title: iMEF

description: original REDseq protocol

source_name: Immortalized mouse embryonic fibroblasts

tag: strain background

value: iMEF (well-differentiated cells)


title: ESC_Oct4KD

status: Public on Dec 31 2014

type: SRA

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

description: modified REDseq protocol

library_source: genomic

data_processing:
library strategy: RED-seq (deep sequencing analysis of Restriction Enzyme Digestion)
Basecalls performed using CASAVA version 1.8.2
Barcode sequences were trimmed and RED-seq reads were aligned to the mm9 genome assembly using Bowtie allowing at most one mismatch in every alignment.
For multimappers, only one alignment was chosen randomly by the -M 1 parameter setting.
Assignment of aligned sequences to individual restriction enzyme cut sites (REs) and differential cut analysis were performed using the Bioconductor package REDseq.
The ChIPpeakAnno package was used to annotate the differentially cut sites to the nearest genes.
Genome_build: mm9
Supplementary_files_format_and_content: The assigned reads for each restriction enzyme site are in bedGraph format (*.bedGraph).

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic stem cells

growth_protocol: Feeder-free growth on gelatin coated dishes in standatd ES medium: KO DMEM + 10% FBS, glutamine, LIF, non-essential amino acids, beta-mercaptoethanol.

extract_protocol:
One million cells were used to construct RED-seq libraries. Cells were washed, pelleted, and resuspended in Swelling buffer (10mM Tris pH8.0, 85mM KCl, 0.5% NP-40, 10mM MgCl2) with 100 units of Sau96I (NEB) and incubated in a thermomixer (Eppendroff) at 37°C for 1 hour, shaking at 900 rpm. Digestion was terminated by adding 40μl of 10% SDS and 20μl of 0.5M EDTA and the chromatin was treated with proteinase K (Ambion) overnight at 55°C. Digested DNA was purified using Phenol/Chloroform/Isoamyl alcohol extractions and precipitated at -80°C for 1 hour.
Digested DNA samples were end-repaired and A-tailed according to Illumina's instructions., and ligated with biotinylated and barcoded adaptors. DNA was purified using Zymo Research DNA clean and concentrate columns following each enzyme reaction. The biotin-adaptor ligated DNA was sonicated in a Covaris sonicator (S220) to generate DNA peak fragments of 200 bp, on average. The sonicated DNA samples were then end-repaired, A-tailed, and ligated with non-biotinylated adaptors. The ligation samples were loaded on 2% agarose gel and DNA was purified within a size range of roughly 200-350 bp in length. Gel-purified DNA was diluted to 250μl with streptavidin binding buffer (20mM HEPES pH 7.6, 500mM NaCl, 1mM EDTA, 0.02% NP-40) and incubated with 30μl of pre-washed streptavidin magnetic beads (NEB) at room temperature for 1 hour. After magnetic separation, the supernatants were removed, and the beads were washed additional three times with streptavidin binding buffer. DNA was eluted from streptavidin magnetic beads by adding 20 μl of 0.1X TE and heating at 60°C for 3 minutes. The elution was repeated three times. The adaptor-ligated material was then PCR amplified with Phusion polymerase (NEB) using 16 cycles of PCR and its concentration was determined using a NanoDrop (Thermo).

treatment_protocol: In one 10 cm2 dish, 1X10^6 cells were infected with 2.5 ug of esiRNA. After 12-15 hours, the media was replaced and cells were cultured until 5 days post-transfection.

tag: genotype/variation

value: Oct4 knockdown

tag: cell line

tag: cell type

value: Mouse embryonic stem cells

tag: material for redseq

value: chromatin DNA


title: ESC_GFPKD

description: modified REDseq protocol

value: GFP knockdown (control)


title: ESC

description: original REDseq protocol

value: wild type

value: Mouse embryonic stem cells (undifferentiated)


title: P1 Sorted corticothalamic projection neurons replicate 1

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

country: USA

institute: Johns Hopkins University

library_source: transcriptomic

data_processing:
100 base pair-paired end reads were mapped to the mouse genome (mm9) using Tophat2 (Kim et al., 2013) with an average of 1.09x108 mapped reads (range 7.62x107-1.33x108; s.d. 1.30x107) and assembled into transcripts using Cufflinks (Trapnell et al., 2010). Individual assemblies were merged using Cuffmerge and UCSC coding genes as a reference.
The merged assembly was used as input for our previously-described long non-coding RNA (lncRNA) identification pipeline (Cabili et al., 2011). Assembled lncRNAs were appended to the list of known UCSC protein-coding genes to establish a suitable reference transcriptome.
Differential expression testing was performed between all pairs of conditions using Cuffdiff2. Data was visualized using the cummeRbund package from Bioconductor (Gentleman et al., 2004; Trapnell et al., 2012b) and additionally integrated into the DeCoN interactive web resource.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file with normalized expression estimates (FPKM) for each gene under each condition

molecule: total RNA

source_name: Corticothalamic projection neurons

extract_protocol:
RNA was recovered from FACS-purified cells using the RecoverAll Total Nucleic Acid Isolation Kit (Ambion) according to manufacturer’s instructions except proteinase K digestion was performed at 50˚C for 3 hours. RNA concentration was quantified with Nanodrop 1000 and quality was determined with an Agilent 2100 Bioanalyzer. RNA Integrity Numbers (RIN) for all samples were between between 6.3 and 9.  Typical yield was between 1 and 2 picograms RNA per sorted event, requiring approximately 100,000 cells to yield 200 ng RNA for library input.
Purified RNA served as input for the standard Illumina RNA-seq library preparation with poly(A) selection.

tag: developmental stage

tag: neuron subtype

value: Corticothal

tag: strain


title: P1 Sorted corticothalamic projection neurons replicate 2


title: P1 Sorted subcerebral projection neurons replicate 2

source_name: Subcerebral projection neurons

value: Subcereb


title: adult_testis_29nt

city: Los Angeles

first: Dario

last: Boffelli

state: CA

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

description: 29nt fraction of small RNA

data_processing: Sequence reads were called with the Illumina Pipeline v1.4. Called reads were processed to trim 5' and 3' adapter sequences (GTTCAGAGTTCTACAGTCCGACGATC and TCGTATGCCGTCTTCTGCTTG, respectively), and remove contaminant microRNA (from mirBase v14), rDNA (28S, 18S, 5S), and tRNA. The remaining reads were aligned against the mouse genome (mmu9) with bowtie v0.12.7, with parameters set to report alignments with up to 1 mismatch, and , if a read aligns to more than one location with the same alignment score, report one randomly selected alignment (relevant parameters: -v1 -M1 –best). Aligned reads were converted to bed format.

source_name: testis tissue

growth_protocol: Mice were housed under standard conditions and fed chow diet ad libitum

extract_protocol: Total RNA was isolated using Trizol and separated by electrophoresis on an 18% polyacrylamide gel. The visible band at ~29nt was excised, extracted from the gel, and used for library construction. Libraries were prepared according to Illumina's Small RNA Sample Preparation Guide (Part # 1004239 RevB).

tag: age

value: 10 weeks

tag: tissue

value: testis

tag: antibody


title: spleen_miwi2

description: RNA IP against MIWI2

source_name: splenocytes

extract_protocol: MIWI2-piRNA complexes were isolated from whole cell lysates of unfractionated splenocytes by incubation with an anti-MIWI2 antibody. piRNAs were recovered by proteinaseK digestion, and used for library construction. Libraries were prepared according to Illumina's Small RNA Sample Preparation Guide (Part # 1004239 RevB).

value: spleen

value: rabbit polyclonal anti-mouse MIWI2 (PIWIL4)

tag: vendor

value: Abcam

tag: catalog number


title: MEL_miwi2

description: RNA IP against MIWI2

source_name: mouse erythroleukemia cells (ATCC TIB-55)

growth_protocol: MEL were maintained in DMEM (Hyclone, South Logan, UT) with 10% FBS (Hyclone) supplemented with penicillin (10 U/ml) and streptomycin (10 U/ml) in a humidified 95% air-5% CO2 atmosphere.

extract_protocol: MIWI2-piRNA complexes were isolated from whole cell lysates by incubation with an anti-MIWI2 antibody. piRNAs were recovered by proteinaseK digestion, and used for library construction. Libraries were prepared according to Illumina's Small RNA Sample Preparation Guide (Part # 1004239 RevB).

value: Friend virus-transformed early mouse erythroblasts


title: E18 Sorted corticothalamic projection neurons replicate 2


title: E18 Sorted corticothalamic projection neurons replicate 1


title: P1 Sorted subcerebral projection neurons replicate 1


title: P1 Sorted callosal projection neurons replicate 2

source_name: Callosal projection neurons

value: CPN


title: E16 Sorted corticothalamic projection neurons replicate 2


title: E16 Sorted corticothalamic projection neurons replicate 1


title: E18 Sorted subcerebral projection neurons replicate 2


title: E18 Sorted subcerebral projection neurons replicate 1


title: E16 Sorted subcerebral projection neurons replicate 2


title: E18 Sorted callosal projection neurons replicate 2


title: E18 Sorted callosal projection neurons replicate 1


title: E16 Sorted subcerebral projection neurons replicate 1


title: E16 Sorted callosal projection neurons replicate 2


title: E16 Sorted callosal projection neurons replicate 1


title: E15 Sorted corticothalamic projection neurons replicate 2


title: E15 Sorted subcerebral projection neurons replicate 2


title: E15 Sorted subcerebral projection neurons replicate 1


title: E15 Sorted callosal projection neurons replicate 2


title: P1 Sorted callosal projection neurons replicate 1


title: E15 Sorted callosal projection neurons replicate 1


title: RNA-Seq, Control cells, Set 1

city: San Francisco

first: Courtney

last: Onodera

address: 1450 Third St, HD374

institute: University of California, San Francisco

description: Cell number-normalized RNA-Seq with ERCC spike-in, Control cells, Set 1

data_processing:
RNA-Seq reads were first trimmed of Illumina adapter sequence. Any pairs with reads containing less than 40 bases of insert sequence were discarded. The remaining trimmed reads were aligned with Tophat (v2.0.10) to a custom genome containing the mm9 mouse assembly with the ERCC spike-in sequences added. The Tophat alignment was guided by a custom reference gene set, consisting of RefSeq genes of length greater than 150 bases (downloaded December 30, 2013 from the UCSC Genome Browser, mm9) as well as the ERCC spike-in sequences. Only properly-paired reads mapping uniquely to the combined mm9+ERCC genome were retained for further analysis. To obtain raw FPKM values for the paired mutant and control libraries, reads were first processed through Cufflinks (v2.2.0), using the custom gene set as a guide but allowing assembly of novel transcripts. Throughout the mapping and quantification procedures, the fr-secondstrand option was invoked whenever possible to indicate the strand-specificity of the sequencing libraries. The custom reference genome was also given to Cufflinks and Cuffdiff for bias correction, and the –max-bundle-frags option was set to 100000000 to enable quantification of highly expressed transcripts. Loess normalization of the paired mutant and control FPKM values obtained from Cuffdiff was performed as described previously [PMID: 23101621]. The loess-normalized FPKM values were used in all subsequent analyses.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-Seq: Tab-delimited text file with Loess-normalized FPKM values for known and novel transcripts.

