title: Mouse feces 09-21

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 21 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 6 and 7 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 21 days prior

value: 6 and 7 days prior


title: Mouse feces 08-21

status: Public on Nov 01 2011

type: SRA

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

country: USA

institute: Washington University School of Medicine

library_source: genomic

data_processing: After parsing each sequencing lane's data by barcode, we excised the barcodes and mapped the reads to an appropriate set of reference genomes using Illumina's ELAND aligner.  The alignment results for each 30-nt (trimmed) sequencing read were evaluated to determine if the read mapped perfectly and uniquely (to only one position in only one reference genome) or if it mapped redundantly (to more than one position within and/or across genomes).  Reads which failed to map perfectly to one of the reference genomes were filtered out and mapped to the Illumina adapter sequences as well as the mouse reference genome to determine what fraction of non-mapping reads were from host-derived DNA or Illumina adapter dimers produced during library creation.  Redundantly mapping reads were also filtered out.  To account for the latter filtering step, the value representing the number of raw hits to each reference genome was normalized using a that genome's "informative genome size", which is (for a given k-mer size) the number of all possible k-mers in that genome that map uniquely (to that genome) when considering all genomes in the analysis.  The processed data files report the "raw counts", the "normalized counts" and the "normalized percentage" (proportion of all normalized counts attributable to a particular species) for each reference genome included in the analysis of each sample.

molecule: genomic DNA

organism: Bacteria

source_name: Mouse feces

growth_protocol: Fecal samples obtained from mice were frozen immediately in liquid nitrogen, stored at -80C, and maintained at this temperature prior to DNA extraction and library preparation.

extract_protocol: Libraries were prepared according a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, 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 Illumina adapter sequence (with or without a 4-nt barcode).  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 II following the manufacturer's protocols.

tag: host organism

value: Mus musculus

tag: host strain

tag: time of gut bacteria

tag: time when gavaged with fermented milk strains


title: Mouse feces 10-21


title: Mouse feces 10-23

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 23 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 1, 2, 8 and 9 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 23 days prior

value: 1, 2, 8 and 9 days prior


title: Mouse feces 07-21


title: Mouse feces 06-21


title: Mouse feces 05-21


title: Mouse feces 04-21


title: Mouse feces 02-21


title: Mouse feces 01-21


title: Mouse feces 09-17

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 17 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 2 and 3 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 17 days prior

value: 2 and 3 days prior


title: Mouse feces 03-21


title: Mouse feces 08-17


title: Mouse feces 07-17


title: Mouse feces 10-17


title: Mouse feces 04-17


title: Mouse feces 03-17


title: Mouse feces 06-17


title: Mouse feces 02-17


title: human_T12_RNA-seq

status: Public on Nov 03 2011

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

description: RNA-seq of human thyroid primary cell with IFN-alpha treatment at 5000 u/ml for 12 hours.

library_source: transcriptomic

data_processing: Single reads split by barcode into individual files using PERL script. The reads with good quality were aligned to reference sequence (RefSeq) databases of human (UCSC hg18) or mouse (UCSC mm9) genomes, RefSeq exons, splicing junctions and contamination databases including ribosome and mitochondria sequences using the BWA alignment algorithm, and the alignment files in SAM format were generated. After filtering reads mapped to contamination databases, the reads that  have one or no mismatch and are uniquely aligned to each exon and splicing-junction sites were extracted and then counted. The read count for each RefSeq transcript was calculated by combining the counts for exons and splicing junctions of the corresponding transcript. The read count at exon, splice-junction, transcript and gene levels were summarized and normalized to relative abundance in Fragments Per Kilobase of exon model per Million (FPKM) in order to compare transcription level among samples.

molecule: total RNA

organism: Homo sapiens

source_name: primary thyroid cell line, IFN-alpha, 12 hrs

growth_protocol: Human thyroid primary cells were prepared from fresh, non-cancerous thyroid tissue adjacent to thyroid tumors that were removed at surgery. Tissue was minced and incubated in 200 U/ml of collagenase solution for 1 hour at 37°C. Cells were harvested and cultured in DMEM supplemented with 10% FBS, penicillin (100 U/ml), and streptomycin (100 µg/ml) (P0). Cells were passaged at 1:2 dilution and cultured until confluent.

extract_protocol: According to the Illumina mRNA Sequencing Sample Preparation Guide. Briefly, 2ug total RNA was hybridized to poly-dT magnetic beads to capture polyA mRNA molecules. Chemical fragmentation, first-strand synthesis with RTase, randomers second-strand synthesis. Then, end repair, 3' A overhang, multiplex adapter ligation (from Illumina indexing kit), size selection by electrophoresis and cut at 200bp. 18 cycles of PCR with a primer bearing an indexing barcode.

treatment_protocol: Confluent human primary thyroid cultures were exposed to human IFNα (5,000 U/ml) for 0, 12 or 24 hours, followed by RNA isolation.

tag: tissue

value: thyroid

tag: treatment

value: 12 hour IFN alpha treatment (5,000 U/ml)


title: Mouse feces 09-16

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 16 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 1 and 2 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 16 days prior

value: 1 and 2 days prior


title: Mouse feces 08-16


title: Mouse feces 06-16


title: Mouse feces 05-17


title: Mouse feces 04-16


title: Mouse feces 03-16


title: Mouse feces 05-16


title: Mouse feces 01-16


title: Mouse feces 10-14

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 14 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 14 days prior


title: Mouse feces 07-14


title: Mouse feces 02-16


title: Mouse feces 05-14


title: Mouse feces 04-14


title: mouse feces NM1200_10.36

description:
Bacteroides caccae ATCC 43185,Bacteroides ovatus ATCC 8483,Bacteroides thetaiotaomicron VPI-5482,Bacteroides uniformis ATCC 8492,Bacteroides vulgatus ATCC 8482,Bacteroides WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii M21/2,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Parabacteroides distasonis ATCC 8503,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Streptococcus thermophilus CNCM I-1630
rRNA-depleted total RNA
RNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 36 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 1, 14, 15, 21, and 22 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

data_processing: After parsing each sequencing lane's data by barcode (where appropriate), we excised the barcodes and mapped the reads to an appropriate set of reference genomes using the ssaha2 algorithm.  Minimum score thresholds for ssaha were selected based on the distribution of scores for all mapped reads of a 32-nt barcoded sample and a 36-nt non-barcoded sample (29 was selected as the minimum score for 32-nt barcoded samples; 33 was the minimum score used for 36-nt and 76-nt non-barcoded samples). Although an 18-nt read is sufficient to map more than 90% of the sequencing reads, even at 32-36 nucleotides a large fraction of reads map to multiple locations (within a genome and/or across genomes). Reads that map non-uniquely were added to each gene in proportion to each gene's fraction of unique-match counts (e.g., a non-unique read that maps equally well to gene A with 18 unique reads and gene B with 2 unique reads will result in 0.9 counts being tallied to gene A and 0.1 counts being tallied to gene B). We added a pseudocount (i.e. added a value of 1) to each gene count prior to normalization to account for differences in sampling depth, although clearly a more appropriate model-based approach to smooth lower expression values is needed in the future, particularly with mixed species samples where one or more species is clearly undersampled. Raw counts were ultimately normalized to reads/kb gene length/million mapped reads (RPKM) following gene count assignments.

