title: 9830-010255B-FF_mRNA-seq

tag: age


title: LJ T1

status: Public on Aug 20 2014

type: SRA

city: La Jolla

first: Lani

last: Gleason

state: CA

address: 8750 Biological Grade

department: Marine Biology Research Division

country: USA

institute: Scripps Institution of Oceanography

description: treated

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequences were removed.
Sequences were used to construct de novo transcriptome assemblies (CLC Genomics Workbench v.6), one for each population.  The 4 population assemblies were then reciprocally blasted and the resulting contigs were trimmed, so all 4 assemblies were comparable.
Assemblies were annotated using Blast2Go.
Reads were mapped back to these assemblies (CLC Genomics Workbench v.6).
Differential expression between geographic regions and between control and heat stress conditions was examined with the program DESeq in R.
Genome_build: no available genome; reference sequences used was de novo transcriptome assemblies from this study
Supplementary_files_format_and_content: tab-delimited text file include normalized expression values for each of the 12 samples for each of the contigs in the reference assembly

molecule: total RNA

organism: Tegula funebralis

source_name: whole animal

extract_protocol:
Whole animals were frozen in liquid nitrogen, ground to a powder, and the RNA of each individual was extracted using standard Trizol reagent methods.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At the start of each experiment, treatment animals were placed in a temperature-programmable incubator (Thermo Precision Model 818) and air temperature was increased by 3 °C every half hour (starting at 15 °C) to simulate a natural rate of heating that snails experience in the intertidal. This gradual increase was continued until the target temperature of 34 °C was reached; the incubator stayed at this target temperature for the remaining 2 hours and 20 min of the experiment.  Each heat stress trial lasted a total of 5.5 hours (including the ramp time), which is an estimate of a typical low tide period for *C. funebralis *in the intertidal.  Control animals were exposed to 15 °C in air in the same incubator for 5.5 hours.

tag: population

value: southern CA

tag: tissue

value: whole animal

tag: location

value: La Jolla, San Diego County


title: 9830-020185B-FF_DSN

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Basecalls performed using CASAVA version 1.8. Quality score is phred33 scale.
Sequenced reads were to hg19 whole genome using MapSplice v12_07 with the default configuration.
The number of fragments derived from genes was estimated using RSEM v1.1.13 with the default setting and the reference transcriptome of UCSC hg19 GAF2.1 KnownGenes on standard chromosomes. Estimated counts were then transformed by upper quartile normalization.
Gene abundance was normalized by the upper quartile across all genes within each lane.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of normalized gene counts for each sample.

Raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns:
http://www.ncbi.nlm.nih.gov/gap/?term=phs000676

organism: Homo sapiens

source_name: breast tumor

extract_protocol:
Fresh-frozen: Autopsy breast tissue sample was flash frozen on dry ice. RNA was retrieved using Qiagen RNeasy mini kit.
DSN: Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used for the construction of sequencing libraries. DSN normalization was then performed to remove rRNA. (ref. Illumina DSN Normalization Sample Preparation Guide)

tag: er (1=positive; 0=negative)

tag: pr (1=positive; 0=negative)

tag: node status (1=positive=1 or more nodes; 0=negative)

tag: grade

tag: tumor size (1= <=2cm; 2= >2cm to <=5cm; 3= >5cm; 4=any size with direct extension to chest wall or skin)

tag: rfs event (0=no relapse; 1=relapsed at any site or died of disease)

tag: rfs months

tag: overall survival event (0=alive; 1=dod or doc)

tag: overall suvival months


title: AB T2

description: treated

value: Aliso Beach, Orange County


title: 982049B-FF_RIBO0

extract_protocol:
Fresh-frozen: Autopsy breast tissue sample was flash frozen on dry ice. RNA was retrieved using Qiagen RNeasy mini kit.
Ribo-zero: rRNA was removed using epicentre's Ribo-Zero rRNA Removal kit cat# RZH110424. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used for the construction of sequencing libraries.


title: m_Cfp1null_RNA_2

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description:
rRNA depleted total RNA
biological replicate 2
technical replicate 1
processed data file: m_Cfp1null_RNA_merged_forward.bigwig
processed data file: m_Cfp1null_RNA_merged_reverse.bigwig

data_processing:
Basecalls performed using Illumina Basecalling Package  VN:1.13.57.0
RNA-seq reads were aligned to the mm9 genome assembly using STAR 2.2.1 to allow for gapped alignments using default settings
A GTF file containing ensEMBL mouse transcript information (release 67) was used to generate a count table with HTSeq in union mode. This only counts 1 isoform per gene using the longest possible transcript. Counts from technical replicates were pooled.
Size factors for each library were determined using the Bioconductor package DESeq (Anders and Huber 2010) and applied to generate a normalized count table for each biological replicate
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were created from BAM using bedtools GenomeCoverageBed with -split option and UCSC wigToBigWig. Tabular count tables were produced by HTSeq.

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: ES cells were grown in gelatinized dishes in Glasgow MEM (Gibco) supplemented with 10% foetal bovine serum (Hyclone) , 1× MEM nonessential amino acids, 1 mM sodium pyruvate, 50 μM 2-mercaptoethanol (Gibco) and LIF.

extract_protocol:
Cells were lysed in TRI reagent (Sigma). Total RNA was then extracted with chloroform, precipitated with isopropanol and DNAse treated (DNA-free, Ambion). Ribosomal RNA from 5 μg of total RNA was depleted using Ribo-Zero kit (Epicentre).
Strand specific RNA-Seq ibraries were prepared using Script-Seq V2 RNA-Seq library preparation kit (Epicentre) according to manufacturer’s instructions.

treatment_protocol: Doxorubicin was purchased from Sigma and used at a final concentration of 1 μM for 6 hours.

tag: strain

tag: genotype

tag: treatment

value: Control


title: 9830-000030B-FF_mRNA-seq

extract_protocol:
Fresh-frozen: Autopsy breast tissue sample was flash frozen on dry ice. RNA was retrieved using Qiagen RNeasy mini kit.
mRNA-seq: Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries. rRNA was removed using standard Illumina protocols.


title: m_Cfp1null_RNA_22

description:
rRNA depleted total RNA
biological replicate 2
technical replicate 2
processed data file: m_Cfp1null_RNA_merged_forward.bigwig
processed data file: m_Cfp1null_RNA_merged_reverse.bigwig


title: AB T1

description: treated


title: 982049B-FF_mRNA-seq


title: AB C2

description: control


title: 040182B-FFPE_DSN

extract_protocol:
FFPE: Autopsy breast tissue sample was formalin-fixed and praffin-embedded. RNA was retrieved using Roche High Pure RNA paraffin kit, Cat# 03270289001.
DSN: Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used for the construction of sequencing libraries. DSN normalization was then performed to remove rRNA. (ref. Illumina DSN Normalization Sample Preparation Guide)


title: m_Cfp1null_RNA_1

description:
rRNA depleted total RNA
biological replicate 1
technical replicate 1
processed data file: m_Cfp1null_RNA_merged_forward.bigwig
processed data file: m_Cfp1null_RNA_merged_reverse.bigwig


title: 040182B-FFPE_RIBO0

extract_protocol:
FFPE: Autopsy breast tissue sample was formalin-fixed and praffin-embedded. RNA was retrieved using Roche High Pure RNA paraffin kit, Cat# 03270289001.
Ribo-zero: rRNA was removed using epicentre's Ribo-Zero rRNA Removal kit cat# RZH110424. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used for the construction of sequencing libraries.


title: AB C1

description: control


title: PP T2

description: treated

value: northern CA

value: Pigeon Point, San Mateo County


title: m_wtES_Dox_RNA_22

description:
rRNA depleted total RNA
biological replicate 2
technical replicate 2
processed data file: m_wtES_Dox_RNA_merged_forward.bigwig
processed data file: m_wtES_Dox_RNA_merged_reverse.bigwig

value: Wildtype (E14Tg2a)

value: Doxorubicin (1mM,  6 hours)


title: 040182B-FF_DSN


title: PP T1

description: treated


title: 982049B-FF_DSN


title: m_wtES_Dox_RNA_12

description:
rRNA depleted total RNA
biological replicate 1
technical replicate 2
processed data file: m_wtES_Dox_RNA_merged_forward.bigwig
processed data file: m_wtES_Dox_RNA_merged_reverse.bigwig


title: 040182B-FF_RIBO0


title: 040182B-FF_mRNA-seq


title: m_wtES_Dox_RNA_2

description:
rRNA depleted total RNA
biological replicate 2
technical replicate 1
processed data file: m_wtES_Dox_RNA_merged_forward.bigwig
processed data file: m_wtES_Dox_RNA_merged_reverse.bigwig


title: PP C1

description: control


title: 020578B-FFPE_DSN


title: m_Cfp1null_RNA_12

description:
rRNA depleted total RNA
biological replicate 1
technical replicate 2
processed data file: m_Cfp1null_RNA_merged_forward.bigwig
processed data file: m_Cfp1null_RNA_merged_reverse.bigwig


title: m_wtES_RNA_22

description:
rRNA depleted total RNA
biological replicate 2
technical replicate 2
processed data file: m_wtES_RNA_merged_forward.bigwig
processed data file: m_wtES_RNA_merged_reverse.bigwig


title: SR T2

description: treated

value: Slide Ranch, Marin County


title: PP C2

description: control


title: 020578B-FFPE_RIBO0


title: SR C2

description: control


title: 020578B-FF_RIBO0


title: m_wtES_RNA_12

description:
rRNA depleted total RNA
biological replicate 1
technical replicate 2
processed data file: m_wtES_RNA_merged_forward.bigwig
processed data file: m_wtES_RNA_merged_reverse.bigwig


title: SR C1

description: control


title: m_wtES_RNA_2

description:
rRNA depleted total RNA
biological replicate 2
technical replicate 1
processed data file: m_wtES_RNA_merged_forward.bigwig
processed data file: m_wtES_RNA_merged_reverse.bigwig


title: 020578B-FF_mRNA-seq


title: m_wtES_RNA_1

description:
rRNA depleted total RNA
biological replicate 1
technical replicate 1
processed data file: m_wtES_RNA_merged_forward.bigwig
processed data file: m_wtES_RNA_merged_reverse.bigwig


title: m_Cfp1null_Dox_RNA_22

description:
rRNA depleted total RNA
biological replicate 2
technical replicate 2
processed data file: m_Cfp1null_Dox_RNA_merged_forward.bigwig
processed data file: m_Cfp1null_Dox_RNA_merged_reverse.bigwig


title: smear under the skin graft (S) with Xen14 bacteria

status: Public on Aug 19 2014

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description:
Xen14 (S)
small RNAs

data_processing:
After indexing and trimming of linker sequences, those reads of at least 15 nt in length that had less than three terminal mismatches in the sequence were sorted and counted for the following analysis. The clean read datasets were blasted with the BOWTIE software according to the following criteria: a 5′ and 3′ linker match of at least 15 nt and an appropriate length (15–29 nt). The pre-miRNAs and mature miRNAs in the miRBase v.20.0 were searched with BLAST to identify Mus musculus miRNAs.
Genome_build: miRBase v.20.0
Supplementary_files_format_and_content: Matrix_Expression.txt reports miRNA counts

source_name: serum

growth_protocol: Recombinant-specific gram-negative pathogen Escherichia coli (Xen14) and gram-positive pathogen Staphylococcus aureus (Xen29) purchased from Caliper (Caliper, USA) were used to induce bacterial infection in the mice at a concentration of 1 × 108 bacteria/100 μL of phosphate buffered saline (PBS). To create mixed gram-negative and gram-positive bacterial infection, 1 × 108 Xen14 bacteria and 1 × 108 Xen29 bacteria/100 μL of PBS were used for wound contamination.

