaded from ENSEMBL) using TopHat (v. 1.2.0) (Trapnell et al. 2009) with the following parameters: -p 3; -m 2; -r 348; -G (GTF of protein-coding transcripts downloaded from ENSEMBL (e64)).
TopHat alignments were supplied to Cufflinks (v.  1.1.0) (Trapnell et al. 2010) for transcript assembly using the following parameters: -p 6; -N (upper quartile normalization); -b [mm9 genome FASTA sequence for bias correction]; -M (GTF from ENSEMBL (e61) of rRNA, tRNA, and mtRNA genomic locations for masking); GTF of protein-coding transcripts from ENSEMBL (e64).
Differentially expressed genes and transcripts were identified using Cuffdiff (v. 1.1.0) with the following parameters: -p 6; -N (upper quartile normalization); -b (mm9 genome fasta sequence for bias correction (Roberts et al. 2011)); -M (GTF of rRNA, tRNA, and mtRNA genomic locations for masking); GTF of protein-coding transcripts from ENSEMBL (e64). Genes and isoforms having a q-value ≤ 0.05 were considered differentially expressed, as reported in the gene_exp.diff and isoform_exp.diff output files from Cuffdiff.

source_name: mouse mammary tumor

extract_protocol:
Total RNA was isolated from cells using the RNeasy mini kit (QIAGEN, Valencia, CA) following manufacturer's protocol with a 15 min DNase treatment before elution. mRNA from 10 µg of total RNA was poly-A selected using Dynal oligo DT beads (Invitrogen, Grand Island, NY) and sheared to ~400 b using Covaris S2. The sample was concentrated to 25 µl using an Amicon Ultra 20K filter. Reverse transcription was performed using random hexamers and SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen, Grand Island, NY). A library was constructed from the resulting cDNA according to the Illumina protocol in the Paired-End DNA Sample Prep Oligo Only Kit.
RNA-seq. Libraries were sequenced on the Illumina GAIIx platform using ver 4 chemistry to obtain 76-base-paired reads.

tag: cell type

tag: shRNA

value: mouse mammary tumor


title: MK_R1


title: MK_C6


title: 26_28_S

status: Public on Jun 07 2014

city: Liege

first: Brett

last: Mommer

state: Wallonia

address: Tour Pharmacie (Bat. B36) Quartier Hôpital, Avenue Hippocrate 15

department: GIGA-Neurosciences

country: Belgium

institute: University of Liege

description: Sample 11

data_processing:
Illumina Casava1.8.2 software used for basecalling to produce the fastq files.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to stickleback BROADS1 v71.1  genome using TopHat 2 (version 2.0.8)
EdgeR's (version 2.11) TMM normalization function was used to adjust for differences in highly expressed genes and to obtain count data at the gene level in modified Counts per Million mapped reads (CPM).
Cufflinks (version 2.1.1) algorithm was used to obtain counts data at the transcript level in Fragments Per Kilobase of exon per Million mapped reads (FPKM).
Genes were removed from differential expression analysis if they were detected in only a single sample and at less than one count per million mapped reads, or if they had zero counts for all samples.
Genome_build: stickleback BROADS1, Ensembl database version 71.1, Feb 2006
Supplementary_files_format_and_content: excel files contain FPKM values (transcript-level; Cufflinks) or logCPM values (gene-level; EdgeR) for each sample. The "logCPM" is the average Counts Per Million mapped reads on the log2 scale.

organism: Gasterosteus aculeatus

source_name: 3dpf embryos_simulated predation risk mother

extract_protocol:
pools of whole embryos from each mother were flash frozen on dry ice, homogenized, and total RNA isolated using AllPrep DNA/RNA Micro Kit (Qiagen). After quality control 1ug of total RNA was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina TruSeq Stranded RNAseq Sample Prep kit )

value: 3 days post-fertilization embryo

value: whole embryo homogenate

tag: maternal treatment

value: simulated predation risk


title: 5_14_C

description: Sample 13

source_name: 3dpf embryos_control mother

tag: developmental stage


title: 24_28_S

description: Sample 10


title: 8_10_S

description: Sample 16


title: 21_14_C

description: Sample 9


title: 5_21_C

description: Sample 14


title: 3_10_S

description: Sample 12


title: WT_cpdA_LPS_3

city: La Jolla

first: Roman

last: Sasik

address: 9500 Gilman Dr.

department: Center for Computational Biology and Bioinformatics

institute: UCSD

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads aligned to mouse transcriptome using bowtie2
Transcript counts summarizid into gene-level summaries
Normalization and differential expression analysis using DESeq
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file of normalized counts

growth_protocol: ES cell-derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
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.

treatment_protocol: Intraperitoneal macrophages were pre-treated with DHA (100 uM for 1 hour) or cpdA (10 uM for 1 hour), then stimulated with LPS (100 ng/ml) for 6 hours

value: Intraperitoneal primary macrophages

tag: strain

tag: pre-treated with

value: small molecule Gpr120 agonist (cpdA 10 uM for 1 ho)

tag: stimulated with

value: LPS (100 ng/ml) for 6 hrs


title: WT_cpdA_LPS_2


title: WT_cpdA_LPS_1


title: 17_10_S

description: Sample 7


title: 10_5_S

description: Sample 1


title: 14_28_S

description: Sample 3


title: 15_5_C

description: Sample 6


title: 15_14_C

description: Sample 4


title: WT_LPS_2


title: 15_2_C

description: Sample 5


title: 20_28_C

description: Sample 8


title: MK_R5


title: 6_21_S

description: Sample 15


title: WT_DHA_LPS_2

value: DHA (100 uM for 1 hr)


title: WT_LPS_1


title: WT_DHA_LPS_3


title: GF Colon RNA-seq Rep 3

city: Durham

first: Christopher

middle: L

last: Frank

state: NC

address: 101 Science Dr.