organism:
Bacteroides
Ruminococcus
Streptococcus thermophilus
Lactobacillus
Collinsella
Clostridia
Parabacteroides
Bifidobacterium animalis subsp. lactis CNCM I-2494

source_name: mouse feces

extract_protocol: Libraries were prepared according 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 (with or without a 4-nt barcode).  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 (IIx) following the manufacturer's protocols.

tag: sample type

value: fecal pellet of a mouse

tag: source


title: Mouse feces 06-14


title: mouse feces NM1200_10.42

description: RNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 42 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 6, 7, 20, 21, 27 and 28 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 42 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 27 and 28 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).


title: Mouse feces 01-17


title: mouse feces NM1200_10.35

description:
Bacteroides caccae ATCC 43185,Bacteroides ovatus ATCC 8483,Bacteroides thetaiotaomicron VPI-5482,Bacteroides uniformis ATCC 8492,Bacteroides vulgatus ATCC 8482,Bacteroides WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii M21/2,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Parabacteroides distasonis ATCC 8503,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Streptococcus thermophilus CNCM I-1630
rRNA-depleted total RNA
RNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 35 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 13, 14, 20 and 21 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).


title: Mouse feces 10-16


title: Mouse feces 01-14


title: Mouse feces 07-16


title: Mouse feces 10-07

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 7 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 7 days prior


title: Mouse feces 03-14


title: Mouse feces 09-07


title: mouse feces NM1200_10.14

description:
Bacteroides caccae ATCC 43185,Bacteroides ovatus ATCC 8483,Bacteroides thetaiotaomicron VPI-5482,Bacteroides uniformis ATCC 8492,Bacteroides vulgatus ATCC 8482,Bacteroides WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii M21/2,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Parabacteroides distasonis ATCC 8503,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Streptococcus thermophilus CNCM I-1630
rRNA-depleted total RNA
RNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 14 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).


title: mouse feces NM1200_9.42


title: Mouse feces 09-14


title: Mouse feces 08-14


title: mouse feces NM1200_10.15

description:
Bacteroides caccae ATCC 43185,Bacteroides ovatus ATCC 8483,Bacteroides thetaiotaomicron VPI-5482,Bacteroides uniformis ATCC 8492,Bacteroides vulgatus ATCC 8482,Bacteroides WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii M21/2,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Parabacteroides distasonis ATCC 8503,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Streptococcus thermophilus CNCM I-1630
rRNA-depleted total RNA
RNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 15 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 1 day prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).


title: mouse feces NM1200_9.36

value: the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 36 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 1, 14, 15, 21, and 22 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).


title: Mouse feces 07-07


title: Mouse feces 06-07


title: Mouse feces 08-07


title: Mouse feces 04-07


title: Mouse feces 02-07


title: Mouse feces 02-14


title: mouse feces NM1200_9.14

value: the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 14 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).


title: Mouse feces 05-07


title: mouse feces NM1200_8.35

value: the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 35 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 13, 14, 20 and 21 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).


title: mouse feces NM1200_9.15

value: the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 15 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 1 day prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).


title: mouse feces NM1200_8.36


title: mouse feces NM1200_8.42


title: Mouse feces 01-07

value: Mus musculus


title: Mouse feces 09-03

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 3 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 3 days prior


title: mouse feces NM1200_8.14


title: mouse feces NM1200_9.35


title: Mouse feces 03-07


title: Mouse feces 10-03


title: mouse feces NM1200_7.36


title: Mouse feces 08-03


title: mouse feces NM1200_8.15


title: mouse feces NM1200_7.42


title: Mouse feces 06-03


title: Mouse feces 07-03


title: Mouse feces 05-03


title: mouse feces NM1200_7.15


title: Mouse feces 04-03


title: mouse feces NM1200_7.14


title: mouse feces NM1200_6.36


title: Mouse feces 02-03


title: Mouse feces 03-03


title: mouse feces NM1200_6.35


title: mouse feces NM1200_6.15


title: Mouse feces 02-42

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 42 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 27 and 28 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 42 days prior

value: 27 and 28 days prior


title: mouse feces NM1200_5.42

description:
Bacteroides caccae ATCC 43185,Bacteroides ovatus ATCC 8483,Bacteroides thetaiotaomicron VPI-5482,Bacteroides uniformis ATCC 8492,Bacteroides vulgatus ATCC 8482,Bacteroides WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii M21/2,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Parabacteroides distasonis ATCC 8503,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Streptococcus thermophilus CNCM I-1630
rRNA-depleted total RNA
RNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 42 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 27 and 28 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).


title: mouse feces NM1200_6.14


title: mouse feces NM1200_5.15


title: mouse feces NM1200_5.14


title: mouse feces NM1200_4.42


title: mouse feces NM1200_4.15


title: mouse feces NM1200_4.14


title: mouse feces NM1200_3.42


title: mouse feces NM1200_3.14


title: Mouse feces 05-35

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 35 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 20 and 21 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 35 days prior

value: 20 and 21 days prior


title: mouse feces NM1200_2.42


title: mouse feces NM1200_3.15


title: mouse feces NM1200_2.14


title: mouse feces NM1200_2.15


title: mouse feces NM1200_1.42


title: Mouse feces 09-01

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 1 day prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 1 day prior


title: Mouse feces 04-02

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 2 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 2 days prior


title: Mouse feces 10-01


title: Mouse feces 08-02


title: Mouse feces 08-01


title: Mouse feces 09-02


title: Mouse feces 07-02


title: Mouse feces 02-02


title: Mouse feces 03-02


title: Mouse feces 01-03


title: Mouse feces 06-02


title: Mouse feces 01-02


title: Mouse feces 10-02


title: Mouse feces 05-02


title: mouse feces NM1200_1.15


title: mouse feces NM1200_6.42


title: mouse feces NM1200_1.14


title: Mouse feces 05-01


title: Mouse feces 06-01


title: Mouse feces 07-01


title: Mouse feces 04-01


title: in vitro culture NM1200_InVitro_1_1.5S

description:
rRNA-depleted total RNA
RNA isolated from a culture of B. animalis subsp. lactis (strain CNCM I-2494) grown to stationary phase in MRS medium.  Biological replicate #1 of 2.

organism: Bifidobacterium animalis subsp. lactis CNCM I-2494

source_name: in vitro culture

value: culture of B. animalis subsp. lactis

tag: strain

value: CNCM I-2494


title: in vitro culture NM1200_InVitro_2_2.5S

description:
rRNA-depleted total RNA
RNA isolated from a culture of B. animalis subsp. lactis (strain CNCM I-2494) grown to stationary phase in MRS medium.  Biological replicate #2 of 2.


title: Mouse feces 03-01


title: Mouse feces 02-01


title: in vitro culture NM1200_InVitro_2_2.5L

description:
rRNA-depleted total RNA
RNA isolated from a culture of B. animalis subsp. lactis (strain CNCM I-2494) grown to logarithmic phase in MRS medium.  Biological replicate #2 of 2.


title: Mouse feces 01-01


title: H3K4me3 ChIP-Seq in GFP-transfected C2C12 cells

city: Stockholm

first: Rickard

last: Sandberg

address: Berzelius vag 35

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description: Chromatin IP against H3K4me3

data_processing: Reads were aligned by Bowtie, with options -n 2 -m 1, against genome build mm9.

