title: EBF1 ChIP-seq [8246.6]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8246.6.bed.gz: mm9

source_name: Pro-B

value: anti EBF1 #0647 homemade

value: 4-5 day culture (Cd19+ cells from Bone marrow)

value: Bone Marrow


title: 05142008_209LAAAXX_B5

status: Public on Mar 17 2012

type: SRA

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description: H3K9,K14Ac ChIPSeq in mES cells

library_source: genomic

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Supplementary_files_format_and_content: Alignment (ylf) files: The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations determined by bowtie. The file contains the locations of the bowtie aligned reads with the following format:
#BWT1 (read category BWT1)
>1 (chromomsome 1)
-12345 (minus strand read)
-9876 (minus strand read)
54321 (plus strand read)
>2 (chromomsome 2)
-67890 (minus strand read)
98765 (plus strand read)
132323 (plus strand read)
#BWT2 (read category BWT2)
etc..

molecule: genomic DNA

organism: Mus musculus

source_name: Chromatin IP against H3K9,K14Ac

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

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: chip antibody

tag: antibody catalog number

value: Upstate 06-599

tag: cell type

value: V6.5 embryonic stem cells


title: 03212008_203MTAAXX_B7

description: H2Bub ChIPseq in mES cells

source_name: Chromatin IP against H2Bub

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

value: Moshe Oren MOSHE OREN LABORATOR


title: Seq for WM262 melanoma cells WCE

description: WM262 WCE

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Supplementary_files_format_and_content: Alignment (ylf) files: The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations determined by bowtie. The file contains the locations of the bowtie aligned reads with the following format:
#BWT1 (read category BWT1)
>1 (chromomsome 1)
-12345 (minus strand read)
-9876 (minus strand read)
54321 (plus strand read)
>2 (chromomsome 2)
-67890 (minus strand read)
98765 (plus strand read)
132323 (plus strand read)
#BWT2 (read category BWT2)
etc..

organism: Homo sapiens

source_name: WM262 WCE

growth_protocol: Melanoma short-term cultures (STCs) were obtained from the Wistar Institute collection, and were derived from patients with metastatic disease. All lines were cultured in RPMI medium (cellgro) containing 10% FBS (cellgro) and penicillin/streptomycin (cellgro). In order to culture WM451-Lu cells, cell culture plates were pre-coated with 1% porcine gel solution (Sigma) to enhance cell adherence.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Melanoma

value: None WCE

tag: cell line


title: RNA-Seq of timepoint 20

status: Public on Mar 16 2012

city: Stanford

first: Hogune

last: Im

state: CA

address: 300 Pasteur Dr. Alway M308

department: Genetics

institute: Stanford

description:
Processed data file:
unk20.bam

library_source: transcriptomic

data_processing:
TopHat  was used to align the reads to the hg19 reference genome, followed by Cufflinks for transcript assembly and RNA expression analysis.
Processed mapped read data was annotated using cufflinks and RefSeq
processed data file build: hg19

molecule: total RNA

source_name: blood cell

growth_protocol: Blood was drawen

extract_protocol:
RNA from different blood component(PMBCs, plasma and sera) was used to prepare RNA-Seq ibraries according to Parkhomchuk D. et. al. 2009. Briefly, Total RNA was treated with DNaseI and rRNA removal by RiboZero. RNA was fragmented by RNA fragmentation kit from Ambion. Resulting RNA was converted to cDNA,  end-repaired using End-repair kit from Epicenter.  The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' 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 300~400 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. Average library fragment size is ~230 bp and SD of ~34 bp.
MicroRNA were isolated from 10 million PBMCs at five time points (Days 4, 21, 116, 185 and 186 from HRV infection) with the mirVanaTM miRNA Isolation Kit (Ambion). microRNA-Seq libraries were prepared from 1 microgram of isolated miRNA according to Illumina’s Small RNA v1.5 Sample Preparation Guide. Each library was sequenced with 36b single-end reads on 1 lane of Illumina’s GAIIx sequencer.

value: PBMC

tag: disease status

value: Healthy

tag: days


title: RNA-Seq of timepoint 21

description:
Processed data file:
unk21.bam


title: RNA-Seq of timepoint 18

description:
Processed data file:
unk18.bam


title: RNA-Seq of timepoint 19

description:
Processed data file:
unk19.bam


title: 07212009_42F6FAAXX_B3

description: Chromatin IP against IgG

source_name: ChipSeq for IgG

growth_protocol: hES cells were grown in mTESR media (Stem Cell Technologies) on plates coated with matrigel (BD Biosciences) in the absence of feeder cells.

value: IgG

value: Santa Cruz SC-2027

value: BGO3 (feeder free)

value: embryonic stem cells


title: CD4+ naive T cell MIRA-Seq in patients with Atopic dermatitis (AD)

city: Seoul

first: Sin-Gi

last: Park

address: 19, Sadang-ro, Dongjak-Gu

department: Department of Bioinformatics & Life science

country: South Korea

institute: Soongsil univ.

description:
Based on the affinity of the MBD2b/MBD3L1 complex (MIRA technique)
MES_processed_data_file : AD_naive_CD4+_T_cell_MES.wig
Final_processed_data_file : AD_processed_data.table

data_processing: The sequence tags were mapped to the human genome with UCSC hg18 (http://genome.ucsc.edu/) assembly based on NCBI build 36.1 through the Solexa Analysis Pipeline (version 0.3.0). Those reads that were mapped to multiple locations were discarded and only those uniquely mapped are retained in the analysis. We obtained about 15~20 million Illumina sequencing reads at every 200 base pair (bp) interval, across the whole genome from MIRA-Seq. As a result, 34 bp reading sequences were obtained. The first and last nucleotides were excluded for exact sequence match. The 34 bp reading sequence was extended toward the 3‘end to cover DNA fragments bound by the MBD proteins. To visualize the data, the readout was converted to browser extensible data (BED) and wiggle (WIG) files compatible with the UCSC Genome Browser (http://genome.ucsc.edu).Tagged overlapping sequences were counted with 200 bp resolution. To find enriched genomic regions, numbers of mapped reads in window of 1 kb were compared with the total number of reads in the genome. MES was calculated as log2 average of gene methylation count in 200 bp interval divided by promoter size (8*200 bp) which is normalized by background total methylation count divided by genome size (15005528*200 bp). The genomic coordinates of promoters and genebodies were downloaded from UCSC Genome Browser database build hg18.

source_name: CD4+ naive T cell

extract_protocol: To obtain naïve CD4+ T cells, peripheral blood mononuclear cells (PBMCs) from blood were isolated by Ficoll-paqueTM PLUS (GE Healthcare bio-Science) density gradient centrifugational method and naïve CD4+ T cells were purified by naïve CD4+ T cells isolation kit II (Miltenyi Biotec). The purity of naïve CD4+ T cells was over 90 % by flow cytometric analysis. For epigenetic analysis, genomic DNA of all the samples was isolated with DNA blood mini kit (QIAGEN). The individual DNAs were pooled and purified using 3M NaOAc (pH 5.2) along with ethanol precipitation method. In each experiment set, genomic DNAs of 12~20 individual sample were pooled to reduce individual variation in further analysis. First, for preparation of DNA for Solexa sequencing, glutathione S-transferase (GST)-tagged with methyl-CPG-binding domain (MBD)-2b and His-tagged MBD-3L1 proteins were prepared. Briefly, the purified genomic DNA was sonicated into 100 to 500 bp fragments and incubated with GST-MBD-2b protein, His-MBD-3L1 protein, and the JM110 bacterial RNA. MagneGST beads (Promega) were pre-blocked with the JM110 bacterial RNA to block nonspecific interaction between nucleic acid and MBD proteins, and incubated in the MIRA binding buffer (10 mM Tris-HCl, pH 7.5, 50 mM NaCl, 1 mM EDTA, 1 mM dithiothreitol, 3 mM MgCl2, 0.1% Triton X-100, 5% glycerol, 25 μg/ml bovine serum albumin) and washed with washing buffer (10 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 mM EDTA, 3 mM MgCl2, 0.1% Triton X-100) at 4°C. Second, for preparation of DNA for confirm the Solexa sequencing, DNA (2 μg) was dissolved in 50 μl of the appropriate buffer and 10 U of MseI (NEB), and incubated at 37 °C overnight. After purification of DNA, pull-down of methylated DNA fragments (restricted using MseI) was performed using the Methylcollector kit (Active Motif) according to the manufacturers' protocols. All DNA was eluted and purified with QIAquick PCR Purification Kit (QIAGEN). To apply Solexa sequencing, the DNAs were ligated to a pair of Solexa adaptors for Illumina Genome Analyzer Sequencing. The ligation products were eluted from 175 to 225 bp fragments on an agarose gel after PCR amplification. Cluster generation and 36 cycles of sequencing were done according to the manufacturer's instructions.

