title: UD input

status: Public on Aug 23 2013

city: Edinburgh

first: Gillian

last: Taylor

address: MRC HGU Crewe Road South

country: United Kingdom

institute: IGMM

data_processing:
Base called with Illumina RTA 1.8.70.0
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-0.12.7
wiggle files were generated in WCB Edinburgh Galaxy server, and normalised to total read number using custom perl scripts
Genome_build: mm9
Supplementary_files_format_and_content: wiggle files include reads per million reads per base pair for 200bp window with 200bp step

source_name: embryonic stem cells

extract_protocol:
Genomic DNA for ChIP was extracted using a Qiagen PCR purification kit.
chromatin was digested with MNase and released at 4C overnight, then histone-DNA complexes were isolated with antibody. H4K16ac antibody = Millipore, cat#07-329 , lot DAM1687546  Rabbit IgG antibody = Santa Cruz, cat#sc-2027 , lot E1512.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: derived from E14s, with the addition of hygromycin-thymidine kinase into the Oct4 locus. E14s are derived from strain 129/Ola mice.

tag: cell line

tag: differentiation

value: undifferentiated

tag: ip/input

value: MNase digested input


title: D3 input

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: differentiated ES cells

tag: strain

value: 3 days retinoic acid


title: UD46c input

data_processing:
Bases called with CASAVA-1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-0.12.7
aligned sam files were converted to bam files using Samtools (v.0.1.7) and bam files were sorted using Samtools, then converted to bed files using Bedtools (version 2.10.1)
bedGraph files were generated from bed files using intTowig tool in WCB Edinburgh Galaxy server, and normalised to RPM number using custom perl scripts
Peak files were generated using SICER (v1.1) (Zang et al, 2009), using input as control library, a window size of 200bp, gap size of 600bp and and FDR of 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: .bedGraph files include reads per million reads per base pair for 200bp window with 200bp step
Supplementary_files_format_and_content: .bed peak files were generated using SICER (v1.1) (Zang et al, 2009), using input as control library, a window size of 200bp, gap size of 600bp and and FDR of 0.01.

source_name: MNase digested input DNA_embryonic stem cells

extract_protocol:
chromatin was digested with MNase and released at 4C overnight, then histone-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols

value: 46c ESC (sox1-GFP)

tag: cell type

value: ESC

tag: chip antibody


title: NPC H4K16ac

source_name: H4K16ac ChIP_differentiated ES cells

value: 5 days to NPCs using NB27 and Neuro2 supplements (GFP facs sorted)

value: NPC

value: H4K16ac antibody (Millipore, catalog# 07-329, lot# 2073125)


title: D3 H4K16ac

value: H4K16ac ChIP


title: UD H4K16ac


title: UD46c H4K16ac

source_name: H4K16ac ChIP_embryonic stem cells


title: SE02_240h_rep2

status: Public on Aug 22 2013

city: Albuquerque

first: Anne

middle: M

last: Ruffing

state: NM

department: Bioenergy and Defense Technologies

country: USA

institute: Sandia National Laboratories

description: Anne M Ruffing and Howland DT Jones. Physiological effects of free fatty acid production in genetically engineered Synechococcus elongatus PCC 7942. Biotechnology and Bioengineering. 2012. 100(9): 2190-2199.

library_source: transcriptomic

data_processing:
Pre-processing: After sequencing, the de-multiplexed data files for each sample were analyzed using FastQC v 0.10.1. This quality check revealed several issues with the read data which were addressed by additional data processing steps. First, adapter sequences were found to be prevalent among the sample reads, despite the fact that data had been de-multiplexed using the Illumina software. Cutadapt 1.0 was used to remove these persistent adapter sequences and to remove nucleotides with low quality scores (phred < 20). FastQC also identified an abundance of polyA/T sequences within the reads. As prokaryotes, cyanobacterial transcripts are not expected to have polyA/T tails; however, previous work has identified a signaling mechanism in cyanobacteria, whereby a polyA tail is added to a transcript to mark it for degradation. Therefore, terminal polyA/T sequences were removed from the reads using Prinseq to improve read alignment. Prinseq was also used to remove any reads less than 20 nucleotides.
Alignment: Bowtie v 0.12.7 was used to align the reads to the S. elongatus PCC 7942 genome index. The genome index was constructed using 3 NCBI files: NC_007604.fna for the S. elongatus PCC 7942 chromosome, NC_007595.fna for plasmid 1, and NC_004990.fna for pUH24. The best alignment for each read was selected, and no reads were discarded due to multiple alignments to the reference genome.  The SAM files constructed by Bowtie were submitted to HTSeq v. 0.5.3p3 to obtain raw counts for each predicted gene feature in the S. elongatus PCC 7942 genome.
Differntial Gene Expression Analysis: The feature counts were then analyzed by EdgeR for differential gene expression analysis. EdgeR includes 3 normalization methods: weighted trimmed mean of M-values (TMM), relative log expression (RLE), and upperquartile normalization. All three normalization methods were applied separately, and the results for each gene feature were averaged. There was good agreement of the differentially expressed genes between the three methods of normalization. EdgeR uses Fisher’s exact test to compute p-values for the calculated fold changes. Fold changes with p-values < 0.05 were considered to be statistically significant.
Genome_build: The genome index was constructed with Bowtie using 3 NCBI files: NC_007604.fna for the S. elongatus PCC 7942 chromosome, NC_007595.fna for plasmid 1, and NC_004990.fna for pUH24.
Genome_build: ASM1252v1
Supplementary_files_format_and_content: Tab-delimited text files include total count values for each feature in the genome.

molecule: total RNA

organism: Synechococcus elongatus PCC 7942 = FACHB-805

growth_protocol: Strains were cultivated in BG-11 media at 30°C in a New Brunswick Scientific Innova 42R incubator shaker with photosynthetic light bank supplying illumination (60 μmol photons m-2 s-1) from alternating cool white and plant fluorescent lights. From solid BG-11/agar media with 1 mM sodium thiosulfate, the strains were inoculated into 4 mL of BG-11 with 40 µg/mL of spectinomycin for SE01 and SE02 and grown under conditions previously described with shaking at 150 rpm. After 5 to 7 days of cultivation, cultures were diluted 100x in 100 mL of BG-11 media (supplemented with spectinomycin for SE01 and SE02) in 500 mL baffled flasks and grown for 4 days to serve as innoculum. Innoculum cultures were added to 400 mL of BG-11 media in 1 L glass media bottles to an initial OD730 of 0.15. The media bottles were sealed with 3-port Omnifit T series caps, including: a vent port containing a Whatman PolyVENT 4 filter to prevent contamination, a sampling port, and a port for bubbling filter-sterilized air supplemented with 1% CO2. After 4 days (96h), IPTG was added to a final concentration of 1 mM.

extract_protocol:
To extract RNA, we used a modified protocol from [(Vijayan et al. 2011), personal communication]. Approximately 50 mL of culture was placed in an ice-cooled centrifuge tube and centrifuged at 3,900 x g for 4 min at 4°C. The supernatant was decanted, and the cell pellets were immediately frozen in liquid nitrogen and stored at -80°C. For extraction, the frozen pellets were thawed on ice and resuspended in 1 mL of AE buffer (50 mM sodium acetate pH 5.2, 10mM EDTA in DEPC treated water). After vortexing to resuspend the pellet, 100 µL of 25% sodium dodecyl sulfate (SDS) and 1 mL of hot acid phenol (acid phenol, pH 4.3 at 65°C) were added, and the mixture was vortexed for 10 s. The mixture was then incubated at 65°C for 10 min with repeated vortexing. After incubation, the tubes were chilled on ice for 5 min. Cellular debris was removed by centrifugation at 12,000 rpm and 4°C for 30 min. The supernatant was extracted and mixed with 1 mL of chloroform. After centrifugation at 3,000 rpm and 4°C for 10 min, the supernatant was extracted and mixed with 1 mL of absolute ethanol. The lysate/ethanol mixture was added to the RNA extraction column from an RNA Clean & Concentrator-25 Kit (Zymo Research Corporation), and the manufacturer’s instructions were followed for RNA purification. Genomic DNA contamination was removed from the RNA mixture using the TURBO DNA-free Kit from Ambion/Life Technologies. The extracted RNA was quantified using the Quant-iT RiboGreen RNA Assay Kit from Life Technologies, and fluorescence was measured with a NanoDrop 3300 Fluorospectrometer. The RNA quality was assessed using the Agilent RNA 6000 Nano Kit and Agilent Bioanalyzer 2100. The Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre) was used to reduce the amount of ribosomal RNA (rRNA) in each sample, and the rRNA-depleted samples were purified using the RNA Clean & Concentrator – 25 Kit from Zymo Research. RNA concentration and quality were assessed again after rRNA removal. Samples were stored at -80°C and sent to Los Alamos National Laboratory for library prep and sequencing.
TruSeq RNA Sample Preparation Kits (Illumina) were used for library construction.

tag: genotype

value: delta-aas, 'tesA

tag: ffa production

value: Yes


title: SE02_100h_rep1


title: SE02_240h_rep3


title: 7942_240h_rep3

description: Pasteur Culture Collection

value: wild type

value: No


title: H3K4me3_ChIPSeq_mt

status: Public on Aug 24 2013

city: Uppsala

first: Lin

last: Jiang

address: Husargatan 3, Box 582

department: Department Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

data_processing:
Alignment: ChIP-sequencing reads were aligned to the Mouse genome July 2007 (NCBI37/mm9) assembly by using Mosaik (version 1.0.1384) (http://bioinformatics.bc.edu/marthlab/Mosaik) with default parameters.
Peaks: The uniquely aligned reads were submitted for calling peaks by using Model-based analysis of ChIP-sequencing (MACS)

source_name: C2C12 myotube

growth_protocol: Near-confluent myoblasts growing with 10% serum and myotubes with~5 days post-differentiation (serum withdrawal). The myotubes were separated from unfused residual cells by light trypsination.