extract_protocol:
Total RNA was extracted from the harvested serum using a mirVana miRNA Isolation Kit (Ambion, USA). The purified RNA yield was determined by the absorbance at 260 nm with an SSP-3000 NanoDrop spectrophotometer (Infinigen Biotech, USA), and RNA quality was evaluated with a BioAnalyzer 2100 system (Agilent Technologies, USA).
RNA smaller than 200 base pairs (bp) was enriched with the mirVana miRNA isolation kit (Ambion). The small RNA samples were sent to GeneTech Biotech Co., Ltd (GeneTech, Taiwan) for small RNA cloning. The population of miRNAs with a length of 15–30 nucleotides (nt) was passively eluted from polyacrylamide gels. The RNA was then precipitated with ethanol and dissolved in water. Small RNAs had linkers ligated to them and bar-coded cDNAs were prepared using a TruSeq Small RNA Sample Prep Kit (Illumina, USA) following the manufacturer’s instructions. Individual libraries were analyzed on a BioAnalyzer (Agilent) for the presence of linked cDNA at the appropriate size (135–165 bp) and 11 bar-coded libraries were pooled into 1 sample by mixing 2.0 ng of the 135–165 bp peak from each sample, as determined by the BioAnalyzer.
Sequencing of the pooled libraries was performed in 1 lane of the Illumina HiSeq2000 Sequencer. Fifty bp single-end reads of the libraries were obtained. After indexing and trimming of linker sequences, those reads of at least 15 nt in length that had less than three terminal mismatches in the sequence were sorted and counted for the following analysis. The clean read datasets were BLASTed with the BOWTIE software according to the following criteria: a 5′ and 3′ linker match of at least 15 nt and an appropriate length (15–29 nt). The pre-miRNAs and mature miRNAs in the miRBase v.20.0 were searched with BLAST to identify Mus musculus miRNAs.

treatment_protocol: Three animal models were used to create bacterial infection routes: subcutaneous injection (hereafter referred to as (I)), cut wound (hereafter referred to as (C)), and skin grafting (hereafter referred to as (S)). In the (I) model, E. coli and/or S. aureus suspensions were injected subcutaneously into the backs of the mice using an Fr. 25 needle. In the (C) model, a 1 cm incision wound was created in the midline of the back, smeared with E. coli and/or S. aureus suspension, and the wound was closed directly with a 4-0 nylon suture. In the (S) model, a 1×1 cm rectangular full- thickness skin graft was lifted from the backs of the mice, E. coli and/or S. aureus suspensions were spread over the wound bed, and the skin graft was reattached and closed with a 4-0 nylon suture. An additional group of animals in each of these three models was inoculated with PBS to serve as a negative control.

tag: infection

value: Xen14 bacteria

tag: animal model

value: smear under the skin graft (S)

tag: rna source

value: serum


title: smear under the skin graft (S) with Xen29 bacteria

description:
Xen29 (S)
small RNAs

value: Xen29 bacteria


title: m_wtES_Dox_RNA_1

description:
rRNA depleted total RNA
biological replicate 1
technical replicate 1
processed data file: m_wtES_Dox_RNA_merged_forward.bigwig
processed data file: m_wtES_Dox_RNA_merged_reverse.bigwig


title: smear in the cut wound (C) with Xen14+Xen29 bacteria

description:
Xen14+Xen 29 (C)
small RNAs

value: Xen14+Xen29 bacteria

value: smear in the cut wound (C)


title: smear in the cut wound (C) with Xen29 bacteria

description:
Xen29 (C)
small RNAs


title: smear in the cut wound (C) with Xen14 bacteria

description:
Xen14 (C)
small RNAs


title: smear under the skin graft (S) with PBS for the control

description:
Contrl (S)
small RNAs

value: PBS


title: smear in the cut wound (C) with PBS for the control

description:
Contrl (C)
small RNAs


title: SR T1

description: treated

tag: population

tag: tissue


title: 020578B-FF_DSN

tag: age

tag: er (1=positive; 0=negative)


title: subcutaneous injection (I) with Xen14 bacteria

description:
Xen14 (I)
small RNAs

value: subcutaneous injection (I)


title: pAminus RNA-seq from mouse ESC R1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

data_processing:
Basecalling using Illumina Casava1.8.2 software.
Map to human genome hg19 or mouse genome mm9 using Tophat (v 2.0.8)
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: hg19 for human samples or mm9 for mouse samples
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: embryonic stem cells

growth_protocol: ES cells were maintained on plates coated with Matrigel (BD Biosciences) in either defined mTeSR medium (StemCell Technologies Inc.) or conditioned medium (CM) with irradiated mouse embryo fibroblasts supplemented with 4 ng/mL human Basic Fibroblast Growth Factor (bFGF).

extract_protocol:
Total RNAs were prepared using Trizol Reagent and treatment with DNase I. 20μg of total RNAs were separated into polyadenylated and nonpolyadenylated fraction by oligo(dT) magnetic beads (Invitrogen). Ribosomal RNAs were further depleted in nonpolyadenylated fractionby using RiboMinus kit (Invitrogen) to get the poly(A)-/ribo- RNA population.
Library was prepared by using Illumina TruSeq RNA Sample Prep Kit V2.

tag: cell line

tag: type

value: pAminus


title: pAplus RNA-seq from mouse ESC R1

value: pAplus


title: subcutaneous injection (I) with Xen14+Xen29 bacteria

description:
Xen14+Xen 29 (I)
small RNAs


title: subcutaneous injection (I) with Xen29 bacteria

description:
Xen29 (I)
small RNAs


title: ko3ab_r2l2 Bisulfite-Seq

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

description: technical replicate of biological replicate 2

library_source: genomic

data_processing:
use moabs to process bisulfite treated data
Genome_build: mm9
Supplementary_files_format_and_content: text; chromosome, start, end, methylation ratio, total reads, methylated reads, strand, next nucletide of cytosine, plus_strand, total reads from plus strand, methylated reads from plus strand, minus strand, total reads from minus strand, methylated reads from minus strand

molecule: genomic DNA

source_name: Dnmt3ab knockout Hematopoietic Stem Cells

growth_protocol: Freshly sorted HSCs (SP KLS CD150+) from each genotype from  >tertiary-transplanted mice

extract_protocol:
Extract genomic DNA using Invitrogen PureLink Genomic DNA kits
Tru-Seq DNA sample prep kit

treatment_protocol: Adapter-ligated fragments were treated with sodium bisulfite (Qiagen)

tag: cell type

value: Murine bone marrow derived primary HSCs

tag: cell surface marker


title: m12_bcell_l2 RNA-Seq

description: technical replicate of biological replicate 1

data_processing:
RUM to make alignments; Customized script to count fragments on gene; DESEQ to do differential expression test;
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated text file for gene's count and fpkm for each sample; XLS file for two sample comparison testing if a gene is differentially expressed;

source_name: wild-type B-Cells

growth_protocol: Freshly sorted wild type and Dnmt3a-KO mouse HSCs (SP-KSL-CD150+)

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

treatment_protocol: PolyA selection

value: Murine bone marrow derived B Cells


title: ko3ab_r2l1 Bisulfite-Seq


title: smear under the skin graft (S) with Xen14+Xen29 bacteria

description:
Xen14+Xen 29 (S)
small RNAs


title: m12_bcell_l1 RNA-Seq


title: ko3ab_r1l1 Bisulfite-Seq


title: ko3ab_hsc_l4 RNA-Seq

source_name: Dnmt-KO Hematopoietic Stem Cells


title: ko3ab_r1l2 Bisulfite-Seq


title: ko3ab_hsc_l1 RNA-Seq


title: ko3ab_hsc_l3 RNA-Seq


title: ko3ab_bcell_l4 RNA-Seq

source_name: Dnmt-KO B-Cells


title: ko3ab_bcell_l2 RNA-Seq


title: ko3ab_bcell_l1 RNA-Seq


title: 48hr Posterior Wound 3

city: Cambridge

first: Kellie

last: Kravarik

state: MA

address: 9 Cambridge Center

department: Biology Department

institute: Whitehead Institute, MIT

description:
P3
RNA from X1's of the pre-pharyngeal region 48 hours after amputation of the tail and pharynx

data_processing:
Bowtie 2.0 to general S. mediterranea transcriptome in Srivastava, 2014 Current Biology using the commands --best -S -5 10 to trim adaptor sequences. Unmapped reads were also reported to a file of unaligned reads.
SAMtools was used to view, sort, index and output raw read counts.
The identifiers for all processed data files can be found in the raw transcriptome related to accession SRP040715, with the exception of  isotigcompIDs which represent the summation of read counts from transcript isotigs.  GBEE01000000 is the direct TSA accession number for the mixed regenerating stage S. mediterranea transcriptome published in Srivastava, M., Mazza-Curll, K. L., van Wolfswinkel, J. C. & Reddien, P. W. Whole-Body Acoel Regeneration Is Controlled by Wnt and Bmp-Admp Signaling. Current Biology (2014). doi:10.1016/j.cub.2014.03.042. I used this transcriptome to map my reads.
Genome_build: GBEE01000000
Supplementary_files_format_and_content: L_*_sequence.PEall.sorted.rawReadCounts.txt: Column A - seqIDs, column B - sequence length, column C - rawreadcounts, and column D - the number of unmapped reads.
Supplementary_files_format_and_content: The raw read count files for all replicates were compiled in a complete matrix (0and48hr.PEall.sorted.totalrawreadcounts.txt), and then raw reads of all putative isotigs (contigs with compX _seq1….compX_seqn sequences) were summed into a single isotigcompX_seq1 row (in the new matrix isotigreadcountsummed.PEall.TotalrawReadCounts.txt).
Supplementary_files_format_and_content: DESeq was used to compute the statistical significance of contigs from 0 to 48A and 0 to 48P using nbinomial(), to the file DESeq_output_AnteriorandPosteriorAnalysis.txt