tag: disease state

value: Atopic dermatitis (AD)

value: CD4+ naive T cell


title: RNA-Seq of timepoint 16

description:
Processed data file:
unk16N.bam

value: Recovery


title: RNA-Seq of timepoint 15

description:
Processed data file:
unk15_new.bam


title: Mll1+/+ TNF

city: Wuhan

first: Min

last: Wu

state: Hubei

address: Room 5005, College of Life Sciences, Wuhan University

department: College of Life Science

country: China

institute: Wuhan University

data_processing:
We removed reads that contain either a base of N or overhalf qualities below 20. Then we got the clean reads.
TopHat was used for gene mapping. We mapped clean reads to the mRNA sequences of mouse, calculated the frequency of each mRNA being covered in four samples afterwards.
DESeq was used for differential expressed genes analysing. We compared every two samples each time, followed by Mll1+/+ TNFvsMll1-/- TNF, Mll1+/+vsMll1 -/--, Mll1+/+ TNFvsMll1+/+, Mll1 -/- TNFvsMll1 -/--. In the results, we picked genes only when its p value below 0.01. We defined these genes differentially expressed genes. We also calculated the RPKM values as the expression level of each gene in the four samples. We could get the fold change of genes through their RPKM values,  decide whether it is a up-regulated gene or a  down-regulated gene.
Genome_build: NCBI Build 37.2
Supplementary_files_format_and_content: Processed data (linked on Series record) includes RPKM values for each Sample.

source_name: Mll1+/+ MEF cell with TNFa treatment

growth_protocol: Both Mll1+/+ and Mll1-/- cells were cultured in DMEM plus 10% FBS.

extract_protocol: Total RNA was extracted with Qiagen Rneasy mini kit. After testing the quality, mRNA was purified and fragmentated. The first and second strand cDNA was synthesized and End repair was performed.  After 3' Ends was adenylated, the adapters was ligated and cDNA was purified. After enrichment and validation, the cDNA templates was sent for sequencing.

treatment_protocol: Cells were treated with 10un/ml TNFa or control medium.  4hr later, cells were harvested and total RNA was isolated.

value: MEF

tag: genotype/variation

value: wild type

tag: agent

value: TNFa (10ng/ml)


title: RNA-Seq of timepoint 12

description:
Processed data file:
unk12_new.bam


title: RNA-Seq of timepoint 13

description:
Processed data file:
unk13_new.bam


title: RNA-Seq of timepoint 14

description:
Processed data file:
unk14_new.bam


title: RNA-Seq of timepoint 10

description:
Processed data file:
unk10_new.bam


title: RNA-Seq of timepoint 11

description:
Processed data file:
unk11_new.bam


title: RNA-Seq of timepoint 7

description:
Processed data file:
UnkVII.bam


title: RNA-Seq of timepoint 5

description:
Processed data file:
UnkV.bam


title: RNA-Seq of timepoint 2

description:
Processed data file:
UnkII.bam


title: RNA-Seq of timepoint 3

description:
Processed data file:
UnkIII.bam


title: RNA-Seq of timepoint 1

description:
Processed data file:
UnkI.bam

value: HRV onset


title: VSV-infected loqs mutant flies

city: Evanston

last: Carthew

state: IL

address: 633 Clark Street

institute: Northwestern University

description: PAGE purified 15-35 nt small RNA fractions

data_processing:
Reads were aligned to the D. melanogaster (build: dm3) and C virus genomes with a seed length of 18 nt, and allowing up to 3 mismatches. Sequencing adaptors were removed using the method of the ABI small RNA Analysis Toolkit.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited text files showing genomic alignments

organism: Drosophila melanogaster

source_name: adult flies

growth_protocol: standard Drosophila rearing protocols

extract_protocol: Total RNA was extracted using Trizol (Invitrogen). Small RNAs between the 18-34 nt size range were PAGE purified from LMW RNA. 200 ng of the small RNAs were used to prepare a library using the SOLiD total RNA expression kit (Ambion).

treatment_protocol: Intrathoraxic injection of viruses

value: loqs mutants

tag: infection

value: Vesicular Stomatitis virus


title: VSV-infected R2D2 mutant flies

value: R2D2 mutants


title: VSV-infected Dcr-2 mutant flies

value: Dcr-2 mutants


title: SINV-infected loqs mutant flies

value: Sindbis virus


title: VSV-infected wiltype flies


title: SINV-infected R2D2 mutant flies


title: CSHL_RnaSeq_NHEK_cell_TAP-Only_shortTotal

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

source_name: NHEK

value: primary cell

value: keratinocyte

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: rnaextract

value: shortTotal

tag: rnaextract description

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Single 36 nt reads

tag: replicate

tag: localization

value: cell

tag: localization description

value: Whole cell

tag: protocol

value: TAP-Only

tag: protocol description

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: CSHL_RnaSeq_HepG2_cytosol_TAP-Only_shortTotal

molecule: cytoplasmic RNA

tag: cell description

value: hepatocellular carcinoma

value: The fluid between the cells outer membrane and the nucleus


title: CSHL_RnaSeq_HepG2_cell_TAP-Only_shortTotal

value: immortalized cell line

tag: line


title: RNA-Seq of timepoint 17

description:
Processed data file:
unk17.bam

tag: cell type

value: PBMC

tag: disease status

value: Healthy

tag: days


title: CSHL_RnaSeq_HepG2_nucleus_TAP-Only_shortTotal

molecule: nuclear RNA

tag: datatype

tag: datatype description

tag: rnaextract

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: RNA-Seq of timepoint 9

description:
Processed data file:
unk09_new.bam

value: RSV onset


title: CSHL_RnaSeq_HeLa-S3_nucleus_TAP-Only_shortTotal

value: RnaSeq

tag: rnaextract description

tag: biorep

tag: labexpid

value: nucleus


title: RNA-Seq of timepoint 8

description:
Processed data file:
UnkVIII.bam


title: CSHL_RnaSeq_HeLa-S3_cell_TAP-Only_shortTotal

value: Sequencing analysis of RNA expression

value: shortTotal

tag: labversion

tag: readtype

tag: readtype description


title: RNA-Seq of timepoint 6

description:
Processed data file:
UnkVI.bam


title: SINV-infected wiltype flies

tag: genotype/variation

value: wild type

tag: infection

value: Sindbis virus


title: CSHL_RnaSeq_NHEK_cytosol_TAP-Only_shortTotal

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

value: iIDR

value: Single 36 nt reads

tag: replicate

tag: localization

value: cytosol

tag: localization description

tag: protocol

tag: protocol description


title: CSHL_RnaSeq_H1-hESC_cell_TAP-Only_shortTotal

growth_protocol: missing

value: stem cell

tag: line

value: cell

value: Whole cell

value: TAP-Only

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: CSHL_RnaSeq_AG04450_cell_TAP-Only_shortTotal

value: primary cell

value: fibroblast of lung

tag: datatype


title: CSHL_RnaSeq_NHEK_nucleus_TAP-Only_shortTotal

value: RnaSeq

tag: datatype description

tag: cell sex

value: F

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in hESC H1 Cells; renlab.H4K8ac.hESC.H1.01.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY17
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11634
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM896166_UCSD.H1.H4K8ac.AY17.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.hESC.H1.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Cell Line H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H4K8ac ChIP-Seq on H1 Cell Line, Library AY17, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13480
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,548,724
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.3904
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.473
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9591
IROC_PERCENTILE: 75
POISSON_SCORE: 0.5482
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.65

