title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in IMR90 Cells; renlab.H3K9me3.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL224
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1723
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121

****************
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: GSM469974_UCSD.IMR90.H3K9me3.UCSD_30WNVAAXX_2.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K9me3.Level1.1
ANALYSIS TITLE: Mapping of IMR90 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the IMR90 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1800
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM469974_UCSD.IMR90.H3K9me3.UCSD_42B3BAAXX_3.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K9me3.Level1.2
ANALYSIS TITLE: Mapping of IMR90 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the IMR90 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1802
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM469974_UCSD.IMR90.H3K9me3.UCSD_301FBAAXX_5.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K9me3.Level1.3
ANALYSIS TITLE: Mapping of IMR90 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the IMR90 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1804
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM469974_UCSD.IMR90.H3K9me3.UCSD_313BFAAXX_3.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K9me3.Level1.4
ANALYSIS TITLE: Mapping of IMR90 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the IMR90 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1806
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM469974_UCSD.IMR90.H3K9me3.wig
ANALYSIS ALIAS: UCSD.IMR90.H3K9me3.Level2.4
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K9me3 in the IMR90 cell line 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.1807
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM469974_UCSD.IMR90.H3K9me3.LL224.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the IMR90 Cell Line, Library LL224 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.4397
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.4748
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.2682
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9446
IROC_PERCENTILE: 88
POISSON_SCORE: 0.5335
POISSON_PERCENTILE: 92

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

ANALYSIS FILE NAME: GSM469974_UCSD.IMR90.H3K9me3.LL224.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the IMR90 Cell Line, Library LL224 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.4505
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 2
BROWSER_TRACK_NAME: IMR90 H3K9me3 24
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K9me3 Library LL224 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.4748
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.2682
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9446
IROC_PERCENTILE: 88
POISSON_SCORE: 0.5335
POISSON_PERCENTILE: 92

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

source_name: IMR90; renlab.H3K9me3.IMR90-01.01

value: IMR90 cells

value: genomic DNA

value: ATCC

value: Cell Line

tag: line

tag: lineage

tag: batch

value: Fetal lung fibroblast

tag: passage

tag: medium

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

tag: Sex

value: Female

value: Histone H3K9me3

value: Branson Tip Sonicator

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: CMV delta2b in Arabidopsis thaliana (col), replicate

status: Public on Jan 20 2010

type: SRA

city: Riverside

first: Qingfa

last: Wu

state: CA

address: 900 University Ave

country: USA

institute: UC Riverside

description:
total small RNAs in systemically infected leaves of A. thaliana
barcode: ATC

library_source: viral RNA

data_processing: All sequences containing perfect match 5' barcode (ATC/CGT/TAC) and at least 6 sucessive perfect-matched nucleotides of  the 3' linker ( CTGTAGGCACCATCAAT / CACTCGGGCACCAAGGA) were kept for later analysis. The barcode and linker sequences were computationally removed by in-house perl script. All trimmed sequences in length of 17~30nt were aligned with CMV genome and the perfect matched reads were used for all further analysis.

molecule: total RNA

organism:
Arabidopsis thaliana
Cucumber mosaic virus (strain FNY)

source_name: leaves of wt Arabidopsis thaliana infected with CMVf-Δ2b

extract_protocol: Small RNAs of 18- to 28-nt extracted by Trizol from the systemically infected leaves 14 days after inoculation with CMVf-Δ2b were purified from 15% denatured polyacrylamide gel. Purified small RNAs were directly ligated to the 3′-linker used for miRNA cloning (Integrated DNA Technology) by T4 RNA ligase 2Tr (New England Biolabs). The ligation products were purified and ligated to the 5′ Solexa linker (GUU CAG AGU UCU ACA GUC CGA CGA UC) by T4 RNA ligase I (New England Biolabs). The final ligation products were reverse transcribed using a primer targeting the 3′-linker (CTGTAGGCACCATCAAT OR CACTCGGGCACCAAGGA ) and the cDNA pool was amplified by PCR and sent for sequencing by the Solexa technology (Illumina). Duplicate libraries were constructed from two independent RNA samples from WT, rdr1, and rdr1 rdr2 rdr6 plants and sequenced by the Solexa platform in Illumina, Inc, and the University of California–Riverside Core Facility, respectively.

tag: a.thaliana genotype

value: wild type (col)

tag: a.thaliana tissue

value: leaves

tag: cmv genotype/variation

tag: cmv strain

value: FNY

tag: collected time

value: 14 days after inoculation


title: DFTD1

status: Public on Jan 01 2010

city: Cambridge

first: Pouya

last: Kheradpour

state: MA

address: 32 Vassar St 32-G822

institute: Massachusetts Institute of Technology

library_source: transcriptomic

data_processing: read counts: number of reads for each unique sequence computed after removing linker

organism: Sarcophilus harrisii

source_name: Facial tumor

growth_protocol: Tissues were harvested from wild Tasmanian devils

extract_protocol: RNA was extracted using Trizol. Total RNA was size fractionated on a PAGE gel, and the 18-24 nt fraction selected. Adaptors were ligated, and the libraries were reverse transcribed and PCR amplified (22 cycles) prior to sequencing.

treatment_protocol: Tissues were stored in RNAlater prior to RNA extraction

tag: animal

tag: tissue

value: Facial tumor


title: Human_PTB_CLIP-seq_D2

status: Public on Dec 24 2009

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

description:
library from dimeric PTB-RNA complex
5’ adaptor: Biotin – 5'-AAUGAUACGGCGACCACCGA-3', 3' adaptor: 5' UCGUAUGCCGUCUUCUGCUUG -3'-puromycin.
library strategy (original submitter annotation): CLIP-seq
library selection (original submitter annotation): CLIP

data_processing:
Sequence reads were obtained using the Illumina Genome Analyzer.
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer. After removal of primer dimmer, the tags longer than 18nt were mapped to the human genome sequence (firstly mapped to hg17 and then coordinates were liftovered to hg18) by allowing 2 mismatches, 2 insertions or deletions, and only those with maximal identity (≥90%) were kept.
Peaks: The four alignment files were combined together for peak finding, as we found that most of the monomeric and dimeric tags are similarly distributed in the genome with high pearson correlation coefficient. The method to detect the peaks above gene-specific randomized background was similar to (Yeo et al., 2009) and described in the paper (Xue et al., 2009).

organism: Homo sapiens

source_name: Hela cells

growth_protocol: HeLa cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) with 10% newborn bovine serum plus 100 U penicillin /streptomycin (Gibico) at 37°C in 5% CO2.

extract_protocol: HeLa cells were UV-irradiated at 400 mj and collected by scraping the cells from 15-cm plates. 3' adaptor was first added to immunoprecipitated PTB-RNA complex, then 10% Novex NUPAGE gel was applied to separate monomeric and dimeric form of complexes. After transfering to NC membrane, corresponding bands were cut and RNA was extracted, separately. After 5' adaptor ligation, RT-PCR was performed following Super Script III product manual.

tag: cell line

value: Hela

tag: clip antibody

value: monoclonal anti-PTB antibody (BB7)

tag: library source

value: dimeric PTB-RNA complex


title: Newborn Human Foreskin Fibroblasts: Bisulfite sequencing

status: Public on Dec 29 2009

city: Singapore

first: Chia-Lin

last: Wei

address: 60 Biopolis Street #02-01

department: Genome Technology & Biology

country: Singapore

institute: Genome Institute of Singapore

description: Fibro DNA methylation mapping data

library_source: genomic

data_processing:
Alignment: Sequence reads were first processed by Illumina Genome Analyzer pipeline for base calling and quality filtering. Reads that passed filtering were aligned to human reference genome, Hg18, via SOAP2 alignment program with less than 2 mismatches. To accommodate the conversion of unmethylated cytosines to thymines by bisulfite conversion, we used a "reduced", three-letter alphabet comprising A, G and {C or T} to represent the genome.
Methylation levels of a C within an aligned read were gauged by the ratio of reads that contained a methylated C at that location vs. all the reads that covered the location.

molecule: genomic DNA

source_name: Primary fibroblast

growth_protocol: WA09 hESC line was cultured feeder-free on MatrigelTM (Becton-Dickinson) in StemPro TM medium (Lifetech, Inc.), and passaged with Accutase (Lifetech, Inc.).  They were harvested at passage 41.  hESC-derived fibroblasts (hESC-Fibro) were derived as a stable proliferating population from spontaneously differentiating passage 40 WA09 hESC cells (Gonzalez et al., 2008); after their differentiation they were expanded in two batches, to passage 11 and passage 13 before harvesting. The neonatal fibroblast line (Fibro) cell line was obtained from GlobalStem, Inc (catalog number GSC-3002, Newborn Human Foreskin Fibroblasts, untreated) and was harvested for analysis at passage 13.  All cell lines were cultured at 37°C, ambient oxygen, and 5% CO2.  The hESC-Fibro and Fibro cell lines were cultured in DMEM+10%FBS and passaged with trypsin.

extract_protocol: Genomic DNA were extracted from the individual cell lines and fragmented via nebulization to sizes between 300 bp to 500 bp.  The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors followed by two consecutive bisulfite treatments using the EpiTect Bisulfite Kit (Qiagen) to ensure maximal conversion rate.  The bisulfite treated DNA was enriched by 10 cycles of PCR with primers complementary to the adaptor sequences by uracil-insensitive Taq polymerase (Pfu Turbo Cx Hotstart DNA Polymerase; Stratagene). Sizes between 250 bp to 300 bp (including the adaptors) were selected and sequenced with the Illumina Genome Analyzer using the PE sequencing method at 75bp read length

tag: cell type

value: Newborn Human Foreskin Fibroblasts


title: Human_PTB_CLIP-seq_D1


title: Jarid1a_ChIPSeq

city: Stanford

first: Anton

last: Valouev

address: 300 Pasteur Dr.

