title: H3K27ac

data_processing:
In brief, all samples were sequenced on an Illumina Genome Analyzer (GAIIx for ChIP-seq and RNA-seq, or HIseq2000 for MNase-seq). Quality assessment and filtering of ChIP-seq and MNase-seq sequences were performed using either the Integrated Eland software or FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) to pre-process FastQ files. Quality score and nucleotide composition at each position of the sequenced tags were assessed by box and bar plotting using FastX-Toolkit standard functions. Quality controls (QC) and filtering of RNA samples were performed using fastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), FASTX-toolkit and Cutadapt (http://code.google.com/p/cutadapt/). Adapters were removed (Cutadapt) and a QC report was generated (fastQC). Sequences were further trimmed at nucleotide 55 and quality filtered as for DNA sample (FASTX-toolkit).
All samples were aligned to human genome (hg19, GRCh37) using Bowtie aligner (allowing 2 mismatches, keeping uniquely aligned reads only)
Piles of tags with same coordinates, due to artifacts of PCR or unannotated regions of the genome were removed according to a thresholding method, except for RNA-seq experiment
Uniquely aligned tags were further elongated after estimating optimal elongation size in silico and enabling to use the original fragment length for further processing.
For ChIP-seq experiments, all samples were input subtracted and signals were scaled so that the same number of units appeared in each experiment after merging of the replicates.
For nucleosome mapping, MNAse-seq experiment in Raji was sequenced in paired-end with higher depth than ChIP-seq in Hiseq2000. Two types of analyses were applied to this data: nucleosomes density and nucleosomes midpoint  that allow to score more specifically for depletion or positioning, respectively. For nucleosome density, paired tags were processed so to be directly connected and to retrieve original fragments (orphan tags were connected to the corresponding pairs using the estimated elongation size computed as described above). The input subtraction step was omitted. For nucleosomes midpoint analyses, the middle of elongated fragments was set as reference allowing locating the maximum signal approximately at the midpoint of the nucleosomes (dyads).
For all experiments, the number of tags covering each nucleotide of the genome was computed and averaged in bins of 50 nucleotides. The scores of bins were rescaled (after input subtraction when applicable) to reduce over-representation of particular genomic regions and signal/noise ratio.
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: wig, contains score of binding, nucleosomes occupancy and short RNAs expression.

extract_protocol:
Total RNA was extracted from 1x107 Raji cells using TRIzol (Life Technologies, USA) according to the manufacturer’s instructions with some modifications to ensure higher recovery rates of small RNAs. This was achieved by addition of 10μg of linear acrylamide (Life Technologies, USA) before RNA precipitation. DNA was digested using the rigorous Turbo DNase (Ambion, USA) treatment as per manufacturer’s instructions. RNA quantity was measured on a Qubit apparatus (Life Technologies, USA) using RNA assay kit the quality was verified using RNA pico chips on a 2100 Bioanalyzer (Agilent Technologies, USA).  Before preparation of sequencing libraries, small RNAs were enriched from 10µg total RNA by using mirVana RNA Isolation kit (Life Technologies, USA) using manufacturer’s protocol for small RNA enrichment.
Strand specific RNA-seq library was constructed with ScriptMiner Small RNA-seq Library Preparation Kit (Epicenter, USA) according to manufacturer’s recommended protocol. Briefly, after both 5’ and 3’ adapter ligation, resulting cDNA library was PCR amplified with 14 amplification cycles. Purified library DNA was run on a 10% TBE-PAGE gel and library DNA corresponding to transcripts between 15nt-50nt was cut from the gel and transferred into 0.5mL tubes with punctured bottoms which were in turn placed in 2mL collection tubes. Gel slices were crushed into 2mL tubes by a 2 minutes centrifugation at 14000g. For library DNA elution by soaking, 0.4ml of 0.3M NaCl was added to each tube, before a 4 hour rotation at room temperature. After removal of gel particles using 0.22μm cellulose acetate filters, 10μg of linear acrylamide (Life Technologies, USA) and 2.5 volumes (approximately 1ml) of ice-cold absolute ethanol were added. After 30 minutes incubation at -80°C, the eluted cDNA was precipitated by centrifugation at 4°C and maximum speed for 45 minutes. The pellet was washed with 1ml of cold 80% ethanol, air dried and resuspended in 20μl of water. The size-selected small RNA library DNA was quantified using a Qubit apparatus with dsDNA High Sensitivity kit (Life Technologies, USA) and verified using DNA High Sensitivity 2100 Bioanalyzer chips (Agilent Technologies, USA).


title: H3K4me1 replicate2

status: Public on Jun 01 2014

type: SRA

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

country: Italy

institute: EMBL

description:
protein associated DNA
H3K4me1_replicate1_replicate2_Scaled_BGSub.wig

library_source: genomic

data_processing:
In brief, all samples were sequenced on an Illumina Genome Analyzer (GAIIx for ChIP-seq and RNA-seq, or HIseq2000 for MNase-seq). Quality assessment and filtering of ChIP-seq and MNase-seq sequences were performed using either the Integrated Eland software or FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) to pre-process FastQ files. Quality score and nucleotide composition at each position of the sequenced tags were assessed by box and bar plotting using FastX-Toolkit standard functions. Quality controls (QC) and filtering of RNA samples were performed using fastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), FASTX-toolkit and Cutadapt (http://code.google.com/p/cutadapt/). Adapters were removed (Cutadapt) and a QC report was generated (fastQC). Sequences were further trimmed at nucleotide 55 and quality filtered as for DNA sample (FASTX-toolkit).
All samples were aligned to human genome (hg19, GRCh37) using Bowtie aligner (allowing 2 mismatches, keeping uniquely aligned reads only)
Piles of tags with same coordinates, due to artifacts of PCR or unannotated regions of the genome were removed according to a thresholding method, except for RNA-seq experiment
Uniquely aligned tags were further elongated after estimating optimal elongation size in silico and enabling to use the original fragment length for further processing.
For ChIP-seq experiments, all samples were input subtracted and signals were scaled so that the same number of units appeared in each experiment after merging of the replicates.
For nucleosome mapping, MNAse-seq experiment in Raji was sequenced in paired-end with higher depth than ChIP-seq in Hiseq2000. Two types of analyses were applied to this data: nucleosomes density and nucleosomes midpoint  that allow to score more specifically for depletion or positioning, respectively. For nucleosome density, paired tags were processed so to be directly connected and to retrieve original fragments (orphan tags were connected to the corresponding pairs using the estimated elongation size computed as described above). The input subtraction step was omitted. For nucleosomes midpoint analyses, the middle of elongated fragments was set as reference allowing locating the maximum signal approximately at the midpoint of the nucleosomes (dyads).
For all experiments, the number of tags covering each nucleotide of the genome was computed and averaged in bins of 50 nucleotides. The scores of bins were rescaled (after input subtraction when applicable) to reduce over-representation of particular genomic regions and signal/noise ratio.
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: wig, contains score of binding, nucleosomes occupancy and short RNAs expression.
Supplementary_files_format_and_content: raw.txt.gz, Eland processed file

molecule: genomic DNA

organism: Homo sapiens

source_name: Raji B-cell line

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS), 100U/ml penicillin, 100mg/ml streptomycin and 2mM L-glutamine (Gibco/Invitrogen) at 37°C and 5% CO2. For the removal of Pol II, cells were treated with 2.5 μg/ml of α-amanitin for the indicated time points for the WT Raji cells.

extract_protocol: Total RNA was extracted from 1x107 Raji cells using TRIzol (Life Technologies, USA) according to the manufacturer’s instructions with some modifications to ensure higher recovery rates of small RNAs. This was achieved by addition of 10μg of linear acrylamide (Life Technologies, USA) before RNA precipitation. DNA was digested using the rigorous Turbo DNase (Ambion, USA) treatment as per manufacturer’s instructions. RNA quantity was measured on a Qubit apparatus (Life Technologies, USA) using RNA assay kit the quality was verified using RNA pico chips on a 2100 Bioanalyzer (Agilent Technologies, USA).  Before preparation of sequencing libraries, small RNAs were enriched from 10µg total RNA by using mirVana RNA Isolation kit (Life Technologies, USA) using manufacturer’s protocol for small RNA enrichment. Strand specific RNA-seq library was constructed with ScriptMiner Small RNA-seq Library Preparation Kit (Epicenter, USA) according to manufacturer’s recommended protocol. Briefly, after both 5’ and 3’ adapter ligation, resulting cDNA library was PCR amplified with 14 amplification cycles. Purified library DNA was run on a 10% TBE-PAGE gel and library DNA corresponding to transcripts between 15nt-50nt was cut from the gel and transferred into 0.5mL tubes with punctured bottoms which were in turn placed in 2mL collection tubes. Gel slices were crushed into 2mL tubes by a 2 minutes centrifugation at 14000g. For library DNA elution by soaking, 0.4ml of 0.3M NaCl was added to each tube, before a 4 hour rotation at room temperature. After removal of gel particles using 0.22μm cellulose acetate filters, 10μg of linear acrylamide (Life Technologies, USA) and 2.5 volumes (approximately 1ml) of ice-cold absolute ethanol were added. After 30 minutes incubation at -80°C, the eluted cDNA was precipitated by centrifugation at 4°C and maximum speed for 45 minutes. The pellet was washed with 1ml of cold 80% ethanol, air dried and resuspended in 20μl of water. The size-selected small RNA library DNA was quantified using a Qubit apparatus with dsDNA High Sensitivity kit (Life Technologies, USA) and verified using DNA High Sensitivity 2100 Bioanalyzer chips (Agilent Technologies, USA).