**********************************************************************

ANALYSIS FILE NAME: GSM896166_UCSD.H1.H4K8ac.AY17.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.hESC.H1.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H4K8ac ChIP-Seq read mappings from the H1 Cell Line, Library AY17, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13600
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: H1 H4K8ac 17
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H4K8ac Library AY17 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,548,724
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.3904
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.473
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9591
IROC_PERCENTILE: 75
POISSON_SCORE: 0.5482
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.65

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H4K8ac.hESC.H1.01.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sample alias

tag: sample common name

value: H1 Cell Line

tag: molecule

value: genomic DNA

tag: disease

value: James Thompson Laboratory

value: Cell Line

tag: lineage

value: Embryonic Stem Cell

tag: passage

value: Between 20 and 40

tag: medium

value: mTeSER

tag: Sex

value: Male

tag: batch

value: Histone H4K8ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Neural Progenitor Cells; renlab.H3K27me3.NPC.03.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK320
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11642
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11641
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM896165_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27me3.AK320.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.NPC.03.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK320, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13544
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,167,237
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0066
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.01
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9667
IROC_PERCENTILE: 87
POISSON_SCORE: 0.0593
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM896165_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27me3.AK320.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.NPC.03.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK320, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13664
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HDNP H3K27me3 20
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK320 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,167,237
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0066
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.01
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9667
IROC_PERCENTILE: 87
POISSON_SCORE: 0.0593
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K27me3.NPC.03.01

value: James Thomson Laboratory

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Histone H3K27me3

value: Active Motif


title: CSHL_RnaSeq_BJ_cell_TAP-Only_shortTotal

source_name: BJ

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: cell description

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID:9916803)

tag: rnaextract

value: shortTotal

tag: rnaextract description

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Single 36 nt reads

tag: replicate

value: TAP-Only

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: CSHL_RnaSeq_A549_cell_TAP-Only_shortTotal

tag: datatype

tag: datatype description

value: Single 101 nt reads

tag: localization

value: cell

tag: localization description

value: Whole cell

tag: protocol

tag: protocol description


title: CSHL_RnaSeq_H1-hESC_nucleus_TAP-Only_shortTotal

tag: cell sex

value: M

value: nucleus

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: CSHL_RnaSeq_HUVEC_nucleus_TAP-Only_shortTotal

source_name: HUVEC

value: primary cell

value: endothelial cell of umbilical vein


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in BMP4 Trophoblast Cells; renlab.H3K27me3.BMP4T.03.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK317
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11636
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM896164_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K27me3.AK317.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.BMP4T.03.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AK317, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13449
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,355,474
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1524
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.2873
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.8682
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3742
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

ANALYSIS FILE NAME: GSM896164_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K27me3.AK317.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.BMP4T.03.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AK317, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13569
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H3K27me3 17
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27me3 Library AK317 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,355,474
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1524
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.2873
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.8682
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3742
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K27me3.BMP4T.03.01

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

tag: passage

tag: medium

tag: Sex

value: Male

tag: batch

value: Histone H3K27me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: CSHL_RnaSeq_SK-N-SH_RA_cell_TAP-Only_shortTotal

tag: datatype

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: rnaextract

value: shortTotal

tag: rnaextract description

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Single 36 nt reads

tag: replicate

value: cell

value: Whole cell

value: TAP-Only

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Neural Progenitor Cells; renlab.H3K27ac.NPC.04.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK319
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11644
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11641
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM896162_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27ac.AK319.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.NPC.04.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK319, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13540
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,052,818
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.035
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0603
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9881
IROC_PERCENTILE: 24
POISSON_SCORE: 0.0961
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM896162_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27ac.AK319.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.NPC.04.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK319, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13660
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HDNP H3K27ac 19
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK319 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,052,818
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.035
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0603
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9881
IROC_PERCENTILE: 24
POISSON_SCORE: 0.0961
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K27ac.NPC.04.01

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Male

value: Histone H3K27ac


title: Reference Epigenome: ChIP-Seq Analysis of H3K14ac in hESC H9 Cells; renlab.H3K14ac.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K14ac in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY15
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11632
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM896161_UCSD.H9.H3K14ac.AY15.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.hESC.H9.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H9 Cell Line H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K14ac ChIP-Seq on H9 Cell Line, Library AY15, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13443
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,197,338
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.5145
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5419
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9711
IROC_PERCENTILE: 75
POISSON_SCORE: 0.6468
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

**********************************************************************

ANALYSIS FILE NAME: GSM896161_UCSD.H9.H3K14ac.AY15.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.hESC.H9.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K14ac ChIP-Seq read mappings from the H9 Cell Line, Library AY15, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13563
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: H9 H3K14ac 15
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K14ac Library AY15 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,197,338
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.5145
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5419
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9711
IROC_PERCENTILE: 75
POISSON_SCORE: 0.6468
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K14ac.hESC.H9.02.01

value: H9 Cell Line

tag: disease

value: James Thompson Laboratory

tag: line

tag: lineage

value: Between 30 and 50

value: mTeSER

value: Female

value: Histone H3K14ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: CSHL_RnaSeq_HeLa-S3_cytosol_TAP-Only_shortTotal

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

value: shortTotal

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

value: iIDR

value: Single 36 nt reads

tag: localization

value: cytosol

tag: localization description

value: The fluid between the cells outer membrane and the nucleus

tag: protocol

value: TAP-Only

tag: protocol description

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: E11.5_hindlimb_ChIP_input_rep4_index12_mate

city: Philadelphia

first: Justin

last: Cotney

state: PA

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

description: input

data_processing:
ChIP-Seq alignments: ChiP-Seq reads were aligned with bowtie (0.12.3) to the mouse genome (mm9) retaining only uniquely mapped reads (command: bowtie -m 1 -p 8 -B 1 --solexa1.3-quals ~/GENOME/mm9/dna/mm9_nh).
ChIP-Seq peak calling: ChIP peaks were identified by MACS (1.37) against input controls.  Default parameters were used for CTCF ChIP-Seq (input control replicates 1 and 2)(command: macs -t ../../s_6_sequence.aligned -c ../../s_5_sequence.aligned --name=Mouse_CTCF_091310_FL_mfold10_p00001 --format=BOWTIE --tsize=74 --gsize=1860000000 --bw=150 --  pvalue=0.00001 --diag --mfold=10 --wig).  Nomodel option was selected for H3K27me3 and H3K27ac ChIP seq (input control replicates 3 and 4 respectively)(command: macs -t ../082310/bowtie/s_5_sequence.aligned -c ../082210/bowtie/s_4_sequence.aligned --name=Mouse_h3k27me3_FL1_p00001 --nomodel --shiftsize=1 --format=BOWTIE --tsi  ze=74 --gsize=1860000000 --bw=150 --pvalue=0.00001 --diag).