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: pre-pharyngeal X1 cells

growth_protocol: Animals were cultured with standard conditions prior to and following wounding. Animals starved for >7 days and between 5-10mm in length were used for all conditions.

extract_protocol:
TRIzol Extraction
Illumina True-Seq V2

treatment_protocol: Animals were wounded, and at the appopriate time point, the pre-pharygial tissue was harvested, macerated, and re-suspended in CMFB + collagase for 5 minutes. They were stained with hoechst 33342 for 45 minutes, and 5 minutes of propridium iodide. The hoechst high, PI low population was then harvested by FACS to isolate live neoblast cells with >2C genome content.

value: Asexual

tag: cell isolation method

value: FACS Isolated

tag: stress

value: Posterior Wound

tag: time

value: pre-pharyngeal X1 cells


title: 48hr Posterior Wound 1

description:
P1
RNA from X1's of the pre-pharyngeal region 48 hours after amputation of the tail and pharynx

tag: strain


title: 48hr Posterior Wound 2

description:
P2
RNA from X1's of the pre-pharyngeal region 48 hours after amputation of the tail and pharynx


title: CD4+_Input_Biotin_ChIPseq

city: New York

first: Willey

last: Liao

state: NY

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

data_processing:
Basecalls performed using CASAVA v1.4
Bowtie v0.12.7 was used to identify sequences mapping uniquely to the genome
Peak calls were determined using BCP (http://rulai.cshl.edu/BCP)
Overlapping peaks between antibody and biotin ChIP methods were merged
Genome_build: mm9
Supplementary_files_format_and_content: BED files for uniquely mapping reads and called BCP peaks for Antibody, Biotin, and overlapping peaks are provided

source_name: CD4+ cells, Foxo1tagBirA mice

extract_protocol:
Lysates were clarified from sonicated nuclei and Foxo1-DNA complexes were isolated with antibody or Streptavidin.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a kit from Epicentre. The blunt, phosphorylated ends were treated with Taq DNA polymerase 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 15-19 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: CD4+, Foxo1tagBirA strepdavidin Input


title: subcutaneous injection (I) with PBS for the control

description:
Contrl (I)
small RNAs


title: 48hr Anterior Wound 3

description:
A3
RNA from X1's of the pre-pharyngeal region 48 hours after amputation of the head

value: Anterior Wound


title: 48hr Anterior Wound 2

description:
A2
RNA from X1's of the pre-pharyngeal region 48 hours after amputation of the head


title: CD4+_Input_Ab_ChIPseq

source_name: CD4+ cells

value: CD4+, Foxo1 Ab Input


title: 48hr Anterior Wound 1

description:
A1
RNA from X1's of the pre-pharyngeal region 48 hours after amputation of the head


title: 0hr 2

description:
2
RNA from X1's of the pre-pharyngeal region

value: control


title: 0hr 3

description:
3
RNA from X1's of the pre-pharyngeal region


title: CD4+_Foxo1_Ab_ChIPseq

value: CD4+, Foxo1 Ab, ChIP

tag: chip antibody

value: Foxo1 antibody (Abcam, Ab39670)


title: WS

status: Public on Aug 18 2014

city: Beijing

first: dan

last: liang

address: No. 35 Qinghua East Road

institute: Beijing Forestry University

data_processing:
Genomic DNA was sequenced by BS technology using Illumina HiSeq2000 sequencer.
Raw sequencing data was processed by the Illumina base-calling pipeline. Low-quality reads that contained more than 50% ’N’s or over 50% of the sequence with low quality value (quality value <20) per read were omitted from the data analysis.
The clean reads were aligned to the reference genome using SOAP aligner (Version 2.01)
The uniquely aligned reads  were used for further analysis.
Genome_build: Poptr2_0
Supplementary_files_format_and_content: Cout files include chromosome ID,C sites' coordinate, the number of methylated reads and non-methylated reads, p-value based on bernoulli distribution.
Cout file format
(1)Chromosome ID
(2)Cytosine position
(3)+/- Watson/Crick chain
(4)Type (CG/CHH/CHG)
(5)Base pattern
(6)Copynum: the same value as repeat rate
(7)Methy reads num
(8)Nonmethy reads num
(9)Binomial distribution expected values

organism: Populus trichocarpa

source_name: WS

growth_protocol: Populus trichocarpa seedlings were planted separately into 10-L plastic pots filled with a mixture of clay, silt and sand (2:2:2, v/v). They were grown under well-watered (WW) conditions in a greenhouse at Beijing Forestry University for 2 months. The plants were supplemented with light for 15 h d-1, and temperature and humidity were kept constant.

extract_protocol: Total DNA was prepared by proteinase K/phenol extraction following the manufacturer’s instructions. The DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of ~250 bp, followed by the blunt ending, dA addition to 3’-end, and adaptor addition following the manufacturer’s protocol.

treatment_protocol: the plantlets were divided into two groups, which were subjected to the following watering regimes: well-watered (WW) treatment (maintaining 100% of field capacity) and water-stress (WS) treatment (maintaining 25% of field capacity). Volumetric soil water content was kept at 24% in the WW treatment, while in the WS treatment the volumetric soil water content was kept at approximately 10%.

tag: protocol


title: Tk_wt_Pyr_plus_TEX

city: Columbus

first: Dominik

last: Jäger

state: Ohio

address: 484 12th West Ave

department: Microbiology

institute: The Ohio State University

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Removal of polyA-tails from Fasta sequences
Size filtering: discarding reads shorter than 12 nt
ead mapping using segemehl version 0.1.2
Genome_build: NC_006624.1
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Unnormalized read coverages in wiggle format (*_plus.wig = plus strand; *_minus_= _minus_strand.wig

organism: Thermococcus kodakarensis KOD1

source_name: cells

growth_protocol: T. kodakarensis cultures were grown anaerobically at 85°C in a nutrient-rich artificial sea water (ASW-YT) medium that contained 5 g/l yeast extract (Y), 5 g/l tryptone (T), the required trace minerals and vitamins (Santangelo et al., 2007; Santangelo et al., 2011) and, either 2 g/l S° (S° medium) or 5 g/l sodium pyruvate (Pyr medium). The growth of cultures was followed by optical density measurements at 600nm (OD600) and aliquots (500 ml) were removed for RNA isolation when the OD600 reached 0.2, or sulfur (Fisher Scientific Inc.) was added to final concentrations of 2 g/liter, to cultures growing in Pyr medium, and a 500 ml aliquot was then removed after an additional 20 min incubation at 85°C.

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) according to the manufacturer
Total RNA was freed of residual genomic DNA by DNase I treatment. For depletion of processed transcripts, equal amounts of T. kodakarensis RNA were incubated with TerminatorTM 5'-phosphate-dependent exonuclease (TEX) (Epicentre #TER51020) as previously described (Sharma et al., 2010).  Libraries for Solexa sequencing (HiSeq) of cDNA were constructed by vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/), as described previously for eukaryotic microRNA (Berezikov et al., 2006) but omitting the RNA size-fractionation step prior to cDNA synthesis

treatment_protocol: Cells were removed from suspension by centrifugation (4000g; 30 min) at 4ºC, the resulting cell pellet immediately resuspended in TRIzol (Invitrogen), snap-frozen in liquid nitrogen and stored at -70ºC. After thawing, total RNA was extracted using the TRIzol manufacturer's protocol, incubated at 37ºC for 1h with DNAse I (Thermo Fisher Scientific Inc.)

tag: growth phase

value: exponential

tag: medium

value: ASW-YT-P

tag: tex-treated

value: yes


title: pAplus RNA-seq from human ESC H9


title: Tk_wt_S0_20min_plus_TEX


title: 0hr 1

description:
1
RNA from X1's of the pre-pharyngeal region


title: WW

source_name: WW

value: well-watered (WW) treatment (maintaining 100% of field capacity)


title: pAminus RNA-seq from human ESC H9

value: pAminus


title: ko3ab_hsc_l2 RNA-Seq

value: Murine bone marrow derived primary HSCs


title: CCA

city: Saint Louis

first: Weixiong

last: Zhang

state: MO

address: Campus Box 1045 One Brookings Drive

institute: Washington university in St Louis

data_processing:
Raw RNA-Seq reads with low quality were firstly discarded. Sequencing adaptors were trimmed using an in-house method that recursively searches for the longest substring of the adaptor appearing within a sequence read. If a raw sequence read did not have a substring of the adaptor longer than 6nt, it was considered as having no adaptor.
The adaptor-trimmed sequences with no ambiguous reads, which were referred to as qualified reads, were then mapped to the cDNA sequences of Cassava using Bowtie 0.12.7 (Langmead et al. 2009) allowing no more than one mismatch.
Reads Count Per Million (CPM) were calculated for each transcript
Raw count of reads were also normalized using upper-quatertile normalization method for differential expression analysis
Genome_build: n/a
Supplementary_files_format_and_content: tab-delimited text files include CPM values and upper-quartile normalized counts for each sample (PACid from Phytozome and Mesculenta_147_PfamAB.txt rom comailab.genomecenter.ucdavis.edu)