department: Pathology

institute: Stanford University

description: Chromatin IP against Jarid1a

data_processing: Enrichment analysis was performed using QuEST software (http://mendel.stanford.edu/sidowlab/downloads/quest/)

organism: Mus musculus

source_name: Embryonic stem cells (chromatin IP fraction)

growth_protocol: standard passaging

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

tag: chip antibody


title: ES_input

description: Total input DNA

source_name: Embryonic stem cells (total chromatin)


title: Human_PTB_CLIP-seq_M2

description:
library from monomeric PTB-RNA complex
5’ adaptor: Biotin – 5'-AAUGAUACGGCGACCACCGA-3', 3' adaptor: 5' UCGUAUGCCGUCUUCUGCUUG -3'-puromycin.
library strategy (original submitter annotation): CLIP-seq
library selection (original submitter annotation): CLIP

value: monomeric PTB-RNA complex


title: P_furiosus_small_RNA

status: Public on Dec 28 2009

city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

data_processing: Reads were aligned to the reference genome with Bowtie to identify uniquely mapping reads.  Those reads that mapped to the CRISPR loci were identified and counted.

organism: Pyrococcus furiosus

source_name: Cultured organisms

growth_protocol: cells were grown by the University of Georgia  Bioexpression and Fermentation Facility in the presence of maltose at 90 C

extract_protocol: Total RNA extracted using standard Trizol extraction. Total RNA fractionated on 15% polyacrylamide gel and size selected to enrich for RNAs of 18-50 nt and 3' and 5' adaptors sequentially ligated to the RNAs.

tag: strain


title: Suz12_ChIPSeq

description: Chromatin IP against Suz12


title: Ezh2_ChIPSeq

description: Chromatin IP against Ezh2


title: Human_PTB_CLIP-seq_M1


title: spe-9 Day8

status: Public on Dec 31 2009

city: New Haven

first: Frank

middle: J

last: Slack

address: 266 Whitney Ave

department: MCDB

institute: Yale University

data_processing: The raw data were aligned to the C. elegans genome (genome build WormBase WS190) using the SOAP program (ver. 1.10 Li, R. et al., Bioinformatics 24: 713-714. 2008) with the following command options: -w 5 -S 3 -A TCGTATGCCGTCTTCTGCTTGT (maximum 2 base pair mismatches were allowed as a default option). Then, the number of times of each read sequenced was examined.

organism: Caenorhabditis elegans

source_name: spe-9 Day8 yound adult

growth_protocol: spe-9 (hc88) mutant animals were cultured at 23dC on regular NGM/OP50 plates after synchronized their growth at the early L1 stage. RNAs were purified at Day 0, 5, 8 and 12 post-L4 molt.

extract_protocol: RNAs enriched for small RNA species (less than 200nt) were prepared using the mirVana miRNA Isolation kit (Ambion) with small RNA enrichment procedure. cDNA libraries for small RNAs were made from 10 µg of RNA using the DGE-Small RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions (As for two biological replicas, named Sample5_spe-9_DAY0_Rep and Sample6_spe-9_DAY8_Rep, 10 µg of total RNAs were used as starting materials).

tag: developmental stage

value: Day8 post-L4 molt

tag: growth condition


title: Jarid2_ChIPSeq

description: Chromatin IP against Jarid2


title: Jurkat_InputDNA

status: Public on Dec 18 2009

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Jordan Hall 104

institute: Indiana University

description: Sheared Input DNA

data_processing:
Alignment (*sorted.txt files): Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. See GSE17954 supplementary readme file for column descriptions (GSE17954_README_Sorted.txt).
Peak detection (*EmpFDR* files) was performed using the Useq application package (http://useq.sourceforge.net). File descriptions are available at http://useq.sourceforge.net/outputFileTypeDescriptions.html

source_name: Input DNA

growth_protocol: Jurkat T cells were grown in RPMI media with 10% FBS

extract_protocol: Crosslinked nuclei were prepared from 1E7 Jurkat T cells.  Chromatin was sheared by sonication and partitioned by immunoprecipitation with antibodies bound to magentic beads.  Crosslinks were revered by heating and DNA was purified by a Qiagen PCR cleanup kit.  ChIP and Input DNA was prepared for sequencing using Illumina’s ChIP-seq kit.  Each ChIP DNA sample was pooled from three independent replicates.  36 bp reads were generated using Illumina’s Genome Analyzer II and standard pipeline software.

value: Jurkat, clone E6-1 T lymphocyte

tag: antibody


title: GM12878_PolII_ChIPSeq

first: Flora

last: Vaccarino

address: 230 South Frontage Road

department: Child Study Center

description: ChIP against Pol II

data_processing: Enriched peak regions corresponding to transcription factor binding sites were identified by first extending all the uniquely mapped tags reads (mapped against hg18) to the averaged sequenced DNA fragment size ~200bps and then accumulated into fragment density signal maps. Peaks in these maps are identified by comparison to a computer simulated null model for each Mb of each chromosome (accounting for the variability in mappability of sequence tags across the human genome. For potential target regions the number of sequenced tags is compared against the normalized number of sequence tags overlapping the region from the matching Input DNA reference sample (GSM487430). Fold enrichment ratios are computed from the ratio of these two sets of counts for each regions as well as p-value using the cumulative distribution function for the binomial distribution. P-value are corrected for multiple hypothesis testing using a Benjamini-Hochberg correction factor and a false discovery rate threshold of 0.05 is imposed. (Rozowsky et al. Nature Biotechnology 27, 66 - 75, 2009)

growth_protocol: GM12878 cells were grown in RPMI media containing 15% FBS

extract_protocol: Nuclei were isolated from cross-linked (1% formaldehyde for 10 minutes at room temperature) GM12878 cells. Nuclei were lysed in RIPA buffer and extracted chromatin was sonicated using Branson Sonifier 250. ChIP DNA was prepared using Pol II antibody. Libraries were prepared according to Illumina's protocols using reagents purchased from different vendors. 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 (Epicenter). The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) (New England Biolab, NEB) 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 (LigaFast, Promega) DNA was PCR amplified (Phusion polymerase, NEB) with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: growth properties

value: Suspension Morphology

tag: lymphoblast antibody

value: RNA Pol II


title: Jurkat_CBP_ChIPseq

description: Chromatin IP against CBP

source_name: CBP ChIP

value: CBP A-22 from Santa Cruz Biotechnology


title: Jurkat_ETS1_ChIPseq

description: Chromatin IP against ETS1

source_name: ETS1 ChIP

value: ETS1 sc355 from Santa Cruz Biotechnology


title: Jurkat_RUNX_ChIPseq

description: Chromatin IP against RUNX

source_name: RUNX ChIP

value: RUNX monoclonal from Nancy Speck


title: H3K27me3_ChIPseq_UPR9_5hrZinc_JM39

status: Public on Dec 17 2009

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

description: Antibody H3K27me3 _Jenuwein

data_processing: Reads (32 bp) were aligned to the Human (UCSC 36.1 (hg18)) reference genome. RNAPII tracks for the different treatment periods (0, 24 and 48 hours) were equalized for the total number of mapped tags by random removal of sequenced tags. For PML, RAR and RXR, enriched intervals were identified using MACs. For RNAPII number of tags within ENSEMBLE genes (from +500 from TSS to end of gene) were counted and gene regulation was expressed as ratio of tags after 24 or 48 hours treatment divided by the tags in the same gene region before treatment.

source_name: UPR9 cells

growth_protocol: Leukemic cells were cultured in normal cell culture containing 10% serum.

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor Diagenode, immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

treatment_protocol: Leukemic cells NB4, MR4, APL were treated with ATRA for 24 or 48 hours, UPR9 cells with zinc for 5 hours.