source_name: embryonic hindlimb bud

growth_protocol: Normal mouse gestation to day 10.5.

extract_protocol: Standard procedure included with Illumina ChIP-Seq kit (IP-102-1001).  For multiplexed samples Illumina Multiplexing adapters and primers (PE-400-1001) were used instead of those provided with the ChIP-Seq kit.  Multiplexed samples were paired-end sequenced with an insert size of 300 bp.  Standard procedure included with Illumina mRNA-seq kit (RS-100-0801).

treatment_protocol: Pregnant mothers were euthanized and embryos were removed and placed in cold PBS.  Forelimb and hindlimb buds were individually removed with forceps.  Total RNA was extracted with RNEasy kit (Qiagen) for RNA-seq. For each ChIP-Seq, limb bud tissue was crosslinked with 1% formaldehyde at room temperature and stored at -80°C. Chromatin was extracted and sheared by sonication. Soluble chromatin was combined Protein G Dynabeads prebound with appropriate antibodies at 4C overnight.  Beads were collected with magnet and washed 5x.  Chromatin was eluted with TE+1%SDS at 65C for 10 minutes.  Crosslinks were reversed at 65C overnight then chromatin was purified with PCR cleanup kit (Qiagen).

tag: strain

tag: tissue

value: hindlimb bud

tag: developmental stage

value: gestational day E11.5

tag: method

value: ChIP-seq

tag: chip antibody

tag: sequencing run type

value: Paired-end 75 multiplexed


title: E10.5_hindlimb_mRNA_seq_rep1

description: polyA-selected RNA

data_processing: RNA-Seq alignments and counts: RNA-Seq reads were aligned with bowtie (0.12.3) to the mouse genome (mm9) retaining only uniquely mapped reads ( command: bowtie -m 1 -B 1 --solexa1.3-quals --sam --sam-nohead ~/GENOME/mm9/dna/mm9_nh+splice30).  Bowtie output was converted to tophatSAM format for use with Cufflinks for calculation of gene expression (RPKM).

source_name: embryonic hindlimb bud, RNA-Seq

extract_protocol: Total RNA was extracted with the RNeasy kit (Qiagen).

treatment_protocol: Pregnant mothers were euthanized, and embryos were removed and placed in cold PBS.  Forelimb and hindlimb buds were individually removed with forceps.

value: gestational day E10.5

value: Single-end 35


title: E10.5_hindlimb_H3K27me3_ChIP_seq_rep1

description: Chromatin IP against H3K27me3.

data_processing:
ChIP-Seq alignments: ChiP-Seq reads were aligned with bowtie (0.12.3) to the mouse genome (mm9) retaining only uniquely mapped reads (command: bowtie -m 1 -p 8 -B 1 --solexa1.3-quals ~/GENOME/mm9/dna/mm9_nh).

ChIP-Seq peak calling: ChIP peaks were identified by MACS (1.37) against input controls.  Default parameters were used for CTCF ChIP-Seq (input control replicates 1 and 2)(command: macs -t ../../s_6_sequence.aligned -c ../../s_5_sequence.aligned --name=Mouse_CTCF_091310_FL_mfold10_p00001 --format=BOWTIE --tsize=74 --gsize=1860000000 --bw=150 --  pvalue=0.00001 --diag --mfold=10 --wig).  Nomodel option was selected for H3K27me3 and H3K27ac ChIP seq (input control replicates 3 and 4 respectively)(command: macs -t ../082310/bowtie/s_5_sequence.aligned -c ../082210/bowtie/s_4_sequence.aligned --name=Mouse_h3k27me3_FL1_p00001 --nomodel --shiftsize=1 --format=BOWTIE --tsi  ze=74 --gsize=1860000000 --bw=150 --pvalue=0.00001 --diag).

source_name: embryonic hindlimb bud, H3K27me3 ChIP

extract_protocol:
For each ChIP-Seq, limb bud tissue was crosslinked with 1% formaldehyde at room temperature and stored at -80Â°C. Chromatin was extracted and sheared by sonication. Soluble chromatin was combined with Protein G Dynabeads prebound with appropriate antibodies at 4C overnight.  Beads were collected with magnet and washed 5x.  Chromatin was eluted with TE+1%SDS at 65C for 10 minutes.  Crosslinks were reversed at 65C overnight, and then chromatin was purified with the PCR cleanup kit (Qiagen).

Standard procedure included with the Illumina ChIP-Seq kit (IP-102-1001).  For multiplexed samples, Illumina Multiplexing adapters and primers (PE-400-1001) were used instead of those provided with the ChIP-Seq kit.  Multiplexed samples were paired-end sequenced with an insert size of 300 bp.  Standard procedure included with the Illumina mRNA-seq kit (RS-100-0801).

tag: antibody vendor

value: Millipore

tag: antibody catalog #

tag: antibody lot#

value: Single-end 75


title: E10.5_hindlimb_mRNA_seq_rep2

description: polyA-selected RNA


title: E11.5_hindlimb_H3K27ac_ChIP_seq_index7_mate

description: Chromatin IP against H3K27ac

value: Abcam


title: E10.5_hindlimb_ChIP_input_rep2

description: Input

source_name: embryonic hindlimb bud, ChIP input


title: E10.5_hindlimb_ChIP_input_rep3

description: Input


title: E10.5_hindlimb_ChIP_input_rep1

description: Input


title: E10.5_forelimb_mRNA_seq_rep2

description: polyA-selected RNA

source_name: embryonic forelimb bud, RNA-Seq

value: forelimb bud


title: E11.5_forelimb_ChIP_input_rep4_index4_mate

description: input

source_name: embryonic forelimb bud


title: CSHL_RnaSeq_MCF-7_cell_TAP-Only_shortTotal

value: immortalized cell line

tag: datatype

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: rnaextract

value: shortTotal

tag: rnaextract description

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

tag: biorep

tag: labexpid

tag: labversion

tag: readtype

tag: readtype description

value: Single 101 nt reads

tag: replicate

value: cell

value: Whole cell


title: E11.5_forelimb_H3K27ac_ChIP_seq_index6_mate

description: Chromatin IP against H3K27ac

tag: strain

tag: tissue

value: gestational day E11.5


title: E10.5_hindlimb_H3K27ac_ChIP_seq_rep2_index_12

description: Chromatin IP against H3K27ac.

source_name: embryonic hindlimb bud, H3K27ac ChIP

value: hindlimb bud

tag: developmental stage


title: CSHL_RnaSeq_H1-hESC_cytosol_TAP-Only_shortTotal

tag: datatype description

value: iIDR

value: Single 36 nt reads

tag: cell sex

value: M

tag: localization

value: cytosol

tag: localization description

value: The fluid between the cells outer membrane and the nucleus

tag: protocol

value: TAP-Only

tag: protocol description

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: E10.5_forelimb_mRNA_seq_rep1

description: polyA-selected RNA

value: forelimb bud

value: gestational day E10.5

tag: sequencing run type

value: Single-end 35


title: E10.5_hindlimb_H3K27ac_ChIP_seq_rep1_index_6

description: Chromatin IP against H3K27ac.

tag: chip antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog #

tag: antibody lot#

value: Paired-end 75 multiplexed


title: E10.5_hindlimb_ChIP_input_rep4_index4

description: Input


title: E10.5_forelimb_H3K27me3_ChIP_seq_rep2

description: Chromatin IP against H3K27me3.

source_name: embryonic forelimb bud, H3K27me3 ChIP

value: Millipore

value: Single-end 75


title: E10.5_forelimb_H3K27me3_ChIP_seq_rep1

description: Chromatin IP against H3K27me3.