organism: Mus musculus

source_name: C2C12 muscle progenitor cells

growth_protocol: Mouse ES-cells were differentiated with B27 and N2 supplement (GIBCO) as monolayers on gelatinized cellbinding surface (Corning) with 0.5uM retinoic acid (all-trans, Sigma) at day 0 and day 2. C2C12 cells were cultured with serum unless for 3h during lipofectamine transfection.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Prep Kit (1003473).

treatment_protocol: Formaldehyde 1% crosslink 9min at 37°C. Cells were mechanically dissociated from the surface before lysis.

tag: cell type

value: GFP-transfected C2C12 cells

tag: differentiation specificity

tag: chip antibody

value: H3K4me3 (Abcam)


title: in vitro culture NM1200_InVitro_1_1.5L

description:
rRNA-depleted total RNA
RNA isolated from a culture of B. animalis subsp. lactis (strain CNCM I-2494) grown to logarithmic phase in MRS medium.  Biological replicate #1 of 2.


title: H3K4me3 ChIP-Seq in Sox3-transfected C2C12 cells

description: Chromatin IP against H3K4me3

value: Sox3-transfected C2C12 cells


title: H3K27me3 ChIP-Seq in GFP-transfected C2C12 cells

description: Chromatin IP against H3K27me3

value: H3K27me3 (Millipore)


title: Heatshock nuclear run-on RNA library 1

city: Seattle

first: Carlos

last: Araya

state: WA

address: 1705 NE Pacific

department: Genome Sciences

institute: University of Washington

description: Nascent RNA

data_processing:
Single-end, chastity-filtered reads were aligned to the UCSC sacCer2 reference genome with MAQ.
Mapped reads from replicates were merged and quality-filtered applying a Q≥30 cutoff.
Average read-depth was calculated for each gene with transcript start and end coordinates (Nagalakshmi et al. 2008).

organism: Saccharomyces cerevisiae

source_name: Heat shock-treated cells

growth_protocol: BY4742 was grown in yeast extract-peptone dextrose (YPD) medium (2% glucose, 2% peptone, 1% yeast extract) at 30°C to exponential growth phase (OD600 = 0.5-0.6)

extract_protocol: RNA was treated with Turbo DNase I, fragmented (Ambion Fragmentation kit) and used for Illumina sequencing library preparation as described (PARKHOMCHUK et al. 2009). Briefly, approximately 50 ng of total RNA was used for first strand synthesis with random hexamers. After subsequent removal of dNTPs with NucAway Spin Columns (Ambion), second strand synthesis was performed in the presence of dUTP. Double-stranded cDNA was purified with the PureLink PCR purification kit (Invitrogen) and subjected to end repair, A-tailing and adaptor ligation steps. DNA libraries were fractionated on a non-denaturing 1xTBE, 6% acrylamide gel (Invitrogen), and fragments between 250-350 bp were excised from the gel and eluted by incubation in TE at room temperature with vigorous shaking for 30 min. Uridine-containing, second strand synthesis products were digested with Uracil-N-Glycosylase (Applied Biosystems). Libraries were amplified via 16 PCR cycles. PCR products were cleaned (PureLink, AMPure) and submitted for sequencing.

treatment_protocol: For heat shock condition yeast cultures of log phase were additonally grown at 39°C for 20 min

tag: pe pcr primer f

tag: pe pcr primer r

tag: sequencing primer

value: TACACTCGGCATTCCTGCTGAACCGCTCTTCCGATCT

tag: affinity selection

value: Biotin-16-UTP selection with Dynabeads MyOne Streptavidin C1

value: 39°C for 20 min


title: Heatshock total RNA library 1

description: Total RNA


title: Heatshock nuclear run-on RNA library 3

description: Nascent RNA


title: Sox3 ChIP-Seq in Sox3-transfected C2C12 cells

description: Chromatin IP against Sox3

value: Sox3 (T. Edlund)


title: Drosophila_2-3d_whole fly_nbr null 1

city: Philadelphia

first: Bonini

last: Nancy

state: PA

address: 415 S University Ave

institute: University of Pennsylvania

description: age-matched nbr[f02257] null mutant flies

data_processing: bowtie

organism: Drosophila melanogaster

source_name: 2-3d nbr[f02257] null fly

growth_protocol: Flies were raised at 25˚C with 12hr/12hr light-dark cycle.

extract_protocol: Total RNA was extracted and purified using TRIzol reagent (Invitrogen). Libraries were prepared according to Illumina's Small RNA Sample Prep kit (v1.5) except 40ug of total RNA was used for each library.

treatment_protocol: Whole flies (pooled male and female; male:female = 1:1) were collected and aged to 2-3d.

tag: age

tag: gender

value: pooled male and female

value: whole fly

tag: genotype


title: Drosophila_2-3d_whole fly_wild type

description: age-matched control flies

source_name: 2-3d 5905 (wild-type) fly

value: control wild type (w, 5905)


title: Heatshock nuclear run-on RNA library 2

description: Nascent RNA


title: Heatshock total RNA library 2

description: Total RNA


title: Total RNA library 1

description: Total RNA

source_name: Log-phase growth cells


title: H3K27me3 ChIP-Seq in Sox3-transfected C2C12 cells

description: Chromatin IP against H3K27me3


title: Nuclear run-on RNA library 1

description: Nascent RNA


title: Nuclear run-on RNA library 3

description: Nascent RNA


title: Heatshock total RNA library 3

description: Total RNA


title: Nuclear run-on RNA library 2

description: Nascent RNA


title: 3' Nuclear run-on RNA library

description: Nascent RNA

value: ACACTCTTTCCCTACACGACGCTCTTCCGATCT


title: Total RNA library 2

description: Total RNA


title: F3 rde-4(ne299)(-/-) (transgene crossed out)

status: Public on Oct 31 2011

first: Gregory

last: Minevich

address: 701 W 168th st HHSC 726

department: Biochemistry

institute: Columbia University

description: small RNAs

data_processing: Sequences were preprocessed to remove flanking adaptor sequences and noise prior to analysis using the Hannon lab FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads were then size filtered using PRINSEQ (Schmieder and Edwards, 2011) so that only small RNAs in the range 20-30nt were considered for alignment.  Alignments of viRNAs to FHV genome (FHV-R1+GFP) were performed using Geneious v5.4.3 (word length = 6) (Drummond AJ, 2011). Aligned reads were further examined for similarity to the C. elegans genome using BLASTN (Zhang et al., 2000) to rule out any small RNAs that might match both C. elegans and FHV genomes.

organism: Caenorhabditis elegans

source_name: F3 progeny of wild-type animals that contained the FR1gfp transgene (and therefore produced viRNAs), but have lost this transgene through outcrossing with non-transgenic wild-type worms

growth_protocol: Worms were cultured on NGM plates seeded with OP50 bacteria, for each sample, 5 medium size plates (8.5 cm) of worms were harvested for RNA

extract_protocol: Worms were lysed using the TRIzol® reagent, and repetitive freezing, thawing and vortexing as previously described (Lee and Ambros, 2001). The mirVana kit (Ambion) was then used for isolation of <200nt RNAs following size selection of small RNAs of 18–30 bases by denaturing polyacrylamide gel fractionation. Small RNA library was constructed using the Illumina v1.5 Small RNA Cluster Generation Kit® and sequenced using the Illumina/Solexa GAIIX platform (Illumina, Inc., San Diego, CA).