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

value: C2C12 myotube

tag: passages


title: SE01_100h_rep3

value: delta-aas


title: SE02_100h_rep2


title: SE01_100h_rep2


title: SE01_240h_rep2


title: 7942_240h_rep2

description: Pasteur Culture Collection


title: SE01_240h_rep3


title: 7942_240h_rep1

description: Pasteur Culture Collection


title: 7942_100h_rep3

description: Pasteur Culture Collection


title: 7942_100h_rep1

description: Pasteur Culture Collection


title: NPC input

source_name: MNase digested input DNA_differentiated ES cells


title: 7942_100h_rep2

description: Pasteur Culture Collection


title: SE02_240h_rep1


title: Chip Seq Analysis of Input in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT rep1

city: Cambridge

first: Rafik

last: Salama

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg18 genome assembly using bwa 0.6.1 with the default parameters
BAM files were filtered and all reads with quality score below 15 are skipped, then the resulting BAM is filtered using the UCSC Duke excluded regions for hg18
Rseg differential was used to identify significant domains in the data using mode 2 versus input
Genome_build: NCBI Build 36.1 (HG18)
Supplementary_files_format_and_content: UCSC bed format of significant regions

organism: Homo sapiens

source_name: IMR90 Human Diploid Fibroblasts

growth_protocol: DMEM supplemented with 10% FBS and antibiotics in 5% oxygen for IMR90 cells

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. After end-repair and addition of an ‘A’ base to the 3’ ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of fourtyfold diluted ‘Adapter oligo mix’ in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with MinElute PCR Purification Kit, and eluted with 32 µl of 10 mM tris buffer at pH8.5. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: 100 nM 4OHT for 6 days in ER:Ras-expressing IMR90 cells to induced ER:Ras

tag: gender

value: female


title: Chip Seq Analysis of Input in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT rep2


title: Chip Seq Analysis of Input in ER:Ras expressing IMR90 human diploid fibroblasts No 4OHT rep3


title: Chip Seq Analysis of Input in ER:Ras expressing IMR90 human diploid fibroblasts No 4OHT rep2


title: Chip Seq Analysis of Input in ER:Ras expressing IMR90 human diploid fibroblasts No 4OHT rep1


title: Chip Seq Analysis of IGG in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT rep3


title: Chip Seq Analysis of IGG in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT rep1


title: Chip Seq Analysis of IGG in ER:Ras expressing IMR90 human diploid fibroblasts No 4OHT rep3


title: Chip Seq Analysis of Input in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT rep3


title: Chip Seq Analysis of IGG in ER:Ras expressing IMR90 human diploid fibroblasts No 4OHT rep1


title: Chip Seq Analysis of IGG in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT rep2


title: Chip Seq Analysis of LMNB1 in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT rep2


title: Chip Seq Analysis of LMNB1 in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT rep3


title: SE01_100h_rep1


title: Chip Seq Analysis of LMNB1 in ER:Ras expressing IMR90 human diploid fibroblasts No 4OHT rep3


title: Chip Seq Analysis of LMNB1 in ER:Ras expressing IMR90 human diploid fibroblasts d6 4OHT rep1


title: SE01_240h_rep1


title: Chip Seq Analysis of LMNB1 in ER:Ras expressing IMR90 human diploid fibroblasts No 4OHT rep2


title: Chip Seq Analysis of LMNB1 in ER:Ras expressing IMR90 human diploid fibroblasts No 4OHT rep1


title: HME-CC-LacZ Untreated Replicate3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: miRNA-Seq

data_processing: Filtered out low quality scores and sequencing artifacts. Using the FastX tool kit, the adaptor sequences were clipped from the 3’ end of the sequence reads and sequences with no adaptor sequence or with less than 16 nucleotides remaining after adaptor removal were excluded from further analysis. Clipped reads were aligned using Bowtie to the hg19 human genome build. We allowed no mismatches in the 15bp seed region of the sequence reads and allowed up to 3 alignments per sequence read.  Processed data provided as miRNA TPM.

source_name: HMECC-Wild Type;log growing, 72 hours post plating

growth_protocol: Cells were grown and maintained in HuMEC Ready Media (Invitrogen) with 4 μg/mL blastocydin as described in Arlander et al, Cancer Res 2008;68(1):89–97

extract_protocol: Illumina Small RNA Sample Preparation Alternative v1.5 Protocol

value: isogenic hTERT-immortalized normal human mammary epithelial cell lines with lentiviral vector transducing the LacZ gene

value: HME-CC

tag: knockdown

value: control


title: HME-CC-ATM1 Untreated Replicate1

description: miRNA-Seq

source_name: HMECC-ATM Deficent;log growing, 72 hours post plating

value: isogenic hTERT-immortalized normal human mammary epithelial cell lines with lentiviral construct expressing an ATM shRNA

value: ATM


title: HME-CC-ATM1 Untreated Replicate2

description: miRNA-Seq


title: HME-CC-ATM1 Untreated Replicate3

description: miRNA-Seq


title: Chip Seq Analysis of IGG in ER:Ras expressing IMR90 human diploid fibroblasts No 4OHT rep2


title: HME-CC-LacZ Untreated Replicate1

description: miRNA-Seq


title: miR21 KO rep1

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

description: mRNA-seq

data_processing:
Basecalls performed using the CASAVA software
Sequenced reads were aligned to the mm9 genome assembly using the TopHat program (Trapnell et al., Bioinformatics, 2009).
Fragments Per Kilobase of transcript per million mapped reads (FPKM) were calculated using a protocol (Trapnell et al., Nat. Prot., 2012). Differentially expressed genes (DEGs) were identified by using Cuffdiff2 with an adjusted p-value cutoff (< 0.05).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file

source_name: Mammary gland

growth_protocol: Mice were handled and housed in accordance with the guidelines of the National Institutes of Diabetes and Digestive and Kidney Diseases (NIDDK, NIH) Animal Care and Use Committee. Generation of miR-21-/- mice was previously described (Hatley, et al. 2010). Mice with a deletion of the Stat5 locus in mammary epithelial cells have previously been reported by Cui et al (Yamaji et al. 2009).

extract_protocol: mRNA-seq: Poly(A) RNA was purified twice from 1 mg total RNA and cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA), and sequenced using HiSeq 2000 (Illumina).

tag: sample tag

tag: tissue

value: Mammary gland

tag: developmental stage

value: 2m old mice


title: miR21 KO rep2

description: mRNA-seq


title: miR21 WT rep2

description: mRNA-seq


title: miR21 WT rep1

description: mRNA-seq


title: 7D rep3

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

description: Sample 9

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 includes FPKM values for each Sample (two spreadsheets; UCSC Genes FPKM, isoform FPKM)

molecule: polyA RNA

source_name: spinal cord_subacute

extract_protocol:
The injured spinal cords were dissected and three 0.5 mm pieces of spinal cord were cut in the injured epicenter. All spinal cords were immediately frozen in liquid nitrogen and processed for RNA isolation. The spinal cords from three mice were combined into one biological replicate for RNA extraction using trizol. Three biological replicates were used for 2D and 7D, two biological replicates were used for sham control.
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).

tag: age

value: spinal cord

tag: sample group

value: 7 day post injury (subacute phase)


title: 7D rep1

description: Sample 7


title: 2D rep1

description: Sample 4

source_name: spinal cord_acute

value: 2 day post injury (acute phase)


title: 2D rep3

description: Sample 6


title: 2D rep2

description: Sample 5


title: 7D rep2

description: Sample 8


title: Early maturation-stage seed coat [small-RNA]

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Seed coats from seeds 6.0 - 7.0 mm in length were collected.

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file. The sequence data are in the qseq format.
Small RNA sequences were first selected for reads containing adapters. Reads were trimmed at the adapter site and reads between 18 – 24 nucleotides were kept for further analysis.
Trimmed reads were first filtered by removing reads that mapped to rRNA and tRNA sequences.  The remaining trimmed reads were aligned to the genome using Bowtie (version 0.12.7) with no mismatch allowed.
Genome_build: Glyma version 1.0
Supplementary_files_format_and_content: tab-delimited text files containing read counts for each trimmed unique sequence

organism: Glycine max

source_name: Soybean early maturation-stage seed coat

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).  Whole seeds containing early-maturation (EM) stage embryos were collected. The embryo was dissected out of the seed coat and the axis was manually separated from the cotyledons of the EM-stage embryo

extract_protocol: Total RNA was isolated from three seed parts (axis, cotyledon, and seed coat) using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions. The TruSeq Small RNA Sample Preparation kit was used to generate libraries with modifications (Illumina, San Diego, CA).  Specifically, 250 ng total RNA was used as input and 15 PCR cycles was used for the final PCR enrichment step. Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82

value: Early maturation-stage

value: seed coat


title: chipseq WT H3K27me3

status: Public on Aug 21 2013

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

data_processing:
Reads were aligned to the mouse reference sequence NCBI Build 37/mm9 with the TopHat algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq, the processed file is in bedgraph format with for both wildtype, Hotair knockout for H3K27me3 and H3K4me3.

source_name: neonatal tail tip fibroblasts, Hotair wildtype

extract_protocol:
Extracted DNA was RNase treated and purified using Qiagen column, and sequencing libraries were made following Illumina’s protocol.
For ChIP-seq libraries, chromatin was solubilized and isolated with corresponding antibodies, and the libraries were made following Illumina protocols.

value: backcross to C57BL6 with over 97% similarity

value: neonatal tail tip fibroblasts

tag: genotype/variation

value: Hotair wildtype


title: chipseq KO H3K27me3

source_name: neonatal tail tip fibroblasts, Hotair knockout

value: Hotair knockout


title: NKX3.1_ChIPSeq

city: Nashville

first: Philip

middle: D

last: Anderson

state: TN

department: Pathology

institute: Vanderbilt University

data_processing:
ChIP-seq reads were aligned to the human genome assembly using Bowtie version 0.12.7 with the following flags: --phred64-quals -S -k1 --best -p6
Read pileup was verified in Integrative Genomics Viewer.
Unmapped reads were discarded.
Equal numbers of mapped Nkx3.1 and control reads were inputted to MACS [version 1.4.1] for peak calling.
IgG reads were used to control for nonspecific Nkx3.1 antibody binding. A shiftsize of 50 nucleotides was specified. Peaks with P values < 1−08 were considered statistically significant. For the processed files, the peaks file contains all the NKX3.1 peaks. The summits file contains the summits of the NKX3.1 peaks, at single nucleotide resolution.
Genome_build: Human genome (Ensembl 37-61)
Supplementary_files_format_and_content: BED files generated with MACS

source_name: LNCaP

growth_protocol: Cells were grown in RPMI supplemented with 10% FBS and 100U/ml Pen-Strep.

extract_protocol:
ChIP was performed for LNCaP cells as described in the protocol supplied in the Chromatin Immunoprecipitation Assay Kit (Millipore).
ChIP-ed DNA was prepared for sequencing on the Illumina Genome Analyzer 2 using the ChIP-Seq DNA Sample Prep Kit (Illumina).

value: Human prostate cancer cells

value: NKX3.1 Santa Cruz (sc-15022)


title: PaP1

city: Chongqing

first: Shuguang

last: Lu

address: 30# Gaotanyan St., Shapingba District,

department: Department of Microbiology

country: China

institute: Third Military Medical University

description: purified genomic DNA of Pseudomonas aeruginosa phage PaP1

data_processing:
Sequencing reads were processed and mapped to the respective reference sequences using the BLASR mapper (http://www.pacbiodevnet.com/SMRT-Analysis/Algorithms/BLASR) and the Pacific Biosciences' SMRT Analysis pipeline (http://www.pacbiodevnet.com/SMRT-Analysis/Software/SMRT-Pipe) using the standard mapping protocol.
To identify modified positions, we used Pacific Biosciences' SMRTPortal analysis platform, v. 1.3.1, which uses an in silico kinetic reference, and a t-test based kinetic score detection of modified base positions (details are available at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf)
Genome_build: NCBI GenBank accession No. NC_019913
Supplementary_files_format_and_content: PaP1_data_modifications.csv files are comma separated text files that contain data for all positions (both strands) in the reference sequence; data includes Qmod score, IPD ratio, and coverage.
Supplementary_files_format_and_content: PaP1_data_modifications.gff files are comma separated text files that contain data for genome positions with Qmod scores greater than 20; Data includes Qmod scores, IPD ratios, coverage, and sequence contexts for a +/- 20 nt window surrounding the modified position

organism: Pseudomonas phage PaP1

source_name: phage PaP1

growth_protocol: Briefly, a liquid culture of the host bacteria during the log phase growth was inoculated with phages (multiplicity of infection of 1/100) and incubated at 37 °C with 200 rpm shaking.