title: E10.5_forelimb_H3K27ac_ChIP_seq_rep1_index_6

description: Chromatin IP against H3K27ac.

source_name: embryonic forelimb bud, H3K27ac ChIP


title: E10.5_hindlimb_H3K27me3_ChIP_seq_rep2

description: Chromatin IP against H3K27me3.


title: E10.5_forelimb_ChIP_input_rep4_index4

description: Input

source_name: embryonic forelimb bud, ChIP input


title: E10.5_forelimb_ChIP_input_rep3

description: Input


title: E10.5_forelimb_ChIP_input_rep2

description: Input


title: E10.5_forelimb_ChIP_input_rep1

description: Input


title: SMC1_KO.R2

status: Public on Mar 15 2012

city: Madrid

first: Silvia

last: Remeseiro

state: Madrid

address: Calle Melchor Fernandez Almagro 3

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: SA1-null Mouse Embryonic Fibroblasts

data_processing:
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (see below) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
SMC1_KO.R1R2vsInputMEF.FDR10.AllFC.bed: mm9 (this file linked to replicate 1 - GSM876519)

source_name: Chromatin IP against SMC1

growth_protocol: MEFs were grown in DMEM supplemented with 20% FBS

extract_protocol: Input and chromatin immunoprecipitated DNA samples were provided by the user. Available sample amounts from 4 to 15ng of DNA (as quantitated by fluorometry) were electrophoresed on agarose gel and independent sample-specific fractions of 100-200 bp were taken. Extracted DNA was processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "ChIP Sequencing Sample Prep Guide" (part # 11257047 Rev. A), with the exception that gel extraction was replaced with Agencourt AMPure XP (BeckmanCoulter) bead purification. Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (14 cycles). The resulting purified DNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on the Genome Analyzer IIx by following manufacturer's protocols.

treatment_protocol: Untreated

tag: genotype/variation

tag: cell type

value: Mouse Embryonic Fibroblasts (MEF)


title: SMC3_WT

description: WT Mouse Embryonic Fibroblasts

data_processing:
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (see below) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
SMC3_WTvsInputMEF.FDR10.AllFC.bed: mm9

source_name: Chromatin IP against SMC3

value: WT


title: SMC1_KO.R1

description: SA1-null Mouse Embryonic Fibroblasts

data_processing:
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (see below) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
SMC1_KO.R1R2vsInputMEF.FDR10.AllFC.bed: mm9


title: SMC3_KO

description: SA1-null Mouse Embryonic Fibroblasts

data_processing:
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (see below) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
SMC3_KOvsInputMEF.FDR10.AllFC.bed: mm9


title: KO_SA1

description: SA1-null Mouse Embryonic Fibroblasts

data_processing:
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (see below) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
KO_SA1vsInputMEF.FDR10.AllFC.bed: mm9

source_name: Chromatin IP against SA1


title: InputMEFs

description: WT and SA1-null Mouse Embryonic Fibroblasts

data_processing:
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (see below) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
InputMEFs.bed: mm9

source_name: input DNA

value: WT/SA1-null (pool)


title: SMC1_WT

description: WT Mouse Embryonic Fibroblasts

data_processing:
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (see below) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
SMC1_WTvsInputMEF.FDR10.AllFC.bed: mm9


title: KO_SA2

description: SA1-null Mouse Embryonic Fibroblasts

data_processing:
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (mm9) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
KO_SA2vsInput.FDR10.AllFC.bed: mm9

source_name: Chromatin IP against SA2


title: Ezh2 ChIP-Seq

city: Boston

first: Michael

last: Hsing

address: 300 Longwood Ave.

department: Cardiology

institute: Children's Hospital Boston

description: Chromatin IP against Ezh2

data_processing: Peaks were detected by Sole-Search

source_name: E12.5 heart apex. 120 hearts

extract_protocol: Multiplexing library prep

tag: age

value: heart apex


title: H3K27me3 ChIP-Seq

description: Chromatin IP against H3K27me3


title: WT_SA2

description: WT Mouse Embryonic Fibroblasts

data_processing:
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (mm9) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
WT_SA2vsInput.FDR10.AllFC.bed: mm9

value: wild type

tag: strain


title: E10.5_forelimb_H3K27ac_ChIP_seq_rep2_index12

description: Chromatin IP against H3K27ac.

tag: tissue


title: input DNA

description: input DNA


title: B. anthracis ethanol-challenged cells (bottom strand)

city: Atlanta

first: Tim

last: Read

address: 615 Michael Street, Suite 301

institute: Emory University

description: 4 technical replicates.

data_processing:
Raw color space data from SOLiD sequencing was mapped to the Bacillus anthracis Ames Ancestor genome (NC_007530.2, NC_007322.2, NC_007323.3) using SOCs software with a mismatch cutoff of 5 nucleotides.

Genome_build: NC_007530.2, NC_007322.2, NC_007323.3
Supplementary_files_format_and_content: *txt: Alignments to the B. anthracis genome using SOCS software.

organism: Bacillus anthracis

source_name: Vegetative bacterial cells, ethanol challenged

growth_protocol: 50 ml cultures were grown to OD600 0.4-0.5, then 50 ml of LB+12% EtOH were added to the culture, resulting in a final concentration of 6% EtOH. Cells were allowed to grow with shaking for 10 minutes and immediately harvested for RNA.

extract_protocol: Phenol-chloroform extraction was used to isolate total RNA, which was enriched using the Ambion MicrobExpress kit. All RNA samples were tested for integrity on a BioRad Experion capillary electrophoresis system. Possible residual DNA was removed by addition of Ambion Turbo DNase. Library preparation for Applied Biosystems SOLiD sequencing was done according to the manufacturer’s Whole Transcriptome Library Preparation protocol.

value: Sterne 34F2

tag: treatment

value: ethanol challenge


title: HBO1_ChIPseq

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description: ChIP against HBO1

data_processing: Raw reads were mapped on the human genome build hg18 using Burrows-Wheeler Aligner (bwa http://bio-bwa.sourceforge.net/). Uniquely mapped reads were kept for further analysis. Samtools and the script genomeCoverageBed were used to produce bedgraph files.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the Genomic DNA Sample Kit (# FC-102-1001). 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  library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: RKO

value: human colon carcinoma

tag: growth conditions

value: untreated cells, normal growth conditions

value: Anti-KAT7/Hbo1/ MYST2 antibody

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. number


title: input DNA

description: input DNA

source_name: RKO_input DNA


title: B. anthracis cold-challenged cells (bottom strand)

description: 4 technical replicates.

source_name: Vegetative bacterial cells, cold challenged

growth_protocol: 50 ml cultures were grown to OD600 0.4-0.5, then 50 ml of previously cooled LB medium (~4°C) was added to cultures, resulting in an average liquid temperature of 19-20°C. Cultures were then shaken in a refrigerated incubator at 17°C for 10 minutes, and RNA was harvested.

value: cold challenge


title: B. anthracis osmotically-challenged cells (bottom strand)

description: 4 technical replicates.

source_name: Vegetative bacterial cells, osmotically challenged

growth_protocol: 50 ml cultures were grown to OD600 0.4-0.5, then 50 ml of LB then 1.5 M NaCl were added to the cultures, resulting in a final concentration of 0.75 M NaCl. Cells were grown for 10 minutes with shaking.

value: osmotic challenge


title: Ribosome protected fragments Wild type 4hpf-2

city: New Haven

first: Antonio

middle: J.