institute: Duke University

data_processing:
Basecalls performed using CASAVA v1.8.2.
First 20bp of DNase-seq reads mapped to NCBI37/mm9 with BWA, RNA-seq mapped to NCBI37/mm9 with Tophat v2.0.8b; in both cases up to 2 mismatches and multireads that map up to 4 locations were allowed.
Putative PCR artifacts filtered from mapped DNase-seq.
DNase-seq peaks called with F-seq v1.84 with default parameters and -f set to zero.
RNA-seq FPKM transcript abundances estimated with Cufflinks and differential testing performed with Cuffdiff v2.0.2, both with -u and -b parameters specified.
Genome_build: mm9.
Supplementary_files_format_and_content: DNase-seq .bigWig files contain single base resolution summed cleavage events (5-prime end of mapped reads); DNase-seq .npf is narrow peak format (BED6+4) with chromosome, start, stop, name, score (for browser display), strand (N/A), signal value (test stat for enrichment), -log10(p-value), q-value (N/A), point-source for peak (0-based offset from start) for the top 100,000 DHS peaks detected by F-seq ; RNA-seq cufflinks files contain gene name, genomic loci, and FPKM abundances.

source_name: Intestinal Epithelial Cells

extract_protocol:
IECs were isolated from the duodenum (anterior 5 cm of midgut), ileum (posterior 6 cm of midgut), and colon (6 cm of terminal hindgut) of 8 to 12-week old mice ; Nuclei were isolated by 0.1% NP-40 lysis for DNase digestions ; Total RNA extracted by cell lysis in TRIzol reagent (Invitrogen) and further purified using Qiagen RNeasy kit according to manufacturer's protocol
DNase-seq libraries were prepared as described (Song and Crawford 2010; PMID:20150147) with 5 µg of DNA pooled from nuclei digested for 2 min, 4 min, and 8 min at 37°C with no exogenous DNase I added ; RNA-seq libraries were prepared with 2 micrograms total RNA used for standard TruSeq library preparation (Illumina) with polyA selection and sequenced with 2 x 50bp paired-end reads

value: Colon

tag: condition

value: germ-free (GF)


title: CV Colon RNA-seq Rep 1

value: conventionalized (CV)


title: WT_DHA_LPS_1


title: GF Colon RNA-seq Rep 1


title: CR Colon RNA-seq Rep 2

value: conventionally-raised (CR)


title: CR Colon RNA-seq Rep 3


title: GF Colon RNA-seq Rep 2


title: CR Colon RNA-seq Rep 1


title: CV Ileum RNA-seq Rep 3

value: Ileum


title: WT_LPS_3


title: CV Ileum RNA-seq Rep 2


title: CV Ileum RNA-seq Rep 1


title: GF Ileum RNA-seq Rep 2


title: CR Ileum RNA-seq Rep 1


title: CR Ileum RNA-seq Rep 2


title: GF Ileum RNA-seq Rep 1


title: CR Duodenum DNase-seq Rep 1

value: Duodenum


title: CR Ileum RNA-seq Rep 3


title: CV Colon DNase-seq Rep 3


title: CR Duodenum DNase-seq Rep 2


title: CV Colon RNA-seq Rep 3


title: CV Colon DNase-seq Rep 1


title: GF Colon DNase-seq Rep 3


title: CV Colon DNase-seq Rep 2


title: CR Ileum RNA-seq Rep 4


title: GF Colon DNase-seq Rep 2


title: CV Colon RNA-seq Rep 2


title: CR Colon DNase-seq Rep 2


title: GF Colon DNase-seq Rep 1


title: CR Colon DNase-seq Rep 3


title: CR Colon DNase-seq Rep 1


title: CV Ileum DNase-seq Rep 3


title: CV Ileum DNase-seq Rep 2


title: GF Ileum DNase-seq Rep 3


title: Y518

city: Changshu

first: Jiang

last: Sun

address: No. 99, South Third Ring Road

institute: Changshu Institute of Technology

data_processing:
base-calling: HCS (illumina) version1.5.15.1 and RTA (Version="1.13.48.0" ).;
filtering: self-software; As there are some adaptor sequences and/or low quality reads present in the raw reads, data filtering is carried out to obtain high quality reads as the clean reads (clean data). The procedure include following steps: 1. Remove reads with adaptor sequences. 2. Remove reads in which the percentage of unknown bases (N) is greater than 10%. 3. Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 20) is greater than 40% in a read, we define this read as low quality.
alignment: SOAPaligner/soap2 (Release 2.21 , 02-14-2011) Paper:Li R., Yu C., Li Y., et al. (2009). SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics, 25 (15). 1966-1967.     ; Parameters:maximum number of mismatches allowed on a read is 2;minimal alignment length (for soft clip) [255] bp is 28; to report repeat hits;align the initial 32 bps as a seed [256] means whole length of read
generation of normalized abundance measurements: RPKM method (Reads Per kb per Million reads); Paper:Audic, S. and J. M. Claverie (1997). The significance of digital gene expression profiles. Genome Res 7(10): 986-95.
Functional annotation ( provide Gene Ontology (GO) annotation information )  : BLAST (version:2.2.23); GO： Annotating the results that from BLAST(-p blastx -e 1e-5 -m 7)sequences to Nr database of NCBI to the terms of GO by use BLAST2GO(default parameters).    KEGG:Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Screening of differentially expressed genes (DEGs)  : ; Referring to "The significance of digital gene expression profiles.FDR ≤ 0.001 and the absolute value of log2Ratio ≥ 1" as the threshold to judge the significance of gene expression difference.
Genome_build: Saccharomyces cerevisiae S288c: chrI,chrII,chrIII,chrIV,chrIX,chrM,chrV,chrVI,chrVII,chrVIII,chrX,chrXI,chrXII,chrXIII,chrXIV,chrXV and chrXVI (total 16 chromosomes);
Supplementary_files_format_and_content: Saccharomyces_cerevisiae.tar.bz2 (format:bzip2 compressed data), includes alignment, normalized abundance and DEGs result.