organism: Manihot esculenta

growth_protocol: Stem segments with three nodes of Cassava (Manihot esculenta Crantz) cultivars were extracted from 8-month-old plants, and inclined in 3-L pots filled with barren red soil: vermiculite (1:1, v/v), fertilized with Hoagland’s solution (Hoagland and Arnon 1950), to propagate and generate well-balanced seedlings. The solution was renewed with 300ml quarter-strength solution once a week. After 2 months of planting, the uniform seedlings were subjected to cold stress treatment. All plants were field grown in Haikou, Hainan, China, during April and June of natural conditions (11h light, 13h dark and 25°C during the day and 18°C at night).  Cassava cultivar SC124 was transferred to normal 24°C illumination incubator (SANYO, Japan) for 2 days to set a homogenization starting point, and then was subjected to three types of cold treatments. 1) Gradual cold acclimation (CA in Figure S1): temperature was decreased from 24°C to 14°C with the rate of -2°C/h to induce mild cold stress. Temperature was then held constant at 14°C for five days to accommodate cold acclimation. RNA was collected at 6h, 24h and 5d after the temperature reaching 14°C. 2) Cold stress after cold acclimation (CCA): after 5 days of cold acclimation and growth under 14°C, plants were watered once with Hoagland’s solution, transferred further to 4°C by -2°C/h gradient cooling, and cultivated at constant 4°C for another 5d. 3) Cold shock (CS): plants grown under 25°C were subjected to dramatic temperature decline to 4°C with a rate of -4°C/h to ensure the temperature reached 4°C at the same time as the CCA treatment. In the two latter treatments, RNA was collected at 6h, 24h and 5d after temperature reaching 4°C. In parallel, plants grown under the normal condition (NC) of 24°C were watered once with Hoagland’s solution every 5 days, and RNA was collected at 0d, 5d and 10d. The mixture samples of SC124 (details were given below) were subjected to small-RNA and mRNA expression profiling by NextGen deep sequencing.

extract_protocol:
Three organs/tissues (folded leaf, fully expanded leaf and roots) of Cassava cultivar SC124 harvested at 6h, 24h and 5d for three cold treatments of CA, CCA and CS, for gene expression profiling at the stages of initial response, secondary response, and functional adaption to cold stresses. Total RNA of each sample was isolated individually, and then pooled with an equal amount from each sample into one for profiling. As a result, four mRNA libraries and four small-RNA libraries, corresponding to the conditions of CA, CCA, CS and NC, were constructed.
The four mRNA libraries were sequenced by RNA-seq by Illumina GAII following Illumina RNA-seq protocol. Briefly, total RNAs were isolated, purified and reversely transcribed, the resulting cDNA products were subsequently digested with NlaIII and the 3′-cDNA fragments captured with the oligo(dT) beads, and then ligated to the Illumina GEX NlaIII Adapter 1. The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, which cutting 17 bp downstream of the recognition site (CATG) to produce tags. After removing 3′fragments with magnetic beads precipitation and MmeI digestion, an Illumina GEX adapter 2 was introduced at the end of tags. The resulting adapter-ligated cDNA tags were subjected to 15 cycles of linear PCR amplified, purified and sequenced with the method of sequencing by synthesis (SBS) using Illumina GAII

tag: cultivar

tag: harvest time

value: 6h, 24h and 5d

tag: treatment


title: NC

description: normal condition (NC) of 24°C were watered once with Hoagland’s solution every 5 days

source_name: folded leaf, fully expanded leaf and roots

tag: tissue


title: HiC crwn4

city: Zurich

first: Stefan

last: Grob

address: Zollikerstrasse 107

department: Institute of Plant Biology

country: Switzerland

institute: University of Zurich

data_processing:
library strategy: HiC-seq
alignment using bowtie version 0.12.7 with the following parameters: -v 0 -m 1 -a
The aligned read-pairs were used to create an interaction matrix, in which each row (and column) corresponds to one fragment, and values represent the number of read-pairs aligned to the respective fragments.
Matrices were corrected for systematic biases using the approach from Jin et al., 2013
Matrices were binned into larger stretches along the genome (windows of size 10 kb, 25 kb, 50 kb, 100 kb, and 250 kb)
Genome_build: TAIR10
Supplementary_files_format_and_content: .txt formated file, containing pairs of genomic bin numbers and their interaction counts

organism: Arabidopsis thaliana

source_name: aerial tissue of 14-day-old seedlings

extract_protocol:
HiC template DNA was prepared according to Lieberman et al. 2009 with minor changes. For detailed protocol see attached publication
HiC libraries were prepared based on TruSeq DNA Library Preparation Protocol with minor changes. For detailed descriptio see attached publication

tag: ecotype

value: Columbia

tag: genotype/variation

value: homozygous crwn4-1

tag: age

value: 14-day-old seedlings

value: aerial tissue of seedlings


title: ko3ab_bcell_l3 RNA-Seq

tag: cell type

value: Murine bone marrow derived B Cells

tag: cell surface marker


title: HiC crwn1

value: homozygous crwn1-1


title: CUTLL1 carrying a second shRNA targeting LUNAR1_3

first: Thomas

last: Trimarchi

address: 550 First Ave Smilow 1307

department: Pathology

institute: NYU School of Medicine

description:
shLnc2_2
Strand-specific RNA-SEQ (dUTP method)

data_processing:
Basecalls performed using CASAVA
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Differential gene expression analysis was performed using cuffdiffv2.1
Genome_build: hg19
Supplementary_files_format_and_content: TAB-delimited text with FPKM values

source_name: CUTLL1 cells

growth_protocol: Cell lines were grown in RPMI with 10% FBS, 1X glutamax and 1X pen-strep.

extract_protocol:
RNeasy kit (Qiagen)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method.

value: human T-ALL cell line

tag: cell line


title: Tk_wt_stat_plus_TEX

value: stationary

value: ASW-YT-S


title: CUTLL1 carrying an shRNA targeting LUNAR1_5

description:
shLnc1_4
Strand-specific RNA-SEQ (dUTP method)


title: TK_wt_exp_plus_TEX


title: CS

description: plants grown under 25°C were subjected to dramatic temperature decline to 4°C with a rate of -4°C/h to ensure the temperature reached 4°C at the same time as the CCA treatment

value: folded leaf, fully expanded leaf and roots


title: CUTLL1 carrying an shRNA targeting LUNAR1_3

description:
shLnc1_2
Strand-specific RNA-SEQ (dUTP method)


title: TK_wt_exp_minus_TEX

value: exponential

value: no


title: CUTLL1 carrying a second shRNA targeting LUNAR1_2

description:
shLnc2_1
Strand-specific RNA-SEQ (dUTP method)


title: CUTLL1 carrying an shRNA targeting LUNAR1_2

description:
shLnc1_1
Strand-specific RNA-SEQ (dUTP method)


title: CA

description: temperature was decreased from 24°C to 14°C with the rate of -2°C/h to induce mild cold stress. Temperature was then held constant at 14°C for five days to accommodate cold acclimation


title: CUTLL1 carrying an shRNA targeting LUNAR1_1

description:
shLnc1_0
Strand-specific RNA-SEQ (dUTP method)


title: CD4+_Foxo1_Biotin_ChIPseq

value: CD4+, Foxo1tagBirA strepdavidin ChIP

value: Strepdavidin


title: CUTLL1 carrying a second shRNA targeting LUNAR1_5

description:
shLnc2_4
Strand-specific RNA-SEQ (dUTP method)


title: CUTLL1 carrying an shRNA targeting Renilla_3

description:
shRen_2
Strand-specific RNA-SEQ (dUTP method)


title: CUTLL1 carrying a second shRNA targeting LUNAR1_4

description:
shLnc2_3
Strand-specific RNA-SEQ (dUTP method)


title: CUTLL1 carrying an shRNA targeting Renilla_4

description:
shRen_3
Strand-specific RNA-SEQ (dUTP method)


title: HPBALL cells treated with GSI

description:
hpball_gsi
Strand-specific RNA-SEQ (dUTP method)

source_name: HPBALL cells

value: HPBALL


title: CUTLL1 carrying an shRNA targeting Renilla_2

description:
shRen_1
Strand-specific RNA-SEQ (dUTP method)


title: CUTLL1 carrying a second shRNA targeting LUNAR1_1

description:
shLnc2_0
Strand-specific RNA-SEQ (dUTP method)


title: CUTLL1 carrying an shRNA targeting LUNAR1_4

description:
shLnc1_3
Strand-specific RNA-SEQ (dUTP method)


title: CUTLL1 cells treated with GSI

description:
cutll1_gsi
Strand-specific RNA-SEQ (dUTP method)


title: HiC Col

value: wildtype


title: CUTLL1 carrying an shRNA targeting Renilla_5

description:
shRen_4
Strand-specific RNA-SEQ (dUTP method)


title: CUTLL1 cells treated with DMSO

description:
cutll1_dmso
Strand-specific RNA-SEQ (dUTP method)


title: Primary T-ALL sample_9

description:
TALL_15
Strand-specific RNA-SEQ (dUTP method)

source_name: primary T-ALL

value: human primary T-ALL


title: Primary T-ALL sample_10

description:
TALL_16
Strand-specific RNA-SEQ (dUTP method)


title: Primary T-ALL sample_8

description:
TALL_14
Strand-specific RNA-SEQ (dUTP method)


title: Primary T-ALL sample_7

description:
TALL_12
Strand-specific RNA-SEQ (dUTP method)


title: Primary T-ALL sample_6

description:
TALL_09
Strand-specific RNA-SEQ (dUTP method)


title: Primary T-ALL sample_5

description:
TALL_08
Strand-specific RNA-SEQ (dUTP method)


title: Primary T-ALL sample_2

description:
TALL_03
Strand-specific RNA-SEQ (dUTP method)


title: Primary T-ALL sample_4

description:
TALL_06
Strand-specific RNA-SEQ (dUTP method)


title: Primary T-ALL sample_3

description:
TALL_04
Strand-specific RNA-SEQ (dUTP method)


title: Human whole thymus extract_2

description:
Thymus_ferrando
Strand-specific RNA-SEQ (dUTP method)

source_name: human thymus

value: thymus


title: Primary T-ALL sample_1

description:
TALL_01
Strand-specific RNA-SEQ (dUTP method)