last: Giraldez

state: CT

address: 333 Cedar Street

institute: Yale University

data_processing:
Ribo_Wt_4_B.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence

organism: Danio rerio

source_name: Whole embryo, wild type

extract_protocol: Ribosome protected fragments were obtained from 80 embryos per sample according to an adapted protocol from (Ignolia et al, 2009). Embryos were incubated with 0.1 ug/ml cycloheximide in Methylene blue water for 5 min, then snap frozen in 25ul Lysis buffer and clarified for 10 min at 10g 4degC. Supernatant was incubated with RNaseI and DNase at room temperature for 45 minutes with gentle mixing, then digested extracts (50ul) were overlain in a 100ul cushion of 1.8M sucrose in 20mM total Tris HCL ph8.0; 140mM KCl; 5 mM MgCl2; 100 ug/ml Cycloheximide; 0.5 mM DTT; 40U/ml SUPERas In (Ambion #AM2694) for 14 h at 55.000 rpm in a TLS55 rotor in a Beckman TL100 ultracentrifuge. The bottom 30 ul was mixed with 4ul of PNK buffer and 4 ul of Proteinase K and incubated at 37degC for 30 minutes. RNA was extracted using Trizol, then run on a 15% Urea gel to excise the 28-38 nt region. To construct barcoded Illumina small RNA libraries, samples were eluted overnight in 300 mM NaOAc pH 5.5; 1 mM EDTA; 0.1U/ul SUPERas In (Ambion #AM2694), followed by Ethanol precipitation. RFP and RNA input fragments were 3?-dephosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer (without ATP) for 1 h at 37degC, followed by 10 min incubation at 75degC and ethanol precipitation. Samples were resuspended and ligated to Illumina v1.5 3' adapter using T4 RNA Ligase 2, truncated K227Q, and RNAseOUT Recombinant Ribonuclease Inhibitor for 6h at 20degC, then separated on a 10% Urea gel to extract the 3' ligation products. These were 5' phosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer with 1mM ATP for 30 min at 37degC and precipitated in ethanol. 5' ligation was performed using T4 RNA Ligase 1 for 6 hrs at 20degC with individual 100uM barcoded 5' adapters, then separated on a 10% Urea gel. Gel-purified samples were reverse transcribed using SuperScript II Reverse Transcriptase according to the Invitrogen protocol, then amplified using Phusion High-Fidelity DNA Polymerase. PCR was carried out with an initial 30s denaturation at 98degC followed by 4 cycles of 30s denaturation at 98degC and 15s extension at 72degC, followed by 10-15 cycles of 10s denaturation at 98degC, 30s annealing at 50degC, and 15s extension at 72degC. Reactions were separated on a non-denaturing 8% polyacrylamide TBE gel and correct sized DNA fragments were sequenced using Illumina HiSeq2000. In parallel, RNA input from 20 embryos was extracted using Trizol, then poly(A) selected using biotinylated oligo(dT40) at room temperature and eluted. Samples were then alkaline fragmented for 20min at 95degC using 2 mM EDTA; 10 mM Na2CO3; 90 mM NaHCO3 pH 9.3; then neutralized with 560ul of ice-cold NaOAc (300mM) pH 5.5 and RNA precipitated with isopropanol. Small RNA sequencing libraries were constructed as above, selecting for fragments in the 30-50 nt range.

tag: sample type

value: ribosome protected fragments

value: whole embryo

tag: genotype

tag: developmental stage


title: Ribosome protected fragments Wild type 6hpf-2

data_processing:
Ribo_Wt_6_B.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Ribosome protected fragments Wild type 4hpf

data_processing:
Ribo_Wt_4_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Ribosome protected fragments Wild type 6hpf

data_processing:
Ribo_Wt_6_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: B. anthracis vegeative cell control (bottom strand)

description: 4 technical replicates.

source_name: Vegetative bacterial cells, control

growth_protocol: 50 ml cultures were grown to OD600 0.4-0.5 in LB before harvesting.

value: control


title: Ribosome protected fragments MZdicer 4hpf-2

data_processing:
Ribo_Dicer_4_B.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence

source_name: Whole embryo, MZdicer

value: MZdicer mutant


title: Ribosome protected fragments MZdicer 4hpf

data_processing:
Ribo_Dicer_4_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Ribosome protected fragments MZdicer 6hpf

data_processing:
Ribo_Dicer_6_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Ribosome protected fragments Wild type 2hpf

data_processing:
Ribo_Wt_2_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Ribosome protected fragments Wild type 2hpf-2

data_processing:
Ribo_Wt_2_B.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Ribosome protected fragments MZdicer 6hpf-2

data_processing:
Ribo_Dicer_6_B.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Input mRNA-Seq Wild type 6hpf-2

data_processing:
Input_Wt_6_B.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence

molecule: polyA RNA

value: input mRNA

tag: genetic background

value: TUAB


title: Ribosome protected fragments MZdicer 2hpf-2

data_processing:
Ribo_Dicer_2_B.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Input mRNA-Seq Wild type 4hpf

data_processing:
Input_Wt_4_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Ribosome protected fragments MZdicer 2hpf

data_processing:
Ribo_Dicer_2_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Input mRNA-Seq Wild type 4hpf-2

data_processing:
Input_Wt_4_B.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: WT_SA1

description: WT Mouse Embryonic Fibroblasts

data_processing:
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (mm9) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
WT_SA1vsInput.FDR10.AllFC.bed: mm9

value: Mouse Embryonic Fibroblasts (MEF)

tag: chip antibody


title: Input mRNA-Seq Wild type 2hpf-2

data_processing:
Input_Wt_2_B.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence

value: wild type


title: Input mRNA-Seq MZdicer 6hpf

data_processing:
Input_Dicer_6_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Input

data_processing:
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (mm9) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
Input.bed: mm9

source_name: Pool of all samples Input

value: wild type/SA1-null (pool)


title: Input mRNA-Seq MZdicer 2hpf

data_processing:
Input_Dicer_2_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Conjugation-8h

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

data_processing: Sequence image analysis was performed using the Firecrest, Bustard and GERALD programs (Illumina). The low quality bases (Q<5) at the ends of the reads were trimmed. Tophat (Trapnell et al. 2009) were used to map the sequenced reads to the current T. thermophila reference genome (Coyne et al. 2008; October, 2008 release) (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/t_thermophila/annotation_dbs/final_release_oct2008/) and find the reads spanning one exon-exon junction. The NUCmer in MUMmer package (Delcher et al. 2002) and a custom script were used to find the reads possibly spanning two or more exon-exon junctions. The mapped reads allowed up to two mismatches and only the canonical GT-AG junction reads were accepted. Transcripts were assembled using the Cufflinks software (Trapnell et al. 2010), and was compared to the predicted gene models using cuffcompare (Trapnell et al. 2010) and custom scripts. Putative ORFs of assembled transcripts were found using GetOrf in EMBOSS package (Rice et al. 2000).

organism: Tetrahymena thermophila

source_name: Tetrahymena conjugation, 8 hour cells, mating type V & VI

growth_protocol: Cells were cultured using 1X SPP (1%PP), 30 degrees, 150 rpm shaking.

extract_protocol:
Total RNA extracted using  Qiashredder (Cat # 79654) and the RNeasy kit (cat. # 74624), from Qiagen. Contains RNA Protect Cell Reagent (Cat. # 76526) and RNeasy Plus Mini Kit (50 samples).
Poly-A mRNA was selected using Dynal magnetic beads (Invitrogen) and fragmented by heating at 94 â. First strand cDNA were synthesized with random hexamer primers and second strand cDNA with DNA polymerase. Double strand cDNA was end-repaired and a single adenosine moiety was added. The Illumina adapters were ligated and gel-electrophoresis was used to select DNA fragments between 200â250 bps in size. Libraries were amplified by PCR with Phusion polymerase. Sequencing libraries were denatured with sodium hydroxide and diluted in hybridization buffer for loading onto a single lane of an Illumina GA flowcell. Cluster formation, primer hybridization and pair-end sequencing were performed using proprietary reagents according to hte manufacturer's recommended protocol (https://icom.illumina.com/).

