title: IgG_1_BCBL1_ChIP-Seq

description: BCBL1 cells per IP with IgG  control antibody

data_processing:
Tag_Lana_1_ChIP-Seq_hg18_align_IgG.bed; genome build: hg18
Alignment: Alignment was performed using BOWTIE
Solexa ChIP-Seq experiments were performed with 2x106 BCLB1 cells per IP with either LANA monoclonal antibody or control mouse IgG.  BCBL1cells are KSHV positive human Pleural Effusion Lymphoma (PEL) cell line.  For Peak calling, A combination of fold ratio and Poisson model for the tag distribution was used to define peaks as follows: (i) Identification of genomic regions (of length 1000bp) enriched with ChIP-seq sequence tags using fold ratio – A genomic region is considered as sequence enriched if the fold ratio, calculated using number of reads normalized to the total reads within that region in ChIP (antibody treatment) sample divided by the number of reads normalized to the total reads in control sample (IgG control) in the same region, is higher than the given cutoff. Nearby enriched regions were merged to make broader enriched genomic regions. A cutoff of 3 was applied to find the initial genomic regions of enrichment at this stage. (ii) Creating the read overlapping profile for each identified region from step 1, by extending the sequence reads from the 5’ end to the 3’ end of the reads up to 300 bps (the average length of the ChIP-DNA fragment sequenced from the Solexa GA with Illumina standard ChIP-seq protocol) for the experiment sample. (iii) Peak identification, by using Poisson model – by counting the number of overlapped reads at each nucleotide position and defining the genomic position with the highest number as the peak position within the significant region.  Finally, only those genomic regions that have fold ratio > 10 and peak score > 8 and p value < 0.001 (as determined by Poisson background model) are considered as statistically significant.   Peak score is calculated as the average value of raw counts within a given region of significant fold enrichment relative to control IgG levels.  The average is measured for overlapping tags at every base after extending the tags to their average tag length within the significant region.


title: Endometrial Non-recurrent 27

status: Public on Jan 11 2012

type: SRA

city: Columbus

first: Fei

last: Gu

state: Ohio

department: Molecular Virology, Immunology & Medical Genetics

country: USA

institute: The Ohio State University

description:
MBDCap using MethylMiner Methylated DNA Enrichment Kit (Invitrogen, ME 10025)
library strategy: Endometrial samples: MBDCao-seq. Breast cells: MBDCap-seq.
library selection: Endometrial samples: MBDCap. Breast cells: MBDCap-seq.

library_source: genomic

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.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human endometrial specimen

growth_protocol: Endometrial samples: N/A. Breast cells: Breast cells were routinely cultured in dishes and changed medium every 3 days.

extract_protocol:
Genomic DNA was isolated by standard methods or by the QIAamp DNA Mini Kit (Qiagen) following the manufacturer's protocol.
Methylated DNA was eluted by the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) according to the manufacturer's instructions. Briefly, one microgram of genomic DNA was sonicated and captured by MBD proteins. The methylated DNA was eluted in 1 M salt buffer. DNA in each eluted fraction was precipitated by glycogen, sodium acetate and ethanol, and was resuspended in TE buffer. Eluted DNA was used to generate libraries for sequencing following the standard protocols from Illumina. MBDCap-seq libraries were sequenced using the Illumina Genome Analyzer II as per manufacturer's instructions.
Illumina ChIP protocol

treatment_protocol: Endometrial samples: N/A. Breast cells: No treatment.

tag: tissue

value: Human endometrial specimen

tag: cell type

value: primary tissues

tag: disease status

value: Non-recurrent

tag: chromatin selection

value: MBD protein


title: mRNA-seq for the K timepoint of the traditional timecourse

status: Public on Jan 06 2012

city: San Francisco

first: Gloria

last: Brar

state: CA

address: 1700 4th Street, BH404

institute: UCSF

description:
mRNA
s_tK-mrna_091211_l2_sequence

library_source: transcriptomic

data_processing: Alignments were performed using the first 25 nt of each read.  mRNA  wiggle files are generated using location assignment that is  distributed along the length of the read ('coverage' mapping), while  footprint wiggle files are generated using a single location  assignment to a position 13 nt from the 5' end of the read ('start' mapping; corresponding to the ribosome P-site position). csv files  describe annotated uORF and AUG units and include RPKM quantitation of  genome-wide expression of annotated genes using the included SK1 gff  file [Yassour et al., Genome Biol 11, R87 (2010)]. All the processed data files are available on Series records [processed_wig_files.tar.gz].