treatment_protocol: The samples were harvested 48 hours after triggering of viral propagation. Viral induction was achieved by heat-shocking young adults first for 1 hour at 37ºC and then for an additional 3 hours at 33ºC

value: whole organism


title: rde-4(ne299) (-/-) (negative control)

description: small RNAs

source_name: rde-4(-/-) mutants (negative control as no viRNAs are expected to be produced)


title: FR1gfp (positive control)

description: small RNAs

source_name: FR1gfp-transgenic worms that can mount an RNAi response and should contain viRNAs (positive control)


title: Mouse feces 09-28

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 28 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 6, 7, 13 and 14 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

tag: host organism

value: Mus musculus

tag: host strain

tag: time of gut bacteria

value: 28 days prior

value: 6, 7, 13 and 14 days prior


title: Total RNA library 3

description: Total RNA

tag: treatment


title: 5-hmC-mediated epigenetic dynamics  (Mecp2.KO.2) [5hmC Capture and Seq]

status: Public on Oct 30 2011

city: Atlanta

first: Keith

middle: E

last: Szulwach

state: GA

address: 615 Michael Street, Whitehead Suite 301

department: Human Genetics

institute: Emory University

description:
Mecp2.KO.2
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture

data_processing: Processed data not provided.

source_name: Mecp2-/ytm1.1Bird Cerebellum

extract_protocol: Genomic DNA was purified from tissue using Wizard genomic DNA purification kit (Promega) with additional Proteinase K treatment and rehydrated in 10 mM Tris (pH 7.9). Genomic DNA samples were sonicated to 100-500 bp by Misonix sonicator 3000 (using microtip, 3 pulses of 30 seconds each with 2 min of rest and a power output level of two) or Bioruptor UCD-200 sonicator (Diagenode, Sparta). Output selector switch was set on High (H), and sonication interval was 30 seconds with 30 cycles of sonication performed. 5-hmC labelling reactions were performed in a 100-ÂµL solution containing 50 mM HEPES buffer (pH 7.9), 25 mM MgCl2, 300 ng/Î¼L sonicated genomic DNA (100-500 bp), 250 Î¼M UDP-6-N3-Glu or UDP-Glu, and 2.25 Î¼M wild-type BGT. The reactions were incubated for 1 hr at 37 Â°C. After the reaction, the DNA substrates were purified by Qiagen DNA purification kit or by phenol-chloroform precipitation and reconstituted in H2O. Biotin addition by click chemistry was performed by adding 150 Î¼M dibenzocyclooctyne modified biotin into the DNA solution, and the reaction mixture was incubated for 2 hr at 37 Â°C. The DNA samples were then purified by Qiagen DNA purification kit. Biotin Labeled 5-hmC DNAs were purified/enriched by Pierce Monomeric Avidin Kit (Thermo) following manufacturerâs recommendations. After elution, the biotin-5-N3-gmC containing DNA was concentrated by 10 K Amicon Ultra-0.5 mL Centrifugal Filters (Millipore) and purified by Qiagen DNA purification kit. 25 ng genomic DNA, 5-hmC-captured DNA, or control captured DNA (in the absence of biotin) were used to initiate library preparation following the Illumina protocol for âPreparing Samples for ChIP Sequencing of DNAâ (Part# 111257047 Rev. A). DNA fragments ~150-300 bp were gel purified after the adapter ligation step and amplified by 18 cycles PCR.

value: 5hmC enriched DNA

tag: Sex

value: Male


title: 5-hmC-mediated epigenetic dynamics  (Input.2) [5hmC Capture and Seq]

description:
Input.2
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture

source_name: C57/BL6 Cerebellum

value: Non-enriched genomic DNA


title: 5-hmC-mediated epigenetic dynamics  (Input.1) [5hmC Capture and Seq]

description:
Input.1
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (1yr.Hipp.2) [5hmC Capture and Seq]

description:
1yr.Hipp.2
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture

source_name: C57/BL6 Hippocampus


title: 5-hmC-mediated epigenetic dynamics  (1yr.Hipp.1) [5hmC Capture and Seq]

description:
1yr.Hipp.1
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (6wk.Hipp.3) [5hmC Capture and Seq]

description:
6wk.Hipp.3
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (6wk.Hipp.2) [5hmC Capture and Seq]

description:
6wk.Hipp.2
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (P7.Cb.2) [5hmC Capture and Seq]

description:
P7.Cb.2
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (6wk.Cb.1) [5hmC Capture and Seq]

description:
6wk.Cb.1
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (1yr.Cb.1) [5hmC Capture and Seq]

description:
1yr.Cb.1
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (P7.Hipp.1) [5hmC Capture and Seq]

description:
P7.Hipp.1
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (Female.Input) [5hmC Capture and Seq]

description:
Female.Input
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture

source_name: Human Cerebellum

value: Female


title: 5-hmC-mediated epigenetic dynamics  (P7.Hipp.2) [5hmC Capture and Seq]

description:
P7.Hipp.2
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (P7.Cb.1) [5hmC Capture and Seq]

description:
P7.Cb.1
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (6wk.Cb.2) [5hmC Capture and Seq]

description:
6wk.Cb.2
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (Male.Cb.Input) [5hmC Capture and Seq]

description:
Male.Cb.Input
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (Male.Cb.2) [5hmC Capture and Seq]

description:
Male.Cb.2
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: F3 FR1gfp; rde-4(ne299)(-/-)

description: small RNAs

source_name: FR1gfp; rde-4(-/-) worms that are two generations away from their rde-4(+/-) grandparents, i.e. worms that can themselves not produce viRNAs, but may have inherited viRNA from their grandparents

tag: tissue


title: Tumor brain tissue

first: Leslie

middle: Y

last: Chen

address: 401 Terry Avenue North

institute: Institute for Systems Biology

data_processing: Alignment: Sequencing reads were mapped to the human genomes GRCh 37 using RNASEQR and other programs. Only uniquely mapped reads were recorded. Three mismatches were allowed in the process of RNASEQR, ERANGE. Default threshold were applied in the other programs.

extract_protocol: Total RNA was extracted from 0.5 gram of frozen tissue using the miRNeasy mini kit (Qiagen, Germantown, MD), and the RNA quality was checked using Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). We performed 75-bp single-end RNA sequencing (RNA-seq) on the Illumina Genome analyzer II following the manufacturer’s suggestion (Illumina, San Diego, CA).  In short, 10 µg high quality RNA was used to enrich poly-adenylated RNA, which was then fragmented, reverse transcribed followed by the synthesis of the second strand.  Each double-stranded cDNA fragment resulting was then blunt-ended, adenylated, ligated to adaptors, and size-purified for ~200 bp fragments.  These size-selected cDNA templates were further enriched using PCR and checked for quality on the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). We performed 75-bp sequencing using the SBS sequencing kit v2 (Illumina, San Diego, CA) one lane for each sample, and obtained 25.3 million, and 23.2 million high quality sequences for the tumor and the peripheral brain RNA samples, respectively.

value: Tumor brain tissue

tag: phenotype

value: glioblastoma multiforme


title: Peripheral brain tissue

value: Peripheral brain tissue


title: 5-hmC-mediated epigenetic dynamics  (Mecp2.KO.1) [5hmC Capture and Seq]

description:
Mecp2.KO.1
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture

tag: strain


title: 5-hmC-mediated epigenetic dynamics  (Rata.Brainstem) [5hmC Capture and Seq]

description:
Rata.Brainstem
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture

organism: Rattus norvegicus

source_name: Rat Brainstem

value: Sprague Dawley


title: 5-hmC-mediated epigenetic dynamics  (6wk.Hipp.1) [5hmC Capture and Seq]

description:
6wk.Hipp.1
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: 5-hmC-mediated epigenetic dynamics  (1yr.Cb.2) [5hmC Capture and Seq]

description:
1yr.Cb.2
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: Soluble_20min_(S20A_20110519_4)

status: Public on Oct 27 2011

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Solubilized MNase-protected DNA fragments, 20 minute digestion