tag: cell line

value: Raji B

tag: antibody vendor/catalog

value: Abcam (ab8895)

tag: antibody


title: GM12878-PU.1-Rep2-Robotic-SL46184

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

country: USA

institute: STANFORD UNIVERSITY

data_processing:
base calling: Casava1.8
read alignment: Bowtie 0.12.7
bedgraph track generation: custom-written python script
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million)

growth_protocol: GM12878 cells were grown under the standard ENCODE protocols (http://genome.ucsc.edu/encode/protocols/cell/human/Jurkat_protocol.pdf and http://genome.ucsc.edu/encode/protocols/cell/human/GM12878_protocol.pdf)

extract_protocol:
Cells were fixed using 1% formaldehyde or 1% formaldehyde at 37C
Libraries were generated following Illumina's DNA Sample Prep Kit protocol

tag: chip-antibody

value: rabbit polyclonal, SPI1/PU.1, Santa Cruz sc-22805


title: H3K4me1 replicate1


title: GM12878-ZBTB33-Rep1-Manual-SL45080

value: mouse monoclonal Kaiso/ZBTB33, Santa Cruz sc-23871


title: GM12878-PU.1-Rep1-Manual-SL45076


title: GM12878-PU.1-Rep2-Manual-SL45077


title: GM12878-PU.1-Rep1-Robotic-SL46183


title: GM12878-NRSF-Rep3-Robotic-WellH1-SL46172

value: mouse monoclonal NRSF, custom generated (Johnson et al. 2007, PMID:17540862)


title: GM12878-NRSF-Rep3-Robotic-WellH12-SL46218


title: GM12878-p300-1F4_E10-Rep2-Robotic-SL46208

value: mouse monoclonal p300, custom generated, 1F4_E10


title: GM12878-p300-1F4_E10-Rep2-Manual-SL45093


title: GM12878-p300-1F4_E10-Rep1-Robotic-SL46207


title: GM12878-p300-1F4_E10-Rep1-Manual-SL45092


title: GM12878-NRSF-Rep3-Robotic-WellG2-SL46176


title: GM12878-NRSF-Rep3-Robotic-WellG3-SL46182


title: GM12878-NRSF-Rep3-Robotic-WellB2-SL46173


title: GM12878-NRSF-Rep3-Robotic-WellG11-SL46216


title: GM12878-NRSF-Rep3-Robotic-WellF3-SL46181


title: GM12878-NRSF-Rep3-Robotic-WellA1-SL46171


title: GM12878-NRSF-Rep3-Robotic-WellB11-SL46211


title: GM12878-NRSF-Rep3-Robotic-WellA12-SL46217


title: Suz12_ChIPExo-Jarid2-WT

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing: Reads from ChIP-exo were mapped by Peconic LLC (State College, PA) to the mouse genome (NCBI 37, mm9) using BWA (version 0.5.9) with default options allowing one gap open and a maximum number of three alignments for any read that aligned across the genome.

organism: Mus musculus

source_name: Primary CD4+ Th cells

growth_protocol: CD4+ T cells were co-cultured with irradiated (3000 Rads) T cell-depleted splenocytes in presence of 1 μg/ml of anti-CD3 (145-2C11) and 1μg/ml of anti-CD28 (37.51) for 4 days with combinations of antibodies and cytokines that included 10 ng/ml of IL-6, 10 ng/ml of IL-21, and 0.5 ng/ml of TGFβ with 10 μg/ml of anti-IL-4 (11B11), anti-IL-12 (C17.8), and anti-IFNγ (XMG1.2)  for Th17 differentiation.

extract_protocol: In brief, 10 million Th17 cells were fixed, lysed and sonicated to 200 base pairs. Sheared chromatin was submitted to Peconic LLC (http://www.peconicgenomics.com/) along with antibodies for ChIP-exo.

tag: cell type

value: Activated CD4+ T cells skewed towards a Th17 subset.

tag: strain

tag: genotype

tag: chip antibody

value: Suz12 (Cell Signaling, D39F6)

tag: chip antibody manufacturer

value: Cell Signaling

tag: chip antibody catalog #


title: GM12878-NRSF-Rep3-Manual-SL45074


title: GM12878-NRSF-Rep1-Robotic-WellD3-SL46179


title: GM12878-NRSF-Rep2-Manual-SL45073


title: GM12878-Input-Rep3-SL45098

value: n/a, input sample


title: GM12878-Input-Rep4-SL45099


title: GM12878-Input-Rep2-SL45097


title: GM12878-NRSF-Rep1-Manual-SL45072


title: GM12878-Input-Rep1-SL45096


title: GM12878-H3K27ac-Rep4-Robotic-SL46200

value: mouse monoclonal H3K27ac, Wako 306-34849


title: GM12878-H3K27ac-Rep3-Manual-SL45090


title: GM12878-H3K27ac-Rep3-Robotic-SL46199


title: GM12878-H3K27ac-Rep4-Manual-SL45091


title: GM12878-H3K27ac-Rep2-Robotic-SL46198


title: GM12878-H3K27ac-Rep2-Manual-SL45089


title: GM12878-NRSF-Rep4-Manual-SL45075


title: GM12878-GABP-Rep2-Robotic-SL46175

value: mouse monoclonal GABP, Santa Cruz sc-28312


title: GM12878-GABP-Rep1-Robotic-SL46174


title: GM12878-H3K27ac-Rep1-Manual-SL45088


title: GM12878-H3K27ac-Rep1-Robotic-SL46197


title: GM12878-GABP-Rep2-Manual-SL45069


title: GM12878-37C-PU.1-Robotic-SL46212


title: GM12878-37C-p300-sc585-lotE3113-Rep2-Robotic-SL46205

value: rabbit polyclonal p300, Santa Cruz sc-585, Lot#E3113


title: GM12878-37C-p300-sc585-lotE3113-Rep1-Robotic-SL46202


title: GM12878-37C-p300-1F4_E10-Rep2-Manual-SL45095


title: GM12878-NRSF-Rep2-Robotic-WellE3-SL46180


title: GM12878-37C-p300-1F4_E10-Rep2-Robotic-SL46209


title: GM12878-37C-NRSF-Robotic-SL46206


title: GM12878-37C-Input-Rep2-SL45101


title: GM12878-37C-H3K27ac-Robotic-SL46215


title: GM12878-37C-GABP-Robotic-SL46201


title: ES1

city: Brookline

first: Yuting

last: Liu

state: MA

address: 82 Walnut St. Unit 3

department: Department of Genetics

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).
The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012).  Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012) and human body map lincRNA annotations (Cabili et al., 2011).
processed data file for protein-coding genes:
processed_FPKM_genes_human_pancreatic_lineage_140112.txt
processed data file for lncRNAs:
processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

molecule: total RNA

source_name: human embryonic stem cells

growth_protocol: Human ESC line H9 was used to differentiate into definitive endoderm cells and pancreatic progenitors as previously described (Jiang et al., 2011). The following antibodies (all were purchased from BD) were used to label different cell populations: PE-conjugated mouse anti-human SSEA4 and APC-conjugated mouse anti-human CD184 for undifferentiated human ESCs (SSEA4+/CD184-); APC-conjugated mouse anti-human CD184 IgG and PE-conjugated mouse anti-human CD117 for definitive endoderm (CD184+/CD117+); PE-conjugated mouse anti-human CD24 and FITC-conjugated rat anti-human CD49f for pancreatic progenitors (CD24high/CD49flow).

extract_protocol:
Total RNA was purified from 1,000 sorted cells using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra-low input RNA kit (Clontech, US).
The amplified cDNA (10-40 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illumina’s construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in Illumina Hiseq 2000 instrument (pair-end 100bp).

treatment_protocol: Primary human islet were obtained from Integrated Islet Distribution Program (IIDP, study number BS208) and processed according to a previous report with minor modification (Dorrell et al., 2008; Dorrell et al., 2011). The following antibodies were used to label desired cell populations: HPi2 (mouse IgG1), and HPa1 (mouse IgM) as primary antibodies (kindly provided by Dr. Streeter), Alexa647-conjugated donkey anti-mouse IgG and Alexa488-conjugated donkey anti-mouse IgM as secondary antibodies. Beta cells were recognized as HPi+/HPa-, and HPi+/HPa+ for alpha cells as described (Dorrell et al., 2011).

value: human embryonic stem cells


title: Tyr1P3D12 replicate1

description:
protein associated DNA
Tyr1P3D12_replicate1_replicate2_Scaled_BGSub.wig

value: Tyr1P 3D12


title: GM12878-37C-ZBTB33-Robotic-SL46213


title: HS_1 (HE007)

city: Bronx

first: Herb

last: Lachman

state: NY

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

data_processing:
We obtained 101-bp mate-paired reads from DNA fragments of with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-Seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8). We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18). The category of transcripts is described at http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html. Transcript abundances were measured in Transcripts Per Million (TPM), which is calculated by multiplying the estimated fraction of transcripts made up by a given gene by 106.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: neuronal aggregates (day 50) derived from induced pluripotent stem cells

extract_protocol:
total cellular RNA was isolated using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, total RNA were extracted to produce cDNA using DT-T7 primers. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For the HS experiment, a group of 49 day old aggregates was placed in an incubator set at 39 degrees C for 24 hours, while control sets of aggregates were maintained at 37 degrees C. The incubator conditions were otherwise unchanged (ambient O2, 5% CO2, 85% humidity).

tag: tissue

value: 3-dimensional neuronal aggregates that resemble a first trimester telencephalon

tag: sample group

value: 39C for 24 hrs


title: Control_1 (HE006)

value: 37C control


title: Control_2 (HE008)


title: HS_2 (HE009)


title: NF-13

city: Milwaukee

first: Liang

last: Wang

state: Wisconsin

address: 8701 Watertown Plank Rd.

department: Pathology

institute: Medical College of Wisconsin

description:
microRNA  from sample F
Characterization of human plasma-derived exosomal RNAs

data_processing:
eRNA were developed to process data from RNA sequencing. Raw reads were firstly extracted from FASTQ files, and trimmed with sequencing quality control of Q > 13 , and then cleaned up 3’ adaptor sequences within read sequences. Those prepared sequences filtered with the length ≥16 nt were combined into a FASTA file and aligned against human miRNA sequences downloaded from miRBase (Release 19, 2043 entries) and human genome reference sequences downloaded from NCBI ftp site (Release 103) with Bowtie (version 0.12.8).
Genome_build: miRNA from miRBase (release19)
Supplementary_files_format_and_content: Data frame of normalized miRNA transcription level  in *.txt

source_name: blood

growth_protocol: we selected plasma samples from 7 anonymous blood donors and split each sample into two for technical replication.