extract_protocol:
EDTA (20 mM), proteinase K (50 μg mL-1), and sodium dodecyl sulfate (0.5%, w/v) were added to the purified phage stock solution (PaP1 or PaP3). The mixture was incubated at 56 °C for 1 h, then an equal volume of phenol–chloroform–isoamyl alcohol solution (25:24:1) was added, followed by centrifugation at 5,000 g for 10 min. The aqueous layer was collected and extracted with chloroform at 5,000 g for 10 min. Finally, the collected aqueous layer was mixed with 0.6 volumes of isopropanol, and stored overnight at –20 °C. The next day, the mixture was centrifuged for 10 min at 12,000 g and 4 °C, and the precipitated DNA was collected and washed with 70% and 100% ethanol, respectively. The PaP1 DNA was suspended in TE buffer (pH 8.0) and stored at –20 °C for subsequent use.
Genomic DNA was randomly sheared to an avearge size of approximately 2,000 bp, end repaired, and ligated to blunt end hairpin adapters for form standard SMRTbell templates

treatment_protocol: The culture showed signs of lysis after ~5 h, and a few drops of chloroform were added. The culture was then centrifuged at 10,000 g for 5 min, and the supernatant (crude PaP1 suspensions) was concentrated and purified via PEG8000 (Sigma-Aldrich, St. Louis, MO) precipitation as described previously . The PaP1 particles were purified using PEG8000 and further purified using CsCl gradient ultracentrifugation.

tag: dna type

value: dsDNA

tag: genus

value: PaP1-like phages

tag: family

value: myovirus


title: HME-CC-LacZ Untreated Replicate2

description: miRNA-Seq

tag: cell type

value: isogenic hTERT-immortalized normal human mammary epithelial cell lines with lentiviral vector transducing the LacZ gene

tag: cell line

value: HME-CC

value: control


title: chipseq WT H3K4me3

tag: strain


title: rnaseq ko1

data_processing:
Reads were aligned to the mouse reference sequence NCBI Build 37/mm9 with the TopHat algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-seq, per-gene RPKM was calculated for all RefSeq annotated genes submitted in the txt file.

extract_protocol:
Total RNA from cells was extracted with the TRIzol reagent (Invitrogen) and the RNeasy mini kit (Qiagen). Poly-A selected RNA was isolated from total RNA with MicroPoly(A)Purist Kit (Ambion) according to the manufacturer’s instruction.
RNA-seq libraries were prepared following the dUTP protocol.


title: rnaseq ko2


title: Early maturation-stage embryonic axis  [small-RNA]

description: Whole embryonic axis devoid of the plumule from seeds 6.0 - 7.0 mm in length was collected.

source_name: Soybean early maturation-stage embryonic axis part

value: embryonic axis part


title: rnaseq het2

source_name: neonatal tail tip fibroblasts, Hotair heterozygous

value: Hotair heterozygous


title: rnaseq het1


title: Early maturation-stage embryonic cotyledons  [small-RNA]

description: Embryonic cotyledons from seeds 6.0 - 7.0 mm in length were collected.

source_name: Soybean early maturation-stage embryonic cotyledons

value: Williams 82

value: embryonic cotyledons


title: rnaseq wt2


title: Early maturation-stage embryonic axis [RNA-seq]

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file. The sequence data are in the qseq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Glycine max genome (v1.0) using bowtie v0.12.7 with parameters -v 2 -5 6 -3 0 -m 3 --best --strata.
Read counts to Glycine max gene models (v1.1) models were computed using BedTools.
Reads per kilobase per million (RPKM) value was calculated according to Mortazavi et al. (Mortazavi et al., 2008).
Genome_build: Glyma version 1.0
Supplementary_files_format_and_content: tab-delimited text file including gene model and normalized RPKM value.

extract_protocol: Total RNA was isolated from three seed parts (axis, cotyledon, and seed coat) using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions.  Total RNA was treated with RNase-free DNaseI (Ambion, Austin, TX) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300. Approximately 20 nanogram of total RNA was amplified with Nugen Ovation Pico WTA system v.1 (Nugen, San Carlos, CA).  Double-stranded cDNA was generated using WT-Ovation Exon Module (Nugen, San Carlos, CA) and quantified with Picogreen on the Nanodrop ND-3300 (Nanodrop Technologies).  One microgram of double-stranded cDNA was fragmented using NEB Fragmentase for 15 minutes at 37oC for the standard protocol (NEB, Ipswich, MA).  The Illumina TruSeq DNA Sample prep kit was used to prepare the Illumina library with modifications (Illumina, San Diego, CA).  Specifically, the Covaris shearing step was omitted, the final PCR enrichment step was performed using Agilent Pfu Turbo Cx DNA polymerase (Agilent, Santa Clara, CA) instead of the TruSeq PCR mix, and 12 cycles of PCR were performed. Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument. Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing

value: Early maturation-stage


title: CTR rep2

description: Sample 2

source_name: spinal cord_normal

value: female

value: spinal cord

value: sham control (normal)


title: CTR rep1

description: Sample 1


title: E2-03-25

status: Public on Aug 20 2013

city: Saint Louis

first: Nathan

middle: P

last: McNulty

state: MO

address: 4444 Forest Park Ave. (5th Floor)

department: Center for Genome Sciences and Systems Biology

institute: Washington University School of Medicine

description:
Sample was collected from a gnotobiotic mouse colonized at day 0 with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The  'diet group' field indicates the order in which the LF/HPP and HF/HS diets were administered.
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174

data_processing:
Library strategy: COPRO-Seq
Demultiplexing: sequences were demultiplexed by 4 nt barcode, requiring an exact match (sequences without a barcode match were excluded from the analysis)
Trimming: after demultiplexing, all sequences were trimmed to 25 bases to eliminate low-quality bases at the ends of each read
Mapping: sequences were aligned to the reference genomes of the 12 bacteria included in the study using Illumina's ELAND aligner (as provided in GAPipeline-1.4.0). Only perfect, non-redundant matches were carried forward in the analysis.
Normalization: raw counts were normalized based on the informative genome size (IGS) of each organism included in the analysis, as described by McNulty et al. in a previous publication (PMID: 22030749).
Summarization: the proportional representation of each organism in the analysis was determined by dividing its normalized counts within a sample by the total normalized counts for all organisms within that sample.
Genome_build: AAVM00000000.2, AAXF00000000.2, AE015928.1, AAYH00000000.2, CP000139.1, ABFY00000000.2, ABIK00000000.2, AAVN00000000.2, AAXB00000000.2, CP000140.1, AAVO00000000.2; note that one additional genome included in the analysis (that of B. cellulosilyticus WH2) was sequenced as part of this study and has not yet been assigned an NCBI accession number.
Supplementary_files_format_and_content: Tab-delimited text file. The file header (in angle brackets, <>) specifies the sample from which data were derived. Subsequent rows specify the organism/reference genome, raw counts, normalized counts, and normalized relative proportion for each taxon included in the alignment. Additional details are available in the accompanying 'README.txt' file.

organism: Bacteria

source_name: Defined bacterial assemblage from a gnotobiotic mouse

growth_protocol: Bacteria from frozen culture stocks were introduced as an artificial community (AC) into 10-12 week-old male gnotobiotic C57BL/6J mice.  Cells were therefore maintained over the course of the experiment within mice until sampling occurred.

extract_protocol:
DNA was extracted from fecal and cecal samples using mechanical disruption (bead-beating with 0.1 mm zirconium beads) in phenol:chloroform:IAA in the same manner as described by McNulty et al. in a previous publication (PMID: 22030749).
Libraries were prepared according to a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, total bacterial gDNA was sonicated in a BioRuptor XL water bath sonicator, cleaned up and concentrated using a Qiagen PCR Purification column, and end-repaired using Klenow DNA polymerase. The blunt DNA was treated with Klenow fragment (exo minus) to add an adenine overhang, and the A-tailed molecules were ligated to the relevant barcoded Illumina adapter sequence.  Adaptered-DNA was then size-selected by agarose gel electrophoresis.  Fragments of the appropriate size were PCR amplified and purified, after which the purified PCR products were loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer I, II or IIx following the manufacturer's protocols.

treatment_protocol: Immediately after collection, samples were subjected to flash-freezing in liquid nitrogen and storage at -80 C until total community DNA extractions could be performed.

tag: experiment

tag: mouse

tag: days post-colonization

tag: collection site

value: feces

tag: diet group

value: LF/HPP=>HF/HS=>LF/HPP


title: E2-03-19


title: E2-03-29


title: E2-03-21


title: E2-03-27


title: chipseq KO H3K4me3

value: backcross to C57BL6 with over 97% similarity

value: neonatal tail tip fibroblasts

value: Hotair knockout


title: chipseq KO input


title: E2-03-17


title: E2-03-16


title: E2-03-15


title: E2-03-26


title: chipseq WT input

value: Hotair wildtype


title: E2-03-12


title: E2-03-10


title: E2-03-13


title: E2-03-05


title: E2-03-07


title: IgG_ChIPSeq

value: Human prostate cancer cells

tag: chip antibody

value: IgG Santa Cruz (sc-2028)


title: E2-03-03


title: E2-03-02


title: rnaseq wt1


title: E2-03-01-r1


title: E2-02-CEC

value: cecum


title: E2-02-41


title: E2-02-40


title: E2-02-42


title: E2-02-38


title: E2-02-35


title: E2-02-33


title: E2-02-21


title: E2-02-25


title: E2-02-19


title: E2-02-30


title: E2-02-27-r1


title: E2-02-29


title: E2-02-26


title: E2-02-13


title: E2-02-15


title: E2-02-31


title: WildtypeMouseRARαChIPSeq

city: Sacramento

first: Yuqi

last: He

state: California

address: Rm3400, Research III, UC Davis Medical Center, 4645 2nd Ave

institute: UC Davis Medical Center

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie
Peaks were called by using MACS
Genome_build: mm9
Supplementary_files_format_and_content: MACS peaks txt file. Bar file was generated from the bed file outputted from MACS

source_name: Liver

extract_protocol:
Grand in liquid nitrogen, then fixed, sonication, pull down by RARα antibody from Santa Cruz (sc-551x).
Illumina True-Seq Kit

tag: tissue

value: liver

tag: gender

value: Male

value: 3 Month

tag: antibody

value: RARα antibody


title: E2-02-16


title: E2-02-12


title: E2-02-10


title: E2-02-07


title: E2-02-17


title: ZR7530 Exome-Seq

city: Portland

first: Laura

middle: M.

last: Heiser

state: OR

address: 3181 SW Sam Jackson Park Rd.