tag: agent

value: 5 hours zinc


title: H3K9K14ac_ChIPseq_UPR9_5hrZinc_JM37

description: Antibody H3K9K14ac _Diagenode


title: H3K27me3_ChIPseq_UPR9_noZinc_JM38

description: Antibody H3K27me3 _Jenuwein


title: spe-9 Day0

source_name: spe-9 Day0 yound adult

value: Day0 post-L4 molt


title: RXR_ChIPseq_UPR9_5hrZinc_JM35

description: Antibody RXR _sc774

value: RXR


title: H3K9K14ac_ChIPseq_UPR9_noZinc_JM36

description: Antibody H3K9K14ac _Diagenode


title: RXR_ChIPseq_UPR9_noZinc_JM34

description: Antibody RXR _sc774


title: Embryonic stem cells: Bisulfite sequencing

description: hESE DNA methylation mapping data

source_name: Embryonic stem cells

value: Embryonic stem cells


title: RAR_ChIPseq_UPR9_5hrZinc_JM33

description: Antibody RAR _A704

value: RAR


title: PML_ChIPseq_UPR9_noZinc_JM30

description: Antibody PML _H238

value: PML


title: PML_ChIPseq_UPR9_5hrZinc_JM31

description: Antibody PML _H238


title: H3K9K14ac_ChIPseq_MR4_24hrATRA_JM29

description: Antibody H3K9K14ac _Diagenode

source_name: MR4 cells

value: 24 hours ATRA


title: RAR_ChIPseq_UPR9_noZinc_JM32

description: Antibody RAR _A704


title: H3K9me3_ChIPseq_MR4_noATRA_JM28

description: Antibody H3K9K14ac _Diagenode


title: spe-9 Day0 replica


title: PML_ChIP-seq_MR4_noATRA_JM26

description: Antibody PML _H238


title: PML_ChIP-seq_APL74_noATRA_JM24

description: Antibody PML _H238

source_name: APL cells _pz74


title: H3K9me3_ChIPseq_NB4_24hrATRA_JM23

description: Antibody H3K9me3 _Jenuwein

source_name: NB4 cells


title: RXR_ChIP-seq_APL74_noATRA_JM25

description: Antibody RXR _sc774


title: GenomicDNA_NB4_noATRA_JM40


title: H3K9me3_ChIPseq_NB4_noATRA_JM22

description: Antibody H3K9me3 _Jenuwein


title: spe-9 Day12

source_name: spe-9 Day12 yound adult

value: Day12 post-L4 molt


title: RAR_ChIPseq_NB4_24hoursATRA_JM21

description: Antibody RAR _A704


title: PML_ChIP-seq_MR4_24hoursATRA_JM27

description: Antibody PML _H238


title: DNAme_MeCap-seq_NB4_noATRA_JM17

description: GST-MBD

value: MethylCap GST MBD


title: PML_ChIP-seq_NB4_24hoursATRA_JM19

description: Antibody PML _H238


title: DNAme_MeCap-seq_NB4_48hoursATRA_JM18

description: GST-MBD

value: 48 hours ATRA


title: spe-9 Day5

source_name: spe-9 Day5 yound adult

value: Day5 post-L4 molt


title: RXR_ChIP-seq_NB4_24hoursATRA_JM20

description: Antibody RXR _sc774


title: Mili IP_Tdrd9-/- replicate1

status: Public on Jan 06 2010

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
library source: Protein-associated small RNAs
library selection: Immunoprecipitation and gel elution of ~28-30 nt RNAs by radioactive spike labelling

data_processing: Alignment with mouse genome July 2007, mm9 assembly

source_name: Mili IP_Tdrd9-/-

growth_protocol: Mouse testes extract

extract_protocol:
Illumina small RNA library preparation kit
Immunoprecipitation and gel elution of ~28-30 nt RNAs by radioactive spike labelling

treatment_protocol: Lysate preparation

value: testes

tag: dev stage

value: 14 dpp


title: Mili IP_Tdrd9-/- replicate2


title: H3K27me3_ChIP-seq_APL164_48hoursATRA_JM16

description: Antibody H3K27me3 _Jenuwein

source_name: APL cells _pz164


title: H3K9K14ac_ChIP-seq_APL164_48hoursATRA_JM15

description: Antibody H3K9K14ac _Diagenode


title: H3K27me3_ChIP-seq_APL164_noATRA_JM14

description: Antibody H3K27me3 _Jenuwein


title: H3K9K14ac_ChIP-seq_APL164_noATRA_JM13

description: Antibody H3K9K14ac _Diagenode


title: RNApolII_ChIP-seq_NB4_24hoursATRA_JM11

description: Antibody RNApolII _8WG16

value: RNAPII


title: RNApolII_ChIP-seq_NB4_48hoursATRA_JM12

description: Antibody RNApolII _8WG16


title: H3K9K14ac_ChIP-seq_NB4_24hoursATRA, JM8a and JM8b

description: Antibody H3K9K14ac _Diagenode


title: H3K27me3_ChIP-seq_NB4_24hoursATRA, JM9a and JM9b

description: Antibody H3K27me3 _Jenuwein


title: H3K27me3_ChIP-seq_NB4_noATRA, JM7a and JM7b

description: Antibody H3K27me3 _Jenuwein


title: RXR_ChIP-seq_APL164_noATRA, JM5

description: Antibody RXR _sc774


title: H3K9K14ac_ChIP-seq_NB4_noATRA, JM6a and JM6b

description: Antibody H3K9K14ac _Diagenode


title: RAR_ChIP-seq_NB4_noATRA, JM3

description: Antibody RAR _A704


title: RXR_ChIP-seq_NB4_noATRA, JM2a and JM2b

description: Antibody RXR _sc774


title: PML_ChIP-seq_NB4_noATRA, JM1a and JM1b

description: Antibody PML _H238


title: PML_ChIP-seq_APL164_noATRA, JM4

description: Antibody PML _H238


title: Mili IP_Tdrd9+/- replicate2

source_name: Mili IP_Tdrd9+/-


title: Miwi-IP

status: Public on Jan 04 2010

city: New York

first: Nicolas

last: Robine

state: NY

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
IP against Miwi
IP and gel-purification, RNA-seq.
Sequencing of small RNAs from Mili IP, Miwi IP, and total RNA from mouse adult testes extract.

data_processing:
Raw sequences were clipped by 3' linker sequences recognition, and clipped sequences longer than 18 nt were selected for analysis.
The processed data files (*seq ) are the result of the pipeline: Raw files -> remove the linker sequences -> count the number of each sequence.

source_name: Miwi immuprecipitate

growth_protocol: Mouse testes were dissected from euthanized adult male swiss webster mice.

extract_protocol: The anti-Mili or anti-Miwi antibody was immobilized onto magnetic beads, and beads were suspended in testes extract for 1 hour.  Retained beads were washed 6 times with 1X PBS, then total RNA from the IP was extracted with Tri-reagent.  Total RNA from whole testes extract was also extracted with Tri-reagent.  Adapters were ligated to the small RNA component from the IP or total RNA, and a cDNA library was produced by reverse-transcription of the adapter-ligated small RNAs.  The cDNA library was gel purified, quantitated, and coupled to a flow cell for sequencing on the Illumina Genome Analyzer II.

treatment_protocol: Testes extract was produced by decapsulating testicles, washing and resuspending spermatogenic tubules in protein extraction buffer, then douncing tubules with 20 strokes of a Type B  glass pestle.  Extract was then cleared with a 30 minute, 10,000 g spin, and snap frozen.

tag: stage

value: adult

tag: size selection

value: anti-Miwi


title: Embryo_Cap_shortRNA_3'_RNAseq_untreated

status: Public on Dec 11 2009

city: Research Triangle Park

first: Sergei

last: Nechaev

state: NC

address: 111 Alexander Dr

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS/NIH

data_processing: Alignment: Sequence reads were obtained, trimmed to 26nt starting at the 5'-most nucleotide and mapped to the Drosophila melanogaster DM3 (April, 2006) genome using the MOM  maximum oligonucleotide mapping tool. All unique reads mapping with two or fewer mismatches were retained. Reads from biological replicates were merged and formatted to .bedgraph format for Forward and Reverse stands.

organism: Drosophila melanogaster

source_name: Embryos

growth_protocol: Embryos were grown on grape agar plates at 25'C

extract_protocol: Nuclei prepared by gentle hypotonic cell lysis in the presence of Mg and centrifugation through 2M sucrose cushion were used to extract total RNA with Trizol reagent  according to the manufacturer's instructions. Ten microgram of nuclear RNA was size-selected on a gel to obtain species 25-100nt, which were extracted from the gel, treated, sequentially, with 5' polyphosphatase and 5' terminator exonuclease, and the remaining capped species were ligated to a custom 3' small RNA linker designed to sequence the cloned RNA directly from its 3' end. After purification on a gel, RNA was treated, sequentially, with alkaline phosphatase and tobacco acid pyrophosphatase, after which the RNA was ligated to a custom 5' small RNA linker (Illumina). Subsequent reverse transcription and library amplification was performed according to the recommendations from the Illumina small RNA cloning kit using a custom RT primer and other standard reagents from the kit.

value: Oregon R

value: Whole embryos

tag: cell source

value: Whole embryos collected between 0 and 16 hours after egg laying

tag: passages

tag: molecule

value: small capped nuclear RNA


title: S2_Cap_longtRNA_5'_RNAseq_untreated_rep2

source_name: S2 cells

growth_protocol: Cells were grown in Schneider's Media supplemented with 10% of heat-inactivated bovine fetal serum, at 26'C, in 175 cm3 culture flasks

extract_protocol: Total RNA from nuclei was treated, sequentially, with 5' polyphosphatase and 5' terminator exonuclease to degrade uncapped species, fragmented by partial alkaline hydrolysis and size-selected on a gel to obtain RNA species in 80-200nt range. RNA was treated, sequentially, with T4 polynucleotide kinase in the presence of ATP and 5' terminator exonuclease, to degrade non-5'-end RNA fragments. RNA was ligated to the 3' RNA linker (Illumina) and purified on a gel. RNA was then treated, sequentially, with alkaline phosphatase and tobacco acid pyrophosphatase, followed by ligation to the 5' RNA linker (Illumina). Subsequent reverse transcription and library amplification was performed according to the recommendations from the Illumina small RNA cloning kit using reagents from the kit.

value: Drosophila Schneider 2 cells

value: obtained from the Drosophila Genome Research Center, derived from Oregon R embryos on the verge of hatching.

value: Immortal. Used within 5 to 10 passages after thawing

value: long capped nuclear RNA, fragmented


title: Mili IP_Tdrd9+/- replicate1

tag: tissue


title: Embryo_Cap_shortRNA_5'_RNAseq_untreated

extract_protocol: Nuclei prepared by gentle hypotonic cell lysis in the presence of Mg and centrifugation through 2M sucrose cushion were used to extract total RNA with Trizol reagent  according to the manufacturer's instructions. Ten microgram of nuclear RNA was size-selecten on a gel to obtain species 25-100nt, which were extracted from the gel, treated, sequentially, with 5' polyphosphatase and 5' terminator exonuclease, and the remaining capped species were ligated to the 3' small RNA linker (Illumina). After purification on a gel, RNA was treated, sequentially, with alkaline phosphatase and tobacco acid pyrophosphatase, after which the RNA was ligated to the 5' small RNA linker (Illumina). Subsequent reverse transcription and library amplification was performed according to the recommendations from the Illumina small RNA cloning kit using reagents from the kit.