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae sporulation media

extract_protocol: Small RNA fragments were size selected via gel purification,  dephosphorylated, polyA tailed, and reverse transcribed. The resulting  cDNA was circulizarized and PCR amplified [Ingolia et al.,n, Science,  (Mar 12, 2009)]. More at  Brar et al, PMID 22194413.

tag: strain


title: footprints for mata/a strain 4hr, fig s6b

description:
Ribosome-protected mRNA
aa_4_f_oCJ33


title: footprints for A14201 meiotic replicate 2

description:
Ribosome-protected mRNA
14201f2_082311_oCJ31


title: footprints for gb15 meiotic replicate 2

description:
Ribosome-protected mRNA
gb15f2_082311_l3


title: mrna for gb15 meiotic replicate 2

description:
mRNA
gb15m2_082311_l5


title: footprints for A14201 meiotic replicate 1

description:
Ribosome-protected mRNA
14201f1_082311_oCJ30


title: footprints for mata/a strain 2hr, fig s6b

description:
Ribosome-protected mRNA
aa_2_f_oCJ31


title: mrna for gb15 meiotic replicate 1

description:
mRNA
gb15m1_082311_l4


title: Control ES cells 96hr, untreated DNA-Seq

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description: Sample 1

data_processing:
mm8-ESC-Control-NT-summary.graph.variableStep.scaled.wig; genome build: mm8
mm8-ESC-Control-NT.bed; genome build: mm8
Sequenced 36-bp reads were aligned to the reference genome (mouse NCBI36/mm8 assembly) using Bowtie 0.12.2 (36). Those reads that mapped to unique genomic locations with at most two mismatches were retained. Roughly ∼50–65% of all reads were mapped to unique genomic locations. To increase the mapping efficiency, we trimmed one base from the 3′-end of the unmapped reads, aligned the residual 36-bp reads to the reference genome and retained those that mapped to unique genomic locations. This procedure was repeated until the residual reads were of length 18, and, in each iteration, reads that mapped to unique genomic locations were retained for further analysis. The reads that mapped to unique genomic locations but whose corresponding 5'- to 3'-sequence in the reference genome neither started with CGG nor ended with GGC were considered noise and discarded. The rationale for this is because the MspI cleaves the DNA containing its recognition site CCGG at the inner C position (C/CGG) (37), the DNA fragments that is sequenced must all start with CGG or end with GGC (complementary strand). Reads that start or end with anything other than CGG or GGC, respectively, are likely to be byproducts of DNA degradation or sequencing errors. The resulting mapped reads for the four samples (control KD treated, control KD untreated, Tet1 KD treated and Tet1 KD untreated) were normalized by total reads in each sample so that the number of reads mapping to a specific site is directly comparable across all four samples. *wig files contain normalized and scaled data in wiggle format.
A site was defined as a 5hmC site only if the normalized read count at this site in the control untreated sample is at least 1.5-fold higher than that in the control treated sample. A 5hmC site was defined to have reduced 5hmC levels in Tet1 KD mESCs only if the 5hmC levels in Tet1 KD cells is at least 1.5 fold less compared to that in Control KD cells.

organism: Mus musculus

source_name: Control ES_96hr_untreated DNA-Seq

growth_protocol: The cells were routinely maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore), and were used at passage 20–35 for experiments. For siRNA transfections, mESCs were cultured on gelatin-coated plates in normal mESC medium.

extract_protocol: MspI-digested DNA from treated and untreated samples derived from control and Tet1 KD mESCs were size-selected (40–220 bp) and sequenced using Illumina GAII.

treatment_protocol: Cells were lysed 96 h after transfection in Trizol reagent, and the genomic DNA were prepared according to manufacturer's instructions. For genome-wide mapping of 5hmC, the genomic DNA obtained from control KD and Tet1 KD cells were processed using the QUEST 5hmC detection kit (Zymo Research) according to manufacturer's instructions (5-hmc: 5-hydroxymethylcytosine).

tag: cell line

value: embryonic stem cells

tag: transfected with

value: control siRNA

tag: passages


title: Tet1-KD ES cells 96hr, untreated DNA-Seq

description: Sample 3

data_processing:
mm8-ESC-Tet1-KD-NT-summary.graph.variableStep.scaled.wig; genome build: mm8
mm8-ESC-Tet1-KD-NT.bed; genome build: mm8
Sequenced 36-bp reads were aligned to the reference genome (mouse NCBI36/mm8 assembly) using Bowtie 0.12.2 (36). Those reads that mapped to unique genomic locations with at most two mismatches were retained. Roughly ∼50–65% of all reads were mapped to unique genomic locations. To increase the mapping efficiency, we trimmed one base from the 3′-end of the unmapped reads, aligned the residual 36-bp reads to the reference genome and retained those that mapped to unique genomic locations. This procedure was repeated until the residual reads were of length 18, and, in each iteration, reads that mapped to unique genomic locations were retained for further analysis. The reads that mapped to unique genomic locations but whose corresponding 5'- to 3'-sequence in the reference genome neither started with CGG nor ended with GGC were considered noise and discarded. The rationale for this is because the MspI cleaves the DNA containing its recognition site CCGG at the inner C position (C/CGG) (37), the DNA fragments that is sequenced must all start with CGG or end with GGC (complementary strand). Reads that start or end with anything other than CGG or GGC, respectively, are likely to be byproducts of DNA degradation or sequencing errors. The resulting mapped reads for the four samples (control KD treated, control KD untreated, Tet1 KD treated and Tet1 KD untreated) were normalized by total reads in each sample so that the number of reads mapping to a specific site is directly comparable across all four samples. *wig files contain normalized and scaled data in wiggle format.
A site was defined as a 5hmC site only if the normalized read count at this site in the control untreated sample is at least 1.5-fold higher than that in the control treated sample. A 5hmC site was defined to have reduced 5hmC levels in Tet1 KD mESCs only if the 5hmC levels in Tet1 KD cells is at least 1.5 fold less compared to that in Control KD cells.