source_name: Saccharomyces cerevisiae

growth_protocol: A single colony of Saccharomyces cerevisiae 2-10515 and Y518 was inoculated into a 100 ml flask with 10 ml medium as described by (Jie & Hongyu, 2009) and incubated at 180 rpm and 30°C for 18 h, then used as seeds for subsequent fermentation. The seeds were inoculated into 500 ml flasks containing 50 ml medium with 10% (v/v) of inoculation and fermented (the same condition with seeds) for 24 h.

extract_protocol:
Cells were harvested, washed twice with DEPC water. Total RNA was isolated using RNeasy Mini Kit (QIAGEN, Germany) and purified using RNase-Free DNase Set (QIAGEN, Germany) as the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Saccharomyces cerevisiae Y518

tag: growth condition

value: fermentation for 24 h

tag: genotype/variation

value: mutant


title: GF Ileum DNase-seq Rep 2

tag: tissue


title: GF Ileum DNase-seq Rep 1


title: ReutH16_F16

city: Yokohama

first: Toshiaki

last: Fukui

address: Nagatsuta 4259

department: Department of Bioengineering

country: Japan

institute: Tokyo Institute of Technology

description: mRNA-enriched

data_processing:
Illumina Casava 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of R. eutropha using BWA with default paramters.
The alignments with mismatch or mapped to the five rRNA regions of R. eutropha H16 were discarded by using custom Perl scripts.
Reads Per Kilobase per Megabase of library size (RPKM) for each coding DNA sequence was calculated by using custom Perl scripts.
Genome_build: R. eutropha H16 Chromosome 1 (NC_008313.1), Chromosome 2 (NC_008314.1) and megaplasmid pHG1 (NC_005241.1).
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values and P-values.

organism: Cupriavidus necator H16

source_name: R. eutropha H16, growth phase

growth_protocol: R. eutropha wild H16 was cultivated in a 500 ml flask on a reciprocal shaker (115 strokes/min) at 30˚C with 100 ml of a nitrogen-limited mineral salts medium. A filter-sterilized solution of fructose was added to the medium at a final concentration of 0.5% (w/v).

extract_protocol:
Total RNA was isolated from the cells by using RNeasy Midi Kit (Qiagen), and treated with DNase I. 25-50 μg of total RNA was then subjected to repeated treatment using RiboMinus Transcriptome Isolation Kits (Yeast and Bacteria) (Invitrogen) for mRNA enrichment.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cells in 10 ml culture broth at 16, 26, and 36 h on fructose were harvested by centrifugation.

tag: strain/background

value: wild-type

tag: phase

value: growth

tag: cultivation

value: fructose for 16 h


title: ReutH16_F36

description: mRNA-enriched

source_name: R. eutropha H16, stationary phase

value: stationary

value: fructose for 36 h


title: ReutH16_F26

description: mRNA-enriched

source_name: R. eutropha H16, PHA production phase

value: PHA production

value: fructose for 26 h


title: CR Ileum DNase-seq Rep 1


title: CR Ileum DNase-seq Rep 2


title: A3.01 H3K4me3

status: Public on Jun 06 2014

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were mapped to hg18 genome using CASAVA 1.6
The following reads were removed for down-stream analysis: multiple match, mismatch >2
Sequencing tags were shifted by +75 bp for positive strand and -75 bp for negative strand. The shifted sequencing tags were counted in non-overlapping 200bp genomic windows.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files with BED graph format

growth_protocol: A3.01, ACH2 and NCHA cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS, 5% penicillin–streptomycin and 2 mmol/l glutamine

extract_protocol:
Cells were resuspended with digestion buffer (50mM Tris-HCL, pH7.6, 1mM  CaCl2, 0.2% triton X-100) and 5mM butyrate, 0.5mM PMSF, x proteinase  inhibitor. The chromatins were digested with Mnase and enzyme was  inactivated by adding the stop buffer (10mM Tris, pH7.6, 5mM EDTA). Pre-  cleared Dynabeads Protein A (100.02D, Life Technologies, Carlsbad, CA) were  bound with antibodies specific to the histone H3, tri methylated at K4  (rabbit polyclonal, ab8580, Abcam, Cambridge, UK) and acetylated at K9  (rabbit polyclonal, ab4441, Abcam, Cambridge, UK). Digested chromatins were  incubated with bead-bound antibody for overnight in RIPA buffer (10 mM  Tris, pH7.4, 1mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, and 1% Triton X-  100). Bead complex was captured by magnetic stand and washed sequentially  twice with RIPA buffer, RIPA + 0.3 M NaCl, and LiCl buffer (0.25 M LiCl,  0.5% NP40, 0.5% Na- Deoxycholate) and once with 1X TE + 0.2% Triton X-100,  and 1X TE. Proteinase K digestion and phenol/chloroform extraction was  performed to isolate the DNA.
Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3’ ends by  Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina’s adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen, Germantown, MD). After purified twice, DNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Phusion PCR master mix (Thermo Scientific, Hudson, NH).