source_name: Embryonic Stem Cells

growth_protocol: Mouse ES cells were routinely passaged in gelatin-coated 6-well plates every other day. Cells counts were obtained using a Vi-CELL (Beckman Coulter) and 200k cells were seeded per 6-well well in serum/LIF media consisting of 15% FBS, 1x Penicillin/Streptomycin, 1x Non-essential amino acids, 0.057mM beta-mercaptoethanol, and 1000U/mL LIF (ESGro, Millipore) in high glucose DMEM supplemented with GlutaMAX and pyruvate (Gibco, 10569-10).

extract_protocol:
Two independently derived lines of Rosa26CreER;Chd1fl/- ES cells were either control-(EtOH) or tamoxifen-treated as described above. Cells were counted twice at different dilutions on a Vi-CELL counter and total RNA was isolated from equal numbers of viable cells. RNA was isolated using the RNeasy kit with on-column DNase I digestion. Total RNA was quantified using a Qubit fluorometer (Invitrogen). Equal elution volumes of RNA corresponding to approximately 1ug of total RNA were mixed with 1uL of a 1:10 dilution of Mix#1 External RNA Controls Consortium (ERCC) RNA spike-in controls, containing 92 polyadenylated transcripts over a range of concentrations (Life Technologies 4456740). rRNA depletion was performed using the Ribo-Zero rRNA removal kit (Epicentre, MRZH116).
Strand-specific libraries were generated using the Illumina TruSeq Stranded mRNA kit (RS-122-2101). Libraries were prepared using barcoded adaptors, pooled, and sequenced over two lanes of an Illumina HiSeq 2500 in rapid mode for paired-end reads of 100 bases at the UC Davis Genome Center.

treatment_protocol: Rosa26CreER;Chd1fl/- ES cells were control (EtOH)- or tamoxifen-treated (1 μM) for 48-72h and then expanded without tamoxifen for 3-5 cell-number normalized passages in serum/LIF medium prior to further analyses.

tag: genotype

value: Control


title: RNA-Seq, Chd1-/- cells, Set 1

description: Cell number-normalized RNA-Seq with ERCC spike-in, Chd1-/- cells, Set 1


title: MerR-Hg WCE

city: Davis

first: Marc

middle: T

last: Facciotti

state: Ca

address: 451 Health Sciences Drive

department: Biomedical Engineering

institute: University of California, Davis

description: index/barcode: ACGGCT

data_processing:
Casava pipeline version 1.7 was used for base calling
Sequences were barcode sorted and quality trimmed (minimum Phred quality 20, minimum length 25bp) using the FASTX-Toolkit (http:// hannonlab.cshl.edu/fastx_toolkit/). Sequencing primer and adapter contamination were filtered using the TagDust package
A reference genome for S. solfataricus 98/2 (GenBank: CP001800.1) was created using Bowtie.  Quality-filtered reads were then mapped using Bowtie to the reference genome with repeat sequences masked, and SAM format sequence files were converted to sorted BAM files using the samtools package.
Putative protein–DNA binding events were detected using Pique, a microbially focused and freely available peak calling application (available at https://github.com/ryneches/pique, version tag: halo_egw). ChIP-seq coverage data and candidate peaks were visualized and manually curated using the Gaggle Genome Browser
Genome_build: ASM2474v1
Supplementary_files_format_and_content: .txt files are tab delimited files that contain Chromosome(replicon), Start of peak region,  End of peak region,  Peak_Reads, integrated reads in the peak region,      Background_Reads calculated over a local region of the same size as the peak,  Enrichment_Ratio of reads in peak to background; .track files are tab delimited files describing Pique processed reads at each position in a replicon - columns are replicon, strand, base pair position, reads.  The .track files can be visualized with the Gaggle Genome Browser.  The .txt files can be loaded into the Gaggle Genome Browser as "bookmarks" for easy navigation from peak to peak.

organism: Saccharolobus solfataricus

source_name: MerR-Hg WCE

growth_protocol: Samples were prepared from a 50mL culture of S. solfataricus WT and merRHA.  Cells were harvested during mid exponential phase at an OD540 of 0.5.

extract_protocol:
Lysates were prepared from sonicated cellsi and MerR-HA/DNA complexes were isolated with an antibody. Whole cell lyate samples labeled "WCE" were prepared without antibody as background.
Illumina libraries were prepared as described in Wilbanks,  G, Larsen  J, Neches  Y, Yao  I, Wu -Y, Kjolby RAS, & Facciotti  T. 2012. A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq Nucleic Acids Research

treatment_protocol: For Hg(II) induction, 0.5µM Hg(II) was added at an OD540 of 0.1, which corresponds to 108 cells/mL and harvested after 1hr. Cells were pelleted and were immediately fixed with 1% (v/v) formaldehyde for 10 min. Fixation was terminated through the addition of glycine to a final concentration of 125mM. Cell pellets were washed twice with 1x PBS pH 7.0, after which the pellets were frozen at -80°C until further use.

tag: treatment

value: 0.0µM HgCl2

tag: chip antibody

tag: magnetic bead


title: RNA-Seq, Control cells, Set 2

description: Cell number-normalized RNA-Seq with ERCC spike-in, Control cells, Set 2


title: Mes_W14 leaf

city: Saint Louis

first: Weixiong

last: Zhang

state: MO

address: Campus Box 1045 One Brookings Drive

institute: Washington university in St Louis

description: small RNA-Seq

data_processing:
The raw sequence reads were first processed to remove reads with no 3' sequencing adaptor or of low quality. The sequence adaptor trimming was done by an in-house program that recursively searches for the longest subsequence of the adaptor appearing within a sequence read. If a raw sequence read did not have a subsequence of the adaptor that was longer than 4 nt, it was considered to have no adaptor.
Genome_build: Mesculenta_147_v4.fa.gz [Cassava (Mesculenta_147); http://phytozome.jgi.doe.gov/pz/portal.html#!bulk?org=Org_Mesculenta]
Supplementary_files_format_and_content: txt format. Content: 1st column is SEQUENCE;  2nd column is COUNT

organism: Manihot esculenta subsp. flabellifolia

source_name: fully expanded leaf

growth_protocol: KU50, Arg7 and W14 were grown in an experiment field in Haikou, China. Leaves and roots of these three genotypes were sampled at 150 DAP for sequencing of small RNAs

extract_protocol: Total RNA of each sample was isolated individually for profiling. As a result, six small-RNA libraries were constructed.

treatment_protocol: No treatment

tag: cultivar

value: W14 (wild progenitor)

tag: condition

value: Cassava under normal condition

value: leaf


title: MerR+Hg ChIPSeq

description: index/barcode: TAACTT

source_name: MerR+Hg ChIPSeq

value: 0.5µM HgCl2

value: HA (Abcam cat# ab9110)

value: protein A-conjugated magnetic beads (JSR Micro, Magnosphere)


title: Mes_W14 storage root

description: small RNA-Seq

source_name: storage root (150 days after planting)

value: root


title: Mes_Arg7 storage root

description: small RNA-Seq

organism: Manihot esculenta


title: Mes_Arg7 leaf

description: small RNA-Seq


title: Eggs

city: Chongqing

first: Yong

last: Huang

address: Tiansheng Road

country: China

institute: Southwest University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to the transcriptome of Bactrocera dorsalis using SOAP software.
Normalize the expression of miRNA in two samples (control and treatment) to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000

organism: Bactrocera dorsalis

source_name: The whole body

extract_protocol:
About 2000 eggs, 10 larvae, 10 pupae and 8 adults were gathered into four centrifuge tubes, respectively, and stored at −80 °C for RNA extraction. Total RNA from the four samples was extracted using the TriZol reagent (TransGen Biotech, Beijing, China), according to the manufacturer's instructions.
For each library, small RNAs of 18 to 30 bp in length were separated by 15% polyacrylamide gel electrophoresis (PAGE). The ligation between these small RNAs and a 5' and 3' adaptors was performed using T4 RNA Ligase (Takara:D2050). The 5'- and 3'-ligated RNA products were purified and then reverse transcribed for the first-strand cDNA using a SuperScript® II Reverse Transcriptase kit (InvitrogenTM: 18064-014) with the complementary sequence of the 3' adaptor. Thereafter, the cDNAs were used as templates for double-stranded cDNA synthesis using PCR amplification in a Veriti Thermal Cycler (Applied Biosystems), using primers that anneal to the adapters. After second-strand cDNA synthesis, the adaptor sequence primers were used to amplify the PCR products as a small RNA library for deep sequencing.

value: egg


title: Pupae

value: pupa


title: RNA-seq of AMY

city: Palo Alto

first: Jingjing

last: Li

address: 3165 Porter Drive

institute: Stanford University

data_processing:
FASTQ alignment using TopHat v2.0.8 aginst the human RefSeq transcriptome downloaded from UCSC Table Browser.
Gene expression quantification using CUFFLINKS V2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: the FPKM values for gene and each sample were listed in the final excel table

organism: Homo sapiens

source_name: human brain (AMY, amygdala)

extract_protocol:
Tissue blocks were provided from NICHD brain bank. Total RNA was extracted from flash frozen tissue samples using Trizol reagent. Then the total RNA was treated with RNase-Free DNase (Qiagen) followed by purification with RNeasy MinElute Cleanup Kit (Qiagen) following the manufacturer’s instructions.
2 µg of total RNA each sample was subject to RNA-seq library preparation with ScriptSeq™ Complete Gold Kit from Epicentre (Cat. # SCL24EP, Madison, WI) following the manufacturer’s instructions. In brief, ribosomal RNA was depleted from total RNA using Ribo-Zero magnetic beads, then the ribosomal RNA depleted RNA was purified and fragmented. Random primer tailed with Illumina adaptor was used to perform reverse transcription to get cDNA library. Adaptor sequence was added to the other end of cDNA library with a Terminal-Tagging step. cDNA library was amplified with Illumina primers provided with this kit. The product was size selected (350~500 bp) from 2% agarose E-gels (Invitrogen) and sequenced in 1 lane per sample on Illumina’s HiSeq 2000 platform.

value: frozen postmortem brain from NICHD

tag: brain region

value: AMY, amygdala


title: RNA-seq of BA9

source_name: human brain (BA9, Brodmann area 9)

value: BA9, Brodmann area 9


title: Peak lactation

city: Yangling

first: zhuanjian

last: li

address: xinong road

institute: Northwest A&F University

data_processing:
Illumina Casava software used for basecalling.
using clean-fastq_v1.pl to remove adapters and low quality tags as well as contaminants
aligning these data in the NCBI with all EST sequences from bovine and its closely related species goat
Genome_build: n/a
Supplementary_files_format_and_content: tab-delimited text files include count values for each read (first column: length of sequence; second column: frequency; third column: small RNA sequence)

organism: Capra hircus

source_name: mammary gland tissues

growth_protocol: All animal protocols were approved by the Review Committee for the Use of Animal Subjects of Northwest A&F University.

extract_protocol:
The mammary glands were collected from three Xinong Saanen dairy goats at different stages: 30 days after lambing (DAL) and 320 DAL. All samples were immediately frozen in liquid nitrogen and stored at -80 oC
Three samples were then pooled, and the total RNA was isolated from each pooled sample using the Trizol reagent.