title: Human whole thymus extract_1

description:
Thymus_ambion
Strand-specific RNA-SEQ (dUTP method)


title: CUTLL1 carrying an shRNA targeting Renilla_1

description:
shRen_0
Strand-specific RNA-SEQ (dUTP method)


title: 38_infected

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

data_processing:
Cluster generation and sequencing of the pooled RNA-seq library was carried out on an Illumina® Cluster Station and Illumina® Genome Analyzer IIx sequencer according to the manufacturer’s instructions (Illumina). The pooled library was sequenced as single-end read 84-mers using Illumina® version 4.0 sequencing kits and the standard Illumina® Genome Analyzer IIx pipeline. The Illumina® Sequencing Control Software version 2.9 and Real Time Analysis version 1.9 software packages were used for real-time tracking of the sequencing run, real-time image processing, the generation of base intensity values and base calling.
deconvolute the pooled libraries into individual libraries of sample sequence reads based on the unique index barcode
Single-end reads, from each filtered individual sample library, were aligned to the B. taurus reference genome (UMD3.1.73)
For each library, raw counts for each annotated gene were obtained using the featureCounts software from the Subread package [version 1.3.5-p4]. The featureCounts parameters were set to unambiguously assign uniquely aligned single-end reads in a stranded manner  to the exons of genes within the B. taurus reference genome annotation
Differential gene expression analysis was performed using the gene raw counts, obtained from 237 featureCounts, within the Bioconductor edgeR package
Genome_build: UMD3.1.73
Supplementary_files_format_and_content: Tab-delimited text files include raw count values per genes

organism: Bos taurus

source_name: PBL derived mRNA

growth_protocol: 16 age-matched female Holstein-Friesian animals used in this study, the eight M. bovis-infected individuals were selected from a panel of 100 naturally infected animals identified during routine disease surveillance by the Irish Department of 101 Agriculture, Food and the Marine. These animals had a positive SICTT result where the skin-fold 102 thickness response to purified protein derivative (PPD)-bovine exceeded that of PPD-avian, and all 103 of these animals were also test positive for the whole blood IFN-γ-based BOVIGAM® assay 104 (Prionics AG, Zurich, Switzerland). In addition, M. bovis infection was confirmed following detailed 105 post-mortem pathological examination and/or culture. Non-infected control animals were selected 106 from a herd with no recent history of M. bovis infection. The control animals were shown to be 107 negative for both the SICTT and IFN-γ tests.

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

value: peripheral blood leukocyte

value: Holstein-Friesian

tag: Sex

value: Female

tag: status

value: infected

tag: ID


title: H3K27ac WT P22 B2

city: Boston

first: Martin

last: Hemberg

address: 300 Longwood Avenue

department: Ophthalmology

institute: Boston Children's Hospital

description: Sample 15

data_processing:
Reads were aligned to Mm9 using BWA with parameters -q 0 -t 4 -n 5 -k 2 -l 32 -e -1 -o 0
The number of reads in each sample was normalized to 10 million and the total number of ChIP reads minus the input reads in the 2 kb window centered on the position 500 bps upstream of the promoters that had been identified as misregulated based on the microarray
The average number of reads (after normalizing to 10M and subtracting input) was calculated as a function of distance for the TSSs that were misregulated in the KO experiment.
Genome_build: Mm9
Supplementary_files_format_and_content: csv file containing the total number of reads in a fixed window. csv file containing the profiles

source_name: H3K27ac WT P22

extract_protocol:
Cerebella were cross-linked and lysed in RIPA buffer. After sonication, immunoprecipitation reactions were performed with antibodies.
Libraries prepared with the Illumina ChIP-Seq DNA Sample Prep Kit as per the manufacturer’s instructions and sequenced on the Illumina HiSeq 2000 platform (Beijing Genomics Institute)

value: WT

tag: developmental stage

value: Postnatal day 22

value: cerebellum

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: lot #


title: 39_infected

tag: strain


title: H3K4me3 WT P6 B2

description: Sample 17

source_name: H3K4me3 WT P6

value: Postnatal day 6


title: 37_infected


title: H3K9/14ac KO P22 B2

description: Sample 14

source_name: H3K9/14ac KO P22

value: Chd4 cKO

value: Millipore


title: H3K9/14ac WT P22 B2

description: Sample 13

source_name: H3K9/14ac WT P22


title: HPBALL cells treated with DMSO

description:
hpball_dmso
Strand-specific RNA-SEQ (dUTP method)

value: human T-ALL cell line


title: H3K9/14ac WT P6 B2

description: Sample 18

source_name: H3K9/14ac WT P6


title: 35_infected


title: H3K27ac KO P22 B2

description: Sample 16

source_name: H3K27ac KO P22


title: H3K4me3 WT P22 B2

description: Sample 11

source_name: H3K4me3 WT P22


title: H3K4me3 KO P22 B2

description: Sample 12

source_name: H3K4me3 KO P22


title: 33_infected


title: 34_infected


title: H3K9/14ac WT P6 B1

description: Sample 8


title: 29_control

value: control


title: H3K27ac KO P22 B1

description: Sample 6


title: 32_infected


title: 24_control


title: 23_control


title: 22_control


title: H3K9/14ac KO P22 B1

description: Sample 4


title: H3K27ac WT P22 B1

description: Sample 5


title: 20_control


title: 36_infected


title: Input_KO_P22

description: Sample 10


title: 18_control


title: H3K9/14ac WT P22 B1

description: Sample 3


title: 17_control


title: H3K4me3 WT P22 B1

description: Sample 1


title: mRNA-seq_PA64s_PA

status: Public on Aug 17 2014

first: Zhen

last: Zhu

address: No.1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

description: mRNA profiling

data_processing:
Illumina Pipeline version 1.5 was used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then filtered into clean reads.
The distinct clean reads of sRNAs that perfectly matched the mature sequences of known rice miRNAs (miRBase release 19) and ta-siARFs (Zhu et al., 2008) were used to estimate the expression level of each rice miRNA and ta-siRNA. The initial counts of clean reads from different samples were normalized into reads per million mapped reads (RPM) for expression amounts.
mRNA-Seq clean reads were aligned to the gene models in MSU Rice Genome Annotation release 6.1 using SOAP v2.20 with  parameters -m 0 -x 1000 -s 40 -l 32 -v 3 -r 2 -p 3.
The gene expression level was calculated by using reads per kilobase transcriptome per million mapped reads (RPKM) method (Mortazavi et al., 2008), with unique position matched reads.
Genome_build: MSU Rice Genome Annotation release 6.1
Supplementary_files_format_and_content: tab-delimited text files include RPM or RPKM values for each Sample.

organism: Oryza sativa

source_name: Panicles

growth_protocol: Super-hybrid rice LYP9 and its parental lines, sterile line PA64s and restorer line 93-11 were planted in the field under the same environmental conditions. Flag leaf and panicle samples were collected at grain-filling stage. The samples, with at least three biological replications, were collected, frozen in liquid nitrogen and stored at –80 °C for total RNA extraction.

extract_protocol:
Total RNAs were extracted from the collected flag leaf and panicle samples at grain-filling stage of hybrid rice and its parents using TRIzol Reagent (Invitrogen) according to the manufacturer’s protocol.
sRNA libraries and mRNA libraries were prepared for sequencing using standard Illumina protocols.

value: Panicles

value: Grain-filling stage


title: mRNA-seq_LYP9_PA

description: mRNA profiling


title: 16_control


title: mRNA-seq_93-11_PA

description: mRNA profiling


title: mRNA-seq_93-11_FL

description: mRNA profiling

source_name: Flag leaves

value: Flag leaves


title: sRNA-seq_93-11_PA

description: sRNA profiling


title: mRNA-seq_LYP9_FL

description: mRNA profiling


title: Input_WT_P22

description: Sample 9


title: H3K4me3 KO P22 B1

description: Sample 2


title: H3K4me3 WT P6 B1

description: Sample 7


title: sRNA-seq_LYP9_PA

description: sRNA profiling


title: mRNA-seq_PA64s_FL

description: mRNA profiling


title: sRNA-seq_93-11_FL

description: sRNA profiling


title: sRNA-seq_PA64s_PA

description: sRNA profiling


title: sRNA-seq_PA64s_FL

description: sRNA profiling


title: sRNA-seq_LYP9_FL

description: sRNA profiling


title: cd8+nkg2d- 2

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 200 Hawkins Dr, 40025 PFP

institute: University of Iowa

data_processing:
Samples were demultiplexed using CASAVA 1.8.2.
TopHat v 2.0.4 was used to map reads, num-threads=4, max-multihits=10, --GTF= mm9/genes.gtf
htseqcount was used to extract counts from accepted_hits.bam files output by TopHat.
Genome_build: mm9
Supplementary_files_format_and_content: Text, tab-delimited, htseqcount output

extract_protocol:
miRNeasy RNA extraction w/on-column Dnase digestion
TruSeq RNA Sample Preparation Kit v2 for multiplexing and library prep, barcodes are provided in raw file names

value: flow sorted lymph node cells

tag: phenotype


title: cd8+nkg2d+ 2


title: cd8+nkg2d+ 1


title: cd8+nkg2d+ 3


title: cd8+nkg2d- 3


title: cd8+nkg2d- 1


title: Prostate cancer bone metastases bone_marrow_nugen8

status: Public on Aug 16 2014

first: hao

last: zhao

address: 1 Baylor Plaza

institute: BAYLOR COLLEGE OF MEDICINE

description: 140 bp average insert size

data_processing: Tophat1.2; Cufflinks1.0.3, hg19

source_name: bone marrow

extract_protocol:
RNA extraction: A bone marrow biopsy was embedded it Tissue-Tek OCT freezing compound. After sectioning at 6um and staining for H&E to verify the presence of tumor, selected samples were sectioned further at 10um, 4 sections each block, into a microcentrifuge tube.  1ml TriZol was added to each tube and homogenized using a plastic pestle and vortexing. To each sample, 200ul of chloroform were added and shaken for 15 seconds and then incubated for 3 minutes at room temperature.  The samples were then centrifuged at 4decC for 15 minutes at 12000xg.  The upper aqueous phase was isolated into a new tube and 500ul of isopropanol was added and the sample was incubated again at room temperature for 10 minutes.  It was centrifuged again at 12000xg for 10 minutes at 4degC. The supernatant was removed from the tube and the RNA pellet was washed in 1ml of 75% ethanol, vortexed briefly, and then centrifuged at 7500xg for 5minutes at 4degC.  The ethanol wash was discarded and the RNA pellet was air dried for 5-10 minutes before resuspension in water.
Construction of sequencing libraries: The Sequencing Library was constructed by using 50ng of RNA and the NuGEN Ovation RNA-Seq kit.  The double-stranded amplified library was fragmented on a Covaris S2 with end repair, and paired-end adaptor ligation using reagents from New England Biolabs (NEBNextR DNA Sample Prep Master Mix Set 1) for the Illumina platform.