tag: cell line

value: CD4+ T cell line

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number


title: ACH2 H3K4me3

tag: cell type

value: HIV-1 latency T cell line


title: NCHA2 H3K4me3


title: NCHA1 H3K4me3


title: ACH2 H3K9ac


title: Skin-RNAseq

city: Shenzhen

first: Min

last: Xie

state: Guangdong

address: 11th Building,Beishan Industrial Zone

department: Science & Technology department

institute: Beijing Genomics Institute

description: For wool related studies, RNA was extracted from a skin sample collected from the flank of one super-fine strain (fiber diameter=16.5 micron) of Gansu alpine fine wool sheep

data_processing:
Base-calling was implemented with build-in software provided by Illumina.
Mapping paired end reads to the genome assembly with Tophat-2.0.8b(invoked bowtie2-2.1.0):tophat2   -N  3  --read-edit-dist  3   -i  10  -I  200000 --phred64-quals  --library-type  fr-unstranded  -r  50  --mate-std-dev  20  index_file   XX_1.fq.gz   XX_2.fq.gz
Convert BAM files to bedGraph files with BEDTools-Version-2.16.2 : bedtools genomecov   -ibam XX.bam -bg -split -g oar_v3.1.genome >XX.bedgraph
Genome_build: Oar_v3.1 downloaded from NCBI ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Ovis_aries/Oar_v3.1/Primary_Assembly/
Supplementary_files_format_and_content: bedGraph

organism: Ovis aries

source_name: Skin

extract_protocol:
RNA was harvested using Trizol (Invitrogen, CA, USA).
RNA sequencing libraries were constructed using the Illumina mRNA-Seq Prep Kit

tag: breed

value: Gansu alpine fine wool sheep

tag: gender

value: female

tag: age

value: 2 years

value: Skin


title: Lung-RNAseq

description: All the seven tissues were derived from a single ewe.This individual was also sequenced to generate a high quality genome assembly ( NCBI Oar_v3.1 )

source_name: Lung

value: Texel

value: 6 months

value: Lung


title: NCHA2 H3K9ac


title: CR Ileum DNase-seq Rep 4

tag: strain

value: Ileum

value: conventionally-raised (CR)


title: A3.01 H3K9ac


title: NCHA1 H3K9ac


title: 2-10515

value: Saccharomyces cerevisiae 2-10515

value: fermentation for 24 h

value: wild type


title: WATper-RNAseq

source_name: White Adipose

value: White Adipose


title: Heart-RNAseq

source_name: Heart

value: Heart


title: CV Ileum DNase-seq Rep 1

value: conventionalized (CV)


title: gSELEXx9

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
Library strategy: SELEX
Reads were mapped to the genome using Bowtie (Langmead et al., Genome Biol 2009) allowing up to two mismatches and only retaining uniquely mapping reads.
gSELEX peaks were defined using MACS (Zhang et al., Genome Biol 2008) with the following parameters: band width = 100, model fold =32, p<1e-10, and for the definition of SELEX peaks we considered a peak positive when it showed over 50 fold increase.
Genome_build: TAIR8
Supplementary_files_format_and_content: Column 1: chromosome, Column 2: start, Column3: stop

organism: Arabidopsis thaliana

source_name: mature leaves from 3 week old plants

growth_protocol: All plants were grown under long day conditions.

extract_protocol: For the genomic SELEX experiment, Arabidopsis thaliana genomic DNA was extracted from wild type 3 week old plant leaves and fragmented to 100 bp using COVARIS. 2 μg of this DNA was processed for end repair and adaptor ligation following the manufacturer’s instructions (Illumina) and used as indicated above for incubation with purified GST-SUVR5 zinc finger domain protein. Two genomic SELEX experiments were performed, one using only one binding/eluting cycle (x1: control) and one with 9 cycles (x9). The recovered DNA was sequenced using an Illumina Genome Analyzer.

tag: ecotype

value: WT, columbia

value: mature leaves

value: 3 weeks


title: Brain-RNAseq

source_name: Brain

value: female

value: Brain


title: Ovary-RNAseq

source_name: Ovary

value: Ovary


title: Kidney-RNAseq

source_name: Kidney

value: Texel

value: Kidney


title: Liver-RNAseq

source_name: Liver

value: 6 months

value: Liver


title: CR Ileum DNase-seq Rep 3

value: Ileum

tag: condition

value: conventionally-raised (CR)


title: DA

city: QINGDAO

first: Muyan

last: Chen

address: 5 YUSHAN ROAD

institute: Ocean University of China

data_processing:
The original image data was transferred into sequence data by base calling(using CASAVA version 1.5+), (defined as ‘raw reads’) and saved as fastq files that include the detailed reads sequences and the reads quality information.
The raw reads obtained from Solexa sequencing were processed by trimming poor quality reads, 5’ adapter pollution reads, reads without 3’ adapters, reads without insert fragments, reads containing poly(A) stretches, and reads less than 18nt. rRNA, tRNA, snRNA and snoRNA were removed by blasting against the GenBank database (http://blast.ncbi.nlm.nih.gov) and the Rfram database (http://sanger.ac.uk/software/Rfam).
Considering that no miRNA information of the sea cucumber was in miRBase19.0, the remaining clean reads were aligned to search all known precursor/mature miRNAs of all animal species in miRBase 19.0 with perfect matches.
Chose the highest expression miRNA for each mature miRNA family which was regarded as a temporary miRNA database. Clean data was aligned to the above temporary miRNA database and the expression of miRNA is generated by summing the count of reads which can align to the temporary miRNA database without mismatches.
Potentially novel miRNAs were identified using MIREAP (http://sourceforge.net/projects/mireap/) with stem-loop structure prediction

organism: Apostichopus japonicus

source_name: Apostihopus japonicus intestine

extract_protocol:
Total RNA from each tissue sample was extracted using miRNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.
Recovered Small RNAs were ligated sequentially to 5’ and 3’ adapters. Reverse transcription was performed followed by PCR amplification. The purified PCR products were used directly for cluster generation and sequencing analysis using the Illumina’s Solexa Sequencer according to the manufacturer’s instrunctions