source_name: Tet1-KD ES_96hr_untreated DNA-Seq

value: Tet1 siRNA #1


title: Control ES cells 96hr, 5hmC glucosyltransferase treated DNA-Seq

description: Sample 2

data_processing:
mm8-ESC-Control-GT-summary.graph.variableStep.scaled.wig; genome build: mm8
mm8-ESC-Control-GT.bed; genome build: mm8
Sequenced 36-bp reads were aligned to the reference genome (mouse NCBI36/mm8 assembly) using Bowtie 0.12.2 (36). Those reads that mapped to unique genomic locations with at most two mismatches were retained. Roughly ∼50–65% of all reads were mapped to unique genomic locations. To increase the mapping efficiency, we trimmed one base from the 3′-end of the unmapped reads, aligned the residual 36-bp reads to the reference genome and retained those that mapped to unique genomic locations. This procedure was repeated until the residual reads were of length 18, and, in each iteration, reads that mapped to unique genomic locations were retained for further analysis. The reads that mapped to unique genomic locations but whose corresponding 5'- to 3'-sequence in the reference genome neither started with CGG nor ended with GGC were considered noise and discarded. The rationale for this is because the MspI cleaves the DNA containing its recognition site CCGG at the inner C position (C/CGG) (37), the DNA fragments that is sequenced must all start with CGG or end with GGC (complementary strand). Reads that start or end with anything other than CGG or GGC, respectively, are likely to be byproducts of DNA degradation or sequencing errors. The resulting mapped reads for the four samples (control KD treated, control KD untreated, Tet1 KD treated and Tet1 KD untreated) were normalized by total reads in each sample so that the number of reads mapping to a specific site is directly comparable across all four samples. *wig files contain normalized and scaled data in wiggle format.
A site was defined as a 5hmC site only if the normalized read count at this site in the control untreated sample is at least 1.5-fold higher than that in the control treated sample. A 5hmC site was defined to have reduced 5hmC levels in Tet1 KD mESCs only if the 5hmC levels in Tet1 KD cells is at least 1.5 fold less compared to that in Control KD cells.

source_name: Control ES_96hr_5hmC glucosyltransferase treated DNA-Seq


title: Tet1-KD ES cells 96hr, 5hmC glucosyltransferase treated DNA-Seq

description: Sample 4

data_processing:
mm8-ESC-Tet1-KD-GT-summary.graph.variableStep.scaled.wig; genome build: mm8
mm8-ESC-Tet1-KD-GT.bed; genome build: mm8
Sequenced 36-bp reads were aligned to the reference genome (mouse NCBI36/mm8 assembly) using Bowtie 0.12.2 (36). Those reads that mapped to unique genomic locations with at most two mismatches were retained. Roughly ∼50–65% of all reads were mapped to unique genomic locations. To increase the mapping efficiency, we trimmed one base from the 3′-end of the unmapped reads, aligned the residual 36-bp reads to the reference genome and retained those that mapped to unique genomic locations. This procedure was repeated until the residual reads were of length 18, and, in each iteration, reads that mapped to unique genomic locations were retained for further analysis. The reads that mapped to unique genomic locations but whose corresponding 5'- to 3'-sequence in the reference genome neither started with CGG nor ended with GGC were considered noise and discarded. The rationale for this is because the MspI cleaves the DNA containing its recognition site CCGG at the inner C position (C/CGG) (37), the DNA fragments that is sequenced must all start with CGG or end with GGC (complementary strand). Reads that start or end with anything other than CGG or GGC, respectively, are likely to be byproducts of DNA degradation or sequencing errors. The resulting mapped reads for the four samples (control KD treated, control KD untreated, Tet1 KD treated and Tet1 KD untreated) were normalized by total reads in each sample so that the number of reads mapping to a specific site is directly comparable across all four samples. *wig files contain normalized and scaled data in wiggle format.
A site was defined as a 5hmC site only if the normalized read count at this site in the control untreated sample is at least 1.5-fold higher than that in the control treated sample. A 5hmC site was defined to have reduced 5hmC levels in Tet1 KD mESCs only if the 5hmC levels in Tet1 KD cells is at least 1.5 fold less compared to that in Control KD cells.