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 20bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file S20A.Novoalign.sam) Because the DNA sample was pooled with DNA from Drosophila melanogaster, we removed all paired reads that mapped to both organisms. 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file S20A.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: soluble chromatin

extract_protocol: Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and H2A.Z, Genes Dev 21, 1519-1529], and the combined S1+S2 supernatants were clarified by centrifugation in a fixed-angle Sorvall SS34 rotor at 12,000 rpm at 4oC for 10 min at least twice or until no visible pellet remained. ChIP was performed as previously described [Furuyama and Biggins, (2007)], and DNA was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_library_protocol_GEO.pdf.

tag: medium

value: YEPD grown:OD=0.8

tag: antibody

tag: sample type


title: Soluble_2.5min_(S2_5A_20110519_3)

description: Solubilized MNase-protected DNA fragments, 2.5 minute digestion

data_processing: 1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 20bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file S2_5A.Novoalign.sam) Because the DNA sample was pooled with DNA from Drosophila melanogaster, we removed all paired reads that mapped to both organisms. 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file S2_5A.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: Nuclei_20min_(N20_20110622_2)

description: All MNase-protected DNA fragments, 20 minute digestion

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file N20_20110622_2.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file N20_20110622_2.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: total nuclei


title: 5-hmC-mediated epigenetic dynamics  (Female.Cb.2) [5hmC Capture and Seq]

description:
Female.Cb.2
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: Pellet_2.5min_(P2_5_20110519_7)

description: Insoluble MNase-protected DNA fragments, 2.5 minute digestion

data_processing: 1. We used Novoalign to map 25bp paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file P2_5_20110519_7.sam) Because the DNA sample was pooled with DNA from Drosophila melanogaster, we removed all paired reads that mapped to both organisms. 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file P2_5_20110519_7.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: insoluble chromatin


title: Pellet_20min_(P20_20110519_8)

description: Insoluble MNase-protected DNA fragments, 20 minute digestion

data_processing: 1. We used Novoalign to map 25bp paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file P20_20110519_8.sam) Because the DNA sample was pooled with DNA from Drosophila melanogaster, we removed all paired reads that mapped to both organisms. 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file P20_20110519_8.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: 5-hmC-mediated epigenetic dynamics  (Female.Cb.1) [5hmC Capture and Seq]

description:
Female.Cb.1
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: Hsa-Diff

city: Chicago

first: Vincent

middle: J.

last: Lynch

address: 920 E. 58th Street

institute: The University of Chicago

description: Human Differentaited

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (GRCh37) and armadillo (dasNov2) genomes using the Illumina Genome Analyzer Pipeline and custom scripts to map onto Ensembl genomes. All reads mapping with two or fewer mismatches were retained.
Txt files containing the read counts mapped to genomes are provided on the Series record. For human the data is shown as mapped bases per gene while the armadillo is shown as reads mapped per gene. To turn the human data into reads mapped per gene you can divide mapped bases by 74.

source_name: Endometrial stromal cells (ESC)

extract_protocol: For RNA extraction we used a Qiagen RNeasy midi kit following the manufacturers protocol with an on-column DNase treatment. Libraries were prepared according to Illumina's instructions for mRNA-Seq using 75bp reads.

value: ESC


title: 5-hmC-mediated epigenetic dynamics  (Male.Cb.1) [5hmC Capture and Seq]

description:
Male.Cb.1
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging
library strategy: 5hmC Capture and Sequencing
library selection5hmC Capture


title: Nuclei_2.5min_(N2.5_20110622_1)

description: All MNase-protected DNA fragments, 2.5 minute digestion

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file N2.5_20110622_1.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file N2.5_20110622_1.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

extract_protocol: Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and H2A.Z, Genes Dev 21, 1519-1529], and the combined S1+S2 supernatants were clarified by centrifugation in a fixed-angle Sorvall SS34 rotor at 12,000 rpm at 4oC for 10 min at least twice or until no visible pellet remained. ChIP was performed as previously described [Furuyama and Biggins, (2007)], and DNA was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_libarary_protocol_GEO.pdf.


title: Nuclei_20min_(N20A_20110519_2)

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file N20A_20110519_2.sam) Because the DNA sample was pooled with DNA from Drosophila melanogaster, we removed all paired reads that mapped to both organisms. 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file N20A_20110519_2.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

value: All MNase-protected DNA fragments, 20 minute digestion


title: H2O_Sorghum_Shoot_3

city: College Station

first: Patricia

last: Klein

state: TX

department: Department of Horticulture

institute: Texas A&M University

data_processing: Sequences were processed using Illumina's CASAVA v1.6 software.  Sequences were trimmed to 50bp and aligned to the sorghum genome (sbi1 downloaded from ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v6.0/Sbicolor/assembly/) using the ELAND_rna algorithm and raw counts per gene were returned using CASAVA v1.6 software after providing the software with the necessary sorghum reference files.  These included an abundant sequences file containing sorghum chloroplast, mitochondria and repeat sequences, an exon coordinates file and a splice junctions file (both files generated from Sbi1.4.gff3 downloaded from ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v6.0/Sbicolor/annotation/ using a combination of custom perl scripts and those provided with the CASAVA V1.6 software package), genome sequence files and a genome size file.  The raw counts from the output of CASAVA v1.6 were given to the edgeR package [48-50] in R and quantile normalized together within edgeR functions.

organism: Sorghum bicolor

source_name: Shoots from untreated 9d sorghum seedings

growth_protocol: Seeds of Sorghum bicolor genotype BTx623 were germinated by soaking in distilled, aerated water overnight and then transferred to moist germination paper for 3 days.  The seedlings were then transferred to 0.5x Hoagland's solution and allowed to grow for an additional 5 days in a controlled environment chamber with a day length of 12 hrs, 50% humidity, and day and night temperatures of 31C and 22C, respectively.

extract_protocol: RNA was extracted using the Qiagen miRNeasy kit. cDNA was generated using the RNA-Seq kit according to the manufacturer's protocol (Illumina Inc., San Diego, CA).

treatment_protocol: At 8 days, the plants were treated with the denoted solutions for 27 hours.  Three groups of 10 plants each were harvested post-treatment as paired shoots and roots; the roots and shoots sequenced in each run are two parts from the same plants.

tag: line

value: Shoot

tag: rta version


title: PEG_Sorghum_Shoot_1

source_name: Shoots from 9d sorghum seedings treated with 20% PEG-8000 for 27 hrs


title: NaOH_Sorghum_Shoot_1

source_name: Shoots from 9d sorghum seedings treated with 0.2M NaOH for 27 hrs

value: 0.2M NaOH


title: ABA_Sorghum_Shoot_3

source_name: Shoots from 9d sorghum seedings treated with 20µM exogenous ABA for 27 hrs

value: 20µM exogenous ABA for 27 hrs


title: H2O_Sorghum_Shoot_1


title: input DNA

city: Tokyo

first: Ryoji

last: Fujiki

address: 1-1-1 yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

country: Japan

institute: The university of Tokyo

description: input DNA

data_processing: Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: HeLa S3 cells

growth_protocol: HeLa S3 cells were routinely maintained in DMEM supplemented with 10% FBS

extract_protocol:
The genomic DNA was extracted from the immunoprecipitated nucleosomes or the input by QIAquick PCR purification kits (QIAGEN) as described in the manufacture's instruction.
Chromatin was digested with MNase 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 18 cycles and library fragments of ~220 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.