value: 320 days after lambing

value: mammary gland

tag: state

value: peak lactation

tag: breed

value: Xinong Saanen dairy goat


title: Dry period

tag: developmental stage

value: 75 days after lambing

value: dry period


title: RNA-seq of BA40

source_name: human brain (BA40, Brodmann area 40)

value: BA40, Brodmann area 40


title: E15 Sorted corticothalamic projection neurons replicate 1

tag: neuron subtype

value: Corticothal


title: RNA-seq of the corpus callosum #4999

source_name: human brain

tag: disease

value: autism spectrum disorder


title: RNA-seq of the corpus callosum #5403


title: RNA-seq of the corpus callosum #5302


title: RNA-seq of the corpus callosum #5407

value: not available


title: RNA-seq of the corpus callosum #4899


title: RNA-Seq, Chd1-/- cells, Set 2

description: Cell number-normalized RNA-Seq with ERCC spike-in, Chd1-/- cells, Set 2


title: RNA-seq of the corpus callosum #4670


title: RNA-seq of the corpus callosum #5242


title: RNA-seq of the corpus callosum #5391


title: Adults

value: adult


title: Larvae

value: larva


title: RNA-seq of the corpus callosum #5163


title: MerR-Hg ChIPSeq

description: index/barcode: ACCTGG

source_name: MerR-Hg ChIPSeq

tag: strain

value: 0.0µM HgCl2

value: HA (Abcam cat# ab9110)

value: protein A-conjugated magnetic beads (JSR Micro, Magnosphere)


title: RNA-seq of the corpus callosum #5144

tag: tissue

value: frozen postmortem brain from NICHD


title: RNA-seq of the corpus callosum #4727


title: Mo-DC 1h LPS mRNA rep 3

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
mRNA
C3 DC LPS

data_processing:
Basecalls performed using CASAVA version 1.7
Data analysis consisted of a filtering step to eliminate reads consisting mono- and di-nucleotide repeats followed by the identification of exact unique matches using fetchGWI [Iseli C, Ambrosini G, Bucher P, Jongeneel CV (2007) Indexing strategies for rapid searches of short words in genome sequences. PLoS One 2: e579].
Megablast was used to recover unmatched reads (http://www.ncbi.nlm.nih.gov/blast/html/megablast.html). Paired information was used to generate alignments of each read on the genomic region where hits were found by previous steps using SIBsim4 http://sibsim4.sourceforge.net/. Alignments were analyzed using Tromer [Steijger T, Abril JF, Engstrom PG, Kokocinski F, Akerman M, et al. (2013) Assessment of  transcript reconstruction methods for RNA-seq. Nat Methods 10: 1177-1184].
Counts for DC0904 and DC0907 were pooled for subsequent analysis. The sample name for these reads is listed as DC_normal in the processed data file
Counts for DCLPS0910 and DCLPS0913 were pooled for subsequent analysis. The sample name for these reads is listed as DC_treated in the processed data file
Genome_build: hg19
Supplementary_files_format_and_content: Raw count data are provided in tab-delimited format

source_name: Mo-DC 1h LPS mRNA rep 3

growth_protocol: monocytes were cultured in RPMI 10% FCS supplemented with 2-mercaptoethanol (50 μM), GM-CSF (600 U/ml), and IL-4 (750 U/ml)

extract_protocol:
Nascent RNA: nuclei were isolated and lysed, the resulting chromatine was pelleted by centrifugation. Primary RNA was extracted using acid water-saturated hot phenol extraction
Total RNA was extracted using Trizol reagent (Life Technologies)
TruSeq library preparation protocol

treatment_protocol: 1 hour LPS (25ng/ml)

tag: cell type

value: Monocyte-derived denditric cells


title: Control fibroblast

city: Shanghai

first: Jun

last: Mi

address: 280 South Chongqing Rd.

institute: Shanghai Jiao Tong University School of Medicine

description: mRNA profiling

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
TPM
Genome_build: hg19
Supplementary_files_format_and_content: TPM

source_name: Fibroblast

growth_protocol: Primary fibroblasts were isolated from foreskin tissues, and grew in DMEM with 15% FBS less than 5 generations.

extract_protocol:
Fibroblasts were rinsed with PBS twice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary fibroblasts starved overnight,  were treated with 8 ng/ml TGF-B for 96 hours before harvested.

value: foreskin

value: primary fibroblast

tag: agent

value: control


title: RNA-seq of the corpus callosum #5308


title: Mo-DC 1h LPS mRNA rep 2

description:
mRNA
C2 DC LPS

source_name: Mo-DC 1h LPS mRNA rep 2


title: Mo-DC mRNA rep 3

description:
mRNA
C3 DC

source_name: Mo-DC mRNA rep 3


title: Mo-DC 1h LPS nascent RNA rep 3

description:
Nascent/primary RNA
B DC LPS
mRNA-seq sample preparation protocol (PE-102-1002-Paired-end kit)

source_name: Mo-DC 1h LPS nascent RNA rep 3


title: Mo-DC mRNA rep 2

description:
mRNA
C2 DC

source_name: Mo-DC mRNA rep 2


title: Mo-DC nascent RNA rep 3

description:
Nascent/primary RNA
B DC
mRNA-seq sample preparation protocol (PE-102-1002-Paired-end kit)

source_name: Mo-DC nascent RNA rep 3


title: atriplex_43_4

city: Wuhan

first: Qiang

state: Saskatchewan

address: #1 Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were quality trimmed using btrim with parameters: -q, -l 50, -a 20, -S
Reads from known repeat sequences were filtered out by comparison against TAIR Plant Repeats Database using bowtie2 with parameters: --local, -k 2, --maxins 1000, --no-unal, --no-hd
First stage assembly performed with Trinity version 2013-02-25
Second stage assembly performed with cap3 using parameters: -p 99, -o 200
Reads mapped back to Trinity/cap3 assembly, and normalized expression values computed as described in the protocol provided by Trinity authors at http://trinity.sourceforge.net/#Downstream_analyses

organism: Atriplex lentiformis

source_name: leaf

growth_protocol: Atriplex lentiformis plants were grown in two growth chambers under either 23/18℃ or 43/30℃ day/night temperature regime with a 16-hour photoperiod and light intensity of 120 micro Einstein’s photon

extract_protocol:
Total RNA were extracted from A. lentiformis leaf tissues grown at 23ºC and 43ºC using Agilent Plant RNA isolation Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 8 weeks

value: 43 ºC

tag: lipid phenotype

value: 18:3 lipid phenotype

tag: weeks

value: 8 weeks

value: leaf


title: Flag-2MIXL

city: Houston

first: Lalitha

last: Nagarajan

state: TX

address: 6767 Bertner

department: Genetics

institute: Unviersity of Texas MD Anderson Cancer Center

description: Experimental Sample

data_processing:
Illumina analysis pipeline GAPipeline-1.5.0 was used for basecalling and alignment to hg18.
Peak calling was done by MACS v1.3.7.1 at pvalue<=1e-5.
Genome_build: hg18
Supplementary_files_format_and_content: Wig files were generated using MACS v1.3.7.1, and combined using MACS v1.4.  Data for 1MIXL+2MIXL.wig.gz was generated by combining the 1MIXL and 2MIXL set before generation
Supplementary_files_format_and_content: The excel data file contains a set of 4 datasets of identified peaks based on which Experimental Sample was normalized to the combined controls: SET1-1MIXL+2MIXL vs IgG+FLAG, SET2-1MIXL vs IgG & Flag, SET3-2MIXL vs IgG & FLAG, SET4-Overlap of SETS1-3. The file contains, region identification, pvalue, number of tags, fold of enrichment over controls, the location of the peak relative to the nearest gene Loci, number of genes within 5kb, and Identification of those genes.

source_name: U937 clone "2MIXL" containing MIXL1 enforced expression vector, grown for 48 hours before harvest

growth_protocol: U937 empty vector and U937 MIXL1 expression vector clones were grown in 90% RPMI/10% FBS for 48 hours at a starting concentration of 1x105/ml before harvest/extraction.

extract_protocol:
Protein-DNA complexes were isolated from sonicated, crosslinked whole cell lysates using IgG mouse (IgG Control) or Flag antibodies.  Crosslinking was then reversed by heating, and DNA was purified.
Library preparation was performed by Dr. Louis Ramagli of the Sequencing and Microarray Facility (SMF) of MD Anderson Cancer center using the Beckman SPRIworks system.

tag: cell line

tag: vector

value: MIXL1 enforced expression vector

tag: clone

value: Established cell culture from histiocytic lymphoma

value: histiocytic lymphoma

tag: gender

value: male

tag: age

tag: antibody

value: Flag (anti-Flag-M2, Sigma)


title: atriplex_43_3

tag: treatment


title: atriplex_23_4

value: 23 ºC

value: 16:3 lipid phenotype


title: DAOY_INPUT_ChIPseq

city: New York

first: Colin

last: Palmer

state: New York

address: 701 W. 168th Street

department: Microbiology & Immunology

institute: Columbia University

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIP-seq reads were aligned to the human hg19 genome using the short read aligner Bowtie (2.0.0)
Significantly enriched ChIP regions were identified using the Model-based analysis of ChIP-Seq (MACS) (1.4.0) using data from sonication-sheared Input chromatin as control
Genome_build: hg19
Supplementary_files_format_and_content: BED files were generated by MACS. The 5th column of MACS-generated bed files is the -10*log10pvalue of peak region.

source_name: DAOY cells

growth_protocol: Cells were maintained in high glucose 1x DMEM (Gibco) with 10% heat-inactivated FBS and supplemented to 1x for: non-essential amino acids, sodium pyruvate, L-Gln, and pen/strep. Media was also made with 4 uL/L betamercaptoethanol.

extract_protocol:
Sonication-sheared nuclear lysate from DAOY human MB cells was obtained using Covaris sonicator and truChIP High Cell Chromatin Shearing Kit with SDS Shearing Buffer, as per manufacturer's specifications. For ZFX ChIP-seq, ZFX-DNA complexes were isolated using a rabbit polyclonal antibody against Zfx and via IP with Protein A Dynabeads (invitrogen). Sonication-sheared chromatin not subjected to IP was used as the Input control.
Library construction and sequencing were performed at the Yale Center for Genome Analysis. Briefly, magnetic AMPure XP beads (Beckman Coulter) are used to purify the user-sheared DNA samples and remain with the sample throughout library construction.  Following each process step, DNA is selectively precipitated by weight and re-bound to the beads through the addition of a 20% polyethylene glycol, 2.5 M NaCl solution.  Following fragmentation, T4 DNA polymerase and T4 polynucleotide kinase blunt end and phosphorylate the fragments.  The large Klenow fragment then adds a single adenine residue to the 3' end of each fragment and custom adapters (IDT) are ligated using T4 DNA ligase.  The inserts are size-selected in-solution and adapter-ligated DNA fragments are then PCR amplified using custom-made primers (IDT).  During PCR, a unique 6 base index is inserted at one end of each DNA fragment. Samples were sequenced on a single-end version 3 Illumina flow cell on a HiSeq 2000

value: medulloblastoma cell line

value: DAOY

tag: chip antibody


title: Flag-1MIXL

description: Experimental Sample

source_name: U937 clone "1MIXL" containing MIXL1 enforced expression vector, grown for 48 hours before harvest


title: Flag-Control

description: Control Sample

source_name: U937 cells containing empty expression vector, grown for 48 hours before harvest

value: empty expression vector


title: IgG-Control

description: Control Sample

value: Mouse-IgG


title: atriplex_43_2


title: atriplex_23_3


title: Mes_KU50 leaf

description: small RNA-Seq

source_name: fully expanded leaf

tag: cultivar

tag: condition

value: Cassava under normal condition


title: TGF-B-treated fibroblast

description: mRNA profiling

source_name: TGF-B-treated fibroblast

value: foreskin

value: primary fibroblast

value: TGF-B


title: atriplex_43_1

value: 43 ºC

value: 18:3 lipid phenotype

value: 8 weeks


title: atriplex_23_2

value: leaf


title: DAOY_ZFX_ChIPseq

value: ZFX


title: Mes_KU50 storage root

description: small RNA-Seq

source_name: storage root (150 days after planting)

value: root


title: H471_1d-2

status: Public on Dec 30 2014

city: Beijing

first: Fan

state: Beijing

address: 12 South Zhong-Guan-Cun St.