tag: tumor stage

value: metastatic

tag: tissue

value: bone metastatic tumor

tag: disease state

value: castration resistant prostate cancer


title: Prostate cancer bone metastases bone_marrow_nugen3

description: 300 bp average insert size


title: Prostate cancer bone metastases bone_marrow_nugen6

description: 300 bp average insert size


title: Prostate cancer bone metastases bone_marrow_nugen7

description: 140 bp average insert size


title: Prostate cancer bone metastases bone_marrow_nugen4

description: 300 bp average insert size


title: Prostate cancer bone metastases bone_marrow_nugen2

description: 300 bp average insert size


title: Smc1_ChIAPET_rep2

first: Richard

middle: A

last: Young

institute: Whitehead Institute for Biomedical Research

description: ChIA-PET against Smc1 in v6.5 mESCs

data_processing:
Images analysis and base calling was done using the solexa pipeline.
The raw sequences were analyzed for linker barcode composition and separated into non-chimeric PET sequences with homodimeric linkers (AA or BB linkers) derived from specific ligation products, or chimeric PET sequences (AB linkers) with heterodimeric linker derived from nonspecific ligation products. We trimmed the 3’ end of PET sequences after a perfect match of the first 10nt of the liner sequences (Linker A with CTGCTGTCCG; Linker B with CTGCTGTCAT). After removing the linkers, only the 5’ ends of the trimmed PET sequences with length of 27bp were retained because the restriction enzyme EcoP151 cuts 27bp away from its recognition sequence.
The sequences of the two ends of PET sequences were separately mapped to the mm9 mouse genome using the bowtie algorithm with the option “-k 1 -m 1 -v 1”.  These criteria retained only the uniquely mapped reads, with at most a single mismatch for further analysis. Aligned reads were paired with mates and were filtered for redundant sequences to avoid bias from PCR amplification in the library preparation procedure. PET sequences with identical genomic coordinates and strand information at both ends were collapsed into a single PET sequence.
Genome_build: mm9
Supplementary_files_format_and_content: BED12 file: The PET sequences were categorized into intrachromosomal PETs, where the two ends of a PET were on the same chromosome, and interchromosomal PETs, where the two ends were on different chromosomes. The unique intrachromosomal PETs are parsed into BED12 format file.

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

extract_protocol:
100 million murine ES cell were cross-linked by 1% formaldehyde at RT 10 mintues and were sonicated to solubilize the chromatin. The chromatin complexes contain DNA fragments with an average size of 300-800bp were immunoprecipitated by using murine SMC1a antibody.
After end repair, the blunt end DNA were ligated with biotin labled half-linkers which containing flanking ECOP15i sites.  After eluted chromatin complexes from protein bead A, Proximity ligated was performed at extremely dilute conditions at 16 O/N. The purified DNA which digested by Ecop15I were prepared for sequencing according to a modified version of the pair end  DNA protocol. Fragmented DNA was end repaired and subjected to add "A" at 3' end, ligated with PE adaptor provided by Illumina. Amplified fragment 214bp (representing pair end genomic DNA 52bp, 42nt linker and  and ~120bp of adaptor sequence) were isolated by agarose gel electrophoresis and purified. sequencing was performed on Illumina Hi-Seq 2000 with PE 50 cycles.
Linker A: 3'-GAC GAC AGG CTA TAG CGC CGG-5', 5'-CTG CTG TCC  GAT ATC GC-3'.  Linker B: 3'-GAC GAC AGT ATA TAG CGC CGG-5' 5'-CTG CTG TCA  TAT ATC GC-3'

treatment_protocol: None.

value: V6.5 Embryonic stem cells

tag: antibody catalog number

value: Bethyl A300-055A


title: P300-_RNA-seq_rep2

status: Public on Aug 15 2014

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: UCSD

description: mRNA sequencing

data_processing:
Libraries were sequenced using Illumina HiSeq 2000 to obtain 50 bp-long reads. Alignment of mRNA-seq reads was performed using default parameters of Tophat to hg19 reference genome in bam format
Bam files were used to calculate FPKM values with the program cuffdiff (cufflinks) for all annotated refseq isoforms. Matching conditions from two independent experiments were treated as replicates in cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated from bam files using genomeCoverageBed (bedtools) command

source_name: Lung Fibroblasts

growth_protocol: IMR90 human primary lung embryo fibroblasts (ATCC) were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 100 U/ml penicillin, 100 u/ml streptomycin, and 10% fetal bovine serum (FBS) at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted from cells using Qiagen easy RNA kit. Maximum amount of RNA was used to start the library preparation according to the manufacturer's instructions (Illumina).
Sequencing libraries were constructed according to the TrueSeq RNA Illumina protocol

treatment_protocol: 1x10^8 low passage IMR90 lung fibroblasts were grown to confluence in 15 cm dishes. After 24 h, the cells were either mock-infected or infected with e1a WT or mutant e1a expressing adenoviral vectors. 24 h post infection total RNA was isolated

tag: cell type

value: contact-inhibited IMR90

tag: infection

value: P300 binding mutant-infected


title: dl312_RNA-seq_rep2

description: mRNA sequencing

tag: cell line

value: IMR90 human primary lung embryo fibroblasts


title: Coinfection_RNA-seq

description: mRNA sequencing

value: RB binding mutant and P300 binding mutant-infected


title: e1awt_RNA-seq_rep2

description: mRNA sequencing


title: P300-_RNA-seq_rep1

description: mRNA sequencing


title: dl312_RNA-seq_rep1

description: mRNA sequencing


title: RB-_RNA-seq_rep1

description: mRNA sequencing

value: RB binding mutant-infected


title: mock_RNA-seq_rep2

description: mRNA sequencing

value: mock-infected


title: mock_RNA-seq_rep1

description: mRNA sequencing


title: Prostate cancer bone metastases bone_marrow_nugen5

description: 300 bp average insert size


title: IMR90_genomic_DNA_Input_dl1500_ChIP-seq

description: Input chromatin in contacted inhibited IMR90 for ChIP-seq normalization after 24h dl1500 infection

data_processing:
Reads were mapped to the Human (hg19) genome using Bowtie software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects.
A custom algorithm executed by MATLAB was used for further processing. The genome was tiled with 50 bp windows. Each read was extended by 150 bases (so we refer to tags as the extend read counts within a bin) and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other. The input sample was used to estimate the expected counts in a window; the average value for all windows was assigned to windows with zero counts.
The total counts of the input and ChIP samples were normalized to each other. The input sample was used to estimate the expected counts in a window; the average value for all windows was assigned to windows with zero counts.
We used the Poisson distribution to estimate the probability of observing the ChIP counts within a window given the expected counts in the input sample window. We considered all windows with P-values less than 1.0 x 10^ -3 to have significant peaks.
Genome_build: hg19
Supplementary_files_format_and_content: no processed data files

extract_protocol:
24 h post infection (p.i.), formaldehyde was added for 10 min at 37°C. After PBS washing, cross-linked cells were scraped from the plates and washed with 1 ml of PBS containing protease inhibitors (Roche). 2x10^7 Cells were resuspended in 450 ul of lysis buffer and incubated for 10 min on ice and immediately sonicated using Misonix cup-horn sonicator. 100 ul of the lysate (corresponding to 5x10^6 cells) were used for each immunoprecipitation with a given antibody (listed below); 10 ul of the lysate was used as input. After overnight reversal of crosslinking at 65°C, samples were treated with RNase A for 30 min at 37°C, proteinase K for 2 h at 56°C. DNA was subsequently purified using phenol/chloroform extraction and precipitation. DNA concentration was measured using Qubit (Invitrogen). At least 10 ng of dsDNA for both input and IP was used for library preparation according to the manufacturer's instructions (NuGen).
Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the NuGen Ovation Ultralow DR Multiplex System 1-8 kit according to protocol.

treatment_protocol: 1x10^8 low passage IMR90 lung fibroblasts were grown to confluence in 15 cm dishes. After 24 h, the cells were incubated with mock- or the dl1500 adenovirus for 1 h in media with 2% serum. Cells were crosslinked 24 h post infection.


title: IMR90_genomic_DNA_Input_mock_ChIP-seq

description: Input chromatin in contacted inhibited IMR90 for ChIP-seq normalization


title: mock_Pol2_ChIP-seq

description: Chromatin IP against PolII in contact inhibited IMR90

data_processing:
Reads were mapped to the Human (hg19) genome using Bowtie software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects.
A custom algorithm executed by MATLAB was used for further processing. The genome was tiled with 50 bp windows. Each read was extended by 150 bases (so we refer to tags as the extend read counts within a bin) and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other. The input sample was used to estimate the expected counts in a window; the average value for all windows was assigned to windows with zero counts.
The total counts of the input and ChIP samples were normalized to each other. The input sample was used to estimate the expected counts in a window; the average value for all windows was assigned to windows with zero counts.
We used the Poisson distribution to estimate the probability of observing the ChIP counts within a window given the expected counts in the input sample window. We considered all windows with P-values less than 1.0 x 10^ -3 to have significant peaks.
Genome_build: hg19
Supplementary_files_format_and_content: BED and wig files were generated by a custom script executed by MATLAB.Bed files contain the coordinates of the significant windows of enrichment. Alltags wig files represents the density of total IP counts. PoissP wig files represent a -logP-value Poisson distribution to estimate the probability of observing the ChIP counts within a window given the expected counts in the input sample window.