tag: cell type

value: Human epithelial carcinoma cell line

tag: chip antibody


title: PEG_Sorghum_Shoot_3


title: NaOH_Sorghum_Shoot_2


title: NaOH_Sorghum_Shoot_3


title: PEG_Sorghum_Shoot_2


title: H2O_Sorghum_Shoot_2


title: ABA_Sorghum_Shoot_2


title: H2B K120 ub_ChIPSeq

description: Chromatin IP against H2B K120 ub

value: H2B K120 ub (clone:56)


title: Hsa-Undiff

description: Human Undifferentiated


title: ABA_Sorghum_Shoot_1


title: Dno-Preg

description: Armadillo

organism: Dasypus novemcinctus

source_name: Mid-stage pregnant endometrium

value: Endometrium


title: H2O_Sorghum_Root_3

source_name: Roots from untreated 9d sorghum seedings

value: Root


title: NaOH_Sorghum_Root_1

source_name: Roots from 9d sorghum seedings treated with 0.2M NaOH for 27 hrs


title: NaOH_Sorghum_Root_2


title: H2B S112 GlcNAc_ChIPSeq

description: Chromatin IP against H2B S112 GlcNAc

value: H2B S112 GlcNAc Mab (clone:MG048A)


title: MDA-231_shEZH2_HOTAIR_odd

status: Public on Oct 29 2011

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description: ChIRP-seq of HOTAIR from MDA-231 cells (shEZH2)

data_processing: Briefly, raw reads from "even" and "odd" in each samples were aligned using "Bowtie," and merged so that only signals common in both "even" and "odd" are retained (merge.wig files). These files were then converted into SAM formats for peaking calling by MACS. For complete methods please refer to the paper.

growth_protocol: Drosophila cell line: 10% Heat-Inactivated FBS in Schneider medium (pen/strep). Human cell lines: 10% FBS in DMEM (pen/strep)

extract_protocol: Cells are crosslinked in 1% glutaraldehyde and lysates clarified by sonication. lincRNA:chromatin adducts are isolated using specific probes. 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.

tag: cell line

value: MDA-231 cell line overexpressing human HOTAIR with EZH2 knocked down

tag: lincrna probes

value: HOTAIR


title: mouse feces NM1200_7.35

description:
Bacteroides caccae ATCC 43185,Bacteroides ovatus ATCC 8483,Bacteroides thetaiotaomicron VPI-5482,Bacteroides uniformis ATCC 8492,Bacteroides vulgatus ATCC 8482,Bacteroides WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii M21/2,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Parabacteroides distasonis ATCC 8503,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Streptococcus thermophilus CNCM I-1630
rRNA-depleted total RNA
RNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 35 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 13, 14, 20 and 21 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

data_processing: After parsing each sequencing lane's data by barcode (where appropriate), we excised the barcodes and mapped the reads to an appropriate set of reference genomes using the ssaha2 algorithm.  Minimum score thresholds for ssaha were selected based on the distribution of scores for all mapped reads of a 32-nt barcoded sample and a 36-nt non-barcoded sample (29 was selected as the minimum score for 32-nt barcoded samples; 33 was the minimum score used for 36-nt and 76-nt non-barcoded samples). Although an 18-nt read is sufficient to map more than 90% of the sequencing reads, even at 32-36 nucleotides a large fraction of reads map to multiple locations (within a genome and/or across genomes). Reads that map non-uniquely were added to each gene in proportion to each gene's fraction of unique-match counts (e.g., a non-unique read that maps equally well to gene A with 18 unique reads and gene B with 2 unique reads will result in 0.9 counts being tallied to gene A and 0.1 counts being tallied to gene B). We added a pseudocount (i.e. added a value of 1) to each gene count prior to normalization to account for differences in sampling depth, although clearly a more appropriate model-based approach to smooth lower expression values is needed in the future, particularly with mixed species samples where one or more species is clearly undersampled. Raw counts were ultimately normalized to reads/kb gene length/million mapped reads (RPKM) following gene count assignments.

source_name: mouse feces

value: fecal pellet of a mouse

tag: source


title: PEG_Sorghum_Root_2

source_name: Roots from 9d sorghum seedings treated with 20% PEG-8000 for 27 hrs


title: H2O_Sorghum_Root_2


title: NaOH_Sorghum_Root_3


title: H3K4me3_LKOJarid1b

city: Copenhagen

first: Sandra

middle: Ursula

last: Schmitz

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research and Innovation Centre

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genomes using the the BOWTIE tool with parameters: -t --best -k 1 -y -p 4 --solexa1.3-quals --chunkmbs 512 -n 2 -l 28 -e 120 .

source_name: embryonic stem cells

growth_protocol: E14TG2a.4 feeder independent ES cells were cultured on 0.1% gelatin-coated plates in Glasgow medium (Sigma) supplemented with glutamine (Gibco), non-essential amino acids (Gibco), sodium pyruvate (Gibco), 50 ÂµM Ã-mercaptoethanol, and 15% foetal bovine serum (HyClone) in the presence of LIF. Recombinant lentiviruses encoding Jarid1b shRNA were produced by standard methods employing co-transfection of PLKO.1 shRNA and packaging vectors in 293FT cells. ESCs were transduced with lentiviral particles for >16 h, and selected with 2 Âµg/Âµl Puromycin (Invitrogen) 48 h after transduction.

extract_protocol: DNA was adaptor-ligated and amplified using a kit from Illumina (IP-102-1001). The amplified DNA from hme/me-DIP or ChIP-seq experiments was analyzed by Solexa/Illumina high-throughput sequencing. The tags were mapped to the mouse genome (assembly mm9) with the Bowtie alignment tool26. To avoid any PCR bias we allowed only one count (match) per chromosomal position thus eliminating spurious spikes. Peak detection and binding analysis were performed using the MACS program at an FDR cut-off value <0.2. IgG was used for normalization

treatment_protocol: Cells were transduced with LKO scramble or Jarid1b

tag: chip or dip

value: ChIP

value: LKO Jarid1b ESCs

tag: chip/dip antibody

value: H3K4me3 [Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb]

tag: chip/dip antibody vendor

value: Cell Signaling

tag: chip/dip antibody lot#

tag: chip/dip antibody catalog#


title: H2O_Sorghum_Root_1

tag: tissue

tag: treatment


title: PEG_Sorghum_Root_3


title: PEG_Sorghum_Root_1


title: ABA_Sorghum_Root_2

source_name: Roots from 9d sorghum seedings treated with 20µM exogenous ABA for 27 hrs


title: Jarid1b_2

value: E14 ESCs


title: H3K4me3_LKOScr

value: LKO Scr ESCs


title: Jarid1b_1


title: ABA_Sorghum_Root_3


title: ABA_Sorghum_Root_1


title: dnmt3a_wt_kras_lung _tumor_WT1

status: Public on Oct 26 2011

city: Cambridge

first: Qing

last: Gao

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description: Chromatin IP against 5mC

data_processing: Reads were mapped to the mouse genome (mm9) using bowtie with options -m 3, -n 3, -best. If a read mapped to more than one place in the genome one place was selected at random. Reads were extended 400 nt. We only kept 1Kb windows that had at least 10 reads in one of the samples. All gene bodies and promoters were kept in the analysis. We added one pseudocount to all the features (1kb windows, gene bodies and promoters) in all the samples to generate the proccessed files provided (readsin1kbWindows.txt, readsinPromoters.txt, readsinGeneBodies.txt ).