source_name: Tet1-KD ES_96hr_5hmC glucosyltransferase treated DNA-Seq


title: mRNA-seq for exponential vegetative cells of the strain 14201 (used for the ndt80 release timecourse)

description:
mRNA
s_14201exp(veg)-mrna_100219_l7_sequence

source_name: S. cerevisiae vegetative


title: mrna for 14201 meiotic replicate 2

description:
mRNA
14201m2_082311_oCJ33


title: human_wbc.single

status: Public on Jan 05 2012

city: Cambridge

first: Robert

middle: K

last: Bradley

state: MA

address: 77 Massachusetts Avenue, 68-223A

department: Biology

institute: MIT

data_processing:
Alignment: The files human.nagnag.junctions.gff and mouse.nagnag.junctions.gff (see Series supplementary files) give the intron-proximal and intron-distal splice junctions of all NAGNAG splicing events analyzed in this study. The 'start' field specifies the last base of the upstream exon and the 'end' field specifies the first base of the downstream exon (upstream and downstream defined with respect to the gene). For each NAGNAG, we extracted the transcript sequence flanking the proximal and distal 3' splice sites and used Bowtie version 0.12.7 to map reads to these two sequences. We required that short reads have at least 6 nt on either side of the splice junction (an "overhang" of 6 nt), and furthermore that there be no mismatches within the overhang region.
Human genome build: hg19
Mouse genome build: mm9

molecule: polyA RNA

source_name: white blood cells

extract_protocol:
Human: RNA-Seq libraries are from the Body Map 2.0 dataset distributed by Illumina, available at the ENA archive with accession number ERP000546.
Mouse: Tissues from a 10-week-old male were extracted immediately after death and stored in RNAlater per the manufacturerâs instructions (Ambion). Tissue was lysed in Trizol and RNA was extracted with Qiagen miRNeasy mini columns. Using 5ug of total RNA, we performed polyA selection and prepared strand-specific libraries for Illumina sequencing following the dUTP protocol and the SPRIworks Fragment library system (Beckman Coulter). We obtained final insert sizes of approximately 160 bp. We sequenced these libraries using the Illumina HiSeq 2000 and the GAIIx machines.

tag: library type

value: single-end

tag: read length


title: human_prostate.single

source_name: prostate


title: human_skeletal_muscle.single

source_name: skeletal muscle


title: human_ovary.single

source_name: ovary


title: human_testes.single

source_name: testes


title: human_lung.single

source_name: lung


title: human_lymph_node.single

source_name: lymph node


title: human_liver.single

source_name: liver


title: human_kidney.single

source_name: kidney


title: footprints for gb15 meiotic replicate 1

description:
Ribosome-protected mRNA
gb15f1_082311_l2


title: human_heart.single

source_name: heart


title: human_breast.single

source_name: breast


title: human_colon.single

source_name: colon


title: human_brain.single

source_name: brain


title: human_adrenal.single

source_name: adrenal


title: mrna for A14201 meiotic replicate 1

description:
mRNA
14201m1_082311_oCJ32

source_name: S. cerevisiae sporulation media


title: human_adipose.single

source_name: adipose


title: human_thyroid.single

source_name: thyroid


title: Th1-H3K27me3

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

description: Chromatin IP against H3K27me3

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 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 200 bp (SICER).
Peaks: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958) for epigenetics modifcations

source_name: primary CD4+ T cells from spleen and lymph nodes

growth_protocol: In vitro differentiated T helper cells: Wildtype OT-II naïve CD4+CD44loCD62L+CD25- T cells were purified by cell sorting.  Cells were cultured for 3.5 days in the presence of OVA peptide and T-depleted mitomycin C-treated splenocytes in IMDM media, along with neutralizing antibodies under Th1 (IL-12), Th2 (IL-4), Th17 (TGFb+IL-6), or Tfh-like (anti-TGFb+IL-6+IL-21) polarizing conditions.  Ex vivo Tfh cells: C57BL6/J mice were immunized with sheep red blood cells and CD4+CD19-CD44hiCXCR5+PD-1+ splenocytes were isolated 6 days later on the flow cytometer.

extract_protocol: Cell lysates were made by MNase digestion plus sonication and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 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: WT TCR transgenic OT-II

value: in vitro repolarized T helper1 cells

value: FACS sorted naive CD4+T cells cultured in vitro for 2 rounds of polarization under Th1 conditions

tag: chip antibody

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog#


title: [E-MTAB-737] polyA+_spleen_6090097, Batch_5_spleen

status: Public on Jan 04 2012

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

description: Performer: University of Lausanne, Switzerland

data_processing: processed data not provided

extract_protocol:
nucleic_acid_extraction | RNA from tissues was isolated by a modified guanidium thiocynate methods followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns. Selected targets were then amplified by RT-PCR
sequencing | Aliquots of up to 5000 RT-PCRs reactions were pooled together and the sequencing library was prepared with no fragmentation as described by the manufacturer (Illumina). DNA fragments were sequenced on one lane of a Illumina GAIIxl. The sequencing was performed at the University of Lausanne, Lausanne, Switzerland.
bioassay_data_transformation | Illumina pipeline export files were transformed into fastq format by applying this Unix command: awk '{print @$1_$2:$3:$4:$5:$6#$7/$8\n$9\n+\n$10}' file_export.txt > file.fastq