value: anti-PolII (N20) (Santa Cruz, catalog# sc-899X)


title: Input_RB1_RBb-_DNA

description: Input DNA

treatment_protocol: 1x10^8 low passage IMR90 lung fibroblasts were grown to confluence in 15 cm dishes. After 24 h, the cells were incubated with either dl312 (delta e1a), psi5 adenoviral vectors expressing WT e1a, P300 binding mutant e1a, or RB binding mutant e1a for 1 h in media with 2% serum. Cells were crosslinked 24 h post infection.


title: Input_RB1_dl312_DNA

description: Input DNA


title: Input_RB1_P300b-_DNA

description: Input DNA


title: RBb-_RB1_ChIP-seq

description: Chromatin IP against RB1 in contact inhibited IMR90 24 h after infection with adeno recombinant vectors expressing e1a RB binding mutant

value: anti-RB1 (4H1) (Cell Signaling, catalog# 9309L)


title: e1a_WT_RB1_ChIP-seq

description: Chromatin IP against RB1 in contact inhibited IMR90 24 h after infection with adeno recombinant vectors expressing e1a WT


title: Input_RB1_e1a_WT_DNA

description: Input DNA


title: Prostate cancer bone metastases bone_marrow_nugen1

description: 300 bp average insert size


title: RB-_RNA-seq_rep2

description: mRNA sequencing


title: Input_RB1_mock_DNA

description: Input DNA


title: dl312_RB1_ChIP-seq

description: Chromatin IP against RB1 in contact inhibited IMR90 24 h after dl312 infection


title: dl1500_RB1_ChIP-seq

description: Chromatin IP against RB1 in contact inhibited IMR90 24 h after dl1500 infection


title: Input_RB1_dl1500_DNA

description: Input DNA


title: dl1500_P300_ChIP-seq

description: Chromatin IP against P300 in contact inhibited IMR90 24 h after infection with dl1500

value: anti-p300 (N-15) (Santa Cruz, catalog# sc-584)


title: mock_Rb1_ChIP-seq

description: Chromatin IP against RB1 in contact inhibited IMR90


title: mock_P300_ChIP-seq

description: Chromatin IP against P300 in contact inhibited IMR90


title: mg012_9_hr_r3

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

data_processing:
fastq file processed using trim_galore (adapter cut and low-quality read trimming) and aligned to the humang genome (hg19) using tophat2.
Transcripts were assigned to gene and counted using htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html).
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are in tvs format (table separated format). Each file has two columns: 1) gene symbol as in annotation file genes.gtf (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz) and gene count as assessed by the program htseq-count using the same genes.gtf annotation file.

growth_protocol: MCF-7 cells were obtained from the European Collection of Animal Cell Cultures and grown in Dulbecco’s Modified Eagle Media (Sigma) supplemented with 10% fetal bovine serum (Sigma).

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Quiagen) with gDNA eliminator and quantified with Qubit 2.0
Illumina TruSeq RNA sample prep kit was used to prepare triplicate samples

treatment_protocol: Cells were plated in 6-well dishes (300K/well), cultured overnight, and treated the following day with 40µM compound for 3, 6 or 9 h.

tag: treatment

value: compound FDI-6

tag: time

value: 9 h


title: mg011_9_hr_r2


title: HCT116p53-/-_4h_rep2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 box 602

department: Department of Human Genetics

country: Belgium

institute: KU Leuven

description: HCT116p53-/-, 4h after IR, replicate 2

data_processing:
Trimming of adaptor
quality read filtering (low complexity were excluded) and size filtering (>18nt)
The remaining reads were mapped to the human genome (Hg18) using Bowtie with the default parameters (seed length of 28, maximum number of 2 mismatches, and report up to 1 alignment per read)
Reads mapping the reference genome were then aligned to known miRNAs (miRBase version 18, release 11/2011) using BLAST, where 100% identity between reads and known miRNAs sequences was required. A weight of 1 was added to miRNA when no reads was detected in a given sample
miRNAs with an aggregate count of less than 100 in all 16 samples were eliminated; then the total read count for each lane was scaled relative to the library size (total number of reads that mapped to known miRNAs).
Read counts of technical replicates were then merged, and log2 (fold change) values were calculated for each miRNA.
P-values were subsequently calculated using a binomial approximation to Fisher's exact test for each miRNA.
Genome_build: hg18
Supplementary_files_format_and_content: raw counts and normalized counts from mapping compiled in text files
Supplementary_files_format_and_content: allchr_k10m10_bwt_vs_allmappedmiRNAs_raw.countsknown and new miRNAs counts
Supplementary_files_format_and_content: allchr_k10m10_bwt_vs_allmappedmiRNAs_norm.countsmiRNAs with an aggregate count of less than 100 in all 16 samples were eliminated; then the total read count for each lane was scaled relative to the library size (total number of reads that mapped to known miRNAs).

growth_protocol: MCF10A cells were obtained from, and authenticated by, Cancer Research UK (CRUK) Cell Services. HCT116 and HCT116 TP53-/- cell lines were kindly provided by Dr. Bert Vogelstein (Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA). MCF10A cells were grown in Dulbecco’s Modified Eagle’s medium (DMEM/F-12 (1:1), Invitrogen) supplemented with 5% horse serum, 10mg/ml insulin, 20 ng/ml EGF, 100 ng/ml choleratoxin, 500 ng/ml hydrocortisone and 100U/ml penicillin and streptomycin. HCT116 and HCT116 TP53-/- cells were cultured in McCoy's 5A Medium (Invitrogen) supplemented with 10% FBS, 100U/ml penicillin and streptomycin. Cultures were maintained at 37°C and at 5% CO2.

extract_protocol:
Cells were rinsed once with 1xPBS, and lysed in 3ml of Trizol reagent (Invitrogen, Carlsbad, CA, USA). RNA extraction was carried out according to the manufacturer’s instructions. The concentration of purified total RNAs was adjusted to 1 μg/μl with RNase free water.
Ten μg of total RNA was subjected to 15% TBE-urea PAGE before small RNA species between 18-30nt in length were excised and eluted in 0.3M NaCl. The v1.5 small RNA 3’ adapter (Illumina) was ligated using T4 RNA ligase 2, truncated (NEB), and then the small RNA 5’ adapter was ligated using T4 RNA ligase. Reverse transcription was performed using the small RNA RT primer (Illumina) using the 5’ and 3’ adapter-ligated RNAs as a template. Twelve cycles of PCR amplification were carried out using GX1 and GX2 primers with Phusion DNA polymerase. The amplified cDNA preparation was subjected to 6% TBE PAGE, and species of ~100bp were excised and purified. Finally, each cDNA library was validated with an Agilent bioanalyzer using the DNA 1000 kits to confirm size, purity, and concentrations.

treatment_protocol: The day before IR treatment, 1.2x106 MCF10A cells or 1.8x106 HCT116 and HCT116 TP53-/- cells were plated in 9.2cm dishes. Five Gy of IR was administered using the 43855D Faxitron Cabinet X-Ray System, followed by incubation for 4 or 24 hour at 37°C in 5% CO2 before harvesting.

value: irradiation

value: 4 h


title: HCT116p53-/-_0h_rep2

description: HCT116p53-/- control sample (0h), replicate 2

value: control

value: 0 h


title: mg009_6_hr_r3

value: 6 h


title: dl1500_Pol2_ChIP-seq

description: Chromatin IP against PolII in contact inhibited IMR90 24 h after infection with dl1500


title: mg010_9_hr_r1


title: HCT116_24h_rep2

description: HCT116, 24h after IR, replicate 2


title: dl1500_H3K27ac_ChIP-seq

description: Chromatin IP against H3K27ac in contact inhibited IMR90 24 h after infection with dl1500

value: anti-H3K27ac (custom antibody from the laboratory of Michael Grunstein)


title: mg008_6_hr_r2


title: e1awt_RNA-seq_rep1

description: mRNA sequencing

value: contact-inhibited IMR90


title: P300b-_RB1_ChIP-seq

description: Chromatin IP against RB1 in contact inhibited IMR90 24 h after infection with adeno recombinant vectors expressing e1a p300 binding mutant

value: P300 binding mutant-infected


title: mg007_6_hr_r1


title: MCF10A_24h_rep2

description: MCF10A, 24h after IR, replicate 2


title: HCT116_0h_rep2

description: HCT116 control sample (0h), replicate 2


title: mg006_3_hr_r3

value: 3 h


title: HCT116_4h_rep2

description: HCT116, 4h after IR, replicate 2


title: MCF10A_4h_rep2

description: MCF10A, 4h after IR, replicate 2


title: MCF10A_0h_rep2

description: MCF10A control sample (0h,) replicate 2


title: mg004_3_hr_r1


title: HCT116p53-/-_24h_rep1

description: HCT116p53-/-, 24h after IR, replicate 1


title: mg003_0_hr_r3


title: mg005_3_hr_r2


title: mg001_0_hr_r1


title: mg002_0_hr_r2


title: mock_H3K27ac_ChIP-seq

description: Chromatin IP against H3K27ac in contact inhibited IMR90

value: IMR90 human primary lung embryo fibroblasts


title: HCT116p53-/-_24h_rep2

description: HCT116p53-/-, 24h after IR, replicate 2


title: HCT116p53-/-_4h_rep1

description: HCT116p53-/-, 4h after IR, replicate 1


title: MCF10A_24h_rep1

description: MCF10A, 24h after IR, replicate 1


title: HCT116_0h_rep1

description: HCT116 control sample (0h), replicate 1


title: MCF10A_0h_rep1

description: MCF10A control sample (0h,) replicate 1


title: MCF10A_4h_rep1

description: MCF10A, 4h after IR, replicate 1


title: Non-atopic healthy control airway smooth muscle H11

city: Amsterdam

first: Ching Yong

last: Yick

address: Meibergdreef 9

department: Respiratory Medicine

country: Netherlands

institute: Academic Medical Center

data_processing:
The general quality of the sequencing run was checked using the GS Run Browser version 2.6 (Roche).
Sequence reads were mapped against the human genome (hg19; UCSC) using the GS Reference Mapper version 2.6 (Roche).
Comparison of the numbers of reads per gene between asthma and healthy controls was based on the negative binomial distribution and carried out with the R package DESeq including correction for multiple testing.
With 24 subjects in total, 4 biopsy specimens per subject, and a significance level of 0.0001, we expected to find 310 true and 2 false significant genes. This resulted in a false discovery rate of approximately 1%.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated files contain mapped genes and the following information: number of unique matching reads, percent of  all unique matches, percent of all reads

source_name: airway smooth muscle

extract_protocol: 4 endobronchial biopsies per subject were collected during a bronchoscopy. Airway smooth muscle was collected from the biopsies by laser capture microdissection and total RNA isolated with TRIzol. cDNA was prepared using the Ovation RNA-Seq System (NuGEN). cDNA libraries of >350bp were constructed using SPRIworks Fragment Library System II (Beckman Coulter) with the addition of GS FLX Titanium Rapid Library multiplex identifier (MID) adaptors (Roche). Emulsion-based clonal amplification was performed using the GS FLX Titanium emPCR Kit (Lib-L; Roche). RNA-Seq was performed using the GS FLX+ instrument (454/Roche).