institute: CAAS

data_processing:
Primary data analysis and base calling was performed by the Illumina instrument software.
Low quality nucleotides (< Q20) were trimmed from raw sequences for each sample, and then pair-end reads with either of both with length less than 30 bp were removed using an in-house Perl script.
The raw reads were first filtered by removing adaptor sequences and low-quality sequences by using in-house perl script. The retained high quality pair-end reads of rice for each sample were mapped to the rice genome of RGAP at MSU (Kawahara et al., 2013) by tophat (Trapnell et al., 2009) and then assembled with Cufflinks (Trapnellet al., 2010) to construct unique transcipts sequences, using the parameter:-g -b -u -o.
Cuffcompare (Trapnell et al., 2009) was used to compare the assembled transfrags of each sample to the reference annotation, and build up a non-redundant transcripts data set among the samples. The number of mapped clean reads for each gene was counted and normalized into RPKM value (Mortazavi et al., 2008)
Genome_build: Nipponbare
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample with replicates merged.

organism: Oryza sativa

growth_protocol: A pot experiment was arranged in a randomized complete block design with three treatments (well-watered, 1d drought stressed, and 3d drought stressed) and two replications (3 pots/replication) in a greenhouse at the Institute of Crop Sciences of Chinese Academy of Agricultural Sciences (CAAS) (Beijing, China). Three strong seedlings of the three genotypes were equidistantly transplanted into a strip pot (15 cm in height and 50 cm in diameter) ﬁlled with 2 kg of sterilized ﬁeld soil, which contained about 50% available water content (AWC) of the soil measured by soil moisture meters (TZS-W). Seedling of each genotype were planted in 6 pots giving a total of 6 plants; all plants were grown with 14 h daylight at 28 °C and an 10 h dark period at 25 °C under controlled conditions.

extract_protocol:
For all RNA-seq samples, total RNA was extracted with TRIzol Reagent (Invitrogen, Carlsbad, California, USA), and quantified using a Qubit RNA assay kit (Applied Biosystems, Foster City, California, USA). RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA). RNA samples from three independent replicates for each treatment were pooled.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The drought stress treatment was started by withholding water at the tillering stage.The days were counted after the AWC in the soil reached 20% to allow drought measurements at precisely determined intervals, and the soil water content reached 15%, 10% and 7.5% after 1d, 3d and 4d drought treatment, respectively.

tag: genotype

value: introgression line

tag: Stage

value: tillering phase

value: drought treatment for 1 day


title: P28_3d-1

value: donor parent

value: drought treatment for 3 day

tag: tissue


title: H471_1d-1


title: HHZ_3d-2

value: recurrent parent


title: HHZ_3d-1


title: H471_3d-2


title: H471_3d-1


title: HHZ_1d-1


title: P28_3d-2


title: P28_1d-2


title: ChIP-seq Total DNA

first: Bart

last: Deplancke

address: Station 19

department: Institute of Bioengineering (IBI)

institute: EPFL

description: Crosslinked chromatin.

data_processing:
Bowtie2 (version 2.0.0-beta6) was used to align the sequencing reads.
Homer (http://biowhat.ucsd.edu/homer/ngs/index.html) was used to produce visualization files in bedGraph.
Genome_build: Release 5 (BDGP5.66)
Supplementary_files_format_and_content: BedGraph files

organism: Drosophila melanogaster

source_name: wing disc, third instar larvae, input

growth_protocol: yw;; C765-Gal4 tubGal80ts salmE-eGFP flies were grown at 25°C for 120 hours.

extract_protocol:
We adapted a recently published protocol (Simigdala et al.). 5 ml of larvae were disrupted using the gentleMACS dissociator (Milteny). The disrupted material was crosslinked in 1% formaldehyde for 10 min at room temperature. Crosslinking was stopped and formaldehyde quenched with 125 mM glycine for 5 min and washed two times in PBS (PBS Dulbecco, L 182-50, Biochrom AG). The material was separated by a gradient of 10% Ficoll (Ficoll PM 400, 17 0300 50, GE Healthcare) as the upper phase, 20% Ficoll as the middle phase and 30% Ficoll as the lower phase. The duration of the gradient centrifugation was 20 min at 5000 rpm. The discs were enriched at the interphase between 10% and 20%. Imaginal discs were washed once with PBS to clean them from residual Ficoll. All Ficoll solutions were made with PBS.
Libraries were prepared using the Illumina TruSeq ChIP Sample Prep Kit (IP-202-1012, Illumina).

tag: genotype/variation

value: yw;; C765-Gal4 tubGal80ts salmE  482 -eGFP

value: 120 h development

value: imaginal wing disc

tag: developmental stage

value: third instar larvae


title: P28_ck-1

value: normal condition


title: P28_ck-2


title: H471_ck-1


title: ChIP-seq H3K27Ac

description: Crosslinked chromatin.

source_name: wing disc, third instar larvae, H3K27Ac ChIP

value: anti-histone H3 (acetyl K27)


title: H471_ck-2


title: atriplex_23_1

value: 23 ºC

tag: lipid phenotype

value: 16:3 lipid phenotype


title: ChIP-seq H3K79m1-2-3

description: Crosslinked chromatin.

source_name: wing disc, third instar larvae, H3K79m1-2-3 ChIP

value: anti-histone H3 (mono+di+tri methyl K79)


title: ChIP-seq RNApol II

description: Crosslinked chromatin.

source_name: wing disc, third instar larvae, RNApol II ChIP

value: anti RNA-polymerase II-CTD


title: HHZ_ck-1

value: leaf


title: HHZ_ck-2


title: ChIP-seq H3K4m1

description: Crosslinked chromatin.

source_name: wing disc, third instar larvae, H3K4m1 ChIP

value: anti-histone H3 (mono methyl K4)


title: ChIP-seq H3K4m2-3

description: Crosslinked chromatin.

source_name: wing disc, third instar larvae, H3K4m2-3 ChIP

value: anti-histone H3 (di+tri methyl K4)


title: HHZ_1d-2

value: tillering phase

value: drought treatment for 1 day


title: P28_1d-1

value: donor parent


title: 48 h fermentation 2-1

city: wuhan

first: zhu

last: yuanmin

state: hubei

department: College of Life Science and Technology

institute: Huazhong University of Science and Technology

data_processing:
Illumina GA Pipeline v1.3  used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
The number of unambiguous clean tags for each gene was calculated and then normalized to TPM
Genome_build: n/a
Supplementary_files_format_and_content: abundance measurements

organism: Globisporangium splendens

source_name: thallus

growth_protocol: Pythium splendens was maintained on potato dextrose agar (PDA: glucose 30 g/L, potatoes extract 200 g/L and agar 20 g/L) slants at 4 °C

extract_protocol:
Total RNA was isolated using the fungal RNA kit (Omaga)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: filamentous fungi

value: thallus

tag: fermentation stage

tag: product

value: lipid


title: 144 h fermentation 6-1


title: 100 h fermentation 4-1


title: hcc364_shY12_tra

first: Saurabh

last: Asthana

address: 1450 Third Street, Room HD276

department: Helen Diller Family Comprehensive Cancer Center

institute: UCSF

data_processing:
Reads were aligned against NCBI build 37 (hg19) of the human genome using the NCBI Ensembl transcript annotation (version 75) with RSEM, which also yielded gene-level expression quantification.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm

source_name: HCC364 cells, infected with shRNA against YAP1 & treated with Trametinib

extract_protocol:
RNA from each of the indicated cell lines was extracted by RNeasy kit (Qiagen). In total, 2 ug of total RNA was used for deep sequencing library preparation using Illumina Truseq sample prep kits (Illumina) according to the manufacturer's protocols. Sequencing libraries with different indices were pooled and sequenced in paired end format to a length of 100bp using the HiSeq2500 platform at Center for Advanced Technology at UCSF.
Illumina Truseq sample prep kits

value: Lung adenocarcinoma

tag: cell line


title: hcc364_shY12_plx

source_name: HCC364 cells, infected with shRNA against YAP1 & treated with PLX4720


title: hcc364_tra

source_name: HCC364 cells, infected with empty vector & treated with Trametinib


title: hcc364_shY13_tra

value: infected with shRNA against YAP1 & treated with Trametinib


title: hcc364_shY13_dmso

source_name: HCC364 cells, infected with shRNA against YAP1 & treated with DMSO


title: PC8

city: Milwaukee

first: Liang

last: Wang

state: Wisconsin

address: 8701 Watertown Plank Rd.

department: Pathology

institute: Medical College of Wisconsin

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC8

data_processing:
A graphic user interface-based tool to process the sequencing data has been developed. After raw data cleaning, sequences with a length 16nt were combined into a FASTA file and aligned against human miRNA sequences from miRBase (Release 19, 2043 entries) and NCBI human genome reference sequences (Release 103). miRNA profiling was normalized using read counts of a miRNA per million mappable miRNA sequences. miRDeep2  was used to identify novel miRNAs from raw sequencing data. Predicted miRNAs with scores  2 were considered significant.
In the screening cohort, the normalized sequencing data from 192 individuals (23 CRPC and an additional 169 healthy and non-healthy subjects), were first processed to screen the most stably expressed miRNAs with overall coefficient of variation (CV) <5%. The most stably expressed miRNAs were further processed by NormFinder  and Bestkeeper. Diagnostic power with P<0.001 was considered to be eligible for normalization. For the follow up cohort, the raw CT values derived from real-time PCR were used to determine their stabilities.
Genome_build: miRNA from miRBase(release19)
Supplementary_files_format_and_content: Data frame of normalized miRNA transcription level  in *.txt
Supplementary_files_format_and_content: Read counts and distribution of each RNA species in the 23 RNA sequencing libraries.
Supplementary_files_format_and_content: 375 common miRNAs with >5 counts per million mappable reads, and 57 putative miRNAs with normalized read counts >5 per million reads

source_name: blood

extract_protocol:
Exosome isolation and RNA extraction was reported previously. The plasma exosomes were isolated using ExoQuick Solution (SBI, Mountain View, CA).  RNA was extracted with the miRNeasy Micro Kit (QIAGEN, Valencia, CA). RNA quantity was determined by a fluorometer (Qubit 2.0, Life Technologies, Carlsbad, CA). Agilent Small RNA Chip (Agilent Technologies, Santa Clara, CA) was used to determine RNA quality.
Small RNA libraries were constructed with 2ng exosomal RNA from each patient as starting material following the instruction of  the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB). Absolute quantities of each indexed library were determined by real-time qPCR using KAPA Library Quantification Kit. Equally 2nM of each index library was pooled and submitted for sequencing using the Illumina HiSeq2000 platform.