value: degenerated intestine

tag: status

value: deep-aestivation


title: Liver-MeDIP-seq

description: This was the same ewe that was sequenced to generate the reference sheep genome( NCBI Oar_v3.1 )

data_processing:
Base-calling was implemented with build-in software provided by Illumina.
Mapping paired end reads to the genome assembly with bowtie2-2.1.0: bowtie2   --phred64  -3 2  --end-to-end -L  16  -I  100  -X  250     -x index_file  -1  XX_1.fq.gz  -2 XX_2.fq.gz  -S XX.sam
convert SAM file to BAM file: samtools view -S XX.sam -b >XX.bam
Convert BAM files to bedGraph files with BEDTools-Version-2.16.2 : bedtools genomecov   -ibam XX.bam -bg  -g oar_v3.1.genome >XX.bedgraph
Genome_build: Oar_v3.1 downloaded from NCBI ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Ovis_aries/Oar_v3.1/Primary_Assembly/
Supplementary_files_format_and_content: bedGraph

growth_protocol: The sheep was kept at natural environment

extract_protocol:
DNA was isolated using E.Z.N.A. HP Tissue DNA Midi Kit (Omega)
MeDIP DNA libraries were prepared following the protocol as previously described in D. Takai et al. Proc. Natl. Acad. Sci.2002.

value: six month


title: Muscle biospy sample 10

status: Public on Jun 05 2014

city: Singapore

first: Joanna

last: Holbrook

address: 30 Medical Drive

country: Singapore

institute: SICS

data_processing:
Sequencing was performed on the Illumina Genome Analyzer IIx platform, as per manufacturer’s instructions.
Raw reads were filtered and trimmed (i.e. base quality < 20 were removed, read length < 20 bp were removed and entire read pair is removed if one of the trimmed reads become shorter than 20 bp), and then aligned against the Cynomolgus macaque genome (Yan et al., 2011) using RRBSMAP (Xi et al., 2012) with default settings (-p 8 -v 0.1 -w 100 -s 12 -D C-CGG).
We filtered for CpGs with at least 10x read coverage and estimated their methylation ratios using the python script methratio in RRBSMAP.
Genome_build: Cynomolgous macaque genome (BGI)
Supplementary_files_format_and_content: tab-delimited text files include methylation values for each Sample ...

organism: Macaca fascicularis

source_name: Muscle

extract_protocol:
5 µg genomic DNA was fragmented by sequential restriction enzyme digestion for 2 hrs each by 150 U each of MspI and TaqαI (Catalogue Nos.: R0106S and R0149M, New England Biolabs) at optimal temperatures, according to manufacturer’s instructions.
Illumina’s RRBS for Methylation Analysis protocol was followed, except that 10 µL of the methylation adapter oligo was used and the ligation was performed for 15 min at 20 °C in the adapter-ligation step. The purified fragments were then bisulphite treated using the EZ-96 DNA Methylation-Gold Kit (Catalogue No.: D5007, Zymo Research), according to manufacturer’s instructions.

value: Muscle


value: normal intestine

value: non-aestivation


title: Muscle biospy sample 11


title: Muscle biospy sample 2


title: Muscle biospy sample 5


title: Muscle biospy sample 8


title: Muscle biospy sample 7


title: Muscle biospy sample 3


title: Muscle biospy sample 4


title: Muscle biospy sample 1


title: BMR_3%

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

description: Sequenced reads were generated from Spalax galili

data_processing:
Used Spalax galili genome and Rattus norvegicus genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.3.1 with default parameters except  -I 50000  --solexa1.3-quals
Genome_build: Spalax_galili_v1 and rat Ensembl release 64
Supplementary_files_format_and_content: bedGraph file, and the format is: scaffold or contig ID, start, end, transcrptome depth

organism: Nannospalax galili

source_name: brain

growth_protocol: Total RNAs were isolated from the brain of female BMRs under various oxygen concentrations (3%, 6%, 10%, 14%, and 21%) for 6 hours. We also got RNAs from the brain of rats under 6%, 10%, 14%, and 21% oxygen conditions.

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with  30  oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was  performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second  strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with  Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp  fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE  adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR  amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end  sequencing module.

treatment_protocol: total RNA is extracted by TRIzol Reagent

tag: oxygen concentration


title: BMR_14%


title: BMR_10%


title: BMR_6%_2


title: BMR_21%_1


title: gSELEXx1

value: WT, columbia

tag: tissue

value: mature leaves


title: BMR_21%_2


title: Oct4_Otx2ko_tetON_Otx2_nodox

city: Stanford

first: Christa

last: Buecker

state: California

address: 269 Campus Drive

department: Chemical and Systems Biology

institute: Stanford University

description: Mouse embryonic stem cells grown under ESC (serum free, N2B27 based 2i+LIF), no dox treatment

data_processing:
libraries were sequenced with Illumina Genome Analyzer.
unique reads were mapped with bowtie to mm9.
wig files were created using QuEST software (Valouev et al, Nature Methods, 2008) using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: wig files of ChIP-seq reads

source_name: embryonic stem cells (ESC)

growth_protocol: All mouse ESC lines were adapted for a minimum of 5 passages to growth in serum free N2B27 based medium supplemented with MEK inhibitor PD0325901 (0.8μM) and GSK3β inhibitor CHIR99021 (3.3μM) in tissue culture dishes pretreated with 7.5μg/ml polyL-ornithine (Sigma) and 5μg/ml laminine (BD) (Hayashi et al., 2011).  To induce EpiLC differentiation, cells were washed with PBS, trypsinized and strained. 200,000 to 300,000 cells per 10cm2 were plated on tissue culture dishes pretreated with 5μg/ml Fibronectin (Millipore) in N2B27 based medium supplemented with 1% KSR (Invitrogen) and 12μg/ml bFGF (Peprotech). Where indicated 20ng/ml Activin A (R&D Scientific) was added.