tag: material type

tag: organismpart

value: spleen

tag: Sex

tag: biosourcetype

tag: biosourceprovider

value: Clontech


title: [E-MTAB-737] polyA+_testis_7060321, Batch_5_testis

value: testis

value: male


title: [E-MTAB-737] polyA+_muscle_7040106, Batch_5_muscle

value: muscle


title: Th2-H3K27me3

description: Chromatin IP against H3K27me3

tag: cell type

value: in vitro repolarized T helper2 cells

value: FACS sorted naive CD4+T cells cultured in vitro for 2 rounds of polarization under Th2 conditions


title: [E-MTAB-737] polyA+_lung_1100350, Batch_5_lung

value: lung


title: Sorted Tfh like-H3K4me3

description: Chromatin IP against H3K4me3

value: CXCR5+PD1+ sorted in vitro repolarized T follicular helper-like cells

value: FACS sorted naive CD4+T cells cultured in vitro for 2 rounds of polarization under Tfh-like conditions


title: Tfh ex vivo-H3K4me3

description: Chromatin IP against H3K4me3

value: ex vivo sorted T follicular helper cells

value: FACS sorted Tfh cells after immunization with SRBCs on day 6


title: Sorted Tfh like-H3K27me3

description: Chromatin IP against H3K27me3


title: Th17-H3K27me3

description: Chromatin IP against H3K27me3

value: in vitro repolarized T helper17 cells

value: FACS sorted naive CD4+T cells cultured in vitro for 2 rounds of polarization under Th17 conditions


title: Th17-H3K4me3

description: Chromatin IP against H3K4me3

value: WT TCR transgenic OT-II


title: Tfh like-H3K4me3

description: Chromatin IP against H3K4me3

value: in vitro repolarized T follicular helper-like cells


title: Tfh like-H3K27me3

description: Chromatin IP against H3K27me3

value: Millipore


title: [E-MTAB-737] polyA+_liver_6100188, Batch_5_liver

value: liver


title: Tfh ex vivo-H3K27me3

description: Chromatin IP against H3K27me3


title: Th1-H3K4me3

description: Chromatin IP against H3K4me3

value: in vitro repolarized T helper1 cells

value: FACS sorted naive CD4+T cells cultured in vitro for 2 rounds of polarization under Th1 conditions


title: [E-MTAB-737] polyA+_heart_7082801A, Batch_5_heart

value: heart

value: male

value: Clontech


title: [E-MTAB-737] polyA+_kidney_7110096, Batch_5_kidney

value: kidney


title: S4 miRNA

city: Beijing

first: Anjing

last: Ge

address: Changping district of Beijing BeiNong road number 7

department: Plant Science and Technology College

country: China

institute: Beijing University of Agriculture

data_processing: lllumina Pipeline v1.3

organism: Fragaria x ananassa

source_name: fruits from 5 different development stages

extract_protocol: Total RNA was extracted using the modified CTAB method, small RNA was seperated with 4M LiCl, and small RNA library was constructed.

tag: cultivar

value: Sweet Charlie

tag: tissue

value: young green fruitlets, big green fruits, white fruits, pink fruits and mature red fruits


title: FBio-Yy1_ChIPseq

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: streptavidin precipitation against Fbio-Yy1

data_processing:
Alignment: 36-bp short reads were  mapped onto the mouse July, 2007 genome release (mm9) using Bowtie. The alignments were performed allowing zero to two mismatches and keeping only the reads that align to unique positions in the genome.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

growth_protocol: ES cell lines were grown on 0.1% gelatinaized tissue culture dishes in DMEM in presence of  15% Serum and Leukemia inhibitory factor.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: Exponentially growing ES cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin from FBio-Yy1 and control BirA expressing ES cells was precipitated with magnetic streptavidin beads (Invitrogen) and recovered DNA used for hightrouput sequencing.