treatment_protocol: Blood samples were collected from CRPC patients in 10 ml PST plasma separator tubes  and processed within 30 minutes of collection. Patients were consented for participation in an advanced prostate cancer biomarker registry prior to blood collection and processing at the time of androgen deprivation therapy (ADT) failure. For plasma specimens, whole blood collection was first centrifuged at 2,000 rpm for 10 minutes. The supernatant was then fractioned into multiple aliquots for storage at -80°C until use. Patients progressing to CRPC stage after ADT failure were evaluated for exosome based prognostic biomarkers in a screening cohort (n=23) and a follow up cohort (n=100). ADT failure was defined as the date of the first occurrence of either two serial PSA rises during chronic ADT measured at least one week apart with an absolute PSA level greater than 2ng/ml  or appearance of new image based metastasis during ADT or initiation of castrate resistant specific therapy to on-going ADT and in the presence of sub-castrate (<50ng/dL) testosterone levels. To determine endogenous reference controls for qRT-PCR, we examined RNA sequencing profiles in plasma from a total of 192 subjects with various health conditions. This study was approved by Mayo Clinic and the Medical College of Wisconsin Institutional Review Board.

value: exosomes from plasma


title: PC9

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC9


title: hcc364_shY13_plx

value: infected with shRNA against YAP1 & treated with PLX4720


title: hcc364_plx

source_name: HCC364 cells, infected with empty vector & treated with PLX4720


title: hcc364_dmso

source_name: HCC364 cells, infected with empty vector & treated with DMSO


title: PC7

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC7


title: mT7

city: Cold Spring Harbor

first: David

middle: A.

last: Tuveson

state: NY

address: 1 Bungtown Rd.

department: Cancer Center

institute: Cold Spring Harbor Laboratory

data_processing:
The quality of 101 base-pair, paired-end reads was assessed using the FASTQC program. No base-pairs were trimmed.
The RSEM program (version 1.2.11) was used to both align raw reads to the mm9 version of the mouse genome and estimate transcript abundances in transcripts per million (TPM), as well as to estimate read counts per genes as expected counts. For the alignment, RSEM internally called the Bowtie alignment program (v1.1.0). Up to 3 mis-matches were allowed in the first 25 base-pairs, and no more than 200 multiple alignments were allowed.
The DESeq2 program (v1.4.1) was used to calculate differential expression, using the Expected Counts estimated by the RSEM program. 7 biological replicate mN, 6 biological replicate mP, and 6 biological mT organoids were used for this analysis, identifying genes differentially expressed in P vs. N organoids, genes differentially expressed in T vs. N organoids, and genes differentially expressed in T vs. P organoids.
Genome_build: mm9
Supplementary_files_format_and_content: A tab-delimited text file includes the Transcript Per Million (TPM) values for each gene in each sample, and the DESeq output for each gene, including the log2 fold-change and adjusted p values for the P vs. N, T vs. N, and T vs. P organoid comparisons

source_name: 3D organoid cell line

growth_protocol: Mouse organoids were grown to 70-90% confluency in a 50 uL dome of 100% Matrigel overlaid with 500 uL of mouse complete media [DMEM F12 Advanced (Invitrogen), 10 mM HEPES pH 7.2-7.5 (Invitrogen), 1X GlutaMax (Invitrogen),  1X Penicillin/Streptomycin (Invitrogen), 0.5 uM A83-01 (TOCRIS), 0.05 ug/mL mEGF (Invitrogen), 0.1 ug/mL FGF-10 (Peprotech), 0.01 uM Gastrin I (Sigma), 0.1 ug/mL mNoggin (Peprotech), 1.25 mM N-aceylcysteine (Sigma), 10 mM Nicotinamide (Sigma), 1X B27 Supplement (Invitrogen), 10% R-spondin-conditioned media], in 4-6 wells of a 24-well plate.

extract_protocol:
Media was removed from Matrigel domes, and 4-6 wells of organoids were harvested in 1 mL total of Trizol. RNA was extracted using the Trizol Plus RNA Purification Kit (LifeTechnologies) per manufacturer’s instructions, and RNA samples were treated on column with PureLink DNase (Life Technologies).
Sequencing libraries were generated from 1 ug of total RNA using a TruSeq Stranded Total RNA Kit with Ribo-zero human/mouse/rat (Illumina # RS-122-2201) per manufacturer’s instructions. For the final amplification,11 cycles of PCR were used. Libraries were quality checked and quantified using a Bioanalyzer 2100 (Agilent) with a DNA 1000 Kit.

tag: mouse background

tag: mouse genotype

value: KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre

tag: tissue origin

value: histologically confirmed mouse pancreatic adenocarcinoma

tag: Sex

value: female


title: mT9


title: mT8


title: LW14

first: Liheng

address: 1150 Saint Nicholas Avenue, Room 234

department: Department of Medicine

institute: Columbia University Medical Center

data_processing:
Hierarchical Clustering was done in Cluster (de Hoon et al., 2004) and visualized in Treeview (Saldanha, 2004). For each experiment and every gene, the gene expression values in FPKM was median centered and normalized to have unit variance before clustering. One matrix CIM (http: //discover.nci. nih.gov/cimminer/home.do) is used to generate the cluster heatmap.
Supplementary_files_format_and_content: csv files include FPKM values for each Sample

source_name: iPSC-derived neuron sample

extract_protocol:
RNA was extracted using RNeasy Micro Kit (QIAGEN). Quality control of the RNA was carried out with the Agilent Bio-analyzer, Qubit 2.0 at the MPSR of Columbia University. 100 ng of RNA with RIN ≥ 9 were used for generating mRNA-focused libraries.
RNA libraries were prepared using TruSeq RNA Sample Preparation Kit v2

tag: age

value: ~ Differentiation day 45

tag: disease

value: BBS (Bardet-Biedl Syndrome)


title: LW13


title: LW12


title: mT3

value: male


title: PC33

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC33


title: LW11

value: Healthy


title: LW10


title: mP6

value: KrasLSL-G12D; Pdx1-Cre

value: pancreatic ducts from histologically confirmed mPanIN-containing pancreas


title: PC32

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC32


title: PC31

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC31


title: LW09

description: Day 82 neurons

source_name: NKX2.1 GFP/W-hESC-derived neurons

value: ~ Differentiation day 82


title: PC3

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC3


title: LW06

description: Day 27 neurons

value: ~ Differentiation day 27


title: PC6

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC6


title: ChIP-seq H3

description: Crosslinked chromatin.

source_name: wing disc, third instar larvae, H3 ChIP

value: yw;; C765-Gal4 tubGal80ts salmE  482 -eGFP

value: 120 h development

value: imaginal wing disc

value: third instar larvae

tag: chip antibody

value: anti-histone H3


title: PC28

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC28

value: exosomes from plasma


title: mT4

value: KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre


title: mP2


title: PC34

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC34


title: mP5


title: mP4


title: hcc364_shY12_dmso

value: Lung adenocarcinoma

tag: treatment

value: infected with shRNA against YAP1 & treated with DMSO


title: ChIP-seq H3K27m3

description: Crosslinked chromatin.

source_name: wing disc, third instar larvae, H3K27m3 ChIP

value: anti-histone H3 (tri methyl K27)


title: LW07

description: Day 27 neurons


title: mP1

value: female


title: LW04

description: Day 12 progenitors

source_name: NKX2.1 GFP/W-hESC-derived progenitors

value: Differentiated day 12 neuron progenitors


title: LW03

description: Day 12 progenitors

value: Healthy


title: mT5

value: histologically confirmed mouse pancreatic adenocarcinoma

value: male


title: mN12

value: wild-type

value: pancreatic ducts from histologically confirmed normal pancreas


title: PC22

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC22


title: PC23

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC23


title: LW02

description: Day 12 progenitors


title: mP3

value: KrasLSL-G12D; Pdx1-Cre

value: pancreatic ducts from histologically confirmed mPanIN-containing pancreas


title: mN11


title: LW01

description: hESC

source_name: NKX2.1 GFP/W-hESC

value: Undifferentiated hESC


title: PC2

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC2


title: mN10


title: PC20

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC20


title: mN7


title: Stele cell, 16h after cut 4

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

description: 16h after removal of root tip

data_processing:
Reads were aligned to the Arabidopsis genome using Bowtie2
Gene calls were calculated by summing the number of reads hitting a gene, calculated with ngsutils. Genes with coverage of <200bp were discarded.
Genome_build: TAIR10
Supplementary_files_format_and_content: Log2 normalized expression calls for genes (csv file)

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Root Stele cells

growth_protocol: Plants were grown on plates (1xMS, 0.5% Sucrose, 0.8% Agar) for 6 DAS

extract_protocol:
Roots were treated with cell-wall digestion solution as in (Birnbaum et al., Nature Methods, 2005). And Individual flourescent cells were isolated using a mouth glass pipette
mRNA was converted to cDNA and amplified according to Tang et. al, Nature Methods, 2009. Library was constructed using TruSeq DNA Sample Preparation Kit, according to manufacturer protocol

value: 7 DAS

tag: cell type

value: Root Stele cells

tag: genetic background


title: Stele cell, 16h after cut 3

description: 16h after removal of root tip


title: mN6


title: PC19

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC19

tag: tissue

value: exosomes from plasma


title: LW05

description: Day 25 neurons

value: ~ Differentiation day 25


title: mN13


title: Stele cell, 16h after cut 1

description: 16h after removal of root tip


title: Stele cell, 0h after cut 3

description: Immediately after removal of root tip


title: Stele cell, 16h after cut 2

description: 16h after removal of root tip


title: 24 month H3K4me1

first: deqiang

last: sun

address: 2121 W Holcombe Blvd

institute: Texas A&M University

description: technical replicate of biological replicate 1

data_processing:
Reads were mapped with Bowtie2. Uniquely mapped reads were used for peak calling by Macs2 with multiple testing correction q value cutoff 0.01.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.0.6 with 1 mismatch in seed allowed, command=bowtie2 -p12 -k 2 -N 1. Peak calling was performed on uniquely aligned reads (lacking bowtie2 flag XS:i) with Macs2 version 2.0.10.20131216, command=macs2 callpeak -f BAMPE -g mm -m 2 50 --verbose 3 --bdg --SPMR -t treatment.bam -c control.bam , where treatment is immunoprecipitate and control is input DNA.
Genome_build: mm9
Supplementary_files_format_and_content: The narrowPeak are BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. Definition of some specific columns are: 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start. The bigWig files were created from the Macs2 bedgraph files, representing signal density of fragment pileup as signal per million reads More information may be found in the Macs2 documentation.

source_name: Hematopoietic stem cells (HSC)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Genomic DNA were extracted from the cells and fragmented to 200-500 bp via biorupter. Followed by immunoprecipitation with specific antibody, ChIPed DNA were successfully made library using ThruPLEX preparation kit without extra amplification (Rubicon, Ann Arbor, MI)

value: Murine bone marrow derived primary HSCs

tag: cell surface marker

tag: strain

value: Abcam ab8895


title: PC15

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC15


title: PC18

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC18


title: PC14

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC14


title: Stele cell, 0h after cut 2

description: Immediately after removal of root tip


title: PC21

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC21


title: Stele cell, 0h after cut 1

description: Immediately after removal of root tip


title: QC cell 20

source_name: Root QC cells

value: 6 DAS

value: Root QC cells


title: PC1

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC1


title: 24 month H3K27ac

value: Abcam ab4729


title: PC29

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC29


title: PC13

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC13


title: mN5

value: female


title: QC cell 18


title: QC cell 19


title: Control-KD RNA-Seq (II)

description: Control for Knockdown

data_processing:
RUM to make alignments; Customized script to count fragments on gene; DESEQ to do differential expression test;
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated text file for gene's count and fpkm for each sample

source_name: KSL cells

growth_protocol: Sca-1+ cells from 5-FU injected mice were isolated and transduced with retrovirus. After in vitro culture for two days in transduction medium, containing Stempro 34 (Gibco, Carlsbad, CA), nutrient supplement, penicillin/streptomycin, L-glutamine (2mM), mSCF (10ng/ml; R&D Systems Minneapolis, MN) and mTPO (100ng/ml; R&D Systems), KSL-GFP+ cells were sorted for RNA-seq.