extract_protocol:
Human plasma samples were obtained from Mayo Clinic and stored at -80°C before use. Exosomes were isolated from 250 µL of plasma prepared from whole blood using the ExoQuick Exosome Precipitation Solution (SBI) according to the manufacturer’s instructions with minor modifications. Briefly, the plasma was incubated with Thromboplastin D (Thermo) for 15 min at 37oC. After centrifugation at 10,000 rpm for 5 min, the supernatant was mixed with 75 µL of ExoQuick Solution and RNase A (Sigma) at final concentration of 10 µg/mL. The mixture was kept at 4oC overnight and then further mixed with 150 units/mL of murine RNase inhibitor (NEB) before centrifugation at 1500 g for 30 min. The exosome pellet was dissolved in 25 µL 1×PBS, 2 µL of which was reserved for evaluation of exosome size and concentration using NanoSight LM 10 instrument (Particle Characterization Laboratories). The remainder was subjected to RNA extraction immediately. The usage of human biospecimen for this study was approved by Institutional Review Board of Medical College of Wisconsin and Mayo Clinic.
RNA was prepared by using miRNeasy Micro Kit (QIAGEN). Twenty-three µL of exosome suspension was mixed with 700 µL QIAzol Lysis buffer, and was processed by the standard protocol from the manufacturer. The extracted RNA was eluted with 14 µL of RNase-free water. The quantity and quality of the RNA were determined by Agilent Bioanalyzer 2100 with Small RNA Chip and RNA 6000 Pico Kit as indicated (Agilent Technologies).
The concentration and the size distribution of isolated exosomes were measured using NanoSight. Prior to sampling, the sample solutions were homogenized by vortexing, followed by serial dilution to the final dilution of 1:100,000 in 0.2 µm-filtered 1x PBS. NIST (National Institute of Standards and Technology) traceable 97 nm ± 3 nm polystyrene latex standards were added and analyzed in conjunction with the diluted exosome solution to validate the operation of the instrumentation. A blank 0.2 µm-filtered 1x PBS sample was also run as a negative control. Each sample analysis was conducted for 90 seconds. The Nanosight’s automatic analysis settings (High Sensitivity, Blue laser [405 nm, 645 mW]) were utilized for the processing of the data. All samples were evaluated in triplicates.

treatment_protocol: We sequenced microRNAs from the 7 human tissue samples with replicates (A1/A8, B2/B9, C3/C10, D4/D11, E5/E12, F6/F13, G7/G14) using NEBNext Multiplex Small RNA library Prep Set from New England Biolab (NEB). After that, we identified miRNAs in these plasma samples against known human matured miRNAs.

value: exosome from plasma


title: NF-6


title: GM12878-37C-p300-sc585-lotEF2711-Rep3-Robotic-SL46204

value: rabbit polyclonal p300, Santa Cruz sc-585, Lot#F2711


title: NG-14

description:
microRNA from sample G
Characterization of human plasma-derived exosomal RNAs


title: NE-12

description:
microRNA from sample E
Characterization of human plasma-derived exosomal RNAs


title: NC-10

description:
microRNA from sample C
Characterization of human plasma-derived exosomal RNAs


title: ND-11

description:
microRNA  from sample D
Characterization of human plasma-derived exosomal RNAs


title: GM12878-GABP-Rep1-Manual-SL45068


title: NA-8

description:
microRNA  from sample A
Characterization of human plasma-derived exosomal RNAs


title: NG-7

description:
microRNA  from sample G
Characterization of human plasma-derived exosomal RNAs


title: NE-5

description:
microRNA  from sample E
Characterization of human plasma-derived exosomal RNAs


title: ND-4


title: GM12878-37C-p300-1F4_E10-Rep1-Manual-SL45094


title: GM12878-37C-p300-1F4_E10-Rep1-Robotic-SL46203


title: NB-2

description:
microRNA from sample B
Characterization of human plasma-derived exosomal RNAs


title: GM12878-37C-Input-Rep1-SL45100


title: NC-3

description:
microRNA  from sample C
Characterization of human plasma-derived exosomal RNAs


title: NA-1

description:
microRNA from sample A
Characterization of human plasma-derived exosomal RNAs


title: 330

description: mRNA tissue sample from patient 330

data_processing:
eRNA were developed to process data from mRNA sequencing.
Human genome reference sequences downloaded from NCBI ftp site (Release 103) with Bowtie2
TopHat and Bowtie were used for genome mapping.
Cufflinks were sued for transcripts assembling.
Genome_build: human genome reference sequences downloaded from NCBI ftp site (Release 103) with Bowtie2.
Supplementary_files_format_and_content: Data frame of FPKM of mRNAs  in *.txt

source_name: prostate

growth_protocol: we selected tissue samples from 10 anonymous donors.

extract_protocol:
Add 200ul chloroform plus 1mL TRIZOL, and vortex for 15 seconds, and  then centrifuge samples at 12,000g for 15 minutes at 2-8 C. Transfer the aqueous phase to a fresh tube. Add 500ul isopropanol plus 1mL TRIZOL to the this new tube, vortex and centrifuge samples at 12,000g for 10 minutes at 2-8 C again. Following centrifugation, remove the supernatant. Wash RNA pellet with 70% alcohol plus 1ml TRIZOL, vortex, and Centrifuge samples again. Remove supernatant and dry the pellet, then redissolve it in 100ul DEPC water. After Dnase Treatment, RNA was purified using Rneasy Column Purification based on Qiagen’s Rneasy Protocol.
The protocol was based on TruSeq RNA Sample Preparation Kits v2

treatment_protocol: The frozen tissues were homogenized by mortar in liquid nitrogen, followed by 1ml TRIZOL/100mg tissue to be homogenized into a falcon tube.

value: prostate


title: 321

description: mRNA tissue sample from patient 321


title: 428

description: mRNA tissue sample from patient 428


title: 197

description: mRNA tissue sample from patient 197


title: 145

description: mRNA tissue sample from patient 145


title: 1107

description: mRNA tissue sample from patient 1107


title: 1073

description: mRNA tissue sample from patient 1073


title: GM12878-p300-sc585_lotF2711-SL34358

growth_protocol: GM12878 and Jurkat cells were grown under the standard ENCODE protocols (http://genome.ucsc.edu/encode/protocols/cell/human/Jurkat_protocol.pdf and http://genome.ucsc.edu/encode/protocols/cell/human/GM12878_protocol.pdf)

extract_protocol:
Cells were fixed using 1% formaldehyde (NRSF samples) or 1% formaldehyde at 37C (p300 samples).
Libraries were generated following Illumina's DNA Sample Prep Kit protocol

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot#


title: NB-9

description:
microRNA  from sample B
Characterization of human plasma-derived exosomal RNAs


title: GM12878-p300-7H5_F2p-SL31842

value: mose monoclonal p300

tag: chip antibody info

value: custom generated; 7H5_F2


title: GM12878-p300-1F4_E10-Rep2-SL34359

value: custom generated; 1F4_E10


title: GM12878-p300-4C5_A1-SL31833

value: custom generated; 4C5_A1


title: GM12878-p300-5D2_A1-SL31836

value: custom generated; 5D2_A1


title: GM12878-p300-2F6_F7-SL31831

value: custom generated; 2F6_F7


title: GM12878-p300-2F4_A8-SL31832

value: custom generated; 2F4_A8


title: 1067

description: mRNA tissue sample from patient 1067


title: GM12878-p300-1F4_E10-Rep1-SL31838


title: 1014

description: mRNA tissue sample from patient 1014


title: GM12878-p300-sc585_lotE3113-SL34362


title: GM12878-p300-5F7_C9p-SL31841

value: custom generated; 5F7_C9


title: Jurkat-NRSF-plate3549-wellH12-SL31882

source_name: Jurkat-NRSF

value: Jurkat

value: mouse monoclonal NRSF

value: custom generated (Johnson et al. 2007, PMID:17540862)


title: GM12878-p300-3B4_G6-SL31835

value: custom generated; 3B4_G6


title: Jurkat-NRSF-plate3549-wellA1-SL31830


title: GM12878-p300-3H6_B6-SL31834

value: custom generated; 3H6_B6


title: Jurkat-NRSF-plate3549-wellD6-SL31851


title: Jurkat-NRSF-plate3435-wellH12-SL29215


title: Jurkat-NRSF-plate3435-wellD6-SL29214


title: GM12878-p300-1A3_F8-SL31840

value: custom generated; 1A3_F8


title: GM12878-p300-2E10_D10-SL31839

value: custom generated; 2E10_D10


title: 306

description: mRNA tissue sample from patient 306

value: prostate


title: Jurkat-NRSF-plate3435-wellA1-SL29213


title: Jurkat-NRSF-plate3405-wellH12-SL28742


title: Jurkat-NRSF-plate3405-wellD6-SL28741


title: Jurkat-NRSF-plate3405-wellA1-SL28740


title: Jurkat-NRSF-plate3365-wellD6-SL26733


title: Jurkat-NRSF-plate3365-wellD1-SL26732


title: Jurkat-NRSF-plate3365-wellH12-SL26734


title: Jurkat-NRSF-plate3365-wellC1-SL26731


title: Jurkat-NRSF-plate3365-wellB1-SL26730


title: GM12878-NRSF-plate3646-wellF7-SL34383


title: GM12878-NRSF-plate3646-wellG12-SL34384


title: GM12878-NRSF-plate3646-wellF6-SL34382


title: GM12878-NRSF-plate3646-wellF5-SL34380


title: GM12878-NRSF-plate3405-wellF12-SL28745


title: GM12878-NRSF-plate3365-wellF12-SL26737


title: GM12878-NRSF-plate3365-wellE6-SL26736


title: nucleosomes

description: protein associated DNA

value: Raji B


title: GM12878-NRSF-plate3365-wellA2-SL26735


title: PP1

description:
processed data file for protein-coding genes:
processed_FPKM_genes_human_pancreatic_lineage.txt
processed data file for lncRNAs:
processed_FPKM_lncRNAs_human_pancreatic_lineage.txt

data_processing:
All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).
The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012).  Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).
processed data file for protein-coding genes:
processed_FPKM_genes_human_pancreatic_lineage_140112.txt
processed data file for lncRNAs:
processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: pancreatic progenitors cells

treatment_protocol: Primary human islet were obtained from Integrated Islet Distribution Program (IIDP, study number BS208) and processed according to a previous report with minor modification (Dorrell et al., 2008; Dorrell et al., 2011). The following antibodies were used to label desired cell populations: HPi2 (mouse IgG1), and HPa1 (mouse IgM) as primary antibodies (kindly provided by Dr. Streeter), Alexa647-conjugated donkey anti-mouse IgG and Alexa488-conjugated donkey anti-mouse IgM as secondary antibodies. Beta cells were recognized as HPi+/HPa-, and HPi+/HPa+ for alpha cells as described  (Dorrell et al., 2011).