tag: strain

value: BirA-ES cells

tag: chip method

value: streptavidin


title: FBio-Ctrl_ChIPseq

description: streptavidin precipitation against mock


title: [E-MTAB-684] polyA+_lung_1100350, Batch_4_lung_cdna2_rep2

value: lung


title: [E-MTAB-684] polyA+_spleen_6090097, Batch_4_spleen_cdna2

value: spleen


title: [E-MTAB-684] polyA+_muscle_7040106, Batch_4_muscle_cdna2

value: muscle


title: [E-MTAB-684] polyA+_liver_6100188, Batch_4_liver_cdna2


title: [E-MTAB-684] polyA+_testis_7060321, Batch_4_testis_cdna2

value: testis


title: [E-MTAB-737] polyA+_brain_6120217, Batch_5_brain

value: brain


title: Th2-H3K4me3

description: Chromatin IP against H3K4me3

value: WT TCR transgenic OT-II

value: in vitro repolarized T helper2 cells

value: FACS sorted naive CD4+T cells cultured in vitro for 2 rounds of polarization under Th2 conditions

value: Millipore


title: [E-MTAB-684] polyA+_lung_1100350, Batch_4_lung_cdna2_rep1


title: [E-MTAB-684] polyA+_kidney_7110096, Batch_4_kidney_cdna2


title: [E-MTAB-684] polyA+_heart_7082801A, Batch_4_heart_cdna2

value: heart


title: [E-MTAB-684] polyA+_brain_6120217, Batch_4_brain_cdna2

value: male


title: [E-MTAB-684] polyA+_brain_6120217, Batch_4_brain_cdna1_newdil

value: Clontech


title: [E-MTAB-684] polyA+_spleen_6090097, Batch_4_spleen_cdna1


title: [E-MTAB-684] polyA+_liver_6100188, Batch_4_liver_cdna1

value: liver


title: [E-MTAB-684] polyA+_testis_7060321, Batch_4_testis_cdna1_newdil


title: [E-MTAB-684] polyA+_testis_7060321, Batch_4_testis_cdna1_rep1


title: [E-MTAB-684] polyA+_heart_7082801A, Batch_4_heart_cdna1


title: [E-MTAB-684] polyA+_lung_1100350, Batch_4_lung_cdna1


title: [E-MTAB-684] polyA+_kidney_7110096, Batch_4_kidney_cdna1

value: kidney


title: [E-MTAB-684] polyA+_brain_6120217, Batch_4_brain_cdna1


title: SLX-2574.433.s_2

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

description:
Input DNA
MCF-7_Input

data_processing:
Alignments: Sequences generated by the Illumina Genome Analyzer were processed by the Illumina analysis pipeline version 1.6.1, and aligned to the Human Reference Genome (assembly hg18, NCBI Build36.1, March 2008) using BWA version 0.5.523. Reads were filtered by removing those with a BWA alignment quality score less than 15.
Peaks: Enriched regions of the genome were identified by comparing the ChIP samples to input samples using the MACS peak caller version 1.3.7.113. Additional peak calls were determined for the tumour samples using the SWEMBL peak caller version 3.2 (Wilder et. al, in prep) with default parameters except with -R = 0.005.  For tumours without a corresponding input, all the available tumour input reads were combined and down sampled to derive acontrol track for peak calling purposes.

source_name: Human breast cancer cell line

growth_protocol:
Cell culture: MCF-7, ZR75-1, T-47D and BT-474 human cell lines were obtained from ATCC.  MCF-7 cells were grown in DMEM containing 10% heat-inactivated FBS, 2 mM L glutamine, 50 U/ml penicillin and 50 ug/ml streptomycin.  ZR75-1, T-47D and BT-474 cells were grown in RPMI containing 10% heat-inactivated FBS, 2 mM L glutamine, 50 U/ml penicillin and 50 ug/ml streptomycin.  To validate the cell lines, samples were genotyped by Health Protection Agency (http://www.hpa.org.uk) (MCF-7, ZR75-1, T-47D) or by in-house genotyping (BT-474).  TAM-R cells17 were obtained from Dr Iain Hutcheson and Prof. Robert Nicholson (Cardiff) and were maintained in phenol red-free DMEM containing 5% charcoal dextran-treated FBS, 2 mM L glutamine, 50 U/ml penicillin and 50 ug/ml streptomycin and 10 nM 4-hydroxytamoxifen.
Primary tumour material: The ER+ breast cancer tumours were obtained from the Nottingham Tenovus primary breast cancer series, Addenbrooke's Hospital and Imperial Hospital Hammersmith, London, UK with appropriate ethical approval from the repositories. The malignant pericardial effusion and the two distant metastases were obtained from Imperial Hospital Hammersmith, London, UK.

extract_protocol:
For ChIP in the tumours and metastases, the frozen sample was cut into smaller pieces and thawed in 1% (final concentration) formaldehyde for 20 minutes at room temperature. The reaction was quenched by adding 0.1 volume of 2M glycine for 10 minutes. The sample was disaggregated by Dounce homogenisation and processed according to standard ChIP procedures (Schmidt D et al, Methods, doi:S1046-2023(09)00047-4 [pii]). The DNA was subsequently amplified as previously described (Schmidt D et al, Methods, doi:S1046-2023(09)00047-4 [pii]).  For the malignantpericardial effusion, epithelial cells were first enriched using Dynabeads conjugated with Epcam.
For ChIPs from cell line material, proliferating cells were cross-linked and processed for ChIP as previously described (Schmidt D et al, Methods, doi:S1046-2023(09)00047-4 [pii]). For the TAM-R cells, ER ChIP-seq was performed on cells grown in DMEM containing 10% FBS and 10 nM tamoxifen for 24 hours.  For the cocktail experiments, cells weretreated with 100 ng/ml IGF-1, 100 ng/ml EGF, 1 ng/ml TNF-alpha and 10 ng/ml IL-6 for 90 minutes.