title: S2_Cap_longtRNA_5'_RNAseq_untreated_rep1


title: S2_Cap_shortRNA_5'_RNAseq_untreated_rep1+rep2

growth_protocol: Cells were grown in Schneider's Media supplemented with 10% of heat-inactivated bovine fetal serum, at 26'C, in a spinner flask with a spinner set at 65rpm.

extract_protocol: Nuclei prepared by gentle hypotonic cell lysis in the presence of Mg  and centrifugation through 2M sucrose cushion were used to extract total RNA with Trizol reagent  according to the manufacturer's instructions. Ten microgram of nuclear RNA was size-selecten on a gel to obtain species 25-100nt, which were extracted from the gel, treated, sequentially, with 5' polyphosphatase and 5' terminator exonuclease, and the remaining capped species were ligated to the 3' small RNA linker (Illumina). After purification on a gel, RNA was treated, sequentially, with alkaline phosphatase and tobacco acid pyrophosphatase, after which the RNA was ligated to the 5' small RNA linker (Illumina). Subsequent reverse transcription and library amplification was performed according to the recommendations from the Illumina small RNA cloning kit using reagents from the kit.


title: S2_Cap_shortRNA_3'_RNAseq_untreated_rep1+rep2

extract_protocol: Nuclei prepared by gentle hypotonic cell lysis in the presence of Mg  and centrifugation through 2M sucrose cushion were used to extract total RNA with Trizol reagent  according to the manufacturer's instructions. Ten microgram of nuclear RNA was size-selected on a gel to obtain species 25-100nt, which were extracted from the gel, treated, sequentially, with 5' polyphosphatase and 5' terminator exonuclease, and the remaining capped species were ligated to a custom 3' small RNA linker designed to sequence the cloned RNA directly from its 3' end. After purification on a gel, RNA was treated, sequentially, with alkaline phosphatase and tobacco acid pyrophosphatase, after which the RNA was ligated to a custom 5' small RNA linker (Illumina). Subsequent reverse transcription and library amplification was performed according to the recommendations from the Illumina small RNA cloning kit using a custom RT primer and other standard reagents from the kit.


title: S2_Cap_shortRNA_3'_RNAseq_IISdepleted_rep1+rep2

treatment_protocol: dsRNA against TFIIS for 72 hours


title: RNApolII_ChIP-seq_NB4_noATRA_JM10

description: Antibody RNApolII _8WG16


title: total RNA

description:
total RNA
IP and gel-purification, RNA-seq.
Sequencing of small RNAs from Mili IP, Miwi IP, and total RNA from mouse adult testes extract.

source_name: total RNA


title: S2_Cap_shortRNA_3'_RNAseq_LacZdepleted_rep1+rep2

treatment_protocol: dsRNA against beta-galactosidase for 72 hours


title: Xenopus-egg_Y12-associated small RNAs

description:
small RNA associated with Y12 antibody
IP and gel-purification, RNA-seq.
Sequencing of small RNAs from Y12 IP.

organism: Xenopus tropicalis

source_name: Y12-associated small RNA

growth_protocol: Eggs harvested from hormonal-induced ovulation of 3 X.tropicalis females.

extract_protocol: The Y12 antibody was immobilized onto magnetic beads, and beads were suspended in egg extract for 1 hour.  Retained beads were washed 6 times with 1X PBS, then total RNA from the IP was extracted with Tri-reagent.  Adapters were ligated to the small RNA component from the IP, and a cDNA library was produced by reverse-transcription of the adapter-ligated small RNAs.  The cDNA library was gel purified, quantitated, and coupled to a flow cell for sequencing on the Illumina Genome Analyzer II.

treatment_protocol: Whole cell extract was produced from eggs that were manually fractionated by high speed centrifugation.

value: egg


title: ZNF263_ChIP-seq_A

status: Public on Dec 03 2009

description: Chromatin IP against ZNF263

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks were called with Sole-Search (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi)

source_name: K562 cells

growth_protocol: 1. Take out the  K562 vial (1 million cells in 1 ml) from liquid nitrogen and thaw it in 37 degree waterbath. Suspend the washed cells in 10 ml RPMI with 10% FBS  and GIBCO Antibiotic-antimycotic (Cat. No. 15240-062 5ml per 500 ml of culture.  2. Centrifuge at 700 rpm for 5 min.  3. Suspend the cells in 10 ml RPMI with 10%FBS and transfer them into a small cell culture flask (not a spinner flask) to be incubated in CO2 incubator.  4. These cells get into log phase in 5 to 7 days. Start counting at day 3. When the cell density reaches 0.7 to 0.8(x 10?)/mlsplit the culture to about 0.4 million cells per ml with fresh RPMI with 10% FBS (this is the growth medium for K562). From this point on the cells should double every 24 hours,  5. From now on expect the cell density to double every 24 hours. (When the total cell number reaches 2X10>7, they can be stored as stock in liquid nitrogen at 1 million cells/ml (a total of 20 vials) in straight serum ( FBS) containing 10% DMSO)   6. Split the cells when the density reaches around 0.75 million/ml.  7. Grow the cells to required numbers.

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

value: myelogenous leukaemia

tag: cell line

tag: passage


title: S2_Rpb3_S2_Pol_II_ChIPSeq_rep1+rep2

data_processing:
Alignment: Sequence reads were obtained, trimmed to 26nt starting at the 5'-most nucleotide and mapped to the Drosophila melanogaster DM3 (April, 2006) genome using the MOM  maximum oligonucleotide mapping tool. All unique reads mapping with two or fewer mismatches were retained. Reads from biological replicates were merged and formatted to .bedgraph format for Forward and Reverse stands.
The two ChIP-seq replicates were combined to make one .bedgraph file (binned into 25nt windows).

extract_protocol: Chromatin IP against total Pol II

tag: cell type

tag: chip antibody

value: Pol II Rpb3 subunit

value: genomic DNA


title: Tbx3_ChIPSeq

status: Public on Dec 04 2009

first: Yuriy

middle: L

last: Orlov

address: 60 Biopolis Street

department: Computational Systems Biology

description: Chromatin IP against Tbx3

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (mm8) genome using the Illumina Genome Analyzer II Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) using processed data file. Control input DNA sequencing library was used as background for peak calling.

source_name: Embyonic stem cells

growth_protocol: D3 and R1 mouse ESCs were obtained from ATCC and cultured as per manufacturer's recommendation, in the presence of inactivated MEFs supplemented with LIF.

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with Tbx3 antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No treatment was performed for ESCs used for ChIP-sequencing.

value: pluripotent and self-renewing cells


title: ZNF263_ChIP-seq_B

description: Chromatin IP against ZNF263


title: Rhesus male 1 rep1

status: Public on Dec 01 2009

city: Chicago

first: Ran

last: Blekhman

state: IL

institute: University of Chicago

data_processing: In order to compare exon and gene expression levels across species, we used BLAT to identify human exons for which clear orthologs exist in the other two species. To avoid biases due to mapping problems, we removed exons for which multiple plausible orthologs or highly similar paralogs exist. This resulted in the identification of 150,108 orthologous exons in 20,689 genes. We then used MAQ to align reads to their corresponding genome sequences (human: hg18, March 2006 draft; chimpanzee: panTro2, March 2006 draft; rhesus macaque: rheMac2, January 2006 draft) and counted the number of reads that mapped to orthologous exons in each sample. We excluded reads that (i) did not overlap any of the three-species orthologous exons, (ii) had a MAQ mapping quality lower than 20, which might indicate errors or ambiguous mapping, or (iii) mapped to more than a single exon in our list. The number of reads mapped to each gene in each lane is available in the processed data file (ReadCountPerLane.txt).

molecule: polyA RNA

organism: Macaca mulatta

source_name: liver

extract_protocol: We extracted RNA from each tissue sample using Trizol (Invitrogen, Carisbad, CA), and confirmed that the RNA was of high quality both by visualizing the RNA on a gel, and by analyzing it using Agillent’s Bioanalyzer 2100. We then prepared samples for RNA sequencing using Illumina’s technology (Solexa) by using our previously published RNAseq protocol (Marioni et al., 2008; detailed protocol is available at http://giladlab.uchicago.edu). This method involves several steps that are designed to convert total RNA into a library of template molecules suitable for high throughput DNA sequencing.  The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads.  Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and a high concentration of random hexamer primers.  This is followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH.  Finally the short cDNA fragments are prepared for sequencing on the Illumina Genome Analyzer using reagents provided in the Genomic DNA Sequencing Sample Prep Kit available with the system.  A full and detailed protocol is available at http://giladlab.uchicago.edu.

tag: sex

value: male

value: liver


title: Rhesus male 2 rep1


title: Rhesus male 2 rep2


title: Rhesus female 3 rep2

value: female


title: Rhesus female 2 rep2


title: spe-9 Day8 replica

source_name: spe-9 Day8 yound adult

tag: strain

tag: developmental stage

value: Day8 post-L4 molt

tag: growth condition


title: Rhesus female 2 rep1


title: Mili-IP

description:
IP against Mili
IP and gel-purification, RNA-seq.
Sequencing of small RNAs from Mili IP, Miwi IP, and total RNA from mouse adult testes extract.