extract_protocol:
Extract RNA using Qiagen Rneasy Micro kit.
Tru-Seq RNA sample prep kit

treatment_protocol: PolyA selection

value: Murine bone marrow KSL cells transduced with KD retrovirus

tag: genotype/variation

value: Control-KD


title: LncHSC-1-KD RNA-Seq (II)

description: Knockdown LncRNA LncHSC-1


title: m12_gr_l2 RNA-Seq (I)

description:
m12_gr_l2
technical replicate of biological replicate 1

source_name: 12 month Granulocytes

growth_protocol: FACS sorted primary mouse Granulocytes

value: Murine bone marrow derived primary Granulocytes


title: QC cell 16


title: QC cell 15


title: m12_gr_l1 RNA-Seq (I)

description:
m12_gr_l1
technical replicate of biological replicate 1


title: E14_MNase-seq

city: La Jolla

first: Pengfei

last: Yu

address: 9500 Gilman Drive MC 0419

department: Bioengineering

institute: University of California San Diego

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The ChIP-seq data were mapped back into mm9 genome by Bowtie 0.12.7, with unique alignment and ≤ 1 mismatch
Raw RNA-seq data were aligned to mouse (mm9) genome using Tophat with unique alignment and ≤ 1 mismatch.  Cufflinks with default parameters was used to estimate the expression levels.
Raw MNase-seq data were mapped to mouse (mm9) and human(hg19) genome using Bowtie 0.12.7 allowing 2 mis-matches and unique alignment only.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: BED files for mapped data of Mnase-seq and ChIP-seq experiment;

source_name: mouse embryonic stem cells (E14)

growth_protocol: Cells are maintained in standard mouse stem cells medium with Lif. Purimycin was added to the medium for transfected cells.

extract_protocol:
Cells are lysed in 1% SDS lysis buffer and sonicated for ChIP analysis. RNA extraction and amplification from preimplantation embryos and ICM were carried out as described before (Xie et al., 2010).
For ChIP-seq, the libraries were prepared with Illumina's 'TruSeq DNAseq Sample Prep kit'. The libraries were then pooled and quantitated by qPCR. Each pool each was sequenced on one lane for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3. For RNA-seq of ICM and blastocyst, there are two-round of RNA Amplification. The amplified RNAs were subjected to sequencing using Illumina’s small sample RNA-seq protocol.

treatment_protocol: For ChIP-seq, Cells are fixed in 1% Formaldehyde and stoped by lysine. For Mnase-seq, Chromatin was processed by optimizing a previously published protocol (Ozsolak et al., 2007) with 200 units of MNase (Worthington Biochemical Corp.) and incubation at 25 degree for 5 min, which typically yielded 80-90% mononucleosomal DNA.


title: QC cell 17


title: QC cell 14


title: KD_E14_MNase-seq

source_name: E14 cells with SMARCAD1 knockdown

value: shRNA targeting Smarcad1 mRNA


title: QC cell 13


title: PC27

description:
Characterization of human plasma-derived exosomal RNAs
miRNA from patient tissue PC27

source_name: blood


title: F-1

city: Bronx

first: Hwa Jin

last: Jung

address: 1301 Morris Park Avenue

institute: Albert Einstein College of Medicine

data_processing:
Reads were trimmed of adapters using a C++ program and then aligned to mirBase using bowtie.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited data table containing miRNA counts

source_name: Zmpste24-/- MEF

growth_protocol: Zmpste24-/- and WT MEFs, and mouse myoblast cell line C2C12 were cultured in Dulbecco’s modiﬁed Eagle’s medium (DMEM, Gibco) containing 10% fetal bovine serum. Serial passage (P) was performed when the cells reached an 80% conﬂuence.

extract_protocol:
Total RNA was extracted from lympocyte samples via mirVana miRNA isolation kit (AM1560)
All samples were prepared according to Illumina Small RNA prep kit (FC-930-1004)

treatment_protocol: no treatment

value: mouse embryonic fibroblasts


title: QC cell 10


title: QC cell 11


title: F+1

source_name: WT MEF

value: Zmpste24 wild-type


title: LncHSC-2-KD RNA-Seq (II)

description: Knockdown LncRNA LncHSC-2


title: QC cell 9


title: QC cell 8


title: QC cell 6


title: Colo829_MNase-seq

source_name: Human Colo829 melanoma


title: QC cell 3


title: QC cell 2


title: QC cell 1


title: QC cell 5


title: QC cell group and split 4


title: QC cell group and split 2


title: QC cell group and split 3


title: QC cell group and split 1


title: QC cell 12


title: 72_D35

status: Public on Dec 29 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

data_processing:
Reads were basecalled using SCS version 2.9 software and processed using version CASAVA 1.8.2
zipped using gzip
For mRNAseq: Reads were mapped against the Macaca mulatta using Illumina's igenomes source Ensembl, Build: Mmul_1. The transcriptome was mapped using Bowtie/Tophat .
HTSeq was used to generate gene counts
Genome_build: Mmul_1
Supplementary_files_format_and_content: tab-delimited text files include: 1 scaled gene counts for each sample of mRNAseq

organism: Macaca fascicularis

source_name: PBMC

growth_protocol: PBMCs

extract_protocol:
Qiagen miRNeasy Isolation Kit from Trizol homogenates
Illumina mRNA

tag: immunization

value: ZEBOVgp

tag: timepoint (days)

value: day 35

tag: outcome

value: survive

value: PBMC


title: 72_D4

value: day 4


title: 72_D28

value: day -28


title: 72_D7

value: day 7


title: 72_D0

value: day 0


title: 71_D4


title: 71_D35


title: 71_D28


title: 71_D7


title: 70_D35


title: 71_D0


title: 71_D14

value: day 14


title: QC cell 4

value: 6 DAS

value: Root QC cells


title: 24 month input DNA

value: Murine bone marrow derived primary HSCs

value: NOT APPLICABLE


title: 70_D4


title: 70_D7


title: 70_D28


title: QC cell 7


title: 70_D0


title: 70_D14


title: 69_D4

value: MARVgp

value: succumb


title: 69_D7


title: 69_D28


title: 69_D0


title: 72_D14


title: H3

first: wenqin

last: fu

state: Hubei

address: No.1,Shizishan Street

department: College of Plant Science and Technology

data_processing:
Basecalls performed using Illumina Casava1.7 software.
Raw reads including those with adaptors, containing more than 10% of unknown bases, and low quality reads were filtered, then clean reads were mapped to  Brassica_ 95k_ unigene using SOAP2, allowing no more than two mismatched bases.
The gene expression level was calculated by using RPKM method (Reads Per kb per Million reads) according to Mortazavi et al., 2008.
Genome_build: Brassica_ 95k_ unigene
Supplementary_files_format_and_content: Microsoft Excel files include the coverage of each gene, expression of gene(RPKM), total number of reads that aligned to gene, the description of gene and so on.

organism: Brassica napus

source_name: Gynoecium

growth_protocol: Plants were grown in the experimental field

extract_protocol:
Gynoecia were removed and immediately conserved in RNAfixer Stabilization Reagent (BioTeke Corporation) for one week, then transferred to liquid nitrogen and kept at -80°C. Total RNA was extracted using the Polysaccharide and Polyphenol Total RNA Isolation Kit (spin column; Bioteke Corporation).
RNA libraries were prepared for sequencing as the protocols: mRNA is enriched by using the oligo(dT) magnetic beads from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification.

value: Gynoecium

tag: developmental stage

value: 1.5 to 3mm long flower buds

tag: phenotype

value: normal


title: 68_D28


title: 66_D7


title: 66_D4


title: 68_D0


title: 66_D28


title: L8_12Plex_H

city: Boston

first: Joshua

middle: David

last: Campbell

state: MA

address: 72 East Concord St.

institute: Boston University

data_processing:
The 3’ adapter sequence was trimmed using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
Reads longer than 15 nucleotides were aligned to hg19 using Bowtie v0.12.7 allowing up to one mismatch and up to ten genome locations.
The number of reads aligning to mature microRNA loci (miRBase v18) was counted using Bedtools v2.9.0.
MicroRNA counts within each sample were normalized to reads per million (RPM) values by adding a pseudocount of one to each microRNA, dividing by the total number of reads that aligned to all microRNA loci within that sample, multiplying by 1 million, and then applying a Log2 transformation.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data matrix contains RPM normalized and Log2-transformed expression for each microRNA within each sample.

source_name: Lung

extract_protocol:
30 mg of whole lung was homogenized with Trizol and then total RNA was extracted using the QiaCube system (Qiagen, Valencia CA). RNA quality was determined by Agilent Bioanalyzer 2100 (Agilent Technologies Inc, Santa Clara, CA)
One microgram of total RNA from each sample was used for library preparation with the TruSeq Small RNA Sample Prep Kit (Illumina).  RNA adapters were ligated to 3’ and 5’ end of the RNA molecule and the adapter-ligated RNA was reverse transcribed into single-stranded cDNA. The cDNA was then PCR amplified using a common primer and a primer containing one of 12 index sequences. The introduction of the six-base index tag at the PCR step allowed multiplexed sequencing of different samples in a single lane of a flowcell.  One to twelve of these indexed cDNA libraries were pooled in equal amount and gel purified together.  Each library was hybridized to one lane of the 8-lane single-read flowcell on a cBot Cluster Generation System (Illumina) using TruSeq Single-Read Cluster Kit (Illumina). The clustered flowcell is then loaded onto HiSeq 2000 sequencer for a multiplexed sequencing run that consists of a standard 36-cycle sequencing read with the addition of a 7-cycle index read.  A PhiX library was sequenced in lane 4 and used for calibration.