source_name: tumor

growth_protocol: Mice were fed chow diet ad libitum

extract_protocol: MeDIP seq was performed using the Magmedip kit (mc-magme-A10, Diagenode) according to manufacturers’ protocol. In brief, 30 mg DNA was sonicated with the Bioruptor sonicator (Diagenode) to 300-500bp fragments. Sonicated DNA was denatured for 5min at 95°C, quickly chilled on ice and immunoprecipitated with 5-methylcytosine antibody in presence of magnetic beads at rotating wheel overnight at 4°C. Magnetic beads with immunoprecipitated DNA were washed three times. Following Ipure kit’s protocol (Diagenode AL-100-0100), DNA was eluted from the beads and purified. Using Illumina Chip-Seq sample prep kit (IP-102-1001, Illumina), DNA was end-repaired, adenylated and adapters were ligated. DNA was size selected (300-500bp) on 2% agarose gel and gel purified with  Gel extraction kit (Qiagen). DNA was PCR amplified for 18 cycles and purified with PCR purification kit (Qiagen). Libraries were sequenced on the genome analyzer II (Illumina).

treatment_protocol: Adenoviral Cre recombinase was delivered to mice of 6 to 12 week old mice via intratracheal approach.

tag: strain

value: MeDIP antibody

tag: manufacturer/source

value: Diagenode

tag: catalog number

tag: lot/batch number

value: lung tumor

tag: genotype/variation

value: dnmt3a wt kras


title: mouse_colon_control_long_3

first: Eveline

last: Steine

description: Reduced representation bisulphite sequencing

data_processing: A bisulfite-aware short-read aligner was used to align reads to the appropriate RRBS library, allowing up to 2 mismatches.  The RRBS library was generated by in silico MspI digestion, fractionation, and conversion.  Mapped reads were assigned to promoters, if possible, defined as +/-2kb from the transcription start site of NCBI Refseq transcripts. A CpG was defined as scorable if it was assayed by at least 5 reads, and a promoter with least 5 scorable CpGs was itself defined as scorable.  In each sample, the methylation fraction of a promoter was calculated as the mean of scorable CpGs.

source_name: colon

extract_protocol: The library was constructed with the DNA sample kit (Illumina, IP-102-1001). Mouse genomic DNA was digested with MspI.  Small and a large size fragment bands, 40-120 and 120-220 bp, respectively, were isolated from a 3% Nusieve gel. DNA was purified with phenol:chloroform, end-repaired and adenylated. The fragments were ligated to the 3’T-overhang methylated-cytosine-containing adapters. After adapter ligation, DNA was bisulfite treated with Qiagen’s Epitect bisulfite kit, with a modification (adding two additional bisulfite conversion cycles) of the manufacturers’ protocol. Bisulfite-treated DNA was PCR-amplified for 24 cycles. Small and large library fragments (120-220 and 220-310 bp, respectively) with the adapters were size-selected on a 3% Nusieve gel. Libraries were sequenced on the Genome Analyzer II (Illumina).

value: regular drinking water

tag: fragment size

tag: cell type

value: epithelial cells isolated from the colon


title: microRNA form watermelon grafted onto bottle gourd

city: Hangzhou

last: Liu

address: No.198, Shiqiao Road, Jianggan District

country: China

institute: Zhejiang Academy of Agricultural Sciences

data_processing: The raw sequenced sequences (sequ-seqs) were subjected to Illumina pipeline filter (Solexa 0.3). Each of the pipeline filter treated data set was further processed with ACGT101-miR, including classify unique sequence family, adapter (ADT) dimmer (5' ADT, 3' ADT & 5' ADT and 3'ADT hooked together without insertion) filter, junk (80% of A, or C, or G, or T, or 3N; 10 repeat of dimmer, 6 repeat of trimmer, or 5 repeat of tetramer; 7 consecutive A, 8 consecutive C, 6 consecutive G or 7 consecutive T; contained only A and C or only G and T) filter, length filter (<16 nt or > 26 nt were removed), simple sequence (80% of A, or C, or G, or T, or 3N) filter, low copy (< 3) filter, mRNA, RFam & repbase filter (unique seqs were blasted against mRNA, RFam & repbase. If a unique sequence hits any of the mRNA, or RFam & repbase with 1 error allowed, it was filtered out). After a series of filtering, the remaining sequences (we called mappable sequences) were blasted to miRBase 16.0 and genome (chicken and MDV) to identify known and novel miRNAs. Length variation at both 3' and 5 ends and one mismatch inside of the sequence were allowed in alignment.

organism: Citrullus lanatus

source_name: watermelon

growth_protocol: Plants were cultivated in the growth chamber at a photosynthetic photon flux density (PPFD) of 600 μmol m-2 s-1 with a photoperiod of 12 h, 25°C (day) and 17°C (night) temperature, and between 50% and 85% humidity until two true-leaf stage.

extract_protocol: Small RNA fragments (14-30 bases) were isolated from the total RNA pool with a Novex 15% TBE-Urea gel (Invitrogen). The purified small RNAs were then ligated with 5’ adaptors (Illumina, San Diego, CA, USA). To remove these unligated adaptors, the ligation products (40–60 bases in length) were gel purified on a Novex 15% TBE-Urea gel. Subsequently, a 3’ adaptor (Illumina) was ligated to the 5’ ligation products. After gel purification on a Novex 10% TBE-Urea gel (Invitrogen), RNA fragments with adaptors at both ends (70–90 bases in length) were reversely transcribed, and the resulting cDNAs were subjected to 15 PCR cycles using the adaptor primers. The amplification products (around 90 bases) were excised from a 6% TBE-Urea gel (Invitrogen). The purified cDNAs library was used directly for cluster generation and sequencing analysis by an Illumina/Solexa G1 sequencer.

value: L. cv. IVSM9

value: the part above cotyledons

tag: development stage

value: two true-leaf stage

tag: growth condition

value: grafted onto bottle gourd


title: microRNA form self-grafted watermelon

description: microRNA form self-grafted watermelon

value: self-grafted


title: mouse_colon_induced_long_1

treatment_protocol: Mice were given doxycycline drinking water (0.5g/l) for 3 months. Dox water was changed every 3 days.

value: Doxycycline drinking water (0.5g/l) for 3 months. Doxycycline water was changed every 3 days.