source_name: Mili immuprecipitate

value: adult

tag: antibody

value: anti-Mili


title: Rhesus male 3 rep1


title: Rhesus female 1 rep1


title: Chimp male 3 rep2

organism: Pan troglodytes


title: sRNA_delayed_deep_sequencing

status: Public on Dec 15 2009

city: Shantou

first: Zeng-Ming

last: Yang

address: 263 Daxue Road

department: Biology

country: China

institute: Shantou University

description:
small RNA deep sequencing of delayed implantation
small RNA(18-35nt)

data_processing: processed data build: mm9, the 3’ end of the read was determined by the 3’ most perfect match to the first 8 nt of the 3’ adaptor.

growth_protocol: Mature mice (Kunming White outbred strain) were maintained in a controlled environment with a 14-h light/10-h dark cycle. All animal procedures were approved by the Institutional Animal Care and Use Committee of Xiamen University.

extract_protocol:
Total RNAs of delayed and activated uterus were extracted by TRIzol (Invitrogen), followed by a 15% Tris-borate-EDTA (TBE) urea gel electrophoresis. Small RNAs were separated by the size of 18-30 bases from the gel. After purification, small RNAs were ligated to a 5’ RNA adapter (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). Followed by another TBE gel purification and ligated to a 3’ RNA adapter (5’- pUCGUAUGCCGUCUUCUGCUUGidT -3’), the purified small RNAs were reverse transcribed using Illumina’s small RNA RT-Primer (5’-CAAGCAGAAGACGGCATACGA-3’) and amplified by a 15 cycle PCR using Illumina’s small RNA primer set (5’-CAAGCAGAAGACGGCATACGA-3’ and 5’-AATGATACGGCGACCACCGA-3’). PCR products were purified and quantified for Illumina sequencing in Shenzhen Huada Gene Sci-Tech Company (Shenzhen, China).
18-30nt small RNA by gel

treatment_protocol: Female mice were mated with fertile males of the same strain to induce pregnancy (day 1 is the day of vaginal plug). To induce delayed implantation, pregnant mice were ovariectomized under ether anesthesia at 08:30-09:00 h on day 4 of pregnancy. Delayed implantation was maintained from days 5-7 by injecting progesterone (1 mg/mouse, Sigma). Estradiol-17 (25 ng/mouse, Sigma) was given to progesterone-primed delayed implantation mice to initiate implantation on day 7 of pregnancy. The mice were sacrificed to collect uteri 24 h after estrogen treatment for activation group. Delayed implantation was confirmed by flushing the blastocysts from one horn of the uterus. The implantation sites of activated uterus were identified through intravenous injection of 0.1 ml of 1% Chicago blue.

value: uterus


title: Chimp male 2 rep1


title: Rhesus male 1 rep2


title: Oryza sativa L. ssp. indica Degradome

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

description: high-throughput sequencing of degradome sequence

data_processing: The 20 and 21nt distinct reads were subjected to the CleaveLand pipeline for small RNA targets identification as previously described (Addo-Quaye et al., 2009). Briefly, the 20 and 21nt distinct reads were first normalized to give “reads per million” (RPM). Subsequently, the degradome reads were mapped to the rice annotated cDNA (TIGR6.1) and the cDNA hit number of each degradome read was recorded. The RPM abundance then was divided by each degradome reads hit number to give “normalized reads per million” (NRPM). For these cDNA matched reads, a 26nt long mRNA tag is generated by extracting 13nt of sequence upstream and downstream of the 5’ end of the matching degradome sequences. All resulting reads were aligned to each registered miRNA (miRBase 13.0) by the Needle program in the EMBOSS package (Rice et al., 2000). Alignments are then scored according to a previously described method (Allen et al., 2005). All alignments with scores not exceeding 7 and having the 5’ end of the degradome sequence coincident with the 10th nucleotide of complementarity to the small RNA were retained. To clearly represent identified targets in degradome library, all hits were categorized based on the abundance of resulting mRNA tag relative to the overall profile of degradome reads matching the target (Addo-Quaye et al., 2008; Addo-Quaye et al., 2009). The resulting output was trimmed with the optimized score thresholds as previously reported with category I set as 4.5, category II as 4 and category III as 3 (Addo-Quaye et al., 2008).

organism: Oryza sativa Indica Group

source_name: young inflorescences (4~6cm)

growth_protocol: Rice (Oryza sativa) ssp. indica (93-11) plants were grown in the field.

extract_protocol: Approximately 150 μg of total RNA was then selected for polyadenylated RNA using the Oligotex mRNA mini kit (Qiagen). The degradome library was constructed as previously described (German et al., 2008; German et al., 2009). Briefly, using T4 RNA ligase (NEB), a 5’ RNA adapter (cx4669, 5′-GUUCAGAGUUCUACAGUCCGAC-3′, from TaKaRa) was added to the cleavage products which possess a free 5’-phosphate on their 3’ termini. Then the ligated products were purified by Oligotex mRNA mini kit (Qiagen) again and reverse transcribed by a primer (cx4670, 5′-CGAGCACAGAATTAATACGACT(18)V-3′, from Invitrogen) via M-MLV reverse transcriptase (Invitrogen). The generated cDNA library was amplified for 6 cycles (94°C for 30 s, 60°C for 20 s, and 72°C for 3 min) with a pair of primers (forward, cx4671: 5′-GTTCAGAGTTCTACAGTCCGAC-3′ and reverse, cx4672 : 5′-CGAGCACAGAATTAATACGAC-3′, from Invitrogen) using Phusion Taq (NEB). The PCR products were digested with an enzyme Mme I (NEB). Next, a double-strand DNA adapter (top, cx4908: 5′-TCGTATGCCGTCTTCTGCTTG-3′, bottom, cx4674: 5’-CAAGCAGAAGACGGCATACGANN-3’, from Invitrogen) was incorporated into the digested products using T4 DNA ligase (NEB) (Addo-Quaye et al., 2008) and gel purified for PCR amplification (94°C for 30 s, 60°C for 20 s, and 72°C for 20 s) with primers (forward, cx4675: 5′-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGAC-3′, reverse, cx4676: 5’-CAAGCAGAAGACGGCATACGA-3’, from Invitrogen) until a distinct band appeared. PCR products were gel purified and subjected to SBS sequencing.

treatment_protocol: Young inflorescences were ground into a fine power in liquid nitrogen and processed using Trizol reagent (Invitrogen).

tag: genotype

value: Wild-type

value: young inflorescences (4~6cm)


title: sRNA_activation_deep_sequencing

description:
small RNA deep sequencing of activation
small RNA(18-36nt)

source_name: activation


title: Rhesus male 3 rep2


title: Rhesus female 1 rep2


title: Chimp male 1 rep2


title: Chimp male 2 rep2


title: mRNA_activation_digital_gene_expression

description: mRNA tag profiling (digital gene expression) analysis of activation

extract_protocol:
mRNAs were isolated through binding to a magnetic oligo(dT) beads. First strand cDNA was synthesized using the binding mRNA as a template, and followed by the synthesis of the second strand of cDNA. After cDNAs were digested with DpnII, the double stranded cDNA fragment attached to the oligo(dT) bead was collected and ligated to a GEX DpnII adapter 1 at the site of DpnII cleavage. The sequence for MmeI was included in GEX DpnII adapter 1. After purification, products coupled with oligo(dT) bead were digested with MmeI to create a 16 bp tag, followed by ligating to a GEX adapter 2 at the site of MmeI cleavage. After PCR amplification, the purified DNA fragments were used directly for sequencing using the Illumina Cluster Station in Shenzhen Huada Gene Sci-Tech Company.
polyA+ mRNA by oligo dT beads


title: Chimp male 1 rep1


title: Chimp female 2 rep2


title: Chimp female 3 rep2


title: Chimp female 3 rep1


title: Small RNAs from maize leaves

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

description: Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

data_processing: Small RNA reads were analyzed after removal of 3' adapter (5' -TCGTATGCCGTCTTCTGCTTG) and filtering of 5' adapter (5'-GTTCAGAGTTCTACAGTCCGACGATC) or 3' adapter artefacts.

organism: Zea mays

source_name: Leaves

growth_protocol: Plants were grown in a flood irrigated plot at the University of Arizona (Tucson, AZ, USA) in 2007. Young leaves were collected and pooled from several 6-weeks-old seedlings.

extract_protocol: Total RNA was extracted  with the Plant RNA Purification Reagent (Invitrogen). Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000).

tag: cultivar

value: B73 (wild type)

tag: age at harvest

value: 6-weeks-old seedlings


title: Chimp female 1 rep2


title: Human male 3 rep2


title: Chimp female 2 rep1


title: Rhesus female 3 rep1


title: Human male 2 rep2


title: Human male 3 rep1


title: Human male 1 rep1


title: Human male 2 rep1


title: Human male 1 rep2


title: Human female 3 rep2


title: Human female 3 rep1


title: Human female 2 rep2


title: Human female 2 rep1


title: Human female 1 rep2


title: Human female 1 rep1


title: K562_Input

status: Public on Nov 25 2009

city: Madison

first: Emery

middle: H.