institute: OHSU

data_processing:
Library strategy: Exome-Seq
Fastq files aligned using bwa aln and bwa sampe (default parameters) to the hg19 (GRCh37) reference to create a BAM file
Individual BAM files are merged and sorted by chromosomal position
Merged BAM file is scanned for duplicate reads using superDeDuper
Genome_build: hg19
Supplementary_files_format_and_content: Only BAM files were uploaded (see SRA records)

source_name: breast cancer cell line

extract_protocol:
Qiagen Gentra Puregene Cell Kit
Exome libraries of matched pairs of tumour / normal genomic DNAs were generated using the Agilent SureSelect XT kit and Agilent Automation Systems NGS system per manufacturer’s instructions. 1 ug of each genomic DNA was sheared using a Covaris E220 to a peak target size of 150 bp. Fragmented DNA was concentrated using AMPureXP beads (Beckman Coulter), and DNA ends were repaired using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. 3’ A-tailing with exo-minus Klenow polymerase was followed by ligation of Agilent paired-end oligo adapters to the genomic DNA fragment.  Ligated DNA was PCR amplified for 8 cycles and purified using AMPure XP beads and quantitated using the Quant-It BR kit (Invitrogen).  500 ng of sample libraries were hybridized to the Agilent biotinylated SureSelect 37Mb Capture Library at 65°C for 72 hr following the manuufacturer’s protocol. The targeted exon fragments were captured on Dynabeads MyOne Strepavidin T1 (Invitrogen), washed, eluted, and enriched by amplification with Agilent post-capture primer and an indexed reverse primer for multiplexing12 additional cycles. After purification of the PCR products with AMPure XP beads, the quality and quantity of the resulting exome libraries were analyzed using an Agilent Bioanalyzer High Sensitivity chip.

treatment_protocol: Cells in exponential growth phase

value: breast cancer

tag: subtype

value: Luminal


title: ZR75B Exome-Seq


title: E2-02-05


title: E2-02-03


title: E2-02-02


title: E2-02-01-r1


title: ZR751 Exome-Seq


title: UACC812 Exome-Seq


title: E2-01-42


title: E2-01-CEC


title: UACC893 Exome-Seq


title: T47D_KBluc Exome-Seq

value: unknown


title: E2-01-41


title: T47D Exome-Seq


title: E2-01-40


title: SUM44PE Exome-Seq


title: E2-01-38


title: T4 Exome-Seq


title: SUM229PE Exome-Seq


title: E2-01-33


title: SUM1315MO2 Exome-Seq

value: Claudin-low


title: SUM159PT Exome-Seq


title: E2-01-29

value: feces


title: SUM149PT Exome-Seq

value: Basal


title: SUM185PE Exome-Seq


title: E2-01-30

value: LF/HPP=>HF/HS=>LF/HPP


title: E2-01-26


title: E2-01-27


title: SUM225CWN Exome-Seq


title: SUM102PT Exome-Seq


title: E2-01-21


title: E2-01-31


title: SKBR3 Exome-Seq


title: E2-01-25


title: E2-01-19


title: PMC42 Exome-Seq


title: E2-01-17


title: E2-01-16


title: MX1 Exome-Seq


title: MT3 Exome-Seq


title: E2-01-15


title: MFM223 Exome-Seq


title: SUM52PE Exome-Seq


title: E2-01-35


title: E2-01-10


title: E2-01-12


title: E2-01-13


title: MDAMB415 Exome-Seq


title: MDAMB436 Exome-Seq


title: E2-01-07


title: E2-01-03


title: E2-01-01-r1


title: MDAMB157 Exome-Seq


title: E2-01-05


title: MDAMB175VII Exome-Seq


title: MDAMB361 Exome-Seq


title: MDAMB134VI Exome-Seq


title: MCF12A Exome-Seq

value: Non-malignant


title: LY2 Exome-Seq


title: MCF10F Exome-Seq


title: JIMT1 Exome-Seq


title: E1-04-15


title: E1-04-02


title: E1-04-12


title: E1-04-16


title: E1-04-05


title: E1-04-13


title: E1-04-19


title: MDAMB468 Exome-Seq


title: MDAMB231 Exome-Seq


title: MCF10A Exome-Seq


title: E1-03-CEC


title: HCC70 Exome-Seq


title: HCC38 Exome-Seq


title: E1-03-42


title: E2-01-02


title: E1-04-01


title: HCC2218 Exome-Seq


title: E1-03-41


title: E1-03-33


title: HDQP1 Exome-Seq


title: E1-03-30


title: HCC2185 Exome-Seq


title: HCC202 Exome-Seq


title: HCC3153 Exome-Seq


title: E1-03-27


title: HCC1954 Exome-Seq


title: E1-03-26


title: MDAMB453 Exome-Seq


title: HCC1806 Exome-Seq


title: E1-03-19


title: E1-03-15


title: E1-03-13


title: HCC1937 Exome-Seq


title: HCC1428 Exome-Seq


title: HCC1569 Exome-Seq


title: HCC1395 Exome-Seq


title: E1-03-16


title: HCC38BL Exome-Seq


title: E1-03-12


title: HCC1143BL Exome-Seq


title: E1-03-02


title: HCC1143 Exome-Seq


title: E1-03-29


title: HCC1187 Exome-Seq


title: E1-03-05


title: EVSAT Exome-Seq

value: EVSAT


title: E1-03-01


title: E1-01-42


title: E1-01-CEC


title: E1-01-41


title: EFM192A Exome-Seq


title: EFM192C Exome-Seq


title: EFM19 Exome-Seq


title: E1-01-30


title: E1-01-33


title: CAMA1 Exome-Seq


title: E1-01-29


title: CAL51 Exome-Seq


title: E1-01-27


title: CAL851 Exome-Seq


title: CAL148 Exome-Seq


title: BT549 Exome-Seq


title: E1-01-26


title: E1-01-16


title: E1-01-19


title: BT483 Exome-Seq


title: E1-01-15


title: BT20 Exome-Seq


title: E1-01-13


title: E1-01-12


title: BT474 Exome-Seq


title: AU565 Exome-Seq


title: E1-01-02


title: E1-01-05


title: 600MPE Exome-Seq


title: CAL120 Exome-Seq


title: 21PT Exome-Seq


title: 21MT2 Exome-Seq


title: 21NT Exome-Seq


title: E1-01-01


title: mouse_4_day_27

description:
NM601_4.27
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174

data_processing:
Basecalls performed using RTA (experiment NM601, v1.5.35-1.6.47; experiment NM602 v1.13.48).
PhiX reads from spike-in controls were filtered out by aligning all reads to a PhiX reference using Bowtie with default settings.
For experiment NM602, multiplexed sequences were demultiplexed based on a perfect match to each 8 bp barcode used, and barcodes were trimmed.
Reads were aligned to one (experiment NM602) or multiple (experiment NM601) reference genomes using the SSAHA2 aligner.
In some cases, reads mapped non-uniquely (i.e., to multiple locations within or across reference genomes). To account for this, we first tallied read counts by gene for all uniquely mapping sequences. Subsequently, reads that mapped non-uniquely were added to each gene's read count in proportion to each gene's fracton of unique match counts. We also added a pseudocount (i.e., a value of 1) to each gene count prior to normalization to account for differences in sampling depth. Read counts were then subsequently normalized at either a species level (i.e., taking into account all genes for a single species) or at a community level (i.e., taking into account all genes for all species) using DESeq.
Genome_build: AAVM00000000.2, AAXF00000000.2, AE015928.1, AAYH00000000.2, CP000139.1, ABFY00000000.2, ABIK00000000.2, AAVN00000000.2, AAXB00000000.2, CP000140.1, AAVO00000000.2; note that one additional genome included in the analysis (that of B. cellulosilyticus WH2) was sequenced as part of this study and has not yet been assigned an NCBI accession number.
Supplementary_files_format_and_content: Tab-delimited text file. Each file contains four columns of information. Column 1 (feature_name): gene. Column 2 (hits): raw counts attributed to gene. Column 3 (fraction_of_reads): proportion of all reads mapped assigned to gene. Column 4 (average_match_score): average match score reported by the SSAHA2 aligner for all reads assigned to gene.

source_name: Defined (fecal) bacterial assemblage from a gnotobiotic mouse, day 27

extract_protocol:
RNAprotect Bacteria Reagent (Qiagen) was used to stabilize both frozen fecal pellets (experiment NM601) and in vitro cultures (experiment NM602; added prior to pelleting cells) per the manufacturer's instructions. Samples were then mechanically disrupted using acid-washed glass beads in a Mini-BeadBeater-8 in the presence of acid phenol:chloroform:IAA (125:24:1), after which ethanol precipitation was performed. RNA was then further purified using a MEGAclear kit, tested for integrity by gel electrophoresis, and shown to be lacking any contaminating genomic DNA by PCR. rRNA depletion was subsequently performed via two rounds of processing with the MICROBExpress kit and two rounds of rRNA capture using custom oligos attached to magnetic beads (Dynabeads). First-strand cDNA synthesis was then performed using random hexamer priming with SuperScript II, after which second-strand synthesis was achieved using E. coli DNA polymerase in the presence of RNase H.
Libraries were prepared according to a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, cDNA was sonicated in a BioRuptor XL water bath sonicator, cleaned up and concentrated using a Qiagen PCR Purification column, and end-repaired using Klenow DNA polymerase. The blunt DNA was treated with Klenow fragment (exo minus) to add an adenine overhang, and the A-tailed molecules were ligated to the relevant Illumina adapter sequence. Non-barcoded adapters were used to construct libraries from experiment NM601 samples. Adapters incorporating an 8 bp barcode were used to construct libraries from experiment NM602 samples. Adaptered-DNA was then size-selected by agarose gel electrophoresis. Fragments of the appropriate size were PCR amplified and purified, after which the purified PCR products were loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on either the Illumina Genome Analyzer IIx (experiment NM601) or the Illumina HiSeq 2000 (experiment NM602) using the manufacturer's protocols.

treatment_protocol: Sample was collected from a gnotobiotic mouse colonized at day 0 with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at days 14 and 28. This animal was fed a low-fat high-plant polysaccharide (LF/HPP) diet in phase 1 (days 1-14), a high-fat high-sugar (HF/HS) diet in phase 2 (days 15-28) and a low-fat high-plant polysaccharide (LF/HPP) diet in phase 3 (days 29-42).


title: mouse_4_day_26

description:
NM601_4.26
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174

source_name: Defined (fecal) bacterial assemblage from a gnotobiotic mouse, day 26


title: mouse_4_day_29

description:
NM601_4.29
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174

source_name: Defined (fecal) bacterial assemblage from a gnotobiotic mouse, day 29


title: 21MT1 Exome-Seq


title: 184A1 Exome-Seq


title: 184B5 Exome-Seq


title: mouse_4_day_15

description:
NM601_4.15
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174

source_name: Defined (fecal) bacterial assemblage from a gnotobiotic mouse, day 15


title: ZR75B, RNA-Seq

data_processing:
Process with Alexa-seq software pipeline [PMID: 20835245]
Genome_build: hg18
Supplementary_files_format_and_content: Text file with fpkm-like measurement (see PMID:20835245) for each Ensembl (v53) gene

growth_protocol: Cells in exponential growth phase

extract_protocol:
Qiagen RNAeasy
RNAseq libraries for transcriptome analysis were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) and Agilent Automation NGS system per manufacturers' instructions. Sample prep began with 1 _g of total RNA from each sample. Poly-A RNA was purified from the sample with oligo dT magnetic beads, and the poly(A) RNA was fragmented with divalent cations. Fragmented poly-A RNA was converted into cDNA through reverse transcription and were repaired using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. 3' A-tailing with exo-minus Klenow polymerase was followed by ligation of Illumina paired-end oligo adapters to the cDNA fragment.  Ligated DNA was PCR amplified for 15 cycles and purified using AMPure XP beads. After purification of the PCR products with AMPure XP beads, the quality and quantity of the resulting libraries were analyzed using an Agilent Bioanalyzer High Sensitivity chip.