extract_protocol:
cells were fixed with 1% Formaldehyde for 10 minutes, then quenched with 0.125M Glycine. After nuclei extraction as described in Rada et al, Nature 2011. Sonication was carried out using Diagenode bioruptor in 15ml Falcon tubes. Each ChIP was validated using q-PCR against selected loci.
libraries were prepared for Illumina sequencing using descibed protocols. All libraries were sequenced as single reads, 36bp length on the Illumina Genome Analyzer Iix.

tag: esc strain

value: Otx2 knock out

tag: mouse strain

value: Oct4 (Santa Cruz sc-8628)


title: Otx2_Otx2ko_tetON_Otx2_nodox

value: Otx2 (Abcam ab21990-100ug)


title: Muscle biospy sample 9


title: Input_Otx2ko_tetON_Otx2_nodox


title: 13_14_C

description: Sample 2

source_name: 3dpf embryos_control mother

tag: developmental stage

value: 3 days post-fertilization embryo

value: whole embryo homogenate

tag: maternal treatment

value: control


title: Input_Otx2ko_tetON_Otx2_plusdox

description: Mouse embryonic stem cells grown under ESC (serum free, N2B27 based 2i+LIF), dox treatment

tag: antibody


title: FAIRE_EpiLC

description: Mouse embryonic stem cells grown under ESC (serum free, N2B27 based 2i+LIF) or differentiated to EpiLCs (serum free, N2B27 based, bFGF and KOSR) for 48h

source_name: epiblast like cells (EpiLC)

value: R1 ESC


title: Input_EpiLC_plusActivinA


title: H3K4me1_EpiLC_plusActivinA

value: H3K4me1 (Abcam ab8895-50ug)


title: BMR_6%_1


title: H3K4me1_EpiLC_minusActivinA


title: Otx2_EpiLC_minusActivin


title: Oct4_EpiLC_plusActivin


title: H3K27ac_EpiLC_plusActivin

value: H3K27ac (Active Motif 39135)


title: p300_EpiLC_minusActivin

value: p300 (Santa Cruz sc-585)


title: Otx2_EpiLC_plusActivin


title: Oct4_EpiLC_minusActivin


title: Input_2i_Otx2_ChIP_rep1


title: H3K27ac_EpiLC_minusActivin


title: H3K4me1_ESC_rep2


title: Input_ESC_rep1


title: Input_ESC_rep2


title: p300_EpiLC_plusActivin


title: Otx2_Otx2ko_tetON_Otx2_plusdox


title: Oct4_Otx2ko_tetON_Otx2_plusdox


title: H3K4me1_ESC_rep1


title: Muscle biospy sample 6


title: Otx2_ESC_rep2


title: H3K27ac_ESC_rep1


title: Oct4_ESC_rep1


title: Oct4_ESC_rep2


title: Input_EpiLC_minusActivinA


title: FAIRE_ESC


title: R5020-RNAseq

city: Ioannina

first: Angeliki

last: Magklara

address: University Campus

department: Medicine

country: Greece

institute: University of Ioannina

data_processing:
Illumina Casava1.7 software used for basecalling.
For ChIP-seq data, reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v1.1.2 with default parameters
For RNA-seq data, reads reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Refseq database using TopHat with own junction  and gene annotation model
For ChIP-seq data, SAM tools were used for filtering uniquely mapped, paired end reads. MACS was used for peak calling with default parameters.
For RNA-seq data the Cufflinks suite was used for transcript annotation
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq data BED files were generated with the genomic coordinates for PR binding sites.
Supplementary_files_format_and_content: For RNA-seq data, txt files were generated with FPKM values for all transcripts

source_name: T47D cells

growth_protocol: RPMI+10% fetal calf serum

extract_protocol:
Trizol extraction for RNA and ChIPs with an antibody against the progesterone receptor for immunoprecipitated DNA
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: R5020 (progestin) or EtOH

tag: cell line

value: breast cancer cell line

tag: passages


title: p300_ESC_rep2


title: EtOH-RNAseq

tag: cell type


title: Otx2-/-_tetON_Otx2_plusdox

data_processing:
RNA seq libraries were sequenced with Illumina Genome Analyzer
reads were mapped with tophat, FPKM were determined using Cufflinks
Genome_build: mm9 and refseq
Supplementary_files_format_and_content: csv files containing all FPKM

extract_protocol:
RNAs from two independent biological replicates of ESC culture and two independent biological replicates from EpiLCs were extracted with Trizol (Invitrogen), following the manufacturer's recommendations. 10 μg of total RNA were subjected to two rounds of oligo-dT purification using Dynaloligo-dT beads (Invitrogen). 100 ng of the purified RNA were fragmented with 10x fragmentation buffer (Ambion). Fragmented RNA was used for first-strand cDNA synthesis, using random hexamer primers (Invitrogen) and SuperScript II enzyme (Invitrogen). Second strand cDNA was obtained by adding RNaseH (Invitrogen) and DNA Pol I (New England Biolabs) to the first strand cDNA mix.
The resulting double-stranded cDNA was used for Illumina library preparation and sequenced with Illumina Genome Analyzer.

treatment_protocol: All samples were washed once with PBS and lysed directly on the plate with Trizol.