treatment_protocol: For growth, mating type VI cells at a medium cell density (~200K cells/ml) were collected. For starvation, mating type V or VI cells were starved in 10 mM Tris (pH 7.5) for 3 and 15 hours. For conjugation, mating type V and VI cells that had been starved for 18 hours were resuspended in 10 mM Tris (pH 7.5) at 200K cells/ml and mixed, and samples were collected at 2 and 8 hours after the mixture.

tag: mating type

value: V and VI

tag: condition

value: conjugation

tag: time

value: 8 hrs


title: Conjugation-2h

source_name: Tetrahymena conjugation, 2 hour cells, mating type V & VI

value: 2 hrs


title: Input mRNA-Seq MZdicer 4hpf

data_processing:
Input_Dicer_4_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Starvation-3h-V

source_name: Tetrahymena starvation, 3 hour cells, mating type V

value: V

value: starvation

value: 3 hrs


title: Input mRNA-Seq MZdicer 4hpf-2

data_processing:
Input_Dicer_4_B.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Starvation-3h-VI

source_name: Tetrahymena starvation, 3 hour cells, mating type VI

value: VI


title: Input mRNA-Seq Wild type 6hpf

data_processing:
Input_Wt_6_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence


title: Growth-m

source_name: Tetrahymena growth cells with medium density, mating type VI

value: growth


title: InputDNA  Pcl3-shRNA

city: San Francisco

first: Jun

middle: S

last: Song

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

institute: UCSF

description: input DNA

data_processing: Bowtie was used to align the reads to the mouse genome (build MM9), using the parameters -n 2 -y --best -m 1. Skellam distribution was used to call peaks at the p-value cutoff of 10-7.

source_name: mouse embryonic stem cells

growth_protocol: Embryonic stem cells were grown as described previously in Singla et al. Nature Methods 2010 and  Singla et al. Dev Cell 2010.

extract_protocol: 34uL IP samples were treated with End Repair kit (Epicentre, Cat # ER81050, Lot # E85-91206), with 5uL of 10X End Repair buffer, 5uL of 2.5mM dNTPs, 5uL of 10mM ATP, and 1uL of END-IT enzyme mix added to each IP.  Samples incubated at room temperature for 45 minutes.  Samples were purified using Qiagen MinElute kit and eluted to 32uL.  An additional âAâ base was added to the 3â end of DNA fragments by adding 5uL 10X NEBuffer 2 (New England Biolabs, Cat # B7002S, Lot # 0010901), 10uL of 1mM dATP, and 3uL of 5U/uL 3â-5â exo-Klenow Fragment (New England Biolabs, Cat #M0212L, Lot # 0180912).  Samples were incubated at 37â°C for 30 minutes and purified with Qiagen MinElute kit, eluting to 20uL.  Samples were then evaporated using a speedvac to 4uL, and sequencing adapters were ligated to the ends of the DNA fragments  by adding 5uL of 2X Quick Ligase Reaction Buffer (New England Biolabs, Cat # B2200S, Lot # 0010910), 0.5uL of Adapter Oligo mix, 1:10 in H2O (????), and 0.5uL of 1U/uL DNA Ligase (New England Biolabs, Cat # M2200L, Lot # 0980910).  Samples were incubated at room temperature for 15 minutes and purified with Qiagen MinElute kit, eluting to 30uL.  Samples were evaporated in a speedvac for 2 minutes and loaded with 6X Bromophenol blue/xylene cyanol loading dye on a 15 cm 8% polyacrylamide gel in TBE.  100bp DNA ladder loaded in far right and left lanes.  Gel run at 200V for 2 hours and stained with 1X SYBR Gold (Invitrogen Cat # S11494) in 120uL TBE, shaking for 15 minutes.  DNA between 200bps and 400bps were excised from gel with a clean scalpel, minced by centrifuging through a sieve, and shook vigorously overnight at 4â°C in 500uL of Qiagen EB buffer.  The next day, samples were mixed vigorously at 50â°C for 15 minutes and centrifuged at 15,000 RPM for 2 minutes.  The supernatant was transferred to a 0.2 um Nanoseq column (Pall, Cat # ODM02C35, Lot # 09551479) and centrifuged at 15,000 RPM for 2 minutes and the flow-through was collected.  Repeat if necessary.  1/10 volume of 3M NaOAC  (pH 5.2), 4uL of glycogen (20ug/uL), and 2 volumes of 100% ETOH were added to each sample, vortexed, and incubated at -80â°C for 30 minutes.  Samples centrifuged at 15,000 RPM for 15 minutes at 4â°C, washed with 1mL 70% ETOH, and centrifuged again for 5 minutes.  Pellets were airdried and resuspended in 20uL of Qiagen EB buffer.  10uL 5X Phusion HF Buffer (Finnzymes, Cat # F-518, Lot # 82), 1uL 10mM dNTPs, 13.5uL PCR grade H2O, 0.5uL HotStart Phusion Taq (Finnzymes, Cat # F540L, Lot #40), and 2.5uL each of forward and reverse 10mM Solexa PCR primers were added to each sample, and run with the following PCR program:   Step 1: 98â°C for 30 seconds  Step 2: 98â°C for 10 seconds  Step 3: 65â°C for 30 seconds  Step 4: 72â°C for 30 seconds  Step 5: Go to step 2, 17 cycles  Step 6: 72â°C for 5 minutes  Step 7: 4â°C, forever  Samples purified with Qiagen MinElute kit, eluting to 40uL.  Samples were evaporated in speedvac for 2 minutes and loaded on an 8% polyacrylamide gel exactly as before.  DNA was excised from same region of gel as before and treated as before.  The following day, the samples were treated exactly the same as after the first gel and overnight shaking, except the purified DNA was ultimately resuspended in 10uL of Qiagen EB buffer.  Sample DNA concentration was determined using an Invitrogen Qubit Flourimeter and the samples were diluted to 10nM for sequencing.

treatment_protocol: Transfection: Cells were transfected using Lipofectamine 2000 (Invitrogen 11668-019).   0.5Î¼g of DNA was combined with 1Î¼l of Lipofectamine in 50Î¼l of Optimem and incubated for 20min.  ESCs were trypsinized and 2x105 were plated into a well of a 6-well along with Lipofectamine mixture.  Cells were incubated for 18hrs followed by media replacement.  For siRNAs, 300ng of DNA and 3Î¼l of Lipofectamine in 300Î¼l of Optimem was used for the Lipofectamine mixture. Libraries of siRNAs were made using a protocol previously described in Foley and O'Farrell 2004 and in Fazzio et al 2008.

value: BayGenomics gene trap line XG122

tag: knockdown


title: Input mRNA-Seq Wild type 2hpf

data_processing:
Input_Wt_2_A.bed; genome build: danRer7
Tophat v1.2.0 alignment to UCSC danRer7 (Zv9) genome sequence, guided by Ensembl r63 gene models; default settings, limited to reads mapping 5 or fewer times. Reads were trimmed of 3' adapter sequence

value: whole embryo


title: InputDNA Pcl3-shRNA6

description: input DNA

value: E14 ESC

value: Pcl3-TAP and Pcl3-wildtype-shRNA6


title: InputDNA scramble

description: input DNA

value: scramble


title: microRNA-Seq of timepoint6

description:
Processed data file:
110413_COLUMBO_00073_FC64E0P_L7_clip3AD5AD_trim_tag_count.txt

data_processing:
TopHat  was used to align the reads to the hg19 reference genome, followed by Cufflinks for transcript assembly and RNA expression analysis.
Small RNA reads were analyzed after removal of 3' adapter and filtering of 5' adapter or 3' artifacts. Sequences larger than 27 nt were trimmed. Unique sequences were identified and the abundance of counts (number of reads).
processed data file build: hg19

source_name: blood cell

tag: cell type

value: PBMC

tag: disease status

value: Healthy

tag: days


title: sRNA-Seq of TCP

city: Chengdu

first: Sheng-hua

last: Wang

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

description: TCP small RNA (13-40 nt size) sequencing

data_processing: The adaptor sequences in raw reads were removed by a custom Perl script. The small RNA reads with length of 13-40 nt were mapped to the genome (MSU 6.1) using SOAPaligner. Only small RNAs with count greater than or equal to 3, mismatches less than 2 and genomic loci less than 50 were retained.