tag: lane

tag: barcode

value: CTTGTA

tag: multiplex

value: H

value: No


title: L8_12Plex_A

value: ATCACG

value: A


title: L8_12Plex_O

value: TTAGGC

value: O


title: L8_12Plex_E

value: ACTTGA

value: E


title: L8_12Plex_B

value: ACAGTG

value: B


title: L8_12Plex_C

value: TGACCA

value: C


title: L8_12Plex_F

value: TAGCTT

value: F


title: L8_12Plex_G

value: GGCTAC

value: G


title: L8_12Plex_N

value: CGATGT

value: N


title: L7_9Plex_I

value: GATCAG

value: I

value: Yes


title: 68_D4

value: MARVgp

value: day 4

value: succumb

value: PBMC


title: L8_12Plex_J

value: CAGATC

value: J

value: No


title: L7_9Plex_M

value: AGTCAA

value: M


title: L7_9Plex_J


title: L7_9Plex_H

value: CTTGTA

value: H


title: 66_D0

value: day 0


title: L7_9Plex_E

value: ACTTGA

value: E


title: S1

value: Gynoecium

value: 1.5 to 3mm long flower buds

value: female sterile


title: 68_D7

value: MARVgp

value: day 7


title: L6_6Plex_J

value: Yes


title: L7_9Plex_L

value: AGTTCC

value: L


title: L6_6Plex_G

value: GGCTAC

value: G


title: L6_6Plex_H


title: L7_9Plex_K

value: ATGTCA

value: K


title: L6_6Plex_F

value: TAGCTT

value: F


title: L8_12Plex_I

value: GATCAG

value: I

value: No


title: L7_9Plex_G


title: L7_9Plex_F


title: L5_6Plex_J

value: CAGATC

value: J


title: L6_6Plex_E

value: ACTTGA

value: E


title: L5_6Plex_I


title: L5_6Plex_F


title: iPSC shlincp21 day 9 merged replicates

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

description: Partially reprogrammed MEFs at day 9, transfected with shRNA targetting Trp53cor1 (lincRNA-p21)

data_processing:
rsem v1.2.12/bowtie v1.0.1 was used to align to the ensembl transcriptome (mm10, v73) using the settings '--bowtie-m 50'
mapping tag counts were GC normalized using EDASeq v1.11.0
transcripts with more than 20 normalized sequence tags in more than 4 conditions were kept for further analysis
replicates were merged by their mean expression values, using mean_replicates() function in glbase
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing ensembl transcript accession, gene name and normalized abundance estimates for each transcript

source_name: reprogramming MEFs

growth_protocol: reprogramming MEFs were cultured in mouse ESC medium (DMEM supplemented with 15% FBS [GIBCO], nonessential amino acids, sodium pyruvate, 2-mercaptoethanol, penicillin/streptomycin and leukemia inhibitory factor [LIF])

extract_protocol:
TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Reprogramming: For iPSC generation, plasmids expressing Oct4, Sox2, Klf4 and c-Myc (OSKM) were used for transfection. MEFs were spilt at 15,000 cells per well in 12-well plate for iPSC generation. GFP+ colonies were counted at day15. shRNA transfection: shRNAs were transfected using pretroSuper-shRNA constructs

value: MEF

tag: shRNA

value: Trp53cor1 (lincRNA-p21)

tag: time

value: 9 days


title: L5_6Plex_H

value: CTTGTA

value: H


title: iPSC shhnrnpk day 12 merged replicates

description: Partially reprogrammed MEFs at day 12, transfected with shRNA targetting Hnrnpk

value: Hnrnpk

value: 12 days


title: L8_12Plex_D

value: GCCAAT

value: D


title: iPSC shhnrnpk day 9 merged replicates

description: Partially reprogrammed MEFs at day 9, transfected with shRNA targetting Hnrnpk


title: L5_6Plex_G

value: GGCTAC

value: G


title: iPSC shlincp21 day 6 merged replicates

description: Partially reprogrammed MEFs at day 6, transfected with shRNA targetting Trp53cor1 (lincRNA-p21)

value: 6 days


title: L3_3Plex_B

value: ACAGTG

value: B

value: Yes


title: L3_3Plex_D


title: L6_6Plex_I

value: GATCAG

value: I


title: L2_3Plex_D

value: No


title: L2_3Plex_C

value: TGACCA

value: C


title: iPSC shhnrnpk day 6 merged replicates

description: Partially reprogrammed MEFs at day 6, transfected with shRNA targetting Hnrnpk

value: MEF


title: iPSC shluc day 6 merged replicates

description: Partially reprogrammed MEFs at day 6, transfected with shRNA targetting luciferase

value: luciferase (control)


title: L2_3Plex_B


title: iPSC shluc day 9 merged replicates

description: Partially reprogrammed MEFs at day 9, transfected with shRNA targetting luciferase

value: 9 days


title: L3_3Plex_C


title: iPSC shluc day 12 merged replicates

description: Partially reprogrammed MEFs at day 12, transfected with shRNA targetting luciferase

value: 12 days


title: iPSC shlincp21 day 12 merged replicates

description: Partially reprogrammed MEFs at day 12, transfected with shRNA targetting Trp53cor1 (lincRNA-p21)

value: Trp53cor1 (lincRNA-p21)


title: JN126

city: Daejeon

first: Byung-kwan

last: Cho

address: 291 Daehak-ro

country: South Korea

institute: korea advanced institute of science and technology

data_processing:
Basecalls were performed using CLC Genomics Workbench 6.5.
Sequence reads were trimmed for adaptor sequence and aligned to Streptomyces coelicolor genome (NC_003888) using CLC Genomics Workbench 6.5 with parameters mismatch cost = 2, length fraction = 0.5, similarity fraction = 0.8.
ChIP-seq reads were aligned to Streptomyces coelicolor genome (NC_003888) using CLC Genomics Workbench 6.5.
Alignment file was extracted as BAM file using CLC Genomics Workbench 6.5.
BAM file was converted to GFF file using in-house script.
Genome_build: NC_003888
Supplementary_files_format_and_content: GFF alignment

organism: Streptomyces coelicolor

source_name: 6X myc tagged Streptomyces coelicolor M145

growth_protocol: JN126 was grown in solid minimal media supplemented with N-acetylglucosamine and asparagine at 30 °C for 36 hours.

extract_protocol:
Lysates were clarified from sonicated cell and 6ⅹmyc-fused NdgR-DNA complexes were isolated with 9E10 antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were cross-linked by 1% formaldehyde at room temperature for 30 min and quenched unused formaldehyde with 125 mM glycine at room temperature for 5 min.

value: harboring 6X myc-fused NdgR

tag: chip antibody

value: c-Myc Antibody (9E10)

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #


title: vir_acc_2

status: Public on Dec 27 2014

city: St Andrews,

first: Darren

middle: James

last: Parker

state: Fife

address: Dyers Brae House

department: Centre for Biological Diversity

country: United Kingdom

institute: University of St. Andrews

data_processing:
trimmed using SOLiD TRIM (with run options: -p 3 -q 22 -y y -e 2 -d 10)
error corrected using SOLiD Accuracy Enhancer Tools (SAET)
trimmed using CLC Genomics Workbench 5.0.1  (quality score: 0.02)
Reads for each sample were mapped individually to the D. virilis genome (r1.2, available from http://flybase.org/) using CLC Bio
HTSeq was used to quantify the read counts mapping uniquely to the reference using the reference annotation available from Flybase (r1.2).
Genome_build: D. virilis genome (r1.2, available from http://flybase.org/)
Supplementary_files_format_and_content: tab-delimited text files of unique read counts mapping to each gene for each sample

organism: Drosophila virilis

source_name: whole fly pooled (20)

extract_protocol:
Frozen flies were pooled. RNA was extracted from each sample using Tri Reagent (Sigma-Aldrich) followed by RNeasy Mini kit (Qiagen) purification with DNase treatment.
RNA libraries were prepared for sequencing using standard SOLiD protocols

tag: origin

value: Toyama, Japan

tag: age

value: 30 days post-eclosion


title: L1_1Plex_A

value: ATCACG

value: A


title: vir_cont_1

tag: strain

value: 27 days post-eclosion


title: vir_cont_2

value: 28 days post-eclosion


title: L5_6Plex_E

value: ACTTGA

value: E

value: No


title: mont_acc_3

organism: Drosophila montana

source_name: whole fly pooled (10)

value: Oulanka, Finland

value: 26 days post-eclosion


title: mont_acc_2

value: 25 days post-eclosion


title: vir_acc_1

value: 29 days post-eclosion


title: mont_acc_1

value: 24 days post-eclosion


title: SVSC_small RNA seq

city: Guangzhou

first: Yunxue

last: Guo

state: Guangdong

address: Beisan street

institute: Sun Yat-sen university

description: Sample 3

data_processing:
SVSC_sequence_trimmed_Small_RNA_sample_grouped.txt; genome build: mm9
Sequence reads were obtained and mapped to the pig genomes using the Illumina Genome Analyzer Pipeline. All reads with perror (perror=10Q/-10, Q represents quality score) values greater than 0.05, and ambiguous nucleotides (maximum two nucleotides allowed) were removed, and sequences left were first mapped to swine sequences in the miRBase. Sequences containing up to two mismatches (or >90% identity) with swine miRNAs were considered as putative swine miRNAs and assigned the same name as that of the top match. Chromosome locations of the sequencing reads without adaptors were determined using short oligonucleotide analysis package (SOAP) software (http://soap.genomics.org.cn) by mapping the sequences to the pig genome.  The classes of small RNAs identified were classified with Sus_scrofa.Sscrofa 9.63.gtf (ftp://ftp.ensembl.org/pub/release-63/gtf/sus_scrofa/Sus_scrofa.Sscrofa9.63.gtf.gz).

organism: Sus scrofa

source_name: vascular stem cell

growth_protocol: Primary vascular stem cells were isolated from porcine dorsal longissimus dorsi and subcutaneous fat tissue  SVSC were plated in 6-well plates at a density of 10^6 cells/well, IVSC were plated in 6-well plates at a density of 1.5×10^6 cells/well, and the cells were cultured in DMEM/F12 growth medium supplemented with 20% FBS and 100 IU/ml penicillin-streptomycin.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.  Total RNA integrity was checked using 1% agarose gel and an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) with an RNA Integrity Number (RIN) value greater than 7 and 28S/18S>0.7.  For Solexa sequencing, small RNAs from the total swine RNA samples were prepared as follows: approximately 10μg total RNA of each sample was size-fractionated by 15% agarose gel electrophoresis and RNA fragments of length 16-35 nt were collected.  The first ligation reaction was conducted to ligate small RNA 3’ adapters to the isolated small RNA, followed by 5’ adapter ligation (Illumina, CA, USA). The small RNA ligated with 3’ and 5’ adapters was size-fractionated on a 10% agarose gel, and the 70-90 nt fraction (small RNA + adaptors) was isolated.  Reverse transcription, followed by PCR at 12 cycles significantly to enrich the fragments with ligated adapters at each end, was used to create cDNA constructs.  The PCR forward and reverse primers annealed to the ends of the adapters.  The amplification products were purified using 6% Novex TBE PAGE and small RNA libraries were validated using the Agilent Technologies 2100 Bioanalyzer.  The well validated libraries were directly used for cluster generation and 36 cycles of sequencing analysis using the Illumina Cluster Station and 1G Genome Analyzer, following the manufacturer’s protocols.

treatment_protocol: Two days after the cells reached confluence, differentiation of the cells was induced by changing the DMEM/F12 medium into DMEM/F12 differentiation medium containing 20% FBS, 0.5 mM 3-isobutyl-1-methylxanthine (IBMX, Sigma Aldrich), 0.25 μM dexamethasone (Sigma Aldrich), 5 mg/l insulin (Sigma Aldrich) and 100 IU/ml penicillin-streptomycin.  The differentiation medium was replaced by DMEM/F12 medium without IBMX and dexamethasone after three days’ culture.  At day 6, the medium was changed to DMEM/F12 growth medium supplemented with 20% FBS and 100 IU/ml penicillin-streptomycin, and the cells were allowed to differentiate for a further 3 or 4 days.

tag: cell type

value: Adipose Derived vascular stem cell

tag: passages

tag: tissue

value: subcutaneous fat


title: IVSC-MDI_small RNA seq

description: Sample 2

data_processing:
IVSC-MDI_sequence_trimmed-1_Small_RNA_sample_grouped.txt; genome build: mm9
Sequence reads were obtained and mapped to the pig genomes using the Illumina Genome Analyzer Pipeline. All reads with perror (perror=10Q/-10, Q represents quality score) values greater than 0.05, and ambiguous nucleotides (maximum two nucleotides allowed) were removed, and sequences left were first mapped to swine sequences in the miRBase. Sequences containing up to two mismatches (or >90% identity) with swine miRNAs were considered as putative swine miRNAs and assigned the same name as that of the top match. Chromosome locations of the sequencing reads without adaptors were determined using short oligonucleotide analysis package (SOAP) software (http://soap.genomics.org.cn) by mapping the sequences to the pig genome.  The classes of small RNAs identified were classified with Sus_scrofa.Sscrofa 9.63.gtf (ftp://ftp.ensembl.org/pub/release-63/gtf/sus_scrofa/Sus_scrofa.Sscrofa9.63.gtf.gz).