tag: condition

value: Tam-Responsive


title: T47D_Input

description:
Input DNA
T-47D_Input


title: SLX-3231.526.s_5

description:
Input DNA
TAM-R_Input

value: Tam-Resist

value: TAMR


title: SLX-4016.651.s_6

description:
Chromatin IP against FOXA1
MCF-7-Veh.2

tag: antibody

value: anti-FOXA1 (AB5089, Abcam)


title: SLX-2577.443.s_8

description:
Input DNA
BT474_Input


title: SLX-4015.651.s_5

description:
Chromatin IP against FOXA1
MCF-7-Cock90.2


title: ZR75_Input

description:
Input DNA
ZR75_Input


title: SLX-2642.442.s_8

description:
Chromatin IP against ER
Cock90.1

value: anti-ER (SC-543, Santa Cruz Biotechnologies)


title: SLX-4013.651.s_3

description:
Chromatin IP against FOXA1
MCF-7-Cock90.1


title: SLX-3230.526.s_4

description:
Chromatin IP against ER
TAM-R.2


title: SLX-2945.469.s_4

description:
Chromatin IP against ER
Cock90.2


title: SLX-2576.443.s_7

description:
Chromatin IP against ER
BT474.2


title: SLX-2867.466.s_6

description:
Chromatin IP against ER
T47D.2


title: SLX-2645.443.s_5

description:
Chromatin IP against ER
BT474.1


title: SLX-2775.448.s_3

description:
Chromatin IP against ER
T-47D.1


title: [E-MTAB-684] polyA+_testis_7060321, Batch_4_testis_cdna1_rep2


title: [E-MTAB-684] polyA+_muscle_7040106, Batch_4_muscle_cdna1

value: muscle


title: SLX-2866.466.s_7

description:
Chromatin IP against ER
ZR75-1.2


title: SLX-2943.469.s_2

description:
Chromatin IP against ER
MCF-7.3


title: SLX-2774.448.s_2

description:
Chromatin IP against ER
ZR75-1.1


title: SLX-2640.438.s_1

description:
Chromatin IP against ER
MCF-7.1


title: SLX-4121.667.s_4

description:
Input DNA
ERneg1 Input

source_name: Human tumour tissue

value: ER-

value: none (input)


title: SLX-4122.667.s_5

description:
Input DNA
ERneg2 Input


title: SLX-1849.331.s_4

description:
Input DNA
M3 Input

value: Metastasis


title: SLX-4014.651.s_4

description:
Chromatin IP against FOXA1
MCF-7-Veh.1


title: SLX-1848.331.s_3

description:
Input DNA
M2 Input


title: SLX-4118.667.s_1

description:
Input DNA
P6 Input

value: Non-responder


title: SLX-2711.446.s_8

description:
Input DNA
P4 Input


title: SLX-4119.667.s_2

description:
Input DNA
P7 Input


title: SLX-4117.666.s_8

description:
Input DNA
G7 Input

value: Responder


title: SLX-4120.667.s_3

description:
Input DNA
G8 Input


title: SLX-3229.521.s_5

description:
Chromatin IP against ER
TAM-R.1


title: SLX-4114.666.s_5

description:
Input DNA
P5 Input


title: SLX-2712.451.s_1

description:
Input DNA
P3 Input


title: SLX-4116.666.s_7

description:
Input DNA
G6 Input


title: SLX-2629.438.s_7

description:
Input DNA
G4 Input


title: SLX-1880.337.s_8

description:
Input DNA
G2 Input


title: SLX-4113.666.s_4

description:
Chromatin IP against ER
ERneg2


title: SLX-4112.666.s_3

description:
Chromatin IP against ER
ERneg1


title: SLX-1845.332.s_5

description:
Chromatin IP against ER
M2


title: SLX-1846.331.s_1

description:
Chromatin IP against ER
M3


title: SLX-4110.666.s_1

description:
Chromatin IP against ER
P7


title: SLX-1843.327.s_6

description:
Chromatin IP against ER
M1


title: SLX-4109.665.s_8

description:
Chromatin IP against ER
P6_2


title: SLX-2773.448.s_1

description:
Chromatin IP against ER
MCF-7.2


title: SLX-4115.666.s_6

description:
Input DNA
G5 Input


title: SLX-1847.331.s_2

description:
Input DNA
M1 Input


title: [E-MTAB-831] polyA+_spleen_6090097, Batch_6_spleen

extract_protocol:
nucleic_acid_extraction | RNA from tissues was isolated by a modified guanidium thiocynate methods followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns. Selected targets were then amplified by RT-PCR.
sequencing | Aliquots of up to 5000 RT-PCRs reactions were pooled together and the sequencing library was prepared with no fragmentation as described by the manufacturer (Illumina). DNA fragments were sequenced on one lane of a Illumina GAIIxl. The sequencing was performed at the University of Lausanne, Lausanne, Switzerland.
bioassay_data_transformation | Illumina pipeline export files were transformed into fastq format by applying this Unix command: awk '{print @$1_$2:$3:$4:$5:$6#$7/$8\n$9\n+\n$10}' file_export.txt > file.fastq