title: mouse_colon_control_short_2


title: mouse_colon_control_short_1


title: dnmt3a_deficient_kras_lung_tumor_KO2

description: Chromatin IP against 5mC

tag: antibody

value: dnmt3a deficient kras


title: dnmt3a_deficient_kras_lung_tumor_KO1

description: Chromatin IP against 5mC


title: mouse_colon_induced_short_3


title: mouse_colon_control_long_1


title: mouse_colon_induced_long_3


title: mouse_colon_induced_short_2


title: mouse_colon_induced_short_1


title: dnmt3a_wt_kras_lung_tumor_WT2

description: Chromatin IP against 5mC


title: microRNA form watermelon grafted onto squash

value: grafted onto squash


title: sampling retroviral library

status: Public on Oct 25 2011

city: Vienna

first: Ulrich

last: Elling

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

description: sampling retroviral library

data_processing: Illumina GA Pipeline RTA 1.8.7; reads were mapped to the mouse mm9 genome using bowtie 0.12.5

source_name: haploid mouse ES cells

growth_protocol: ES cells were grown in standard ES cell medium

extract_protocol: inverse PCR: In brief, genomic DNA preparations were digested using DpnII or MseI, purified using the QIAquick Gel Extraction Kit, and fragments ligated at a concentration of 3µg/ml over night. The ligase was then heat inactivated and rings were re-digested in ligase buffer using the enzymes NheI and PvuII. Linearized fragments were purified using the QIAquick Gel Extraction Kit and subjected to PCR using Accuprime Taq polymerase (Invitrogen), primers FS Solexa upstream and FS Solexa downstream, and a BioRad Thermal Cycler. The program of 95ºC for 30 sec, 60ºC for 30 sec, and 68ºC for 105 sec was repeated 36 times. Amplicons were loaded on agarose gels, eluted and subjected to deep sequencing using an Illumina Genome Analyzer and primer FS flowcell. The following iPCR primers were used:   upstream primer  AATGATACGGCGACCACCGAGATCGCCAGTCCTCCGATTGA  downstream primer  CAAGCAGAAGACGGCATACGAGTTCCTATTCCGAAGTTCCTATTCTCTA  flowcell sequencing primer  TGATTGACTACCCGTCAGCGGGGGTCTTTCA

treatment_protocol: selection was performed with G418 or ricinus communis

value: haploid mouse ES cells

tag: retrovirus used

value: reFlipROSAß-Geo(Cre)

tag: selection

tag: transfection batch


title: mouse_colon_control_short_3


title: Nrl-KO_rep3

city: BETHESDA

first: HARSHA

middle: KARUR

last: RAJASIMHA

state: MD

address: 6 CENTER DR RM 303D

department: ITMB

institute: NEI

description: RNA-seq of Nrl-/- mouse retina

data_processing: Illumina Casava1.7 software, BWA, Partek

source_name: Retina

growth_protocol: Normal mouse growth protocol.

extract_protocol: Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.

tag: genotype

value: Nrl-/-

tag: age

value: post natal day 21

value: Retina


title: Nrl-KO_rep2

description: RNA-seq of Nrl-/- mouse retina

tag: tissue


title: sequencing ricinus screen inversions

description: sequencing ricinus screen inversions

value: ricinus communis


title: mouse_colon_control_long_2

tag: treatment


title: dnmt3a_deficient_kras_lung_tumor_KO3

description: Chromatin IP against 5mC

tag: strain

value: MeDIP antibody

value: Diagenode

value: lung tumor


title: mouse_colon_induced_long_2

value: epithelial cells isolated from the colon


title: wild-type_rep3

description: RNA-seq of wild type mouse retina

value: wild type


title: UT-A_ChipSeq_HeLa-S3_Input

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromChip

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell lineage

value: ectoderm

tag: treatment description

value: No special treatment or protocol applies

tag: controlid

tag: labversion

value: Illumina, pooled,fseq v 1.84

tag: cell karyotype

value: cancer

tag: cell sex

value: F

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: align_on_cluster_bwa.pl v 1


title: UT-A_ChipSeq_HepG2_Input

tag: cell description

value: hepatocellular carcinoma

value: endoderm

value: M

tag: antibody


title: UT-A_ChipSeq_A549_Input

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: fseq v 1.84


title: UT-A_ChipSeq_MCF-7_vehicle_c-Myc

treatment_protocol: vehicle

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: antibody antibodydescription

value: Rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:MYC

tag: antibody targetdescription

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05

tag: replicate

value: vehicle

value: Charcoal stripped hormone-free FBS for 72 hours (Crawford)

value: c-Myc

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin

value: Santa Cruz Biotech

tag: replicate description

value: tier 1


title: UT-A_ChipSeq_Gliobla_Pol2

source_name: Gliobla

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

tag: treatment

value: No special treatment or protocol applies

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_H54,p-value cutoff:0.05

value: mouse monoclonal, clone 8WG16

value: Gliobla/Input

value: align_on_cluster_bwa.pl v 1


title: UT-A_ChipSeq_K562_CTCF

tag: datatype description

value: Rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

value: baseAlignCounts.pl v 1,1% ENCODE array platform validation tests,p-value cutoff:0.05,fseq v 1.84, iff_K562

value: rabbit polyclonal


title: UT-A_ChipSeq_Gliobla_CTCF

tag: treatment description


title: UT-A_ChipSeq_MCF-7_vehicle_CTCF

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: controlid

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05

value: vehicle

value: Charcoal stripped hormone-free FBS for 72 hours (Crawford)

value: CTCF


title: UT-A_ChipSeq_MCF-7_CTCF

value: ChipSeq

value: Chromatin IP Sequencing

value: No special treatment or protocol applies

tag: labversion

value: tier 1


title: UT-A_ChipSeq_Monocytes-CD14+_Input

tag: cell

value: Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2:not in 2011 analysis

value: fseq v 1.84

tag: cell lineage

value: mesoderm

value: F

value: Input

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: UT-A_ChipSeq_H1-hESC_Pol2

growth_protocol: missing

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: mouse monoclonal, clone 8WG16

value: align_on_cluster_bwa.pl v 1


title: UT-A_ChipSeq_H1-hESC_CTCF

value: Rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

value: CTCF

value: rabbit polyclonal


title: UT-A_ChipSeq_MCF-7_Pol2

value: ChipSeq

value: Chromatin IP Sequencing

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: No special treatment or protocol applies

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05

value: tier 1


title: UT-A_ChipSeq_GM12878_Input

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: fseq v 1.84

tag: cell karyotype

value: normal

value: mesoderm

tag: cell sex

value: F

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: UT-A_ChipSeq_GM12892_CTCF

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

value: align_on_cluster_bwa.pl v 1


title: UT-A_ChipSeq_HUVEC_c-Myc

source_name: HUVEC

value: ChipSeq

value: Chromatin IP Sequencing

value: Rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:MYC

tag: antibody targetdescription

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

tag: antibody vendorname

value: Santa Cruz Biotechnology

value: baseAlignCounts.pl v 1,p-value cutoff:0.01,fseq v 1.84, iff_HUVEC

tag: antibody

value: c-Myc

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin

value: Santa Cruz Biotech

value: HUVEC/Input


title: UT-A_ChipSeq_GM12878_c-Myc

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: No special treatment or protocol applies

tag: antibody vendorid

value: baseAlignCounts.pl v 1,1% ENCODE array platform validation tests,fseq v 1.84, iff_GM12878,p-value cutoff:0.001

tag: replicate

tag: replicate description

value: tier 1


title: UT-A_ChipSeq_HepG2_c-Myc

tag: datatype

tag: datatype description

value: hepatocellular carcinoma

tag: treatment

value: baseAlignCounts.pl v 1,p-value cutoff:0.01,fseq v 1.84, iff_HepG2,1% ENCODE array platform validation tests


title: UT-A_ChipSeq_K562_Input

tag: treatment description

tag: controlid

tag: labversion

value: fseq v 1.84,Illumina

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: cancer

value: mesoderm

value: F

value: Input

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: align_on_cluster_bwa.pl v 1