value: dorsal longissimus dorsi


title: SVSC-MDI_small RNA seq

description: Sample 4

data_processing:
SVSC-MDI_sequence_trimmed-1_Small_RNA_sample_grouped.txt; genome build: mm9
Sequence reads were obtained and mapped to the pig genomes using the Illumina Genome Analyzer Pipeline. All reads with perror (perror=10Q/-10, Q represents quality score) values greater than 0.05, and ambiguous nucleotides (maximum two nucleotides allowed) were removed, and sequences left were first mapped to swine sequences in the miRBase. Sequences containing up to two mismatches (or >90% identity) with swine miRNAs were considered as putative swine miRNAs and assigned the same name as that of the top match. Chromosome locations of the sequencing reads without adaptors were determined using short oligonucleotide analysis package (SOAP) software (http://soap.genomics.org.cn) by mapping the sequences to the pig genome.  The classes of small RNAs identified were classified with Sus_scrofa.Sscrofa 9.63.gtf (ftp://ftp.ensembl.org/pub/release-63/gtf/sus_scrofa/Sus_scrofa.Sscrofa9.63.gtf.gz).
'SVSC-MDI_sequence.txt.gz' raw data file has less data rows and smaller size than the rest of the files, but the exit data were well enough for further analysis after normalization.


title: IVSC_small RNA seq

description: Sample 1

data_processing:
IVSC_sequence_trimmed_Small_RNA_sample_grouped.txt; genome build: mm9
Sequence reads were obtained and mapped to the pig genomes using the Illumina Genome Analyzer Pipeline. All reads with perror (perror=10Q/-10, Q represents quality score) values greater than 0.05, and ambiguous nucleotides (maximum two nucleotides allowed) were removed, and sequences left were first mapped to swine sequences in the miRBase. Sequences containing up to two mismatches (or >90% identity) with swine miRNAs were considered as putative swine miRNAs and assigned the same name as that of the top match. Chromosome locations of the sequencing reads without adaptors were determined using short oligonucleotide analysis package (SOAP) software (http://soap.genomics.org.cn) by mapping the sequences to the pig genome.  The classes of small RNAs identified were classified with Sus_scrofa.Sscrofa 9.63.gtf (ftp://ftp.ensembl.org/pub/release-63/gtf/sus_scrofa/Sus_scrofa.Sscrofa9.63.gtf.gz).


title: astrocyte_pre-sen_rep2

city: Philadelphia

first: Sager

middle: Jayesh

last: Gosai

state: Pennsylvania

address: 433 S University Ave.

department: Biology

institute: Universiry of Pennsylvania

description: processed data file: SenescentAstrocytesDEanalysis_v2.csv

data_processing:
Basecalls performed with Bustard 1.9.3.
3' adapter sequences were trimmed using cutadapt (version 1.2.1 with parameters -e 0.06 -O 6 -m 14)
Redundant reads were compressed using an in-house perl (version 5.8.8) script
Untrimmed reads were aligned to the human genome (hg19) using Tophat (version 2.0.10 with parameters --library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive --transcriptome-max-hits 10 --no-coverage-search –no-novel-juncs)
Non-redundant (compressed) read counts in genes were quantified using HtSeq (parameters : --stranded=yes –mode=intersection-strict) (ambiguous not allowed) (executed with python 2.7)
Differential expression was analyzed using DESeq(1) in the R (version 2.15.2 (2012-10-26) -- "Trick or Treat") statistical environment
Genome_build: hg19
Supplementary_files_format_and_content: CSV format: differential expression of refgene transcripts

source_name: proliferating cells

growth_protocol: Human astrocytes were cultured at 37°C, 5% CO2 in astrocyte medium supplemented with 2% fetal bovine serum, growth supplement, and penicillin/streptomycin all obtained from ScienCell Research Laboratories (Carlsbad, CA). Cells were seeded at a standard density of 1 × 10^4cells/cm2 and cultured until they reached 70% to 80% confluence. At each passage, astrocytes were trypsinized, counted, and the cumulative population doubling level (CPDL) was calculated as we have previously described

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen; Valencia, CA) according to the manufacturer’s instructions and the concentration was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop; Rockland, DE)
Libraries were prepared by selecting poly-A-containing mRNA from total cellular RNA using the Dynabeads mRNA direct kit (Life technologies). The mRNA was fragmented and a 5’phosphate was then added using T4 polynucleotide kinase (Life technologies). A 15% TBE-urea gel was used to size select the library for fragmented products of 60-200 nucleotides. The ends of the fragmented products were ligated with Illumina v1.5 RNA adapters using T4 RNA ligase 2 (New England Biolabs). Superscript II reverse transcriptase (Life technologies) was used to generate a cDNA library that was PCR-amplified using Phusion HiFi DNA polymerase (New England Biolabs). The cDNA library was purified on a 6% TBE gel (Life technologies). The quality of the library was verified prior to sequencing by cloning into Zero Blunt TOPO (Life technologies) and analyzing 6-10 clones by standard sequencing to determine the diversity of the library products, the abundance of rRNA, appropriate size of the products, and the presence of adapters. T he verified size-selected poly-A stranded cDNA library was submitted to the Next-Generation Sequencing Core (NGSC) University of Pennsylvania, Philadelphia PA for sequencing. The Illumina Solexa GAII platform was used to obtain 50-bp single-end sequencing reads, which were analyzed using the v1.5 pipeline.

tag: source tissue

value: fetal cortex 20-22 weeks

value: primary astrocytes

tag: treated with

value: none (untreated control)


title: astrocyte_senescent_rep2

source_name: senescent cells

value: 200 µM hydrogen peroxide for 2hr

tag: rna extraction time point

value: 6 days after the initiation of treatment


title: astrocyte_senescent_rep1


title: mont_cont_1

value: 21 days post-eclosion


title: mont_cont_3

value: 23 days post-eclosion


title: astrocyte_pre-sen_rep1


title: mont_cont_2

value: 22 days post-eclosion


title: hPGCLC day4 rep1

status: Public on Dec 26 2014

city: St Louis

first: Sabine

last: Dietmann

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description: Cultured cells

data_processing:
Low quality bases (q < 20) from the 3' end and adapter sequences were removed with the TrimGalore wrapper scripts (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore).
Reads were mapped to the human (GRCh37/hg19) reference genome with Tophat 2.0.12 (http://ccb.jhu.edu/software/tophat)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Processed data files contain read counts per RefSeq transcripts generated by using the HTSeq 0.6.1 python package (http://www-huber.embl.de/users/anders/HTSeq)

source_name: Day4 hPGCLCs derived from day2 pre-induced cells

extract_protocol:
Total RNA was extracted with the PicoPure RNA Isolation Kit. Total RNA (0.5-2 ng) was reverse transcribed and amplified into cDNA using Ovation RNA-Seq System V2 (Nugen) according to manufacturer’s instructions.
Amplified cDNA was sonicated into 250 bp by Covaris S220 Focused-ultrasonicators. Subsequently, RNASeq library was generated with 500 ng of fragmented cDNA using Ovation Ultralow DR Multiplex System (Nugen). Library was quantified by KAPA Library Quantification Kit (Kapa Biosystems) using QuantStudio 6 Flex Real-Time PCR System (Applied Biosystems).

tag: facs

value: TNAP and mCherry+

tag: gender

value: Male


title: Pre-induced cells day2 rep1

description: Cultured cells

source_name: Day 2 pre-induced cells derived from hESC

value: Unsorted


title: Soma male week7 rep2

description: Primary cells

source_name: Gonadal somatic cells isolated from developmental week 7 genital ridge

value: TNAP and cKIT-


title: Pre-induced cells day2 rep2

description: Cultured cells

value: Day 2 pre-induced cells derived from hESC


title: hPGCLC day4 rep2

description: Cultured cells

value: Day4 hPGCLCs derived from day2 pre-induced cells


title: 4i WIS2 hESC rep1

description: Cultured cells

source_name: Human embryonic stem cell cultured in 4i condition

value: TNAP+


title: 4i WIS2 hESC rep2

description: Cultured cells

value: Human embryonic stem cell cultured in 4i condition


title: Soma male week 7 rep1

description: Primary cells

value: Gonadal somatic cells isolated from developmental week 7 genital ridge


title: TCam-2 rep1

description: Cultured cells

source_name: Seminoma cell line TCam-2

tag: cell line


title: TCam-2 rep2

description: Cultured cells


title: STT5814_GIST_mini

status: Public on Dec 25 2014

city: Stanford

first: Xiangqian

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

description: Experiment type: 3’end RNA Sequencing

data_processing:
Sequenced Reads after filtered by quality, were re-filtered by fastx, and then were mapped to the transcriptome (refMrna, downloaded from the UCSC genome browser, www.genome.ucsc.edu/) by using SOAP2, allowing at most two mismatches
Total numbers of sequenced reads for each gene symbol from the transcriptome mapping were determined and were used to create the gene-expression profile matrix. The library size was then normalized to one million reads (TPM).
The sequencing depth for each library was determined with the estimation of library saturation for transcriptome detection, which showed that our sequencing depths were deep enough to detect almost all of the known mRNAs expressed.
The distances between sequencing reads and 3’end of mRNAs were measured to be around 100-200nt as we expected.
Genome_build: hg19
Supplementary_files_format_and_content: expressional matrix with sample by column and gene by row

source_name: miniGIST

extract_protocol:
Multiple 2mm-diameter cores were taken from diagnostic FFPE material for RNA isolation. Then, total RNA was extracted by using of RecoverAll Total Nucleic Acid Isolation Kit (Ambion).
Poly(A)+RNA was selected and enriched with oligo(dT) using the Oligotex mRNA mini Kit (Qiagen).  The Poly(A) RNA was heat sheared to 100~200nt fragments. The sheared RNA was then subjected to first and second strand cDNA synthesis, followed by additional steps of library construction. The libraries were sent to the Stanford Genomic Center to be sequenced for the first 36bp at the 5’end of mRNA fragments with Illumina GA IIx machines.

treatment_protocol: Clinical tissue samples were formalin-fixed and paraffin-embedded (FFPE).

value: Soft Tissue

tag: tissue group

value: mini GIST (Gastrointestinal stromal tumor)

tag: tissue archive method

value: FFPE

tag: block storage

value: room temperature


title: STT5599_GIST

description: Experiment type: 3’end RNA Sequencing

source_name: GIST

value: overt GIST (Gastrointestinal stromal tumor)


title: STT5817_GIST_mini

description: Experiment type: 3’end RNA Sequencing


title: STT5813_GIST_mini

description: Experiment type: 3’end RNA Sequencing


title: STT5816_GIST_mini

description: Experiment type: 3’end RNA Sequencing


title: STT5952_GIST

description: Experiment type: 3’end RNA Sequencing


title: STT5812_GIST_mini

description: Experiment type: 3’end RNA Sequencing


title: STT5953_GIST

description: Experiment type: 3’end RNA Sequencing


title: STT5597_GIST

description: Experiment type: 3’end RNA Sequencing


title: STT5594_GIST

description: Experiment type: 3’end RNA Sequencing


title: STT5593_GIST

description: Experiment type: 3’end RNA Sequencing


title: STT5808_GIST_mini

description: Experiment type: 3’end RNA Sequencing


title: STT111_GIST

description: Experiment type: 3’end RNA Sequencing