value: pancreatic progenitors cells


title: alpha1

source_name: human pancreatic alpha cells

value: human pancreatic alpha cells


title: DE2

source_name: definitive endoderm cells

value: definitive endoderm cells


title: alpha2


title: PP2


title: PP3


title: DE1


title: ES2

source_name: undifferentiated human ESCs

value: human embryonic stem cells


title: beta1

source_name: human pancreatic beta cells

value: human pancreatic beta cells


title: beta2


title: cKO rep1

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and all short (less than 35 base pairs), low-quality, and non-speccific sequences were discarded.  Sequences were then mapped to the Mus musculus reference genome (Build NCBI-M37.65 ENSEMBL/MGI annotations) using the CLC RNA-Seq reference mapping algorithm (length parameter: 0.9, identity: 0.8)
Reads per million per kilobase (RPMK) values were calculated to rank gene expression.  Observed counts were quantile normalized according to Bolstad et al., Bioinformatics, 2003 and then underwent differential expression analysis using the beta binomial method of Baggerly et al., Bioinformatics, 2003 with False Discovery Rate correction for multiple comparisons according to Benjamini and Hochberg, Journal of the Royal Statistical Society, 1995.
Only genes with mean unnormalized RPMK values greater than two for either the wild type or Sip1 cKO were investigated, estimated to correspond to approximately one mRNA molecule per cell (based on the estimate that typical mammalian cells contain 500,000 molecules of mRNA (Bryant and Manning, 1998) although cells can vary significantly in mRNA content (Islam et al., 2011)).  A minimum change in RPMK between the wild type and Sip1 conditional knockout greater than two was also used in further analysis.  Additionally, only genes with a p-value less than 0.05 (for a 95% confidence interval) and more than a 2.5 fold change in normalized RPMK value are reported.  This fold change threshold was chosen based on experimental data comparing relative gene expression between E15.5 lenses from mixed background Sip1 f/f no Cre control mice and inbred C57Bl/6<har> mice (also submitted to GEO) which indicated that a large proportion of changes below 2.5 fold are likely due to variation in genetic background, not the Sip1 gene deletion.
Genome_build: Build NCBI-M37.65 ENSEMBL/MGI annotations
Supplementary_files_format_and_content: tab-delimited text files include normalized and non-normalized RPKM values for each Sample as well as gene annotation (ID, name, synonyms, and MGI identifier)

source_name: lens

extract_protocol:
Lenses were removed, flash frozen on dry ice, and total RNA was extracted from Sip1 cKO and wild type lenses at E15.5 (30 lenses per biological replicate; three independent biological replicates analyzed for each genotype) using the SV Total RNA Isolation System (Invitrogen).  Illumina® TruSeqTM RNA Sample Preparation Kit v2 was used to prepare the sequence libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mix

value: lens

tag: age

value: 15.5 days post conception

value: Sip1 flox/flox + MLR10Cre (cKO)


title: WT rep2

value: Sip1 flox/flox no Cre (wild type)


title: cKO rep3


title: cKO rep2


title: GM12878-NRSF-plate3646-wellB1-SL34357

tag: cell line

value: mouse monoclonal NRSF

value: custom generated (Johnson et al. 2007, PMID:17540862)


title: WT rep1


title: GM12878-NRSF-plate3405-wellB1-SL28743


title: GM12878-NRSF-plate3405-wellE6-SL28744


title: Jurkat-NRSF-plate3365-wellA1-SL26729

value: Jurkat


title: GM12878-NRSF-plate3646-wellE6-SL34381


title: AG rep2


title: AG rep1


title: SC_rep6

status: Public on May 31 2014

city: East Melbourne

first: Jason

last: Li

address: St Andrews Pl

country: Australia

institute: Peter MacCallum Cancer Centre

description: SC rep6

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the mouse reference genome (mm9) using Tophat v1.4.1 with default parameters.
Counts per gene were obtained using HTSeq with mode intersection-nonempty and Ensembl gtf. Counts were normalised using the limma-voom method.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing limma-voom normalised log2 values for each Sample

source_name: sub-cutaneous tumors that were growing in the absence of an intra-kidney tumor

growth_protocol: 6 sub-cutaneous (SC) Renca (renal tumor cell line) tumors, growing with no concomitant intra-kidney (IK) tumor and 6 SC Renca tumors, growing with a concomitant IK tumor were harvested at day 14 after tumor inoculation.

extract_protocol:
Cells were lysated and total RNA was extracted using a Qiagen RNeasy kit. 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

value: entire tumor composition:tumor cells+ stroma cells

tag: origin

value: Renca cell line tumor injected sub-cutaneously at day 14 post-tumor injection

value: BALB/C


title: AG rep3


title: SC_rep3

description: SC rep3


title: SC_rep4

description: SC rep4


title: SC_rep2

description: SC rep2


title: CD4

description: CD4 T lymphocytes

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using tophat/bowtie with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cutfflinks/cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CD4 T lymphocytes

growth_protocol: 30 intra-kidney Renca (renal tumor cell line) tumors were harvested at day 16 after tumor inoculation in addition to 4 spleens from tumors-bearing mice.

extract_protocol:
Cells (CD4 T cells from spleens and M1, M2 from tumors) were lysated and total RNA was extracted using a Qiagen RNeasy kit. 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: Tumors and spleens were dissociated and stained for FACS sorting using specific membrane antibodies: anti-CD45.2, anti-TCRbeta, anti-CD4, anti-F4/80, anti-CD11b. CD4 T lymphocytes, type-2 and type-1 macrophages were then sorted using a FACS sorter (BD Bioscience).

value: CD4 T cells sorted from in vivo renal tumors

value: Renca cell line tumor injected intra-kidney at day 14 post-tumor injection


title: IK_rep5

description: IK rep5

source_name: sub-cutaneous tumors that were growing in the presence of an intra-kidney tumor


title: IK_rep6

description: IK rep6


title: IK_rep3

description: IK rep3


title: SC_rep5

description: SC rep5


title: M1

description: Type-1 macrophages

source_name: Type-1 macrophages

value: M1 sorted from in vivo renal tumors


title: IK_rep4

description: IK rep4


title: IK_rep1

description: IK rep1


title: M2

description: Type-2 macrophages

source_name: Type-2 macrophages

value: M2 sorted from in vivo renal tumors


title: WT rep3


title: BECs-Stressed

city: Los Angeles

first: Young-Kwon

last: Hong

state: CA

address: 1450 Biggy St. NRT6501

institute: University of Southern California

description: polyA selection prior to cDNA generation

data_processing:
Illumina RTA RTA Version=1.13.48.0, deconvolution and fastq file generation CASAVA-1.7.1a5
Genome_build: hg19
Supplementary_files_format_and_content: wig file

molecule: polyA RNA

source_name: neonatal dermal BECs_stressed

growth_protocol: Human neonatal dermal BECs were isolated from deidentified foreskin specimen and cultured to passage 5 under the previously described culturing condition.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Quality control was performed with Agilent Bioanalyser.
 Illumina TuSeq mRNA v2 according to manufacturer's instructions

treatment_protocol: About one million cells were exposed to a laminar flow at 2 Dyne/cm2 using an orbital shaker installed in a CO2 incubator under 5% CO2 for 12 hours.

tag: developemental stage

value: Neonates

value: foreskin specimen

value: neonatal dermal blood vascular endothelial cells (BECs)

tag: passage

value: Passage 5

tag: culture condition

value: laminar flow at 2 Dyne/cm2


title: phyA-1 3 (ler)

city: Shenzhen

first: Bosheng

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

country: China

institute: SUSTC (current, may different with previous institution )

data_processing:
Bowtie for alignment, v1, default parameter
Cufflink for expression profiling, v2.1.0, default paremeter
Genome_build: TAIR10
Supplementary_files_format_and_content: tabulat, table head : test_id gene_id gene    locus   sample_1        sample_2        status  value_1 value_2 log2(fold_change)       test_stat       p_value q_value significant

organism: Arabidopsis thaliana

growth_protocol: grown in the dark for 4 d and iradiated with 3 hour of Far red light

extract_protocol:
RNAeasy Kit
stander Illumina mRNA-seq protocol

treatment_protocol: The wild-type seedlings and the phyA-1 mutant (both of the Landsberger ecta [Ler] ecotype) were grown in the same conditions used for the phyA ChIP-seq analysis (D4d+FR3h) prior to RNA isolation. Three independent biological replicates were subjected to RNA-seq analysis.

value: seedling

tag: ecotype

value: Ler


title: phyA-1 1 (ler)

tag: genotype


title: phyA-1 2 (ler)


title: Arabidopsis Ler wild type 1

source_name: Arabidopsis Ler wild type

value: wild type


title: Arabidopsis Ler wild type 3


title: 48-5008-DM_RNA-seq

city: Shanghai

first: Gao-Yi

last: Tan

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Streptomyces hygroscopicus subsp. jinggangensis 5008

source_name: 5008/DM_48h culture

growth_protocol: Strain was cultured at 37°C for 48 h in 50 ml fermentation media in 250 ml shaking flasks with reciprocal shaking (220 rpm).