title: mouse_4_day_13

description:
NM601_4.13
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174

source_name: Defined (fecal) bacterial assemblage from a gnotobiotic mouse, day 13


title: mouse_3_day_29

description:
NM601_3.29
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: ZR751, RNA-Seq


title: mouse_3_day_30

description:
NM601_3.30
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174

source_name: Defined (fecal) bacterial assemblage from a gnotobiotic mouse, day 30


title: ZR7530, RNA-Seq


title: mouse_4_day_30

description:
NM601_4.30
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: UACC893, RNA-Seq


title: mouse_3_day_27

description:
NM601_3.27
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: T47D Kbluc, RNA-Seq

value: T47D Kbluc


title: mouse_3_day_15

description:
NM601_3.15
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: SUM52PE, RNA-Seq


title: UACC812, RNA-Seq


title: mouse_3_day_13

description:
NM601_3.13
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: mouse_3_day_16

description:
NM601_3.16
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174

source_name: Defined (fecal) bacterial assemblage from a gnotobiotic mouse, day 16


title: SUM229PE, RNA-Seq


title: mouse_2_day_29

description:
NM601_2.29
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: mouse_2_day_27

description:
NM601_2.27
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: mouse_2_day_30

description:
NM601_2.30
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: mouse_3_day_26

description:
NM601_3.26
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: SUM1315, RNA-Seq


title: mouse_4_day_16

description:
NM601_4.16
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: SUM149PT, RNA-Seq


title: MX1, RNA-Seq


title: mouse_2_day_15

description:
NM601_2.15
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: SKBR3, RNA-Seq


title: T47D, RNA-Seq


title: mouse_2_day_13

description:
NM601_2.13
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: MDAMB361, RNA-Seq


title: mouse_1_day_30

description:
NM601_1.30
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: mouse_1_day_29

description:
NM601_1.29
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: mouse_1_day_27

description:
NM601_1.27
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: MDAMB175, RNA-Seq


title: SUM225CWN, RNA-Seq


title: mouse_1_day_16

description:
NM601_1.16
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: MCF12A, RNA-Seq


title: EFM192B Exome-Seq


title: MDAMB134VI, RNA-Seq


title: MCF10F, RNA-Seq


title: mouse_2_day_16

description:
NM601_2.16
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: MCF10A, RNA-Seq


title: mouse_1_day_15

description:
NM601_1.15
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: mouse_1_day_13

description:
NM601_1.13
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174


title: E2-15-42

description:
Sample was collected from a gnotobiotic mouse colonized at day 0 with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The  'diet group' field indicates the order in which the LF/HPP and HF/HS diets were administered.
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174