last: Bresnick

state: WI

address: 1300 University Avenue 383 MSC

department: Pharmacology

institute: University of Wisconsin-Madison

data_processing:
Alignment: Sequence reads obtained were aligned to the UCSC human genome assembly HG18 using the Eland application (Illumina), allowing no more than two mismatches per sequence. Only sequences that aligned uniquely were used to identify GATA-1 and GATA-2 occupancy peaks. The 32 nt sequence reads were extended by the average length of the ChIP-seq library (327 bp).
Peaks: Binding sites were determined using a multi-pass system. The first pass of the program determines an accurate, statistically significant height cutoff for peaks.  Sequenceable regions of the genome are estimated based on 12 input sample datasets of K562 and HeLa cells (unpublished data). This approach accounts for genomic regions with a lower abundance of sequence reads and provides a basis for randomizing sequence reads from the ChIP-seq experiments. The minimum peak height is then determined, using a false discovery rate of 0.001. The second pass eliminates false peaks that are also present in input data sets. The background model was produced by randomly selecting sequence reads from input libraries and placed in ten files of equal size. Both the ChIP-seq and input data sets are binned using a sliding window of 30 bp. ChIP sample bins that are above height cutoff and are significant vs. input background, using a one sample T-test, are assessed as potential peaks. A third pass to the peak detection removes peaks in duplicated regions. The resulting potential peaks with lengths greater than the average length of chromatin fragments used in the ChIP experiment are reported. The height of a peak reflects the number of overlapped sequence reads for that peak.

source_name: Input control

growth_protocol: Human K562 erythroleukemia cells (ATCC # CCL-243) were cultured in RPMI medium 1640 supplemented with 10% heat inactivated FBS and antibiotic-antimycotic solution (Invitrogen, 15240-104) in a 36-38°C, 5-10% CO2.

extract_protocol: ChIP samples were prepared using 10e8 K562 cells per condition. Chromatin was prepared as described (http://www.genomecenter.ucdavis.edu/farnham/protocol.html). ChIP libraries were created using 15 cycles of amplification. Libraries were run on a 2% agarose gel, and the 150-450 bp fraction was extracted and purified using DNA gel extraction kit (QIAGEN). To estimate the yield of library and its relative amplification value, library DNA was quantitated using a Nanodrop, and serial dilutions of 1.25 nM library were compared to a reference library by real-time PCR using primers complementary to the adapters. Real-time PCR was performed using SYBR® Green Master PCR Mix (Invitrogen). The amplification C(t) value relative to a known reference library was used to estimate the flowcell loading concentration.  The ChIP-seq libraries were run on an Illumina GA2 at the U. California-Davis.

value: input control


title: K562_GATA2_ChIP

source_name: Chromatin IP against GATA2


title: K562_GATA1_ChIP

source_name: Chromatin IP against GATA1


title: Small RNAs from maize tassels

source_name: Male inflorescence (tassels)

growth_protocol: Plants were grown in a flood irrigated plot at the University of Arizona (Tucson, AZ, USA) in 2007. Pre-meiotic tassels were collected and pooled from several 8-week old plants.

value: 8-week old plants

value: pre-meiotic stage

tag: length

value: ranged in length between 2-4 cm long


title: mRNA_delayed_digital_gene_expression

description: mRNA tag profiling (digital gene expression) analysis of delayed implantation


title: Chimp female 1 rep1


title: Small RNAs from maize ears

description:
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.
Small RNAs from maize ears

source_name: Female inflorescence (ears)

growth_protocol: Plants were grown in a flood irrigated plot at the University of Arizona (Tucson, AZ, USA) in 2007. Post-meiotic immature ears were harvested and pooled from 10- and 11-week old plants.

value: 10- and 11-week old plants

value: post-meiotic stage

value: 3-5 cm long with silks about 1-4 cm long


title: Muscle_animal_4908

status: Public on Nov 24 2009

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

data_processing: The raw sequences were trimmed to 30 nucleotides, and it was set as a requirement that any sequence must appear at least three times and be present in at least two of the seven libraries. All identical reads within a library were grouped and converted into unique sequences. Reads containing Ns or long tracks (¡Ý8) of As were removed and the sequences were trimmed for adaptor-sequences. To annotate the unique sequences, a Decypher Tera-BLASTN Search was performed against a database of mature miRNAs obtained from miRBase (release 12.0). Hits with a match of 16 or more nucleotides to a miRNA from the database were gathered, and the count of each miRNA was normalized to the total number of sequence reads per lane.

organism: Sus scrofa

source_name: Longissimus dorsi muscle

extract_protocol: Total RNA was purified using the mirVanaTM miRNA isolation kit (Ambion) following the manufactures protocol and 10 µg total RNA from each sample was used for library constructions following the protocol supplied with the Small RNA Sample Prep Kit (Illumina, protocol version 1004239_RevA, March 2008) with minor modifications. Briefly, the 18-30 base pair fraction of total RNA was excised from 15 % Criterion Tris-Borate-EDTA (TBE)-Urea gels (Bio-Rad) stained with SYBR Safe DNA gel stain (Invitrogen) and visualised using a Dark Reader Transilluminator (Clare Chemical Research). Samples were electrophorised on individual gels throughout the library preparation to avoid cross-contamination. The small RNA was purified, ligated with the SRA 5´ and 3´ adaptors, reverse transcribed and amplified as recommended by the manufacturer. The 90 base pairs PCR products were purified on 4 % low range agarose gels (manufacturer) using the QIAquick Gel Extraction Kit (QIAGEN), eluted in 30 µL elution buffer and dried to a volume of 10 – 15 µL using a SC210A SpeedVac® Plus (ThermoSavant). The concentrations of the libraries were determined using a NanoDrop ND-1000 Spectrophotometer (manufacturer) and the size and purity were determined using an Agilent 2100 Bioanalyzer in combination with the Agilent DNA 1000 Kit. The seven libraries were diluted in buffer EB (QIAGEN) to 10 nM, denaturated with 2 N NaOH to a final DNA concentration of 0.5 nM, diluted to 2 pM with pre-chilled Hybridization buffer (Illumina) and loaded in individual lanes into a 1.0 mm flowcell together with a single lane of a 2 pM PhiX control library (Illumina). Clustering and 36 cycle sequencing were conducted on an Illumina Genome Analyzer (version I) using the Small RNA sequencing primer in combination with clustering and sequencing kits supplied by Illumina. The resulting images were transferred to the pipeline computer (DELL PowerEdge 2900, 8 cores (2 x 4 CPU, 2.6 GHz, 16 GB RAM, 4.7 TB hard drive) during the run using robocopy and analysed using the Genome Analyzer Pipeline Software (version 1.0, Illumina) generating the raw fastq files.

tag: longissimus dorsi muscle, animal

value: 4908, gender:male, age:1.5 years


title: Muscle_animal_3713

value: 3713, gender:male, age:1.5 years


title: Muscle_animal_5342

value: 5342, gender:male, age:1.5 years


title: Muscle_animal_4363

value: 4363, gender:male, age:1.5 years


title: GATA-1_ChIPSeq

city: Cambridge

first: Laura

last: Riva

address: 77 Massachusetts Avenue

department: Biological Engineering

institute: MIT

description: Streptavidin pull down of metabolically biotinylated GATA-1

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse genome (UCSC, mm8) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

source_name: MEL86 erythroid cell line expressing metabolically biotinylated GATA-1 (MEL Bio-GATA-1)

growth_protocol: MEL-bioGATA-1 cells were cultured in 5% CO2 at 37°C in DMEM+ 10% FCS+1% L-Glutamine+ 2% Pen/Strep. Erythrocyte differentiation of MEL cells was induced with 1.7% (v/v) for 24 hrs.

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

value: Induced MEL  bioGATA-1 cells


title: CTCF_ChIPSeq

status: Public on Nov 29 2009

first: Alon

last: Goren

address: 7 Cambridge Center

institute: Broad Institute

description: Chromatin IP against CTCF

data_processing: Alignment: Sequences were aligned to the mm8 reference genome using ARACHNE (Batzoglou, S. et al. ARACHNE: a whole-genome shotgun assembler. Genome research 12, 177-189 (2002)), as described previously (Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007)). Sequences with more than a single best match in the reference genome were discarded. We also created a map of ‘unalignable’ genomic positions to which no unique 36 base read could be uniquely aligned due inherent sequence redundancy for consideration in downstream processing

source_name: V6.5 embryonic stem cells

growth_protocol: Mouse ES cells (V6.5; male; genotype 129SvJaexC57BL/6; passages 10–15) were cultivated in 5% CO2 at 37 °C on irradiated MEFs in DMEM containing 15% FCS, ESGRO, penicillin/streptomycin, Glutamax, non-essential amino acids and 2-mercaptoethanol. ES Cells were passaged two to three times on 0.2% gelatin-coated plates to remove MEF contamination.