organism: Oryza sativa Indica Group

source_name: Tricellular pollen

growth_protocol: Rice grown under natural field conditions.

extract_protocol: Extraction of total RNA was performed using MiR VanaTM RNA Isolation Kit (Ambion), according to the manufacturer's instructions

treatment_protocol: Tissue samples were collected at sunny noon on July. Collected biological samples were frozen in liquid nitrogen and kept -80C until RNA extraction.

tag: subspecies

value: Variety:Guichao No.2

tag: tissue

value: Male gametophyte

value: tricellular pollen (TCP) stage


title: InputDNA Pcl3-shRNA7

description: input DNA

tag: cell line

value: Pcl3-TAP and Pcl3-wildtype-shRNA7


title: Pcl3 ChIP-seq shRNA6

description: Chromatin IP against Pcl3-TAP

value: anti-FlagM2 (Sigma, 088k6018)

tag: antibody manufacturer

value: Sigma

tag: antibody catalog #


title: Pcl3 ChIP-seq shRNA7

description: Chromatin IP against Pcl3-TAP


title: Suz12 ChIP-seq scramble

description: Chromatin IP against Suz12-TAP


title: Suz12 ChIP-seq Pcl3-shRNA

description: Chromatin IP against Suz12-TAP


title: H3K27me3 ChIP-seq scramble

description: Chromatin IP against H3K27me3

value: anti-H3K27me3 (Upstate, 07-449)

value: Upstate


title: CD8 H3K4me3

status: Public on Mar 14 2012

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

description: Chromatin IP against H3K4me3

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9 assembly) using the Illumina Illumina ELAND software.

source_name: Mature CD8+ T cells

extract_protocol: Nuclei were treated with Mnase to generation mononucleosomes. These were then immunoprecipitated with rabbit polyclonal antibodies against H3K4me3 and H3K36me3. DNA fragements were eluted and adaptors ligated to allow for ultra high throughput sequencing

tag: strain

value: Mature CD8+ T cells from thymus


title: CD8 H3K36me3

description: Chromatin IP against H3K36me3


title: CD8 input

description: input


title: H3K27me3 ChIP-seq Pcl3-shRNA

description: Chromatin IP against H3K27me3

tag: genotype


title: microRNA-Seq of timepoint7

description:
Processed data file:
110413_COLUMBO_00073_FC64E0P_L8_clip3AD5AD_trim_tag_count.txt

extract_protocol:
RNA from different blood component(PMBCs, plasma and sera) was used to prepare RNA-Seq ibraries according to Parkhomchuk D. et. al. 2009. Briefly, Total RNA was treated with DNaseI and rRNA removal by RiboZero. RNA was fragmented by RNA fragmentation kit from Ambion. Resulting RNA was converted to cDNA,  end-repaired using End-repair kit from Epicenter.  The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' 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 300~400 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. Average library fragment size is ~230 bp and SD of ~34 bp.
MicroRNA were isolated from 10 million PBMCs at five time points (Days 4, 21, 116, 185 and 186 from HRV infection) with the mirVanaTM miRNA Isolation Kit (Ambion). microRNA-Seq libraries were prepared from 1 microgram of isolated miRNA according to Illumina’s Small RNA v1.5 Sample Preparation Guide. Each library was sequenced with 36b single-end reads on 1 lane of Illumina’s GAIIx sequencer.


title: CD4 H3K4me3

description: Chromatin IP against H3K4me3

source_name: Mature CD4+ T cells

value: Mature CD4+ T cells from thymus


title: CD4 input

description: input


title: mRNAs from Burkholderia glumae BGS2 (BGR1 tofI::Ω) mutant after 10hr LB liquid culture

first: Ingyu

last: Hwang

address: Kwanak Gu Daehak Dong

department: Agricultural Biotechnology

institute: Seoul National University

description:
BGS2_10h
mRNA

data_processing:
The reads were processed using Illumina CASAVA v1.8.2 software and normalized using the RPKM method.

Genome_build: Burkholderia_glumae_BGR1_uid59397
Supplementary_files_format_and_content: *txt: Tab-delimited text file with RPKM counts.

organism: Burkholderia glumae

source_name: Bacteria culture, BGS2, 10hr

growth_protocol: Each bacteria strain was grown either 6hr or 10 hr in LB liquid.

extract_protocol:
Total RNA was extracted by the RNeasy midi kit (Qiagen, Valencia, CA) following the manufacturer's protocol, and ribosomal RNA was removed by the MICROBExpress Kit (Ambion, TX, USA) for mRNA enrichment.

Illumina TruSeq RNA Sample Preparation Kits v2. Non-directional, single-end 50bp sequencing.

value: BGR1 tofI::Ω mutant

tag: culture time


title: CD4 H3K36me3

description: Chromatin IP against H3K36me3


title: mRNAs from Burkholderia glumae BGS9 (BGR1 qsmR::Ω) mutant after 10hr LB liquid culture

description:
BGS9_10h
mRNA

source_name: Bacteria culture, BGS9, 10hr

value: BGR1 qsmR::Ω mutant


title: mRNAs from Burkholderia glumae BGR1 wild type after 10hr LB liquid culture

description:
BGR1_10h
mRNA

source_name: Bacteria culture, BGR1, 10hr

value: wild type


title: mRNAs from Burkholderia glumae BGS2 (BGR1 tofI::Ω) mutant after 6hr LB liquid culture

description:
BGS2_6h
mRNA

source_name: Bacteria culture, BGS2, 6hr


title: Rad21 rep2 WT mES MM8

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: ChIP-Seq for Rad21 in asynchronous mESCs

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Embryonic stem cells

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

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody catalog number

value: Bethyl A300-080A

value: Bethyl

value: V6.5 embryonic stem cells


title: Pol2 Nocodazole mES MM8

description: ChIP-Seq for RNA Pol II in nocodazole treated mESCs

tag: chip antibody

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz SC-899

value: Santa Cruz

tag: treatment

value: 200 ng/ml nocodazole

value: 12 hr


title: Rad21 rep1 WT mES MM8


title: CapG Nocodazole mES MM8

description: ChIP-Seq for CapG in nocodazole treated mESCs

value: CapG

value: Tatsuya Hirano AFR310-4L

value: Tatsuya Hirano


title: CapG WT mES MM8

description: ChIP-Seq for CapG  in asynchronous mESCs


title: Pol2 Asynchronous mES MM8

description: ChIP-Seq for RNA Pol II in asynchronous mESCs - matching nocodazole-treated


title: mRNAs from Burkholderia glumae BGR1 wild type after 6hr LB liquid culture

description:
BGR1_6h
mRNA

source_name: Bacteria culture, BGR1, 6hr


title: mRNAs from Burkholderia glumae BGS9 (BGR1 qsmR::Ω) mutant after 6hr LB liquid culture

description:
BGS9_6h
mRNA

source_name: Bacteria culture, BGS9, 6hr