value: HF/HS=>LF/HPP=>HF/HS


title: E2-15-41


title: LY2, RNA-Seq


title: E2-15-40


title: JIMT1, RNA-Seq


title: MB157, RNA-Seq


title: HS578T, RNA-Seq


title: HCC38, RNA-Seq


title: E2-15-35


title: MDAMB231, RNA-Seq


title: HCC70, RNA-Seq


title: E2-15-31


title: MCF7, RNA-Seq


title: HCC3153, RNA-Seq


title: HCC2218, RNA-Seq


title: E2-15-29


title: HCC202, RNA-Seq


title: E2-15-CEC


title: E2-15-27


title: HCC1954, RNA-Seq


title: HCC1937, RNA-Seq


title: E2-15-26


title: E2-15-19


title: E2-15-25


title: HCC1599, RNA-Seq


title: HCC1569, RNA-Seq


title: E2-15-38


title: HCC1428, RNA-Seq


title: E2-15-17


title: HCC1806, RNA-Seq


title: HCC1419, RNA-Seq


title: E2-15-15


title: HCC1395, RNA-Seq


title: E2-15-16


title: E2-15-33


title: HCC1143, RNA-Seq


title: E2-15-13


title: EFM192C, RNA-Seq


title: E2-15-30


title: EFM192B, RNA-Seq


title: E2-15-10


title: E2-15-12


title: EFM192A, RNA-Seq


title: CAMA1, RNA-Seq


title: E2-15-05


title: E2-15-03


title: E2-15-21


title: BT549, RNA-Seq


title: E2-15-01


title: E2-15-02


title: BT483, RNA-Seq


title: 600MPE, RNA-Seq


title: E2-14-CEC


title: E2-14-42


title: E2-14-40


title: E2-14-41


title: 21MT1, RNA-Seq


title: 21NT, RNA-Seq


title: AU565, RNA-Seq


title: E2-14-33


title: E2-14-31


title: 184B5, RNA-Seq


title: E2-15-07


title: E2-14-30


title: 184A1, RNA-Seq


title: E1-14-42


title: E2-14-29


title: E1-14-41


title: E2-14-26


title: E1-14-33


title: E2-14-25


title: E2-14-27


title: BT474, RNA-Seq


title: E1-14-30


title: E1-14-29


title: E2-14-38


title: 21MT2, RNA-Seq


title: E2-14-19


title: 21PT, RNA-Seq


title: E2-14-17-r1


title: E2-14-35


title: E1-14-26


title: E2-14-16


title: E2-14-15


title: E1-14-15


title: E2-14-13


title: E1-14-19


title: E1-14-CEC


title: E2-14-10


title: E1-14-13


title: E1-14-12


title: E1-14-05


title: E2-14-07


title: E2-14-21


title: E2-14-05-r1


title: E1-14-02


title: E2-14-03


title: E1-14-01


title: E2-14-02


title: E1-13-CEC


title: E1-14-27


title: E2-14-01


title: E2-13-CEC


title: E1-13-41


title: E2-13-42


title: E2-13-41


title: E1-13-30


title: E1-13-42


title: E1-14-16


title: E2-14-12


title: E2-13-40


title: E1-13-33


title: E1-13-29


title: E2-13-38


title: E1-13-27


title: E2-13-31-r1


title: E1-13-26


title: E2-13-30


title: E1-13-19


title: E1-13-16


title: E1-13-15


title: E1-13-13


title: E2-13-29


title: E2-13-33


title: E2-13-27


title: E1-13-12


title: E2-13-26


title: E1-13-05


title: E1-13-02


title: E2-13-25


title: E2-13-19


title: E1-12-CEC


title: E2-13-21


title: E1-13-01


title: E2-13-17


title: E2-13-16


title: E1-12-41


title: E1-12-42


title: E2-13-15-r1


title: E1-12-33


title: E1-12-30


title: E2-13-12


title: E2-13-35


title: E2-13-13


title: E2-13-10


title: E1-12-27


title: E1-12-26


title: E2-13-05


title: E1-12-19


title: E2-13-07


title: E2-13-03


title: E2-13-02


title: E1-12-16


title: E2-13-01


title: E1-12-15


title: E1-12-12


title: E1-12-13


title: E1-12-05


title: E1-12-02


title: E2-12-40


title: E2-12-CEC


title: E2-12-38


title: E2-12-42


title: E2-12-41


title: E1-11-CEC


title: E1-12-29


title: E2-12-35


title: E2-12-31


title: E1-11-41


title: E1-11-42


title: E1-11-33


title: E2-12-33


title: E1-11-30


title: E2-12-30


title: E2-12-27


title: E1-11-26


title: E2-12-29


title: E2-12-26


title: E1-11-27


title: E1-11-15


title: E1-12-01


title: E2-12-25


title: E1-11-12


title: E2-12-12


title: E1-11-01


title: E2-12-21


title: E1-11-16


title: E1-11-13


title: E2-12-19


title: E2-12-07


title: E2-12-16


title: E1-10-CEC


title: E2-12-17


title: E1-11-02


title: E1-11-05


title: E2-12-13


title: E2-12-05-r1


title: E1-10-29


title: E2-12-15


title: E1-10-30


title: E2-12-03


title: E1-11-19


title: E2-12-02


title: E2-12-10


title: E1-10-26


title: E1-10-27


title: E2-12-01-r1


title: E2-11-CEC


title: E1-10-33


title: E2-11-42


title: E1-10-19


title: E1-10-16


title: E1-10-42


title: E2-11-41


title: E2-11-40


title: E1-10-15


title: E1-10-13


title: E1-10-02


title: E2-11-35


title: E1-10-01


title: E2-11-33


title: E2-11-31


title: E1-10-12


title: E2-11-30


title: E1-09-CEC


title: E1-09-42


title: E2-11-27


title: E2-11-26


title: E1-09-33


title: E2-11-29


title: E1-09-29


title: E2-11-21


title: E2-11-25


title: E1-09-30


title: E2-11-19


title: E1-09-27


title: E1-09-26


title: E2-11-17


title: E1-09-19


title: E2-11-16


title: E1-09-16


title: E1-09-15


title: E2-11-13


title: E2-11-38


title: E2-11-15


title: E1-09-12


title: E2-11-12


title: E2-11-07


title: E1-09-41


title: E1-09-13


title: E1-09-05


title: E2-11-10


title: E2-11-05


title: E2-11-02


title: E2-11-01-r1


title: E1-09-02


title: E1-08-CEC


title: E2-10-CEC


title: E2-11-03


title: E1-08-42


title: E1-09-01


title: E1-08-33


title: E1-08-41


title: E2-10-41


title: E1-08-30


title: E1-08-29


title: E1-08-27


title: E2-10-40


title: E1-08-26


title: E2-10-38


title: E1-08-19


title: E2-10-35


title: E2-10-33


title: E2-10-30


title: E2-10-31-r1


title: E2-10-29


title: E1-08-13


title: E1-08-05


title: E1-08-12


title: E1-08-02


title: E2-10-27


title: E2-10-25


title: E1-08-15


title: E1-08-01


title: E2-10-26


title: E2-10-19


title: E1-07-CEC


title: E1-08-16


title: E1-07-42


title: E2-10-42


title: E1-07-41


title: E2-10-21


title: E2-10-15


title: E1-07-33


title: E2-10-16


title: E1-07-30


title: E2-10-13


title: E1-07-29


title: E2-10-10


title: E1-07-27


title: E1-07-19


title: E1-07-26


title: E2-10-07


title: E2-10-03


title: E1-07-15


title: E2-10-05-r1


title: E2-10-17


title: E2-09-CEC


title: E1-07-16


title: E1-07-12


title: E1-07-13


title: E2-09-42


title: E2-10-01-r1


title: E2-09-38


title: E2-10-02


title: E2-10-12


title: E2-09-33


title: E1-06-42


title: E2-09-41


title: E1-07-05


title: E2-09-40


title: E2-09-31


title: E1-06-33


title: E1-06-30


title: E2-09-30


title: E1-06-27


title: E1-06-29


title: E2-09-29


title: E1-06-26


title: E2-09-26


title: E1-06-19


title: E2-09-25


title: E1-07-02


title: E1-06-15


title: E2-09-19


title: E1-06-CEC


title: E1-06-41


title: E1-06-16


title: E1-06-13


title: E1-07-01


title: E2-09-15


title: E2-09-21


title: E1-06-02


title: E2-09-16


title: E2-09-35


title: E1-06-05


title: E2-09-13


title: E2-09-12


title: E1-06-01


title: E1-05-CEC


title: E1-05-42


title: E2-09-27


title: E2-09-07


title: E1-05-41


title: E2-09-05


title: E1-05-30


title: E1-05-33


title: E1-05-29


title: E1-05-27


title: E2-09-01-r1


title: E2-08-42


title: E1-05-19


title: E2-09-17


title: E1-06-12


title: E1-05-26


title: E1-05-16


title: E1-05-15


title: E2-08-38


title: E2-08-41


title: E1-05-13


title: E2-08-35


title: E2-08-40


title: E2-09-10


title: E1-05-05


title: E1-05-12


title: E2-08-33


title: E1-05-02


title: E2-08-30


title: E2-09-03


title: E2-08-29


title: E2-09-02


title: E1-04-CEC


title: E2-08-27-r1


title: E2-08-31


title: E2-08-26


title: E2-08-21


title: E1-04-33


title: E1-04-30


title: E1-04-29


title: E2-08-19


title: E2-08-17


title: E1-04-27


title: E1-04-26


title: E2-08-15


title: E1-02-CEC


title: E1-02-42


title: E2-08-16-r1


title: E2-08-12


title: E2-08-10


title: E1-05-01


title: E1-02-41


title: E2-08-07


title: E1-02-30


title: E1-04-42


title: E1-02-29


title: E1-04-41


title: E1-02-27


title: E2-08-25


title: E1-02-26


title: E2-08-CEC


title: E1-02-19


title: E1-02-16


title: E1-02-15


title: E2-08-13


title: E1-02-12


title: E1-02-13


title: E2-07-42


title: E1-02-33


title: E2-07-41


title: E2-07-38


title: E2-07-CEC


title: E1-02-05


title: E2-07-35


title: E1-02-01


title: E2-08-05-r1


title: E2-07-33


title: E2-07-31


title: E2-07-30


title: E1-02-02


title: E2-08-02


title: E2-08-01-r1


title: E2-07-27


title: E2-07-29


title: Tie2_Trap_rep2

city: Boston

first: Fei

last: Gu

state: MA

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the Ensembl NCBIM37 genome assembly using tophat version 1.4
Genome_build: Ensembl NCBIM37
Supplementary_files_format_and_content: wig files and bigwig files

source_name: Heart

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee of Boston Children’s Hospital.

extract_protocol:
Fragments 150-300 bp were size-selected by 2% agarose gel electrophoresis. Recovered DNA was amplified using Phusion DNA polysome (NEB), multiplexing PCR primer 1.0, and one indexed primer. The amplified libraries were purified with Agencourt AMPure XP beads (Beckman Coulter). The libraries were quantitated using the Quant-iT DNA quantitation kit (Invitrogen). The DNA size distribution of the library was measured by an Agilent Bioanalyzer.
total cytoplasmic RNA, translating ribosome affinity purification (TRAP) RNA
2 µg of pooled input or TRAP RNA were used for two rounds of poly(A) mRNA purification by Dynabeads Oligo(dT)25 (Invitrogen). RNA was reverse transcribed by SuperScript III (Invitrogen) and random hexamer primers. After RNaseH treatment and PolI catalyzed 2nd-strand cDNA synthesis, DNA end repair was achieved by End-it kit (Epicnetre). DNA was then A-tailed with Exo- Klenow (NEB), and adaptors were ligated using Quick T4 DNA Ligase (NEB).

treatment_protocol: Male mice (25-30 g) were anesthetized with isofluorane blended with oxygen. The chest was shaved and cleaned with alcohol. Prior to the incision, 0.1 ml of 0.1% lidocaine was introduced under the skin. The chest cavity was opened by an incision of the left second intercostal space. The pericardial sac was opened and dissected apart, the ascending portion of aorta was dissected from the surrounding tissues and a silk suture was passed underneath the aorta and ligated against a 25- gauge needle. The needle was then removed, resulting in a ligature with a fixed diameter tied around and constricting the aorta. The sham procedure was identical except that the aorta was not ligated.

value: heart

tag: age

value: Adult

tag: sample type

value: TRAP RNA

tag: treatment

value: No surgery

tag: transgene

value: Tie2, an endothelial cell-specific Cre (Tie2-Cre) to activate TRAP in all endothelial cells_Trap_rep2

tag: genetic background

value: 129/C57BL mixed


title: Tie2-Trap_rep1

value: Tie2, an endothelial cell-specific Cre (Tie2-Cre) to activate TRAP in all endothelial cells-Trap_rep1


title: E2-07-26-r1


title: TNT_Trap_rep2

value: TNT, a cardiomyocyte-specific Cre (TNT, a cardiomyocyte-specific Cre (TnT-Cre) to activate TRAP in mouse cardiomyocytes


title: TNT_Trap_rep1


title: E2-07-21


title: E2-07-25


title: CAG-Sham-TRAP_rep3

value: Sham

value: CAG, a ubiquitously expressing TRAP in all cell lineages


title: CAG-Band-input_rep3

value: cytoplasmic RNA

value: Banding


title: E2-07-17-r1

value: feces

value: LF/HPP=>HF/HS=>LF/HPP


title: CAG-Sham-input_rep3


title: E2-07-19


title: E2-07-15


title: Input


title: E2-07-13


title: E2-07-16


title: E2-07-12


title: TnT-Sham-TRAP_rep3

value: TNT, a cardiomyocyte-specific Cre (TnT-Cre) to activate TRAP in mouse cardiomyocytes


title: TnT-Sham-input_rep3


title: TnT-Band-TRAP_rep3


title: E2-07-10


title: E2-08-03


title: TnT-Band-input_rep3


title: E2-07-07


title: E0-12_Input replicate1

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing:
The Raw images were first processed with the Casava 1.7.0.
Base-called sequences with confidence metrics were obtained using OLB-1.9.0.  All multiplexed samples were demultiplexed using Casava 1.7.0
The BWA program was used to align the sequence reads to the Drosophila melanogaster (v5.32) genome, allowing up to 2 edit distance in the seed region and 3 in the full read length. Tags that aligned to more than one  location were excluded from our analysis for both ChIP sample and the corresponding control sample (input chromatin). Only properly aligned reads with mapping quality more than 30 were kept.
Peaks were called using SPP and IDR
Wig files were generated using MACS2
Genome_build: dm3
Supplementary_files_format_and_content: bed (columns are: chrom; chromStart; chromEnd; name; score; strand; signalValue; pValue; qValue; peak; Ref to: http://code.google.com/p/phantompeakqualtools/) and wig

organism: Drosophila melanogaster

extract_protocol:
Chromatin lysates were clarified from homogenized and sonicated tissues; protein-DNA complexes were isolated with antibody.  DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  Briefly, up to 12.5 ng DNA was included in the high molecular weight (HMW) tagmentation reaction (5 minutes at 55 degrees Celsius). Tagmented DNA was purified using a Qiagen MinElute column. Addition of barcoded PCR-compatible sites and library enrichment were performed using 12 cycles of PCR. Amplified DNA was purified using the Qiagen MinElute PCR Purification Kit. Library fragments of approximately 225 bp were gel purified and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a HiSeq2000 according to the manufacturer’s protocol.
Libraries were prepared according to ChIP-seq library kit instruction Nextera DNA prep kit is FC-121-103

tag: developmental stage

tag: fraction

value: input DNA

tag: replicate

tag: transcription factor

tag: antibody name

tag: antibody manufacturer

tag: antibody catalog number


title: prd-RF13_ChIP-seq replicate2

description:
4096.bw
4096.bed

value: ChIP

value: prd

value: Desplan Lab


title: E2-07-05

tag: experiment

tag: mouse

tag: days post-colonization

tag: collection site

tag: diet group


title: CAG-Band-TRAP_rep2

tag: tissue

value: heart

tag: age

value: Adult

value: TRAP RNA


title: CAG-Sham-TRAP_rep2

tag: sample type

tag: treatment

value: 129/C57BL mixed


title: prd-RF13_ChIP-seq replicate1

description:
4096.bw
4096.bed


title: E2-07-03


title: CAG-Band-input_rep2

tag: transgene

tag: genetic background


title: CAG-Band-TRAP_rep3


title: prd-RF12_ChIP-seq replicate2

description:
4095.bw
4095.bed

tag: developmental stage

tag: fraction


title: prd-RF12_ChIP-seq replicate1

description:
4095.bw
4095.bed

tag: replicate

tag: transcription factor


title: CAG-Sham-input_rep2


title: cnc_Input replicate1

source_name: AdultFemale

value: AdultFemale

tag: antibody name

tag: antibody manufacturer


title: E2-07-01-r1

tag: experiment


title: cnc_ChIP-seq replicate1

description:
4082.bw
4082.bed

value: cnc

value: White Lab

tag: antibody catalog number


title: br_Input replicate1


title: TnT-Sham-TRAP_rep2

value: Sham


title: br_ChIP-seq replicate2

description:
4077.bw
4077.bed

value: br

value: Lepesant Lab


title: TNT_Band_TRAP_rep2

value: Banding

value: TNT, a cardiomyocyte-specific Cre (TNT, a cardiomyocyte-specific Cre (TnT-Cre) to activate TRAP in mouse cardiomyocytes


title: E2-06-42

tag: mouse

tag: days post-colonization

value: feces

value: LF/HPP=>HF/HS=>LF/HPP


title: br_ChIP-seq replicate1

description:
4077.bw
4077.bed

value: ChIP


title: E2-06-41

tag: collection site

tag: diet group


title: E2-06-CEC

value: cecum


title: TnT-Sham-input_rep2

tag: tissue

tag: age

value: cytoplasmic RNA

value: TNT, a cardiomyocyte-specific Cre (TnT-Cre) to activate TRAP in mouse cardiomyocytes


title: E2-06-40


title: E2-06-35


title: TNT_Band_input_rep2

value: heart

value: Adult

tag: sample type

tag: treatment


title: E2-07-40


title: CAG-Sham-input_rep1

tag: transgene

value: CAG, a ubiquitously expressing TRAP in all cell lineages

tag: genetic background

value: 129/C57BL mixed


title: E2-06-33


title: CAG-Band-TRAP_rep1

value: TRAP RNA


title: E2-06-38


title: CAG-Band-input_rep1


title: CAG-Sham-TRAP_rep1


title: E2-07-02


title: E2-06-30


title: TNT_Sham_TRAP_rep1


title: E2-06-31


title: E2-06-29


title: cnc_ChIP-seq replicate2

description:
4082.bw
4082.bed

tag: developmental stage

value: AdultFemale

tag: fraction

value: cnc

value: White Lab


title: TNT_Band_TRAP_rep1


title: TNT_Band_input_rep1


title: TNT_Sham_input_rep1

value: Sham


title: E2-06-27


title: GlcA 1

organism: Bacteroides cellulosilyticus

source_name: In vitro bacterial culture, D-Glucuronic acid sodium salt monohydrate

treatment_protocol: Sample was collected from an in vitro culture in which Bacteroides cellulosilyticus WH2 was grown to early log stage in Bacteroidetes minimal media containing a single carbohydrate as a carbon source.