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

tag: gender

value: male


title: ES_Illumina.WCE

description: whole cell extract


title: Muscle_animal_147

value: 147, gender:male, age:1.5 years


title: Control_Input_DNA_sequencing

institute: Genome Institute of Singapore

description: control input DNA sequencing, no IP

value: pluripotent and self-renewing cells


title: Muscle_animal_4365

value: 4365, gender:male, age:2 years


title: Rdf2 KO veg

status: Public on Nov 23 2009

city: Boston

first: Mary

middle: T

last: Couvillion

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: small RNA sequencing

data_processing: The 36nt long Illumina reads were stripped of the 3’ linker and the resulting small RNA sequences were mapped to the sequenced Tetrahmyena macronuclear genome, assembly 2. Only reads matching the  genome 100%, or with one 3'nt mismatch because of untemplated nucleotide addition, were used for further analysis. For annotation, we used The Tetrahymena Genome Database for protein coding genes,  non-coding RNAs and transposons/repeats/IESs. SEQLEN = the small RNA sequence length, in nucleotides. MAPNUM = the number of times the small RNA matches the respective genome sequence. _N indicates an untemplated nt added to the sequence shown.  All small RNAs were converted into DNA for sequencing, therefore U's are represented as T's.

organism: Tetrahymena thermophila

source_name: Rdf2 KO cells

growth_protocol: media: 0.8X - 1X SUPP, 30 degrees C. Cells for "IP" libraries were grown in 1 ug/mL CdCl2 to induce tagged protein expression

extract_protocol: TRIzol (total sRNA), S100 (Argonaute-bound sRNA)

value: Rdf2 KO


title: Rdn2 KO veg

description: small RNA sequencing

source_name: Rdn2 KO cells

value: Rdn2 KO


title: Rdf1 KO veg

description: small RNA sequencing

source_name: Rdf1 KO cells

value: Rdf1 KO


title: Twi12 IP veg

description: small RNA sequencing

source_name: Twi12 IP cells

tag: protein

value: Twi12 IP


title: SB210 veg

description: small RNA sequencing

source_name: SB210 cells

value: wild type


title: Twi10 IP veg

description: small RNA sequencing

source_name: Twi10 IP cells

value: Twi10 IP


title: Twi9 IP veg

description: small RNA sequencing

source_name: Twi9 IP cells

value: Twi9 IP


title: small RNA maize seedling tissues

city: Cold Spring Harbor

first: Jer-M

last: Chia

address: 1, Bungtown Road

institute: Cold Spring Harbor Laboratory

description: 19-24nt RNA gel-extracted from total RNA in seedling tissue

data_processing: Triimmed: solexa sequences were converted to fasta, the adaptor sequence (CTGTAGGCACCATCAAT) was pattern matched and trimmed off. Only sequences were the adaptor was identified (with at least 6nt) is included in this set

source_name: Total RNA from maize seedling tissues

extract_protocol: small RNA libraries contructed from root, seedling, tassel, ear, and pollen

tag: tissue

value: seedling


title: Chimp male 3 rep1

source_name: liver

value: liver


title: Rice_AGO1b

first: Yijun

last: Qi

address: No.7 Science Park Road,Zhongguancun Life Science Park

institute: National Institute of Biological Sciences, Beijing

description: small RNA

data_processing: The adaptor sequences in Illumina 1G sequencing reads were removed by using ‘‘vectorstrip’’ in the EMBOSS package. The small RNA reads with length of 19–27 nt were mapped to the genome using Blast. Only small RNAs with perfect genomic matches were retained.

organism: Oryza sativa

source_name: Seedling

growth_protocol: Rice plants were grown in growth chambers with 12-h light/dark cycles, 28 oC during the day and 23 oC during the night.

extract_protocol: Small RNAs were ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified using a pair of Illumina cloning primers and then provided for Illumina sequencing.

treatment_protocol: RNAs were extracted from total extract and immunopurified AGO1 complexes by Trizol reagents. Bigger RNAs were removed by PEG precipitation, and enriched small RNAs were seperated on 15% PAGE/7M Urea gel, and small RNA within the range of 18-28 nt were purified from the gel.

tag: protein complex


title: small RNA maize tassel tissues

description: 19-24nt RNA gel-extracted from total RNA in tassel tissue

source_name: Total RNA from maize tassel tissues

value: tassel


title: h3k27me3_4hr

city: Singapore

first: Vipin

last: Narang

address: 60 Biopolis Street, #02-01, Genome

description: Chromatin IP against H3K27me3 4 hrs post treatment

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm8 (February, 2006) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed as described in (Chen et al. 2008, PMID: 18555785)

source_name: mouse bone marrow-derived macrophages

growth_protocol: Primary bone-marrow-derived macrophages were derived from 6-8 week old female Fvb mice as described in (De Santa et al. 2007, PMID: 17825402). Fetal livers were obtained from E14.5 embryos in a mixed L129-C57BL/6 background.

extract_protocol: ChIP experiments were carried out as described in (De Santa et al. 2007, PMID: 17825402). Libraries for sequencing experiments were generated from 0.5x10^9 cells (Jmjd3) or 1x10^8 cells per point in all other cases. ChIP DNA was ligated to Solexa/Illumina adaptors followed by PCR amplification with limited cycles. The amplified DNA was size selected (~ 200 bp to 300 bp) and subjected to sequencing by Solexa/Illumina protocol. Over 10 million uniquely mapped tags were generated for each ChIP sample.

treatment_protocol: Macrophages were stimulated with lipopolysaccharide (LPS) and interferon gamma (IFNγ)

value: mouse bone marrow-derived macrophages

tag: treatment

value: LPS+IFNγ treated for 4 hrs


title: h3k27me3_0hr

description: Chromatin IP against H3K27me3 in untreated macrophages

tag: cell type

value: untreated


title: Twi8 IP veg

description: small RNA sequencing

source_name: Twi8 IP cells

value: Twi8 IP


title: RNApolII_0hr

description: Chromatin IP against RNA-Polymerase II in untreated macrophages

tag: chip antibody

value: RNA-polymerase II


title: RNApolII_2hr

description: Chromatin IP against RNA-Polymerase II 2 hrs post treatment

value: LPS+IFNγ treated for 2 hrs


title: RNApolII_4hr

description: Chromatin IP against RNA-Polymerase II 4 hrs post treatment


title: small RNA maize root tissues

description: 19-24nt RNA gel-extracted from total RNA in root tissue

source_name: Total RNA from maize root tissues

value: root


title: h3k4me3_4hr

description: Chromatin IP against H3K4me3 4 hrs post treatment


title: small RNA maize ear tissues

description: 19-24nt RNA gel-extracted from total RNA in ear tissue

source_name: Total RNA from maize ear tissues

value: ear


title: Twi7 IP veg

description: small RNA sequencing

source_name: Twi7 IP cells

value: Twi7 IP


title: small RNA maize pollen tissues

description: 19-24nt RNA gel-extracted from total RNA in pollen tissue

source_name: Total RNA from maize pollen tissues

value: pollen


title: h3k4me3_0hr

description: Chromatin IP against H3K4me3 in untreated macrophages


title: Rice_AGO1c

description: small RNA


title: jmjd3_2hr

description: Chromatin IP against jmjd3 2 hrs post treatment

value: LPS+IFNγ treated for 2hrs


title: CU522 veg

description: small RNA sequencing

source_name: CU522 cells

value: wild type


title: Rice_AGO1a

description: small RNA


title: Twi2 IP veg

description: small RNA sequencing

source_name: Twi2 IP cells

value: Twi2 IP


title: ES-S-lane3

status: Public on Nov 05 2009

city: The Bronx

first: Eric

last: Bouhassira

address: 1300 Morris Park avenue

institute: Albert Einstein College of Medicine

description: Human ES cells, S phase

data_processing:
The data were processed using the GAPipeline-1.3.2, which includes
1. Image analysis (Firecrest)-Uses the raw TIF files to locate clusters on the image, and outputs the cluster intensity, X,Y positions, and an estimate of the noise for each cluster. The output from image analysis provides the input for base calling.
2. Base calling (Bustard)-Uses cluster intensities and noise estimate to output the sequence of bases read from each cluster, along with a confidence level for each base.
3. Sequence analysis (Gerald and Eland)-Allows for alignment to a reference sequence, filtering of data based on predefined criteria, and visualization of the result. Uniquely matching reads (with 0, 1 or 2 mismatches) were further processed with custom smoothing algorithms. See publication (PMID:19767418).

source_name: Human embryonic stem cells

growth_protocol: matrigel

extract_protocol: DNA from sorted cells in S or G1 was extracted, sheared by sonication to a length of about 500bp and Solexa linkers were ligated using standard procedures.  Purified DNA is subjected to mechanical fragmentation by nebulization (compressed air at 32-35psi for 6 minutes on ice).  The resulting double-stranded (ds) overhang fragments are end-repaired by incubation in the presence of T4 DNA polymerase and Klenow polymerase. The polished fragments are phosphorylated by T4 PNK, followed by the addition of a single ‘A’ base to the 3' end of the blunt-ended phosphorylated fragments.  This ‘A’ base prepares the DNA fragments for ligation to proprietary adapter oligonucleotides (Illumina single-read or paired-read sequences) which have a ‘T’ base at their 3' end.     Ligation products are size-selected by gel electrophoresis and purification (2% low-range agarose with ethidium bromide).  Following 1-2 hours at 80-110V (room temperature), the library range is visualized under brief UV and the desired size (200-500bp) excised with a clean scalpel.  Purified DNA libraries are subjected to a final PCR amplification step (15 cycles).  All amplified libraries are quantitatively and qualitatively assessed by Nanodrop ND-1000 (Thermo Scientific, DE, USA) UV/Vis spectroscopy and DNA bioanalyzer 2100 (Agilent, CA, USA) microfluidics.

value: embryonic stem cells

tag: cell cycle phase

value: S


title: ES-G1-lane1

description: Human ES cells, G1 phase


title: ES-S-lane2

description: Human ES cells, S phase


title: ES-G1-lane2

description: Human ES cells, G1 phase


title: ES-G1

description: Human ES cells, G1 phase


title: ES-G1-lane3

description: Human ES cells, G1 phase


title: ES-S-lane1

description: Human ES cells, S phase


title: ERY-S

description: Human erythroid cells, S phase

data_processing: The SoliD data were matched to the HG18 genome with the ABI software called Mapreads (http://solidsoftwaretools.com/gf/project/mapreads/) and Corona Lite (http://solidsoftwaretools.com/gf/project/corona). Uniquely matching reads (with 0, 1 or 2 mismatches) were further processed with custom smoothing algorithms. See publication (PMID: 19767418).