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
Following "TruSeq RNA Sample Preparation Guide"

treatment_protocol: The mycelia was collected from the fermentation medium by centrifugation at 12,000 rpm for 5 min, resuspended in 1 mL TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US), and broken in a precellys homogenizer (6,500 rpm, 1×30 s; Peqlab) with glass beads (150–212 μm, Sigma). Cell debris was removed by centrifugation at 12,000 rpm for 5 min, and the extracted supernatants were stored at -80°C.

tag: genotype/variation

value: shbR1/shbR3 double mutant (DM)

value: Mycelia


title: Arabidopsis Ler wild type 2


title: 48-5008-WT_RNA-seq

source_name: 5008_48h culture


title: SC_rep1

description: SC rep1

tag: cell type

value: entire tumor composition:tumor cells+ stroma cells

tag: strain


title: Pabyssi_RNAseq

city: Gif-sur-Yvette

first: Claire

last: Toffano-Nioche

address: Avenue de la Terrasse, b. 21

department: UFR des Sciences

country: France

institute: CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay

data_processing:
Mapping performed with bowtie.0.12.7 (parameters : -q -m 1)
ncRNA were identified and classified into long five_prime_UTR (utr5), small_regulatory_ncRNA (sRNA), or antisense_RNA (asRNA) using the detrprok_wf.1 (Galaxy Tool Shed)
Genome_build: NC_000868.2
Supplementary_files_format_and_content: gff files include overlapping read count

organism: Pyrococcus abyssi

source_name: cells

growth_protocol: Pyrococcus abyssi GE5 was grown anaerobically in ASW-YT rich medium, containing artificial seawater, yeast extract and tryptone40 at 92 °C.

extract_protocol:
Total RNAs were extracted using the TRIzol method (Invitrogen). A pool of equal amounts of each sample was checked for integrity by 2100 Bioanalyzer (Agilent Technologies Inc.) and treated to enrich in primary transcripts using a 5'-phosphate-dependent exonuclease (Terminator, Epicenter). RNA samples were subsequently purified and concentrated using the RNA Clean-Up and Concentration Kit (Norgen Biotek Corp).
The strand-specific RNA-seq template library was prepared starting from a pool of total samples (50 ng) following the directional mRNA-seq library preparation protocol provided by Illumina Inc.

treatment_protocol: After two overnight transfers, cells were diluted to 2 × 106 cells/mL. After an initial growth of 3 h, samples (10 mL) were taken every 1.5 h until cells reach the stationary phase (11 h of growth). Samples were quickly cooled down in liquid nitrogen, spinned, and the pellets were frozen at −80°C


title: IK_rep2

description: IK rep2

value: Renca cell line tumor injected sub-cutaneously at day 14 post-tumor injection


title: RME1O_RSF1W_IME1cO_IME1ncO - Repl 4

status: Public on May 30 2014

city: St. Louis

first: Barak

middle: A

last: Cohen

state: Missouri

address: Campus Box 8510, Department of Genetics

institute: Washington University School of Medicine

description: Each row represents an independent biological replicate of the strain. Genotype of the strain is indicated in the "title" column. The Illumina library from each replicate was run on 2-3 independent sequencing lanes (technical replicates) until we obtained at least 4 million raw reads per replicate. Each raw file has the sequences obtained from each run for the given sample. The sequencing reads for each sample were combined across all sequencing runs before processing.

data_processing:
If present, adapter dimers were removed. The sequencing reads were aligned to the Verified and Uncharacterized open reading frames (ORFs) in the S. cerevisiae reference genome (S288C , genome release R63-1-1, Saccharomyces Genome Database (SGD, http://www.yeastgenome.org/)) using Bowtie, version 0.12.7 (Langmead et. al. (2009), Genome Biol 10: R25). Only unique alignments with maximum 2 mismatches in the --best alignment mode were accepted.
Genome_build: S288C , genome release R63-1-1, Saccharomyces Genome Database (SGD, http://www.yeastgenome.org/)
Supplementary_files_format_and_content: The counts for all the reads aligned to a given ORF were summed to give the raw counts per ORF.

organism: Saccharomyces cerevisiae

source_name: Vineyard background strain with indicated Vineyard (W) or Oak (O) versions of four Sporulation QTN

growth_protocol: Two replicates each of the 16 strains in the vineyard background allele replacement panel were grown for 14 hours at 30C in 96-well blocks containing 500ul of Yeast Peptone Dextrose (YPD) medium with 2% dextrose. The replicates were pooled and diluted 1:50 into 250 ml conical flasks containing 50ml of 1% potassium acetate to induce sporulation. Cultures were grown for 30 hours and sporulation efficiencies were measured as described in Gerke et.al. (2009), Science 323: 498-501. The entire procedure was repeated on different days until we had four biological replicates for each strain.

extract_protocol:
Total RNA was extracted using standard procedures. mRNA was extracted with the DynaI mRNA DIRECT™ kit (Life Technologies) and fragmented with a Covaris Focused ultrasonicator.
mRNA extraction and fragmentation, random hexamer priming of cDNA and Illumina library preparations were done using standard procedures.
Illumina libraries were prepared from the cDNA of each of the 64 samples. We obtained libraries from all the samples except the strain with vineyard alleles of RME1nc, RSF1c, IME1nc and oak allele of IME1c which had only 3 replicates for the subsequent analyses. The libraries were indexed separately and pooled into one sequencing reaction. The pool was run on multiple lanes until we obtained a minimum of 4 million reads per sample. The sequencing reads from each run were de-multiplexed before sequencing reads from each sample were processed independently. The sequencing reads for each sample were combined across all sequencing runs before data processing.

treatment_protocol: Growth was stopped after 2 hours in potassium acetate by spinning cells down and freezing the cell pellets at -80⁰C. Cells were harvested at this stage. The entire procedure including total RNA extraction was repeated on different days until we had four biological replicates for each strain.

tag: strain background

value: Background is vineyard strain BC187


title: RME1W_RSF1O_IME1cO_IME1ncO - Repl 4


title: RME1O_RSF1O_IME1cW_IME1ncW - Repl 4


title: RME1O_RSF1W_IME1cW_IME1ncW - Repl 4


title: RME1O_RSF1W_IME1cO_IME1ncW - Repl 4


title: RME1W_RSF1W_IME1cW_IME1ncO - Repl 4


title: RME1W_RSF1W_IME1cW_IME1ncW - Repl 4


title: RME1W_RSF1O_IME1cW_IME1ncO - Repl 4


title: RME1O_RSF1O_IME1cO_IME1ncW - Repl 4


title: RME1W_RSF1O_IME1cW_IME1ncW - Repl 4


title: RME1O_RSF1O_IME1cW_IME1ncO - Repl 4


title: RME1W_RSF1W_IME1cO_IME1ncO - Repl 4


title: RME1W_RSF1W_IME1cO_IME1ncW - Repl 4


title: RME1O_RSF1O_IME1cO_IME1ncO - Repl 4


title: RME1W_RSF1W_IME1cW_IME1ncW - Repl 3


title: RME1W_RSF1W_IME1cW_IME1ncO - Repl 3


title: RME1O_RSF1W_IME1cO_IME1ncW - Repl 3


title: RME1O_RSF1W_IME1cW_IME1ncW - Repl 3


title: RME1O_RSF1W_IME1cW_IME1ncO - Repl 3


title: RME1W_RSF1W_IME1cO_IME1ncW - Repl 3


title: RME1O_RSF1O_IME1cW_IME1ncW - Repl 3


title: RME1W_RSF1O_IME1cW_IME1ncW - Repl 3


title: RME1W_RSF1W_IME1cO_IME1ncO - Repl 3


title: RME1W_RSF1O_IME1cO_IME1ncW - Repl 3


title: RME1W_RSF1O_IME1cO_IME1ncW - Repl 4


title: RME1O_RSF1W_IME1cW_IME1ncO - Repl 4


title: RME1O_RSF1O_IME1cO_IME1ncW - Repl 3


title: RME1O_RSF1O_IME1cW_IME1ncO - Repl 3


title: RME1O_RSF1W_IME1cO_IME1ncO - Repl 3


title: RME1O_RSF1W_IME1cW_IME1ncW - Repl 2


title: RME1W_RSF1W_IME1cO_IME1ncW - Repl 2


title: RME1O_RSF1O_IME1cO_IME1ncO - Repl 3


title: RME1W_RSF1O_IME1cW_IME1ncW - Repl 2


title: RME1O_RSF1O_IME1cW_IME1ncW - Repl 2


title: RME1W_RSF1O_IME1cW_IME1ncO - Repl 2


title: RME1W_RSF1O_IME1cO_IME1ncW - Repl 2


title: RME1O_RSF1W_IME1cO_IME1ncW - Repl 2


title: RME1W_RSF1W_IME1cW_IME1ncW - Repl 2


title: RME1W_RSF1W_IME1cO_IME1ncO - Repl 2


title: BECs-Static

source_name: neonatal dermal BECs_control

tag: tissue

value: static


title: RME1W_RSF1O_IME1cO_IME1ncO - Repl 3


title: RME1O_RSF1O_IME1cW_IME1ncO - Repl 2


title: RME1O_RSF1W_IME1cW_IME1ncO - Repl 2


title: RME1O_RSF1W_IME1cO_IME1ncO - Repl 2


title: RME1W_RSF1O_IME1cO_IME1ncO - Repl 2


title: RME1W_RSF1W_IME1cW_IME1ncW - Repl 1


title: RME1O_RSF1O_IME1cO_IME1ncO - Repl 2


title: RME1W_RSF1O_IME1cW_IME1ncW - Repl 1


title: RME1O_RSF1O_IME1cW_IME1ncW - Repl 1


title: RME1O_RSF1W_IME1cW_IME1ncW - Repl 1


title: RME1W_RSF1W_IME1cO_IME1ncW - Repl 1


title: RME1W_RSF1O_IME1cO_IME1ncW - Repl 1


title: RME1W_RSF1O_IME1cW_IME1ncO - Repl 1


title: RME1O_RSF1W_IME1cW_IME1ncO - Repl 1


title: RME1O_RSF1W_IME1cO_IME1ncW - Repl 1


title: RME1W_RSF1W_IME1cO_IME1ncO - Repl 1


title: RME1W_RSF1O_IME1cW_IME1ncO - Repl 3


title: RME1O_RSF1O_IME1cO_IME1ncW - Repl 2


title: RME1O_RSF1O_IME1cW_IME1ncO - Repl 1


title: RME1O_RSF1O_IME1cO_IME1ncW - Repl 1


title: IDGSW3_125_rep1_d35

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

description: Sample 28

data_processing:
TopHat with default settings and sample type "fr-secondstrand" for directional libraries
ArrayStar (DNASTAR) with default RNA sequencing settings.  Imported BAM files from TopHat output.
Genome_build: mm9
Supplementary_files_format_and_content: tab deliminated text files include RPKM values for each sample