tag: strain

tag: carbohydrate


title: Fuc 2

source_name: In vitro bacterial culture, L-(-)-Fucose

value: L-(-)-Fucose


title: E2-06-26


title: OSX 2

source_name: In vitro bacterial culture, Xylan from oat spelts

value: Xylan from oat spelts


title: E2-06-25

value: feces


title: GalNAc 1

source_name: In vitro bacterial culture, N-Acetyl-D-galactosamine

value: N-Acetyl-D-galactosamine


title: New_Tie2_TRAP_l2

description:
No surgery
TRAP RNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the Ensembl NCBIM37 genome assembly using tophat version 1.4
reads were count using htseq-count version 0.5.3
Genome_build: Ensembl NCBIM37
Supplementary_files_format_and_content: RPKM

value: No surgery


title: New_Tie2_TRAP_l1

description:
No surgery
TRAP RNA


title: E2-06-21

value: LF/HPP=>HF/HS=>LF/HPP


title: New_Tie2_input_l2

description:
No surgery
cytoplasmic RNA


title: E2-06-17


title: New_Tie2_input_l1

description:
No surgery
cytoplasmic RNA


title: Pul 1

source_name: In vitro bacterial culture, Pullulan from Aureobasidium pullulans

value: Pullulan from Aureobasidium pullulans


title: E2-06-16

source_name: Defined bacterial assemblage from a gnotobiotic mouse


title: AG 2

source_name: In vitro bacterial culture, Arabinogalactan (Larch Wood)

value: Arabinogalactan (Larch Wood)


title: E2-06-15


title: Cello 3

source_name: In vitro bacterial culture, D-(+)-Cellobiose

value: D-(+)-Cellobiose


title: E2-06-13


title: New_CAG_TRAP_l2

description:
No surgery
TRAP RNA

value: heart

value: Adult


title: Arab 3

source_name: In vitro bacterial culture, Arabinan (Sugar Beet)

value: Arabinan (Sugar Beet)


title: Fuc 1


title: Rha 3

source_name: In vitro bacterial culture, L-Rhamnose monohydrate

value: L-Rhamnose monohydrate


title: E2-06-12


title: New_CAG_input_l2

description:
No surgery
cytoplasmic RNA


title: E2-06-10


title: New_CAG_Band_TRAP_rep2_l2

description:
Banding
TRAP RNA

value: Banding


title: CS 2

source_name: In vitro bacterial culture, Chondroitin sulfate A sodium salt from bovine trachea


title: E2-06-07


title: Pul 3


title: New_CAG_Band_TRAP_rep2_l1

description:
Banding
TRAP RNA


title: E2-06-05-r1


title: Fru 2

source_name: In vitro bacterial culture, D-(-)-Fructose

value: D-(-)-Fructose


title: GlcA 3

value: D-Glucuronic acid sodium salt monohydrate


title: New_CAG_Band_TRAP_rep1_l2

description:
Banding
TRAP RNA


title: GalA 1

source_name: In vitro bacterial culture, D-Galacturonic acid sodium salt

value: D-Galacturonic acid sodium salt


title: New_CAG_TRAP_l1

description:
No surgery
TRAP RNA


title: E2-06-19


title: Man 1

source_name: In vitro bacterial culture, D-(+)-Mannose

value: D-(+)-Mannose


title: E2-06-03


title: E2-05-42


title: E2-06-02


title: GlcMan 2

source_name: In vitro bacterial culture, Glucomannan (Konjac; Low Viscosity)

value: Glucomannan (Konjac; Low Viscosity)


title: E2-06-01-r1

value: feces


title: New_CAG_Band_input_rep1_l2

description:
Banding
cytoplasmic RNA

source_name: Heart


title: New_CAG_Band_input_rep2_l2

description:
Banding
cytoplasmic RNA


title: New_CAG_input_l1

description:
No surgery
cytoplasmic RNA


title: Rib 2

source_name: In vitro bacterial culture, D-(-)-Ribose

value: D-(-)-Ribose


title: New_CAG_Band_TRAP_rep1_l1

description:
Banding
TRAP RNA


title: New_CAG_Band_input_rep2_l1

description:
Banding
cytoplasmic RNA


title: E2-05-40


title: PGA 1

source_name: In vitro bacterial culture, Polygalacturonic Acid (PGA)

value: Polygalacturonic Acid (PGA)


title: Suc 1

source_name: In vitro bacterial culture, Sucrose

value: Sucrose


title: GlcNAc 1

source_name: In vitro bacterial culture, N-Acetyl-D-glucosamine

value: N-Acetyl-D-glucosamine


title: Rha 1


title: E2-05-41

value: LF/HPP=>HF/HS=>LF/HPP


title: E2-05-CEC

value: cecum


title: New_CAG_Sham_TRAP_rep2_l2

description:
Sham
TRAP RNA

value: heart

value: Sham


title: New_CAG_Band_input_rep1_l1

description:
Banding
cytoplasmic RNA

value: Adult


title: New_CAG_Sham_TRAP_rep2_l1

description:
Sham
TRAP RNA


title: E2-05-38


title: Lam 2

source_name: In vitro bacterial culture, Laminarin from Laminaria digitata

value: Laminarin from Laminaria digitata


title: GlcNAc 3


title: E2-05-35


title: New_CAG_Sham_TRAP_rep1_l1

description:
Sham
TRAP RNA


title: E2-05-33


title: New_CAG_Sham_input_rep2_l2

description:
Sham
cytoplasmic RNA


title: E2-05-31


title: New_CAG_Sham_input_rep2_l1

description:
Sham
cytoplasmic RNA


title: GalNAc 2

source_name: In vitro bacterial culture, N-Acetyl-D-galactosamine

value: N-Acetyl-D-galactosamine


title: New_CAG_Sham_input_rep1_l2

description:
Sham
cytoplasmic RNA


title: Glc 2

source_name: In vitro bacterial culture, D-(+)-Glucose

value: D-(+)-Glucose


title: BBG 1

source_name: In vitro bacterial culture, β-Glucan (Barley; Low Viscosity)

value: β-Glucan (Barley; Low Viscosity)


title: E2-05-30

source_name: Defined bacterial assemblage from a gnotobiotic mouse


title: XG 2

source_name: In vitro bacterial culture, Xyloglucan (Tamarind)

value: Xyloglucan (Tamarind)


title: E2-05-27


title: E2-05-29


title: WAX 1

source_name: In vitro bacterial culture, Arabinoxylan (Wheat Flour; Low Viscosity)


title: B replicate 5

city: New York

first: Doron

last: Betel

state: NY

address: 1305 York Avenue (Box 140)

department: Medicine

institute: Weill Cornell Medical College

description: Ambion Human Brain Reference RNA

data_processing:
Basecalls and demux was performed using CASAVA version 1.8.0
All sequenced libraries were mapped to the human genome (hg19) using TopHat(v.2.0.3) (Trapnell et al., 2013) with the following parameters: '-r 70 --mate-std-dec 90'. A custom GTF file that includes both RefSeq information (from UCSC genome browser) and the ERCC transcript information was used (--GTF \$SEQCLB/hg19\_150\_ERCC.gtf) along with the transcriptome index option (--transcriptome-index \$SEQCLIB/hg19\_150\_ERCC). Genes shorter than 150 bp were excluded from this GTF file.
HTSeq (v.0.5.3p3) was used to generate the count matrix with the following parameters: 'htseq-count -m intersection-strict -s no' with the same GTF file used for the alignment step ($SEQCLIB/hg19\_150\_ERCC.gtf)
FPKM values were generated by Cufflinks
genome build: hg19
processed data files format and content: tab delimited text files of gene read counts or FPKM values

source_name: Ambion Human Brain Reference RNA (HBRR)

extract_protocol: Standard Illumina RNA-seq protocol and reagents

tag: sample composition

value: Several brain regions from 23 adult donors

tag: ercc

value: 2% by volume of ERCC mix #2

tag: replicate number


title: New_CAG_Sham_TRAP_rep1_l2

description:
Sham
TRAP RNA


title: Rib 3

tag: experiment


title: A replicate 5

source_name: Strategene Universal Human Reference RNA (UHRR) from 10 human cell lines

value: 10 human cell lines (B lymphocyte, brain, breast, cervix, liposarcoma, liver, macrophage, skin, testis, and T lymphocyte)

value: 2% by volume of ERCC mix #1


title: B replicate 4

description: Ambion Human Brain Reference RNA


title: E2-05-21

tag: mouse

tag: days post-colonization

value: feces


title: E2-05-25

tag: collection site

tag: diet group


title: Ara 2

source_name: In vitro bacterial culture, D-(-)-Arabinose

value: D-(-)-Arabinose


title: Xyl 1

source_name: In vitro bacterial culture, D-(+)-Xylose

value: D-(+)-Xylose


title: E2-05-26

value: LF/HPP=>HF/HS=>LF/HPP


title: A replicate 4

description: Strategene Universal Human Reference RNA


title: A replicate 3


title: E2-05-19


title: E2-05-17-r1


title: B replicate 2

description: Ambion Human Brain Reference RNA


title: E2-05-15


title: A replicate 2


title: E2-05-12


title: Suc 2

value: Sucrose


title: E2-05-13


title: BBG 2


title: PGA 3

value: Polygalacturonic Acid (PGA)


title: GlcNH3 2

source_name: In vitro bacterial culture, D-(+)-Glucosamine hydrochloride

value: D-(+)-Glucosamine hydrochloride


title: E2-05-10


title: B replicate 1

description: Ambion Human Brain Reference RNA


title: New_CAG_Sham_input_rep1_l1

description:
Sham
cytoplasmic RNA

source_name: Heart

tag: tissue

value: heart

tag: age

value: Adult

value: Sham


title: A replicate 1


title: Pul 2

source_name: In vitro bacterial culture, Pullulan from Aureobasidium pullulans

value: Pullulan from Aureobasidium pullulans


title: B replicate 3

description: Ambion Human Brain Reference RNA


title: E2-05-05


title: APpot 1

source_name: In vitro bacterial culture, Amylopectin from potato starch

value: Amylopectin from potato starch


title: BBG 3

value: β-Glucan (Barley; Low Viscosity)


title: Cello 1

source_name: In vitro bacterial culture, D-(+)-Cellobiose

value: D-(+)-Cellobiose


title: WAX 3

value: Arabinoxylan (Wheat Flour; Low Viscosity)


title: E2-04-CEC

value: cecum


title: E2-05-01-r1


title: Rha 2

source_name: In vitro bacterial culture, L-Rhamnose monohydrate

value: L-Rhamnose monohydrate


title: E2-05-02

value: feces


title: E2-05-16


title: E2-04-42


title: Cello 2


title: Man 3

source_name: In vitro bacterial culture, D-(+)-Mannose

value: D-(+)-Mannose


title: E2-04-41


title: Suc 3

source_name: In vitro bacterial culture, Sucrose


title: E2-04-40


title: GalA 3

source_name: In vitro bacterial culture, D-Galacturonic acid sodium salt

value: D-Galacturonic acid sodium salt


title: E2-05-07

value: LF/HPP=>HF/HS=>LF/HPP


title: GalA 2


title: E2-04-35


title: E2-04-38


title: Xyl 2

value: D-(+)-Xylose


title: E2-04-33


title: XG 1

value: Xyloglucan (Tamarind)


title: Lam 3

source_name: In vitro bacterial culture, Laminarin from Laminaria digitata

value: Laminarin from Laminaria digitata


title: E2-05-03

source_name: Defined bacterial assemblage from a gnotobiotic mouse


title: E2-04-31


title: E2-04-30


title: E2-04-29


title: Xyl 3


title: Dex 1

source_name: In vitro bacterial culture, Dextran from Leuconostoc mesenteroides

value: Dextran from Leuconostoc mesenteroides


title: Rib 1

source_name: In vitro bacterial culture, D-(-)-Ribose

value: D-(-)-Ribose


title: E2-04-25


title: GlcNH3 1

value: D-(+)-Glucosamine hydrochloride


title: E2-04-21


title: OSX 1

source_name: In vitro bacterial culture, Xylan from oat spelts

value: Xylan from oat spelts


title: OSX 3


title: E2-04-17


title: E2-04-19-r1


title: GlcNAc 2

source_name: In vitro bacterial culture, N-Acetyl-D-glucosamine

value: N-Acetyl-D-glucosamine


title: Arab 1

source_name: In vitro bacterial culture, Arabinan (Sugar Beet)