source_name: Human erythroid cells

value: erythroid cells


title: ES-S

description: Human ES cells, S phase


title: ERY-G1

description: Human erythroid cells, G1 phase


title: MB_14day_seedling

status: Public on Nov 20 2009

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description:
Gene Expression between two maize reciprocal hybrids (Mo17xB73)
mRNA-seq on Mo17XB73 (MB_14day_seedling)
Sequencing library construction was completed using the Illumina mRNA-Seq sample preparation kit.

data_processing: The Illumina reads were aligned to maize gene models (Release 4a.53, http://www.maizesequence.org) with short read aligner NOVOALIGN (http://www.novocraft.com). Two mismatches across 35 bp were allowed and only the reads that uniquely mapped to gene models were considered for further analysis. In total, 4.5 million reads from B73xMo17 and 5.2 million reads from Mo17Xb73 were mapped to 26,394 gene models.

growth_protocol: kernels planted in growth chambers (PGW-40, Percival Scientific, http://www.percival-scientific.com). Temperature and light cycle were set as 25 degrees for 15 hours of light and 20 degrees for 9 hours of dark. During the light period the light intensity at the surface of the growth medium was maintained between 650 and 800 umol m-2 sec -1.

extract_protocol: RNAs were purified using DNaseI treatment followed by cleanup with the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) as per manufacturer instructions.  Sequencing library construction was completed using the Illumina mRNA-Seq sample preparation kit.

treatment_protocol: Two genotypes compared without treatment

value: above ground Seedling

tag: age

value: 14 days after planting


title: Mop1/mop1-SAM

description:
SAM gene expression in mop1 non-mutants sibs
mRNA was amplified from SAM tissue

data_processing:
The Illumina reads were aligned to maize gene models (Release 4a.53, http://www.maizesequence.org) with short read aligner NOVOALIGN (http://www.novocraft.com). Two mismatches across 35 bp were allowed and only the reads that uniquely mapped to gene models were considered for further analysis.
There are two samples in the experiment: mop1-mutant vs. mop1-non-mutant.
Each sample has two techincal Solexa runs. The processed data for each sample is the merged data for final analysis across the technical reps for each sample.

source_name: Shoot apical meristem

extract_protocol: At 14-days after planting SAMs were collected using the PALM MicroBeam System (115V Z, P.A.L.M. Microlaser Technologies, http://www.palm-microlaser.com.). Plants homozygous and heterozygous for the mop1-1 mutant allele were distinguished using two pairs of primers: a pair of mop1-specific primers consisting of RDRF3 (sequence: 5’-TCTCCACCGCCCACTTGAT-3’) and RDRR2 (sequence: 5’-ATGGCCAGCAGGGTGTCGCAGAT-3’) and a primer pair consisting of the Mutator TIR primer Mu-TIR (5’-AGA GAA GCC AAC GCC AWC GCC TCY ATT TCG TC-3’) and the mop1-specific primer RDRF3. Twelve mop1-1/mop1-1 and ten Mop1/mop1-1 SAMs were used to form mop1 and non-mutant pools. Collected SAM tissues were used for RNA extraction, RNA amplification and synthesis of double stranded cDNAs according to our previous published procedures (Ohstu, et al., 2007). These procedures preferentially target polyadenylated transcripts.

value: Mop1/mop1 (non-mutant)

tag: stage

value: 14-day after planting


title: mop1/mop1-SAM

description:
SAM gene expression in mop1 mutants
mRNA was amplified from SAM tissue

value: mop1/mop1 (mutant)


title: BM_14day_seedling

description:
Gene Expression between two maize reciprocal hybrids (B73xMo17)
mRNA-seq on B73XMo17 (BM_14day_seedling)
Sequencing library construction was completed using the Illumina mRNA-Seq sample preparation kit.


title: Dmel_loq_sRNAseq

status: Public on Nov 04 2009

first: Trevis

middle: M

last: Alleyne

address: 303 E. Superior Street

department: Feinberg School of Medicine

institute: Northwestern University

description: small RNA discovery and profiling

data_processing: Reads were aligned to the D. melanogaster (build: dm3) and C virus genomes allowing 6 colourspace matches, with up to 3 mismatches in the first 18 colours.  Sequencing adaptors were removed using the method of the ABI small RNA Analysis Toolkit.

source_name: 4-6 day old adult flies

growth_protocol: Standard fly husbandry

extract_protocol: Library constructed using the SOLiD Small RNA expression kit, directional cloning of small RNAs based on a 5' Phosphate group

value: loquacious mutant

tag: rna

value: 18-35 small RNAs

value: female


title: H3K9me3-Control shRNA_ChIPseq

first: Mikael

last: Huss

description:
Anti-H3K9Me3 (ab8898; Abcam) antibody was used for ChIP of control shRNA knockdown sample.
A pool of 3 ChIP samples was used.

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches.
The control knockdown and Eset knockdown cells were directly compared for H3K9me3 enrichment, and the regions that were enriched in the control sample were identified.

The following supplementary files contain alignments:
GSM440257_CME036_R00057_lane7_s_7_sorted.txt
GSM440257_CME036_R00057_lane8_s_8_sorted.txt
GSM440257_CME036_R00089_lane2_s_2_sorted.txt

source_name: embryonic stem cells, control shRNA

growth_protocol: E14 mouse ES cells, cultured under feeder-free conditions, were maintained in Dulbecco's Modified Eagle-Medium (DMEM, GIBCO), with 15 % heat-inactivated ES qualified fetal bovine serum (FBS, GIBCO), 0.055 mM beta-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1 mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon). Control shRNA and Eset shRNA knockdown samples were obtained by transfecting ES cells with the respective shRNAs using lipofectamine-2000(invitrogen). The transfected ES cells were maintained in the ES medium with 0.8ug/ml puromycin.

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. ChIP-enriched DNA from multiple ChIP experiments was pooled and quantified using PicoGreen dsDNA quantitation kit (Invitrogen). The ChIP-enriched DNA was processed for Solexa sequencing using ChIP-Seq Sample Prep Kit (Illumina).

treatment_protocol: The ES cells were fixed in 1% formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 0.1 M glycine before harvest for extract preparation.

tag: cell line

tag: knockdown

value: control

tag: antibody

value: anti-H3K9Me3 antibody


title: Dmel_wt_sRNAseq

description: small RNA discovery and profiling

tag: genotype

value: wildtype


title: AGO1 IP dcr-2 knockdown

status: Public on Nov 15 2009

first: Benjamin

last: Czech

address: 1 Bungtown Rd

description: small RNA sequencing

data_processing: The 36nt Illumina reads were stripped of the 3’ linker, collapsed, and the resulting small RNA sequences were matched without mismatches to the Drosophila release 5 genome, and to the genomes of Drosophila C virus, Flock house virus and Cricket paralysis virus with up to 3 mismatches. Only reads that met these conditions were subjected to further analyses. For annotations we used a combination of UCSC, miRBase, and Flybase tracks for protein coding genes, repeats/transposons, non-coding RNAs and microRNAs, as well as custom tracks (for synthetic markers, endo-siRNAs from structured loci, miR and miR* strands) with different priorities (annotation priority list available upon request). For comparison of small RNA counts between libraries, reads were normalized to the same total number after bioinformatic removal of those sequences that matched to synthetic cloning markers or assumed degradation products of abundant cellular RNAs (rRNAs, snoRNAs and tRNAs). SEQ = the sequence of the small RNA. LENGTH = the length of the small RNA. NAME = annotation name of the small RNA. READS = read count in respective library. All small RNAs were converted into DNA for sequencing, therefore U's are represented as T's.

source_name: S2-NP cells

growth_protocol: 25°C in Schneider's medium (Invitrogen) supplemented with 10% FBS and 1% pen-strep (Invitrogen)

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen) and size-fractionated by PAGE.

treatment_protocol: ~3X10^6 S2-NP cells were soaked in 1.5 mL serum-free Schneider’s medium containing 10 µg dsRNAs in 6-well plates, and 3 mL serum-containing medium was added 45 minutes later. After 4 days of initial dsRNA treatment, cells were treated with dsRNAs for a second round and harvested another 4 days later. For IP libraries, cell extracts were prepared, evenly split and subjected to immunoprecipitation using antibodies against AGO1 (Abcam) or the FLAG epitope (Sigma), respectively, as described (Czech et al., 2008; Zhou et al., 2008). RNAs were recovered from the immunoprecipitated samples using Trizol (Invitrogen) and used for production of small RNA libraries.

value: AGO1 IP dcr-2 knockdown

value: S2-NP cells


title: oxidized ("mock")

description: small RNA sequencing

value: oxidized ("mock")


title: Dmel_r2d2_sRNAseq

description: small RNA discovery and profiling

value: R2D2 mutant


title: Eset_ChIPseq

description:
Custom-made rabbit polyclonal antibody was used for ChIP.
A pool of 20 ChIP samples was used.

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches.

The following supplementary files contain alignments:
GSM440256_CME039_R00087_lane7_s_7_sorted.txt
GSM440256_CME039_R00087_lane8_s_8_sorted.txt

The supplementary file 'GSM440256_Eset_peaks.bed' contains the peak calls for the Eset enzyme ChIP-seq library (CME039). Peaks were called using MACS.

source_name: embryonic stem cells, unperturbed

value: embryonic stem cells

value: unperturbed

value: rabbit polyclonal anti-Eset antibody