tag: es cell line

value: Otx2-/- ESC

tag: growth

value: under ESC (serum free, N2B27 based 2i+LIF) with dox treatment


title: Otx2-/-_tetON_Otx2_nodox

value: under ESC (serum free, N2B27 based 2i+LIF) with no dox treatment


title: PR-ChIP-seq

tag: chip antibody

value: PR

tag: chip antibody catalog #

tag: chip antibody manufacturer

value: Santa Cruz


title: input DNA

value: input


title: RAT_6%_1

description: Sequenced reads were generated from Rattus norvegicus

organism: Rattus norvegicus


title: RAT_10%


title: DxB_male_chow_8wk_adipose_pooled3

city: Los Angeles

first: Yehudit

last: Hasin-Brumshtein

address: 695 Charles E. Young Drive South

department: David Geffen School of Medicine, Cardiology

institute: UCLA

description: Processed files contain allele counts for SNPs

data_processing:
Base calling was performed with CASAVA
Reads were aligned to mm9 genome where DBA/2J SNPs were masked to N, with mrsFAST allowing up to 3 mismatches. Paired reads were treated as independent.
Reads that faile to map with mrsFAST were aligned to the same genome with Tophat v1.
Selection of Uniquely mapped reads, that overlap a known SNP
Count alleles at each known SNP postions
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited tables of allele specific counts for each covered SNP in each sample

source_name: adipose gonadal fat pad

extract_protocol:
tissue was removed and frozen in liquid nitrogen, RNA was extracted from frozen tissue using Qiazol and Qiagen miRNeasy kit
Standard Illumina protocols

tag: cross

value: DxB

value: gonadal fat pad

tag: age

value: 8 wks


title: H3K27ac_ESC_rep2


title: Otx2-/-_ESC

value: under ESC (serum free, N2B27 based 2i+LIF)


title: p300_ESC_rep1


title: Otx2-/-_EpiLC

value: differentiated to EpiLCs (serum free, N2B27 based, bFGF and KOSR)


title: E14_EpiLC

value: E14 ESC


title: BxD_male_chow_8wk_adipose_pooled3

value: BxD


title: BxD_female_chow_8wk_adipose_pooled3


title: DxB_female_chow_8wk_adipose_pooled2


title: E14_ESC


title: WT

city: Baltimore

first: Yulian

last: Zhou

address: 725 N. Wolfe Street

institute: JHMI

description: Sample 4

data_processing:
Raw reads were mapped to the reference genome (mm10) using TopHat and the relative abundance of each transcript was calculated with Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each Sample.

source_name: Whole retina

extract_protocol:
Three batches of total RNA were extracted using Trizol (Invitrogen) and the RNeasy kit (Qiagen). Each batch was prepared from 4-8 P10 retinas (2-4 mice) per genotype.
Three batches of RNA were pooled for RNAseq library construction using the TruSeq RNA Sample Prep Kit v2 (Illumina).

treatment_protocol: 20 μg 4HT intraperitoneal injection at P3

tag: strain

value: mixed (contains at least C57BL6 and 129)

tag: genotype/variation

value: WT

value: total retina


title: NdpKO

description: Sample 2

value: NdpKO

tag: tissue


title: beta catenin stabilization

description: Sample 3


title: R1_EpiLC_plusActA

value: R1 ESC

tag: mouse strain

value: differentiated to EpiLCs (serum free, N2B27 based, bFGF and KOSR) for 48h with 20ng/ml Actin A


title: R1_EpiLC_noActA

value: differentiated to EpiLCs (serum free, N2B27 based, bFGF and KOSR) for 48h with no Actin A


title: RAT_14%

tag: oxygen concentration


title: R1_ESC_rep2


title: NdpKO rescue

description: Sample 1

tag: developmental stage


title: RAT_6%_2


title: fog2 sperm (polyA replicate 1)

status: Public on Jun 04 2014

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
NR_sperm_fog2
processed data file: data_mRNA_rpkm.txt

data_processing:
Sequencing reads for each sample and stage were seperately mapped to the transcriptome using bwa with default parameters. For small RNAs reads were mapped to the genome
For mRNAs reads were aggregated across all isoforms of a given gene.
For mRNAs aggregated reads were converted to reads per million mapped reads per kilobase of transcript length (RPKM).
For small RNAs reads were annotated based on the strand and the annotation (i. e. sense or antisense with regards to a given annotation).
For small RNAs all reads of a given annotation were aggregated and converted into reads per million (RPM)
Genome_build: WS190
Supplementary_files_format_and_content: Tab separated txt-file with gene identifiers and expression values in RPKM for mRNAs and RPM for small RNAs.

source_name: sperm poly(A)-extracted mRNA library

growth_protocol: Strains were maintained using previously described methods(Brenner, 1974; Stiernagle, 2006) on OP50 seeded NGM plates at permissive temperatures.

extract_protocol:
mRNA-Seq: PolyA RNA was fragmented into approximately 250 nt fragments by chemical fragmentation (200 mM tris acetate pH 8.2, 500 mM potassium acetate, 150 mM magnesium acetate) at 94°C for exactly 3.5 min in a thermocycler. Fragmented RNAs were isolated with RNA Clean beads (Beckman Coulter, USA) according to manufacturerâ??s instructions. Fractionation was checked by capillary electophoresis in a RNA Pico 6000 chip using the Bioanalyzer (Agilent Technologies, USA). First strand cDNA synthesis was accomplished using Superscript III Reverse Transcriptase and random hexamers (Invitrogen, USA), followed by second strand synthesis using DNA Polymerase I and RNaseH (Invitrogen USA). Double-stranded DNA was purified with Agencourt AMPure beads XP (Beckman Coulter, USA) and quality was checked by capillary gelelectrophoresis on the Bioanalyzer with the Agilent DNA 1000 kit (Agilent Technologies, USA). dsDNA libraries subsequently processed for sequencing using the Genomic DNA Sample Prep Kit (Illumina, USA) according to the manufacturerâ??s protocol.
Oocytes: Adult wild-type hermaphrodites (N2) were cut using a razorblade in PBS containing 0.5% BSA and 0.02%Tween. Oocytes were picked by mouth pipetting under a stereo microscope (Leica), washed thoroughly in PBS and lyzed in TriZol LS (Invitrogen, USA). Sperm: Sperm was isolated in principle as described previously(L¹Hernault & Roberts, 1995) from males worms obtained from a fog-2(q71) mutant background strain. Males were cut in cold PBS containing protease inhibitors (Sigma-Aldrich, Germany). Sperm was subsequently purified by filtration (3x40µm, 2x10µm, 1x6µm nylon mesh) and washed twice in cold PBS. Sperm was then activated by incubation in PBS containing 200µg/mL Pronase (Sigma-Aldrich, Germany) for 30 minutes at 24°C and suspended in Trizol LS (Invitrogen, USA) for RNA extraction. 1-cell embryos: 1-cell embryos were obtained by fluorescence activated cell sorting (eFACS) as described previously(Stoeckius et al, 2009) in an FACSAriaIII flow cytometer (BD Biosciences, USA).  Whole worm: Adult worms were washed from NGM plates with M9-Buffer and subsequently washed at least 3 times with M9-Buffer. RNA was isolated from whole worms by bead homogenization (6000 rpm, 5 seconds) in a Precellys24 (Precellys, USA) in Trizol LS reagent (Invitrogen, USA) according to the manufacturers protocols.