value: Arabinan (Sugar Beet)


title: E2-04-15


title: E2-04-16


title: Man 2


title: Glc 1

source_name: In vitro bacterial culture, D-(+)-Glucose

value: D-(+)-Glucose


title: E2-04-12


title: WAX 2

source_name: In vitro bacterial culture, Arabinoxylan (Wheat Flour; Low Viscosity)


title: E2-04-13


title: XG 3

source_name: In vitro bacterial culture, Xyloglucan (Tamarind)


title: E2-04-07


title: E2-04-05-r1


title: E2-04-03


title: Glc 3


title: Gal 2

source_name: In vitro bacterial culture, D-(+)-Galactose

value: D-(+)-Galactose


title: E2-04-27


title: GlcA 2

source_name: In vitro bacterial culture, D-Glucuronic acid sodium salt monohydrate


title: E2-04-02


title: E2-04-26


title: Gal 3


title: E2-04-01-r1


title: APpot 3

source_name: In vitro bacterial culture, Amylopectin from potato starch

value: Amylopectin from potato starch


title: E2-03-CEC

value: cecum


title: Ara 1

source_name: In vitro bacterial culture, D-(-)-Arabinose

value: D-(-)-Arabinose


title: Ara 3


title: E2-03-40

value: feces


title: E2-03-42


title: E2-04-10


title: AG 1

source_name: In vitro bacterial culture, Arabinogalactan (Larch Wood)

value: Arabinogalactan (Larch Wood)


title: E2-03-33

value: LF/HPP=>HF/HS=>LF/HPP


title: E2-03-41


title: Dex 3


title: Lam 1


title: CS 1

source_name: In vitro bacterial culture, Chondroitin sulfate A sodium salt from bovine trachea


title: E2-03-38


title: E2-03-30


title: Gal 1


title: GalMan 2

source_name: In vitro bacterial culture, Galactomannan (Carob; Low Viscosity)

value: Galactomannan (Carob; Low Viscosity)


title: E2-03-31


title: PGpot 3

source_name: In vitro bacterial culture, Pectic Galactan (Potato)

value: Pectic Galactan (Potato)


title: AG 3


title: PGA 2

source_name: In vitro bacterial culture, Polygalacturonic Acid (PGA)

value: Polygalacturonic Acid (PGA)


title: PGpot 1


title: CS 3

value: Chondroitin sulfate A sodium salt from bovine trachea


title: GlcMan 3

source_name: In vitro bacterial culture, Glucomannan (Konjac; Low Viscosity)

value: Glucomannan (Konjac; Low Viscosity)


title: PGpot 2


title: GalMan 1


title: Fru 1

source_name: In vitro bacterial culture, D-(-)-Fructose

value: D-(-)-Fructose


title: Dex 2

source_name: In vitro bacterial culture, Dextran from Leuconostoc mesenteroides

value: Dextran from Leuconostoc mesenteroides


title: APpot 2


title: E2-03-35

source_name: Defined bacterial assemblage from a gnotobiotic mouse


title: GalMan 3


title: Fru 3


title: RCASBP-A-RNAseq

status: Public on Aug 19 2013

city: Berlin

first: Peter

last: Hansen

address: Augustenburger Platz 1

department: Institute for Medical Genetics and Human Genetics

country: Germany

institute: Charité-Universitätsmedizin Berlin

description: cDNA from polyA selected RNA

data_processing: The  Reads Per Kilobase of transcript per Million mapped reads (RPKM) values were then calculated for all transcripts (i)  in dependence on the formula introduced by Mortazavi et. al. Nat Methods 2008  : RPKM(i)= (reads(i) * 10^9)/(length(i) * no.of.reads), with reads(i) = number of reads mapped to the transcript; length(i) =  length of this specific transcript ; no.of.reads = the number of mapped reads. The RPKM values were calculated for each isoform separately, taking into account the compensatory effect between isoforms of the same gene.

organism: Gallus gallus

source_name: empty vector infected chMM

growth_protocol: Chicken micromass cultures were routinely prepared by generating a single cell suspension of embryonic mesenchymal chicken limb bud cells (HH24) (2 × 10^7 cells/ml) and the appropriate virus was added before plating. Cultures were plated as 10µl droplets and cells were cultured for 9 days in chMM medium (DMEM/HAM’S F12 (Gibco) with 10% FBS (PAA), 0.2% chicken serum (Sigma), 1% L-glutamin (Gibco), 1% penicillin/streptomycin (Gibco) before harvest.

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were enriched with antibody. For ChIP-seq library preparation ethanol precipitated DNA from ChIP was redissolved in 46 µl of water and subjected to library preparation using the NEBnext ChIP-Seq Library Prep Master Mix for Illumina (New England Biolabs) selecting for a fragment size range of 300-450 bp according to manufacturer's instructions. Sequencing was performed on an Illumina GAIIx sequencer with 36 bp single reads using TruSeq v5 sequencing chemistry and TruSeq v5 Cluster Generation Kits. For RNA-seq, total RNA from chicken micromass cultures was isolated using peqGOLD TriFast Reagent (peqLAB) and subsequent purification with RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. mRNA for RNA-seq libraries was purified using the Oligotex mRNA Mini Kit (Qiagen) from 6 µg of total RNA. RNA-seq libraries were constructed using the NEBNext mRNA Library Prep Master Mix Set for Illumina according to manufacturer's instructions selecting for a fragment size range of 300-500 bp. Sequencing was performed on an Illumina GAIIx sequencer with 115 bp single reads using TruSeq v5 sequencing chemistry and TruSeq v5 Cluster Generation Kits.

tag: cell type

value: chicken micromass

tag: days of incubation

tag: virus used for infection

value: RCASBP(A)-empty

tag: chip antibody


title: R9308-34 rep2

city: hangzhou

first: Rongrong

last: Zhai

address: No. 359, Tiyuchang Rd

institute: China National Rice Research Institute

data_processing:
Basecalls performed using CASAVA version 1.8
The raw reads were filtered to obtain high-quality reads by removing low-quality reads containing more than 30% Q<20 bases. Then  the low-quality bases (Q<20) at the 5’ and 3’ ends of the remaining reads were discarded. Passed filter reads were mapped onto the Nipponbare reference genome (IRGSP build 5.0) by RSEM (v1.1.11)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated to detect gene expression levels.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Oryza sativa

source_name: Root

growth_protocol: Rice seeds were surface-sterilized with 3% H2O2 for 10 min and then rinsed with distilled water several times. After soaking in distilled water at 37℃ for 2d, germinated seeds were sowed in the field of the China National Rice Research Institute, Fuyang, China, for approximately 30 d. Then 40 seedlings of each genotype were transplanted in plots on a floating foamed plastic in a pool full of nutrient solution. Roots were sampled with ten replicates at the tillering stage and heading stage to measure root traits and estimate heterosis. Meantime, for RNA-Seq analysis, two roots of every genotype at either stage were collected and stored at -80℃ before use.

extract_protocol:
Total RNA was extracted from roots using TRIzol regent (Invitrogen) and purified with Oligotex mRNA Midi Kit (QIAGEN). RNA quality was checked by the Bioanalyzer 2100 (Aligent) and all samples had RNA Integrity Number (RIN) value more than 8.5. The sequencing library was prepared according to manufacturer′s instructions (Illumina). The poly-A containing mRNA was isolated from total RNA using two rounds of purification with poly-T oligo-attached magnetic beads and subsequently fragmented by the RNA fragmentation kit. The first strand cDNA was generated using reverse transcriptase and random primers. After the second strand cDNA synthesis and adaptor ligation, cDNA fragments of 200 bp were isolated by gel electrophoresis and enriched by 18 cycles of PCR. The products were loaded on Illumina Hiseq2000 instrument for pair-end 100 bp×2 sequencing for 100 cycles.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: root

tag: developmental stage

value: Heading stage


title: R9308-34 rep1

tag: strain


title: Xieqingzao B-34 rep1

value: cv.Xieqingzao B


title: GlcMan 1

tag: carbohydrate


title: Xieqingzao B-12 rep2

value: Tillering stage


title: Arab 2

source_name: In vitro bacterial culture, Arabinan (Sugar Beet)

value: Arabinan (Sugar Beet)


title: Xieyou 9308-34 rep2

value: cv. Xieyou9308


title: Isolated PST haustoria rep 2

city: Davis

first: Dario

last: Cantu

address: One Shields Ave

department: Plant Sciences

institute: UC Davis

data_processing:
Reads were trimmed at the 3' end using a minimum quality treshold of Q3; reads that after trimming were shorter than 40 were discared
Reads were then mapped using Bowtie (0.12.8) as single end reads, with parameters --best -v 2 --sam
Sam files were parsed to extract the read counts.
Genome_build: BioProject: 181960 genome  (Submission SUB141196)
Supplementary_files_format_and_content: quality trimmed reads mapped mapped onto the reference and whose counts are presented in Table 1.txt
Supplementary_files_format_and_content: Table 1.txt: tab separated txt file with read counts determined by mapping the sequencing reads

organism: Puccinia striiformis f. sp. tritici 08/21

source_name: Isolated PST haustoria

extract_protocol:
Total RNA was extracted from both the infected wheat leaf material and purified haustoria using TRIzol reagent (Invitrogen, UK) and treated with DNA™-free DNase (Manufacturer) and the Removal Reagents kit (Ambion, UK) following the manufacturer’s instructions. The quantity and quality of RNA extracted was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, UK).
cDNA libraries were prepared using the illumina TruSeq RNA Sample preparation Kit (illumina, US) for RNA extracted from infected material (sample Inf) and the haustoria sample  H2 and using the Clontech SMARTer Ultra Low Input RNA Kit (Clontech, Takara Bio Europe, France) for RNA extracted from the haustoria sample  H1.

value: UK race 08/21

tag: sample type

value: Isolated fungal haustoria

value: haustoria


title: HOXD13-wt-RNAseq

description: cDNA from polyA selected RNA

source_name: Hoxd13(wt) expressing chMM


title: Input-PITX1

data_processing: Peaks were called using MACS2 with appropriate input controls and the following settings: ( -g 1. 0e9 -q None -p 1e-1 --too-large --bw (as determined by spp-get binding characteristics))

source_name: sonified chromatin from Pitx1(wt) expressing chMM


title: Input-HOXD13-Q317K

source_name: sonified chromatin from Hoxd13(Q317K) expressing chMM


title: Xieyou 9308-34 rep1


title: PST infected wheat leaves

source_name: PST infected wheat leaves

value: pool of stripe rust infected wheat leaves

tag: host

value: Triticum aestivum (cv. Avocet S)


title: Isolated PST haustoria rep 1


title: Xieqingzao B-12 rep1


title: Input-HOXD13-Q317R

source_name: sonified chromatin from Hoxd13(Q317R) expressing chMM


title: R9308-12 rep2