growth_protocol: Custom αMEM powdered tissue culture medium was purchased from Cellgro (Manassas, VA) and supplemented with 2.20g/L NaHCO3 (S233-3) (Fisher Scientific, Waltham, MA). Fetal Bovine Serum (FBS) (SH30396) was purchased from HyClone (Logan, Utah) and heat inactivated by incubation at 55°C for 30 minutes. Penicillin-Streptomycin Solution (SV30010) was purchased from Fisher Scientific, (Waltham, MA) and recombinant mouse interferon-gamma (rmIFN-γ) from Gibco/Invitrogen (Camarillo, CA). 10cm and 6 well collagen IV coated plates were purchased from BD Biosciences (San Jose, CA). IDG-SW3 cells (6) were expanded in 10cm collagen coated at 33°C in αMEM with 10% heat inactivated FBS, 100 units/mL penicillin/streptomycin, and 50U/mL IFNγ.  Cells were harvested with 0.05% Trypsin/0.53mM EDTA (Fisher Scientific, Waltham, MA) and plated in 6 well collagen coated plates at 40,000 cells/cm2. To induce osteocytogenesis, two days after plating, cells were transferred to 37°C and media was changed to osteogenic media (αMEM with 10% heat inactivated FBS, 100 units/mL penicillin/streptomycin, 50μg/mL ascorbic acid (A4034, Sigma, St. Louis, MO) and 4mM β-glycerol phosphate (G9422, Sigma, St. Louis, MO) without IFNγ. Osteogenic media was changed three times weekly.

extract_protocol:
Directional RNA-seq libraries were prepared with the Epicentre (Madison, WI) ScriptSeq v2 RNA-seq Library Preparation Kit per manufacturer’s instructions.  Ribosomal RNA depletion (RNA 6000 Nano Kit) and final library quality (High Sensitivity DNA kit) was analyzed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
RNA was isolated using the TRI-Regent protocol (MRC, Cincinnati, OH) with an additional LiCl extraction. Eight μg of total RNA was DNase1 treated (Invitrogen) then ribosomal RNA was depleted using the RiboMinus Eukaryote Kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions

treatment_protocol: Basal mRNA samples at days 3, 7, 14, 21, 28, and 35 were not treated with any compound or vehicle.  The vitamin D experiments were treated with 100nM of 1,25(OH)2D3 (or ethanol vehicle) for 24 hours prior to RNA harvesting.

value: osteocytic cells

tag: differentiation day


title: RME1O_RSF1O_IME1cO_IME1ncO - Repl 1


title: IDGSW3_125_rep2_d35

description: Sample 29


title: IDGSW3_125_rep3_d35

description: Sample 30


title: RME1W_RSF1O_IME1cO_IME1ncO - Repl 1


title: IDGSW3_vehicle_rep3_d35

description: Sample 27


title: RME1W_RSF1W_IME1cW_IME1ncO - Repl 1


title: IDGSW3_125_rep3_d3

description: Sample 24


title: IDGSW3_vehicle_rep2_d35

description: Sample 26


title: IDGSW3_vehicle_rep1_d35

description: Sample 25


title: IDGSW3_125_rep2_d3

description: Sample 23


title: IDGSW3_vehicle_rep2_d3

description: Sample 20


title: IDGSW3_vehicle_rep1_d3

description: Sample 19


title: IDGSW3_vehicle_rep3_d3

description: Sample 21


title: IDGSW3_125_rep1_d3

description: Sample 22


title: cV6

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

description:
Sample 54
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv

data_processing:
We built custom exon-junction library for mapping. Human and mouse libraries were based on Ensembl66 annotation, while chimpanzee and rhesus macaque libraries were based on liftovered human annotation.
We used Bowtie2 with a default parameter setting to align the reads to the respective genomes, human version hg19, chimp panTro3, rhesus rheMac2 and mouse version mm9 from the Ensembl66, as well as custom exon-junction libraries.
We kept reads with alignment score > 150, and among those that mapped to two locations, only those with a difference in alignment score >= 5. Among reads that mapped to an exon and exon junction, those with higher scores were kept.
To calculate three species comparable gene expression, only reads in CDS regions which could be recipical liftoverable between human chimpanzee/rhesus macaque were considered. To calculate four species comparable gene expression, which could be recipical liftoverable between human and all other three species were considered.
Genome_build: Pan_troglodytes-2.1.3
Supplementary_files_format_and_content: Gene expression was quantified as 1000*P*N/(L-99) where N is the number of reads aligned to liftoverable CDS regions and L is the total length of these regions, P is coefficient used to normalize read number, which equal to mean of read number of all samples divided by read number of current sample.

organism: Pan troglodytes

source_name: VC

extract_protocol:
Total RNA was extracted by a Trizol (Invitrogen) procedure according to the manufacturer's instructions. All RNA quality was assessed using an Agilent 2100 Bioanalyser.
Sequencing libraries were prepared using the TruSeq RNA-Seq Sample Prep Kit (Illumina) according to the manufacturer's instructions.
Polyadenylated RNA was isolated using a poly-dT bead procedure and then chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded complementary DNA were repaired. After 3'-end adenylation of these products, Illumina Single-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were then PCR-amplified (15 cycles). The RNA-seq libraries were sequenced (100 cycles) on the Illumina Hiseq 2000 platform.

tag: strain/background

value: primary visual cortex

tag: Sex

value: M

tag: age (years)


title: cC4

description:
Sample 58
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv

source_name: CBC

value: cerebellar cortex

value: F


title: cC6

description:
Sample 60
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: cV4

description:
Sample 52
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: cC5

description:
Sample 59
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: cC1

description:
Sample 55
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: cC3

description:
Sample 57
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: cV5

description:
Sample 53
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: cV3

description:
Sample 51
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: cV2

description:
Sample 50
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: IDGSW3_basal_rep2_d35

description: Sample 17

extract_protocol:
Directional RNA-seq libraries were prepared with Illumina Small RNA Sample Prep Kit and TruSEq RNA Sample Preparation Kits v2 according to the directional mRNA-seq Sample Preparation protocol (Illumina, San Diego, CA) with the following modification – the library was purified using 2 rounds of purification with AMPure Beads in 1.5mL tubes instead of a 96 well plate format. Ribosomal RNA depletion (RNA 6000 Nano Kit) and final library quality (High Sensitivity DNA kit) was analyzed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
RNA was isolated using the TRI-Regent protocol (MRC, Cincinnati, OH) with an additional LiCl extraction. Eight μg of total RNA was DNase1 treated (Invitrogen) then ribosomal RNA was depleted using the RiboMinus Eukaryote Kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions


title: IDGSW3_basal_rep1_d35

description: Sample 16


title: cV1

description:
Sample 49
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: MandLPSandIFNg_3

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

description: Barcode: CGTTACCA

data_processing:
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 50bpX25bp pair-end sequencing. Second mate was used for sample demultiplexing, at which point individual single-end (demultiplexed) fastqs were aligned to mm9 genome using TopHat with following options -G mm9.mrna.10.31.gtf --prefilter-multihits --segment-length 20 --max-multihits 15. Geneexpression was obtained using ESAT software tool (http://garberlab.umassmed.edu/software/esat/) focused on analysis of 3’end targetedRNA-Seq. The following parameters were used: -task "score3P" –normalizedOutput -window 1000 -maxExtension 3000 -maxIntoGene 2000 -stranded –collapseIsoforms.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file that includes normalized expression data

source_name: Macrophages, LPS and IFNg

extract_protocol:
Bone-marrow derived macrophages were generated from C57BL/6 mice and stimulated with either Il4 or combination of LPS&IFNg or left unstimulated for 24 h
mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen). For cDNA synthesis, we used custom oligo-dT primer with a barcode and adapter-linker sequence (CCTACACGACGCTCTTCCGATCT—XXXXXXXX-T15). After first strand synthesis samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded using consecutive acid-alkali treatment. Then, second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (New EnglandBiolabs, Ipswich, MA) and after SPRI clean-up, mixture was PCR enriched 14 cycles andSPRI purified to yield final strand specific 3'end RNA-seq libraries
3'end DGE

value: bone-marrow derived macrophages


title: cC2

description:
Sample 56
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: IDGSW3_basal_rep2_d28

description: Sample 14


title: MandLPSandIFNg_1

description: Barcode: AACTTGAC


title: IDGSW3_basal_rep3_d28

description: Sample 15


title: cP5

description:
Sample 47
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv

source_name: PFC

value: prefrontal cortex


title: cP4

description:
Sample 46
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: MandIL4_3