value: airway smooth muscle layer from airway wall

tag: health status

value: Non-atopic healthy control


title: Non-atopic healthy control airway smooth muscle H12


title: Non-atopic healthy control airway smooth muscle H7


title: Non-atopic healthy control airway smooth muscle H9


title: Non-atopic healthy control airway smooth muscle H8


title: Non-atopic healthy control airway smooth muscle H10


title: Atopic healthy control airway smooth muscle H5

value: Atopic healthy control


title: Atopic healthy control airway smooth muscle H4


title: Atopic healthy control airway smooth muscle H6


title: Atopic healthy control airway smooth muscle H3


title: Atopic healthy control airway smooth muscle H2


title: Atopic asthma airway smooth muscle A10

value: Atopic asthma


title: Atopic asthma airway smooth muscle A11


title: Atopic asthma airway smooth muscle A8


title: Atopic healthy control airway smooth muscle H1


title: Atopic asthma airway smooth muscle A6


title: HCT116p53-/-_0h_rep1

description: HCT116p53-/- control sample (0h), replicate 1


title: Atopic asthma airway smooth muscle A9


title: Atopic asthma airway smooth muscle A5


title: HCT116_24h_rep1

description: HCT116, 24h after IR, replicate 1


title: Atopic asthma airway smooth muscle A4


title: Atopic asthma airway smooth muscle A3


title: Atopic asthma airway smooth muscle A2


title: HCT116_4h_rep1

description: HCT116, 4h after IR, replicate 1


title: Atopic asthma airway smooth muscle A12


title: pUPF1_1

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

data_processing:
The 3'-adapter sequence was first removed (using fastx_clipper -a TGGAATT), and reads with a length of <15 nts were discarded.
Reads were mapped to the human genome (hg19) using Bowtie2 (local mode) with parameters "--local -5 4 -3 4". Reads with a mapping quality score (MAPQ) of ≥10 were selected for further analysis.
mRNA abundance was measured using reads per kilobase per million reads (RPKM) based on exonic regions of RefSeq sequences.
Genome_build: hg19
Supplementary_files_format_and_content: uniquely mapped reads, the 5th column in bed file represents read number

source_name: Human embryonic kidney (HEK) 293T cells

growth_protocol: HEK293T cells (24 x 107/3 x 150-mm dishes) were incubated in 200 nM okadaic acid for three hours.

extract_protocol:
Cellular RNAs bound by p-UPF1 were immunoprecipitated using anti-p-UPF1(S1116) (Millipore, anti-phospho-Upf1(Ser1127)) and Dynabeads protein A magnetic beads (Life Technologies). The RNA in bead-bound RNA p-UPF1(S1116) complexes was digested to primarily  100 nts by incubation for 30 min at 4°C with RNase I (1U/l; Life Technologies); for RNA size estimations after RNase I digestion, ~200 ng of RNA were radio-labeled using  32P-ATP (Perkin Elmer) and T4 polynucleotide kinase (New England Biolabs) and subsequently visualized using a Typhoon 9410 Variable Mode Imager (GE Healthcare) after electrophoresis in 6M urea 15% polyacrylamide. After extensive washing, bound complexes were eluted using IP elution buffer (Kurosaki and Maquat 2013), and RNA fragments were purified using TRIzol Reagent and then separated in 6M urea 15% polyacrylamide in parallel with a DynaMarker Prestain Marker for Small RNA (BioDynamics Laboratory). Small-range RNAs (~25-40 nts) were excised from 6M urea 15% polyacrylamide and agitated overnight at 25°C in RNA extraction buffer (20 mM Tris, 300mM sodium acetate, 2 mM EDTA, 0.2 % v/v SDS). RNAs were eluted from 6M urea 15% polyacrylamide gel using a Coaster Spin-X column (Corning) and further purified using TRIzol Reagent followed by ethanol precipitation. In parallel, control IPs using rabbit IgG were performed. Additional control samples were prepared without IP.
Purified 25-40-nt RNA fragments were treated with recombinant shrimp alkaline phosphatase (New England Biolabs) to remove 3'-phosphates and subsequently phosphorylated at 5'-hydroxyl groups using T4 polynucleotide kinase (New England Biolabs). Phosphorylated RNA fragments were purified with RNeasy Mini Columns (Qiagen). A 3'-adenylated adapter was ligated to the phosphorylated RNA fragments using truncated T4 RNA ligase (New England Biolabs). An RT primer was annealed to the adapted RNAs to prevent adapter self-ligation, followed by 5' RNA adapter ligation using T4 RNA ligase (New England Biolabs). After RT of adapter-ligated RNAs, cDNAs were amplified using 15 PCR cycles. Amplified cDNAs were purified in 8% polyacrylamide, and the quality and quantity of cDNAs were assessed using an Agilent Bioanalyzer and qPCR. cDNAs were then sequenced using the Illumina HiSeq 2500 platform.

value: Human embryonic kidney

tag: ip antibody


title: IgG_2

value: rabbit IgG


title: pUPF1_2


title: Ctl_1


title: Ctl_2


title: Atopic asthma airway smooth muscle A1


title: Trichy1_Control

city: Coimbatore

first: Raveendran

last: Muthurajan

state: Tamil Nadu

address: Tamil Nadu Agricultural University

department: Department of Plant Biotechnology

country: India

institute: Tamil Nadu Agricultural University

data_processing:
Basecalls performed using Torrent Suite 3.4.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequences using Torrent Suite 3.4.2
Quality reads were mapped Oryza sativa whole genome TIGR ver. 7.0 using using CLC Genomics workbench ver. 6.5.1 using maximum number of mismatches allowed 2
Genome_build: MSU Rice Genome Annotation Project Release 7
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Eleusine coracana

source_name: Leaf, Trichy 1, without salinity stress

growth_protocol: Finger millet genotypes were raised in perforated pots (having 3-4 mm holes on the side walls and bottom) filled with fine field soil mixed with required amount of fertilizer and three pots were arranged in trays. Seedlings were grown under normal conditions upto 20 days.

extract_protocol:
Total RNA was isolated using ONESTEP RNA reagent following manufacturer's protocol. Residual genomic DNA was removed with DNase I. DNase treated RNA was purified from using shrimpex Spin column Concentration module according to the protocol. The quality of the obtained total RNA before and after DNase treatment was analyzed using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Ribosomal RNA depletion was carried out using Ribominus Plant Kit for RNA-Seq.
Whole transcriptome library was prepared using Ion Total-RNA Seq kit V2 as per manufacturer's guidelines. rRNA depleted total RNA was fragmented using RNAse III enzyme. Fragmented RNA was purified using Magnetic Bead Clean up module. The fragmented RNA was hybridized and ligated with Ion adapters. Reverse transcription reaction was carried out to convert the RNA into cDNA. The cDNA was purified using Magnetic Bead concentration module. cDNA was amplified by using Barcoded 5’ PCR primer and 3’ PCR primer. Amplified cDNA was then purified using Magnetic Bead Clean up module. Concentration of the purified cDNA was measured with a NanoDrop® Spectrophotometer. Yield and Size distribution of the library was determined using Agilent Bioanalyzer 2100. Equal volume of each library was mixed to prepare a pool of library. The pooled barcoded libraries were amplified using emulsion PCR. After ePCR, the templates are denatured and bead enrichment step is performed to separate the beads with templates from non-template beads. The enriched beads are then loaded onto the Ion P1 Chip and sequenced using Ion Proton sequencer.

treatment_protocol: Control pots were maintained in well watered condition.

value: Top two fully expanded and intact young leaf near shoot apex


title: Atopic asthma airway smooth muscle A7


title: WC1

city: Dallas

first: kenian

last: chen

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Reads were mapped to reference genome (version mm9) using Tophat (version 1.3.3) which uses the Bowtie (version 0.12.7)read mapper, Tophat was fed with the option of“–no-novel-juncs”and  option "–G" which supplies Tophat with known transcript GTF file (download from cufflinks website)
Mapped reads were assembled into RNA transcripts using the Cufflinks software (version 1.3.0). Cufflinks was run using the annotation file (downloaded from Cufflinks web site) of known genes and the mapped reads produced by Tophat. FPKM values (Fragments Per Kilobase of exon model per Million mapped fragments, a normalized gene expression value that are comparable between different samples and genes) together with confidence intervals were estimated for each replicate.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample

source_name: whole cortex

extract_protocol:
Total RNA was extracted using the miRNeasy kit (Qiagen) under manufactor’s protocols. The quality was accessed by BioanalyzerTM. Samples with high RNA integrity number (RIN) (>8) were used for library construction. 100ng total RNAs were used for each sequencing library.
RNA samples were polyA selected and paired-end sequencing libraries were constructed using TruSeq RNA Sample Prep Kit as described in the TruSeq RNA Sample Preparation V2 Guide (Illumina).

value: FVN/Swiss

value: cerebral cortex


title: CO12_Control

source_name: Leaf, CO12, without salinity stress


title: WC2


title: Endothelial2

source_name: cerebral cortex

value: endothelial cells


title: CO12_Stress

source_name: Leaf, CO12, salinity stressed

treatment_protocol: Salinity stress was imposed to a set of plants by NaCl to a concentration of 300mM at 4 leaf stage (20 days after showing).


title: Trichy1_stress

source_name: Leaf, Trichy 1, salinity stressed


title: Endothelial1