tag: temperature

tag: rna source

value: sperm

tag: library

value: poly(A)-extracted mRNA library


title: 1-cell embryos (small RNA replicate 1)

description:
1cell_1
processed data file: data_small_RNA_rRNA.txt
processed data file: data_small_RNA_miRNA_prec.txt
processed data file: data_small_RNA_miRNA.txt
processed data file: data_small_RNA_u21RNA.txt
processed data file: data_small_RNA_tRNA.txt
processed data file: data_small_RNA_snoRNA.txt
processed data file: data_small_RNA_snRNA.txt
processed data file: data_small_RNA_exon.txt
processed data file: data_small_RNA_intron.txt

source_name: 1-cell small RNA library

extract_protocol:
For small RNA-seq: 1 µg of total RNA per sample were used for small RNA library preparation. First total RNA was treated with RNA 5â?? polyphosphatase (Epicentre Biotechnologies, USA) prior to small RNA library preparation to allow for subsequent cloning of multiphosphorylated endo-siRNAs. Small RNA cloning and library preparation was then performed with the TruSeq Small RNA Sample Preparation Kit (Illumina, USA) according to the manufacturer protocol.
Oocytes: Adult wild-type hermaphrodites (N2) were cut using a razorblade in PBS containing 0.5% BSA and 0.02%Tween. Oocytes were picked by mouth pipetting under a stereo microscope (Leica), washed thoroughly in PBS and lyzed in TriZol LS (Invitrogen, USA). Sperm: Sperm was isolated in principle as described previously(L¹Hernault & Roberts, 1995) from males worms obtained from a fog-2(q71) mutant background strain. Males were cut in cold PBS containing protease inhibitors (Sigma-Aldrich, Germany). Sperm was subsequently purified by filtration (3x40µm, 2x10µm, 1x6µm nylon mesh) and washed twice in cold PBS. Sperm was then activated by incubation in PBS containing 200µg/mL Pronase (Sigma-Aldrich, Germany) for 30 minutes at 24°C and suspended in Trizol LS (Invitrogen, USA) for RNA extraction. 1-cell embryos: 1-cell embryos were obtained by fluorescence activated cell sorting (eFACS) as described previously(Stoeckius et al, 2009) in an FACSAriaIII flow cytometer (BD Biosciences, USA).  Whole worm: Adult worms were washed from NGM plates with M9-Buffer and subsequently washed at least 3 times with M9-Buffer. RNA was isolated from whole worms by bead homogenization (6000 rpm, 5 seconds) in a Precellys24 (Precellys, USA) in Trizol LS reagent (Invitrogen, USA) according to the manufacturers protocols.

value: fem-1(hc17ts)/TX189(OMA-1::GFP) (mother) X CB4856 (father)

value: 1-cell embyro

value: small RNA library


title: CB4856 whole worm (small RNA replicate 1)

description:
HW_1
processed data file: data_small_RNA_rRNA.txt
processed data file: data_small_RNA_miRNA_prec.txt
processed data file: data_small_RNA_miRNA.txt
processed data file: data_small_RNA_u21RNA.txt
processed data file: data_small_RNA_tRNA.txt
processed data file: data_small_RNA_snoRNA.txt
processed data file: data_small_RNA_snRNA.txt
processed data file: data_small_RNA_exon.txt
processed data file: data_small_RNA_intron.txt

source_name: whole worm small RNA library

value: whole worm


title: RAT_21%


title: N2_background whole worm (polyA replicate 3)

description:
NR_poly_3
processed data file: data_mRNA_rpkm.txt

source_name: whole worm poly(A)-extracted mRNA library


title: N2_background whole worm (polyA replicate 1)

description:
NR_poly_1
processed data file: data_mRNA_rpkm.txt


title: CB4856 sperm (polyA low purity)

description:
HW_sperm_lp
processed data file: data_mRNA_rpkm.txt


title: CB4856 whole worm (polyA replicate 3)

description:
HW_poly_3
processed data file: data_mRNA_rpkm.txt


title: CB4856 whole worm (polyA replicate 1)

description:
HW_poly_1
processed data file: data_mRNA_rpkm.txt


title: 1-cell embryos (ribominus replicate 3)

description:
1cell_ribo_3
processed data file: data_mRNA_rpkm.txt

source_name: 1-cell embyro RiboMinus-extracted mRNA library

value: RiboMinus-extracted mRNA library


title: 1-cell embryos (ribominus replicate 2)

description:
1cell_ribo_2
processed data file: data_mRNA_rpkm.txt


title: 1-cell embryos (ribominus replicate 1)

description:
1cell_ribo_1
processed data file: data_mRNA_rpkm.txt