description: Barcode: GTCTGATG

source_name: Macrophages, IL4


title: IDGSW3_basal_rep3_d21

description: Sample 12


title: cP3

description:
Sample 45
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: IDGSW3_basal_rep2_d21

description: Sample 11


title: MandIL4_2

description: Barcode: GTATAACA


title: cP2

description:
Sample 44
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: MandIL4_1

description: Barcode: CCAGAGCT


title: IDGSW3_basal_rep1_d21

description: Sample 10


title: cK6

description:
Sample 42
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv

source_name: kidney

value: kidney


title: Ctrl_2

description: Barcode: GTCGCCTT

source_name: Macrophages, unstimulated


title: IDGSW3_basal_rep2_d14

description: Sample 8


title: cK5

description:
Sample 41
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: IDGSW3_basal_rep3_d14

description: Sample 9


title: cP1

description:
Sample 43
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: LCL RISC-Associated Small RNA (Abcam AB57113 Immunoprecipitation)

city: Durham

first: Adam

middle: Wesley

last: Whisnant

state: NC

address: 213 Research Drive 427 CARL Bldg

department: Molecular Genetics and Microbiology

institute: Duke University

description:
RISC-associated small RNA
LCLrip

data_processing:
Reads were processed using the FASTX-Toolkit and were aligned to the human genome (NCBI, Hg19) and human miRNA library (miRBase19), using Bowtie. Reads of at least 15 nt were retained if they mapped to the indicated library with 0 mismatch.
Analysis of tailed reads was completed using custom Perl scripts written in house. Briefly, deep sequencing reads obtained from the above pipeline were aligned with Bowtie to miRBase19 hairpins with no mismatches, and reads which were unaligned were retained. These reads were confirmed to have a discrete 5′ prime start site and were then assigned to the human miRNA of closest length with a complete, perfect match along the length of the mature miRNA. Then the sequence 3′ of the potentially tailed, mature miRNA was checked against all pre-miRNA hairpins capable of generating it, and miRNAs were designated tailed if the 3′ sequence extension did not align to any pre-miRNA hairpin.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files have two columns: pre-miRNA and Reads per Million (RPM).  The pre-miRNA is the name of the hairpin as annotated in miRbase v19.  RPM is the total number of reads that align to that hairpin divided by the total number of reads (in millions) for that library.

source_name: LCL B-cell line

growth_protocol: Roswell Park Memorial Institute medium (RPMI) supplemented with 15% FBS

extract_protocol:
Immunoprecipitation of RISC with followed by mirVana miRNA isolation as previously described (Flores et al, 2013 [PMID 23536669])
Illumina TruSeq Small RNA Sample Preparation Kit was used to ligate adapters with small RNA purified with the mirVana miRNA Isolation Kit.  Reverse transcription was performed with Invitrogen SuperScript III and PCR amplification using Promega's GoTaq Green Master Mix

value: LCL B-cell line

tag: immunoprecipitation antibody

value: Anti-Ago2 (Abcam, catalog# AB57113, lot# GR111546-1)

tag: illumina 3' index


title: MandLPSandIFNg_2

description: Barcode: CAGCAAGG


title: Ctrl_1

description: Barcode: AGTTGCTT


title: IDGSW3_basal_rep3_d35

description: Sample 18

tag: cell line


title: LCL Total Small RNA

description:
Total small RNA
LCLtotal

extract_protocol:
TRIzol total RNA isolation followed by the mirVana miRNA isolation kit
Illumina TruSeq Small RNA Sample Preparation Kit was used to ligate adapters with small RNA purified with the mirVana miRNA Isolation Kit.  Reverse transcription was performed with Invitrogen SuperScript III and PCR amplification using Promega's GoTaq Green Master Mix


title: IDGSW3_basal_rep3_d7

description: Sample 6


title: cP6

description:
Sample 48
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: SH-SY5Y RISC-Associated Small RNA (Diagenode 2A8 Immunoprecipitation)

description:
RISC-associated small RNA
SY5YripM

source_name: SH-SY5Y neuroblastoma cell line

growth_protocol: 1:1 mixture of Minimal Essential Medium Eagle (MEME) and Ham’s F-12 medium with 10% FBS and 1% non-essential amino acids

value: SH-SY5Y neuroblastoma cell line

value: Anti-Ago (Diagenode, catalog# 2A8, provided by Zissimos Mourelatous)


title: IDGSW3_basal_rep2_d7

description: Sample 5


title: IDGSW3_basal_rep1_d28

description: Sample 13


title: cK3

description:
Sample 39
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: cK2

description:
Sample 38
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: A549 RISC-Associated Small RNA (Diagenode 2A8 Immunoprecipitation)

description:
RISC-associated small RNA
A549ripM

source_name: A549 alveolar basal epithelial cell line

growth_protocol: Roswell Park Memorial Institute medium (RPMI) supplemented with 10% FBS


title: IDGSW3_basal_rep1_d7

description: Sample 4


title: cK1

description:
Sample 37
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: RME1O_RSF1W_IME1cO_IME1ncO - Repl 1

description: Each row represents an independent biological replicate of the strain. Genotype of the strain is indicated in the "title" column. The Illumina library from each replicate was run on 2-3 independent sequencing lanes (technical replicates) until we obtained at least 4 million raw reads per replicate. Each raw file has the sequences obtained from each run for the given sample. The sequencing reads for each sample were combined across all sequencing runs before processing.


title: IDGSW3_basal_rep3_d3

description: Sample 3


title: A549 Total Small RNA

description:
Total small RNA
A549total

value: A549 alveolar basal epithelial cell line


title: C8166 RISC-Associated Small RNA (Diagenode 2A8 Immunoprecipitation)

description:
RISC-associated small RNA
C8166ripM

source_name: C8166 T-cell line

value: C8166 T-cell line


title: IDGSW3_basal_rep2_d3

description: Sample 2


title: cM6

description:
Sample 36
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv

source_name: muscle

value: muscle


title: cM5

description:
Sample 35
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: IDGSW3_basal_rep1_d3

description: Sample 1


title: cM4

description:
Sample 34
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: C8166 Total Small RNA

description:
Total small RNA
C8166total


title: 293 RISC-Associated Small RNA (Diagenode 2A8 Immunoprecipitation)

description:
RISC-associated small RNA
293ripM

source_name: 293 embryonic kidney cell line

growth_protocol: Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

value: 293 embryonic kidney cell line


title: cM3

description:
Sample 33
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: Input_IDGSW3_d3

data_processing:
ChIP-seq runs were all 50bp.  Barcoded samples were run over 4 lanes total and the fastq data were concatenated prior to BOWTIE mapping.  12 barcoded samples were run in each lane, over 4 lanes total.  Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using BOWTIE [-m 1 -- best] to mm9 [UCSCmouse genome build 9].  Replicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/] and QuEST [http://mendel.stanford.edu/sidowlab/downloads/quest/].
QuEST 2.4 was run using the recommend settings for transcription factor (TF) like binding with the following exceptions: kde_bandwith=30, region_size=600, ChIP threshold=30, enrichment fold=3, rescue fold=3
HOMER analysis was run using the default settings for peak finding.  Histone peaks were called with a 2-fold enrichment over input instead of 4-fold (for transcription factors) given the nature of histone chip-seq.
False Discovery Rate (FDR) cut off was 0.001 (0.1%) for all peaks.
Genome_build: mm9
Supplementary_files_format_and_content: *.bed files contain the ChIP-seq peak locations, *.bedgraph files are for display in the UCSC genome browser

extract_protocol:
Chromatin immunoprecipitation was performed as described previously (Meyer MB, Mol Endo. 2012). Briefly, samples were subjected to immuno-precipitation using either a control IgG antibody or the indicated experimental antibody (VDR, RXR, H3K4me1, H3K4me2, H3K4me3, H3K27Ac, H3K5Ac, H3K9Ac, H4K20me1, H3K36me3, or H3K9me3).  To remove the calcified matrix from the differentiated cells, the cells were subjected to three 15 minute 300mM EDTA washes following fixation. Subsequently, matrix mix was subjected to 2x10 pulses with a Polytron Homogenizer (Power Gen 125, Fisher Scientific) while in NCP 1 buffer (Hepes 10mM pH 6.5, EDTA 10mM, EGTA 0.5mM, Triton X-100 0.25%).  Resulting cell pellet was resuspended in NCP 2 buffer (Hepes 10mM pH 6.5, EDTA 1mM, EGTA 0.5mM, NaCl 200mM) and remainder of protocol was followed.  The isolated DNA (or Input DNA acquired prior to precipitation) was then validated by quantitative real time PCR (qPCR) and further prepared for ChIP-seq analysis.
ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions.  During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols.  ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp.  Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina HiSeq2000 sequencers by the University of Wisconsin-Madison DNA Sequencing Facility in the University of Wisconsin-Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver.  3) on an Illumina cBot (Illumina, Carlsbad, CA) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 50mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver.  3). Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina Carlsbad, CA) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane. and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  The transcription factor ChIP sample was repeated in biological replicate in the same manner (minimum of 2 replicates).  Histone modifications were analyzed as single samples. Sequences were mapped to the mouse genome (mm9) using BOWTIE (--best –m 1) to yield unique alignments.

treatment_protocol: For VDR and RXR ChIP-seq, IDG-SW3 cells were treated with 100nM of 1,25(OH)2D3 for 3 hours prior to ChIP assay.

value: Day 3

tag: chip antibody


title: IDGSW3_basal_rep1_d14

description: Sample 7

value: osteocytic cells


title: Input_IDGSW3_d35

value: Day 35


title: cM1

description:
Sample 31
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: H3K9me3_IDGSW3_d35

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot#


title: hC6

description:
Sample 30
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv

data_processing:
We built custom exon-junction library for mapping. Human and mouse libraries were based on Ensembl66 annotation, while chimpanzee and rhesus macaque libraries were based on liftovered human annotation.
We used Bowtie2 with a default parameter setting to align the reads to the respective genomes, human version hg19, chimp panTro3, rhesus rheMac2 and mouse version mm9 from the Ensembl66, as well as custom exon-junction libraries.
We kept reads with alignment score > 150, and among those that mapped to two locations, only those with a difference in alignment score >= 5. Among reads that mapped to an exon and exon junction, those with higher scores were kept.
To calculate three species comparable gene expression, only reads in CDS regions which could be recipical liftoverable between human chimpanzee/rhesus macaque were considered. To calculate four species comparable gene expression, which could be recipical liftoverable between human and all other three species were considered.
Genome_build: GRCh37
Supplementary_files_format_and_content: Gene expression was quantified as 1000*P*N/(L-99) where N is the number of reads aligned to liftoverable CDS regions and L is the total length of these regions, P is coefficient used to normalize read number, which equal to mean of read number of all samples divided by read number of current sample.

value: cerebellar cortex

value: M

tag: age (days)


title: 293 Total Small RNA

description:
Total small RNA
293total


title: H3K36me3_IDGSW3_d35


title: rC6

description:
Sample 90
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv

data_processing:
We built custom exon-junction library for mapping. Human and mouse libraries were based on Ensembl66 annotation, while chimpanzee and rhesus macaque libraries were based on liftovered human annotation.
We used Bowtie2 with a default parameter setting to align the reads to the respective genomes, human version hg19, chimp panTro3, rhesus rheMac2 and mouse version mm9 from the Ensembl66, as well as custom exon-junction libraries.
We kept reads with alignment score > 150, and among those that mapped to two locations, only those with a difference in alignment score >= 5. Among reads that mapped to an exon and exon junction, those with higher scores were kept.
To calculate three species comparable gene expression, only reads in CDS regions which could be recipical liftoverable between human chimpanzee/rhesus macaque were considered. To calculate four species comparable gene expression, which could be recipical liftoverable between human and all other three species were considered.
Genome_build: rheMac2
Supplementary_files_format_and_content: Gene expression was quantified as 1000*P*N/(L-99) where N is the number of reads aligned to liftoverable CDS regions and L is the total length of these regions, P is coefficient used to normalize read number, which equal to mean of read number of all samples divided by read number of current sample.

organism: Macaca mulatta


title: H4K20me1_IDGSW3_d35


title: 293 RISC-Associated Small RNA (Abcam AB57113 Immunoprecipitation)

description:
RISC-associated small RNA
293ripAb


title: cM2

description:
Sample 32
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv

value: F


title: SH-SY5Y Total Small RNA

description:
Total small RNA
SY5Ytotal


title: H3K9Ac_IDGSW3_d35

value: Millipore


title: hC5

description:
Sample 29
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rC5

description:
Sample 89
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: cK4

description:
Sample 40
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv

value: kidney


title: hC4

description:
Sample 28
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rC4

description:
Sample 88
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hC3

description:
Sample 27
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: H4K5Ac_IDGSW3_d35


title: H3K4me3_IDGSW3_d35


title: rC2

description:
Sample 86
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hC2

description:
Sample 26
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hC1

description:
Sample 25
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rC3

description:
Sample 87
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rC1

description:
Sample 85
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: H3K27Ac_IDGSW3_d35


title: H3K4me2_IDGSW3_d35


title: hV5

description:
Sample 23
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv

value: primary visual cortex


title: rV5

description:
Sample 83
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rV6

description:
Sample 84
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: H3K9me3_IDGSW3_d3


title: rV4

description:
Sample 82
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hV6

description:
Sample 24
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: H3K4me1_IDGSW3_d35


title: hV3

description:
Sample 21
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: H3K36me3_IDGSW3_d3


title: rV2

description:
Sample 80
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: H3K9Ac_IDGSW3_d3


title: rV3

description:
Sample 81
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hV1

description:
Sample 19
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hV2

description:
Sample 20
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rV1

description:
Sample 79
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: H4K20me1_IDGSW3_d3


title: H4K5Ac_IDGSW3_d3


title: H3K27Ac_IDGSW3_d3


title: rP6

description:
Sample 78
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv

value: prefrontal cortex


title: hP6

description:
Sample 18
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rP5

description:
Sample 77
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rP4

description:
Sample 76
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rP3

description:
Sample 75
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: H3K4me3_IDGSW3_d3


title: hP3

description:
Sample 15
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: H3K4me2_IDGSW3_d3


title: hV4

description:
Sample 22
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: H3K4me1_IDGSW3_d3


title: hP2

description:
Sample 14
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rP1

description:
Sample 73
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: RXR_125_rep2_IDGSW3_d35

value: RXR ΔN-197

value: Santa Cruz


title: hK6

description:
Sample 12
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rP2

description:
Sample 74
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hP1

description:
Sample 13
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rK6

description:
Sample 72
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hK5

description:
Sample 11
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rK5

description:
Sample 71
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hK4

description:
Sample 10
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hK3

description:
Sample 9
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rK4

description:
Sample 70
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rK3

description:
Sample 69
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rK2

description:
Sample 68
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: VDR_125_rep2_IDGSW3_d35

value: VDR C-20


title: hK2

description:
Sample 8
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: RXR_veh_rep1_IDGSW3_d35


title: hP5

description:
Sample 17
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hP4

description:
Sample 16
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: VDR_125_rep1_IDGSW3_d35


title: rK1

description:
Sample 67
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hM6

description:
Sample 6
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: VDR_Veh_rep2_IDGSW3_d35


title: mC6

description:
Sample 120
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv

data_processing:
We built custom exon-junction library for mapping. Human and mouse libraries were based on Ensembl66 annotation, while chimpanzee and rhesus macaque libraries were based on liftovered human annotation.
We used Bowtie2 with a default parameter setting to align the reads to the respective genomes, human version hg19, chimp panTro3, rhesus rheMac2 and mouse version mm9 from the Ensembl66, as well as custom exon-junction libraries.
We kept reads with alignment score > 150, and among those that mapped to two locations, only those with a difference in alignment score >= 5. Among reads that mapped to an exon and exon junction, those with higher scores were kept.
To calculate three species comparable gene expression, only reads in CDS regions which could be recipical liftoverable between human chimpanzee/rhesus macaque were considered. To calculate four species comparable gene expression, which could be recipical liftoverable between human and all other three species were considered.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Gene expression was quantified as 1000*P*N/(L-99) where N is the number of reads aligned to liftoverable CDS regions and L is the total length of these regions, P is coefficient used to normalize read number, which equal to mean of read number of all samples divided by read number of current sample.


title: hK1

description:
Sample 7
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: VDR_Veh_rep1_IDGSW3_d35


title: RXR_125_rep1_IDGSW3_d35


title: mC5

description:
Sample 119
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hM4

description:
Sample 4
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rM4

description:
Sample 64
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mC4

description:
Sample 118
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rM3

description:
Sample 63
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: RXR_veh_rep2_IDGSW3_d35


title: mC3

description:
Sample 117
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mC2

description:
Sample 116
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rM2

description:
Sample 62
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hM1

description:
Sample 1
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rM1

description:
Sample 61
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mV6

description:
Sample 114
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mV4

description:
Sample 112
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mV5

description:
Sample 113
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mC1

description:
Sample 115
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mV2

description:
Sample 110
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mV1

description:
Sample 109
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mV3

description:
Sample 111
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mP6

description:
Sample 108
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mP3

description:
Sample 105
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mP4

description:
Sample 106
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mP1

description:
Sample 103
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mK6

description:
Sample 102
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mP5

description:
Sample 107
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mP2

description:
Sample 104
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mK2

description:
Sample 98
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mK4

description:
Sample 100
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mK1

description:
Sample 97
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mK3

description:
Sample 99
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hM2

description:
Sample 2
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rM6

description:
Sample 66
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hM5

description:
Sample 5
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mK5

description:
Sample 101
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mM6

description:
Sample 96
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: hM3

description:
Sample 3
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: rM5

description:
Sample 65
mRNA
Processed data file: 3_species_comparable_gene_RPKM.tsv
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mM4

description:
Sample 94
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: pHBI1::HBI1-YFP

city: Jinan

first: Mingyi

last: Bai

state: Shandong

address: 27 Shandananlu

department: Life of Scienec

institute: Shandong University

data_processing:
Total reads were mapped to the Arabidopsis genome (TAIR10; www.Arabidopsis.org) using the Tophat software. The unique mapping reads were analyzed with PRI-CAT online software with default parameters (http://www.ab.wur.nl/pricat/) (Muino et al., 2011) and cutoff (FDR<0.05) to define the HBI1-binding peaks. Two nearest neighbor genes flanking binding site, and genes that contain binding site within the transcribed region were defined as putative HBI1 target genes.
Genome_build: TAIR10

source_name: Seedling

growth_protocol: The pHBI1::HBI1-YFP and 35S::YFP plants were grown in a greenhouse with a 16-h light/8-h dark cycle at 22-24℃ for 4-weeks.

extract_protocol:
For ChIP-Seq, library was constructed from 10 ng of ChIP DNA, pooled from twelve biological repeats to reduce sample variation.
Libraries were constructed with barcodes using NEBNext ChIP-Seq Library Prep Reagent Set for Illumina kit (New England Biolabs).

tag: genotype/variation

tag: Stage

value: 4 weeks plants

tag: antibody

value: YFP antibody (Homemade)


title: YFP


title: HBI1-Ox 2#

data_processing:
The sequence reads were mapped to the Arabidopsis genome using Tophat software, and differential gene expression was analyzed using DeSeq software.
Genome_build: TAIR10

growth_protocol: Wild type Arabidopsis, 35S::HBI1-YFP and Col were grown on half-strength MS medium for 5 days under constant light.

extract_protocol:
Total RNA was extracted with Spectrum Plant Total RNA Kit (Sigma)
Libraries were constructed with barcodes using TruSeqTM RNA Sample Preparation Kit (Ilumina)

value: 5 days plants


title: mM3

description:
Sample 93
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv

value: muscle


title: mM2

description:
Sample 92
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: mM1

description:
Sample 91
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv


title: Col 1#