value: spleen


title: SLX-4103.665.s_2

description:
Chromatin IP against ER
P5_2


title: SLX-4108.665.s_7

description:
Chromatin IP against ER
P6_1


title: SLX-2706.446.s_3

description:
Chromatin IP against ER
P4


title: SLX-2707.446.s_4

description:
Chromatin IP against ER
P3


title: SLX-4102.665.s_1

description:
Chromatin IP against ER
P5_1


title: SLX-2625.438.s_3

description:
Chromatin IP against ER
P2


title: SLX-1202.250.s_1

description:
Input DNA
G1 Input


title: SLX-2624.438.s_2

description:
Chromatin IP against ER
P1


title: [E-MTAB-831] polyA+_lung_1100350, Batch_6_lung

value: lung


title: [E-MTAB-831] polyA+_liver_6100188, Batch_6_liver

value: male


title: SLX-4105.665.s_4

description:
Chromatin IP against ER
G5_2


title: SLX-4106.665.s_5

description:
Chromatin IP against ER
G6


title: SLX-4104.665.s_3

description:
Chromatin IP against ER
G5_1


title: [E-MTAB-831] polyA+_kidney_7110096, Batch_6_kidney

value: Clontech


title: SLX-2627.438.s_5

description:
Chromatin IP against ER
G4


title: Input HeLa cells

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

description: Input DNA

data_processing: Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using BWA package.

source_name: Input HeLa cells

growth_protocol: Cells were synchronized by serum starvation followed by hydroxyurea block as following: first near-confluent cells were cultured for 36h in serum-deprived medium (0.5% FBS). Then, cells were subcultured, and allowed to attach to the culture dishes in DMEM containing 10% FBS for three hours. Subsequently, 2mM hydroxyurea (Sigma Aldrich) was added to the medium for 16 hours to arrest cells at the onset of S phase. Cells were released from the HU block by washing three times with PBS and adding fresh medium containing 10% FBS.

extract_protocol: Immunoprecipitated chromatin was sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by ligation mediated PCR (LMPCR). After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel, barcoded and sequenced on SOLiD/AB sequencer in multiplexed way to produce 50 base pair long reads.

treatment_protocol: ChIP was performed according the Millipore's EZ ChIP protocol, with the following specifications: cells were crosslinked for 10 minutes by 1% freshly made formaldehyde. Crosslinking was stopped by 5 minutes of 100mM glycine. Cells were then washed twice with PBS, and scraped in 1 mL of ChIP lysis buffer. Lysates were sonicated for 8 minutes at maximum power on a Covaris S2 (Covaris). For ChIP-qPCR 1 million cells were used for each reaction; for ChIP-seq, 25 million cells were used for each reaction. IPs were performed using BSA-blocked Fast Flow Agarose G beads (Millipore, 16-266).  A rabbit polyclonal E2F7 antibody (sc-66870, Santa Cruz) was used for immunoblotting (1:1000), conventional ChIP (1 ug per reaction), and ChIP-seq (10 ug per reaction). To improve signal-to-noise ratios in the ChIP-seq experiments, a double-IP protocol was used. Antibody-chromatin complexes were eluted from the beads using 200 uL of buffer containing 1% SDS and 100mM NaHCO3, and dissolved in 10 mL of ChIP dilution buffer. The I.P. was then repeated with 5 ug antibody, and processed according to the EZ ChIP protocol.

tag: cell line

value: HeLa

tag: timepoint

value: mid to late S-phase


title: [E-MTAB-831] polyA+_heart_7082801A, Batch_6_heart

value: heart


title: [E-MTAB-831] polyA+_brain_6120217, Batch_6_brain

value: brain


title: SLX-1881.334.s_1

description:
Chromatin IP against ER
G2


title: SLX-2626.438.s_4

description:
Chromatin IP against ER
G3


title: [E-MTAB-831] polyA+_testis_7060321, Batch_6_testis

value: testis


title: E2F7 in HeLa cells run1 and run2

description:
ChIP DNA
E2F7 ChIP-seq sample was sequenced in 2 independent runs and data were combined for the analysis

value: rabbit polyclonal E2F7, Santa Cruz, sc-66870


title: [E-MTAB-831] polyA+_muscle_7040106, Batch_6_muscle


title: SLX-1201.250.s_4

description:
Chromatin IP against ER
G1

value: anti-ER (SC-543, Santa Cruz Biotechnologies)


title: H3K4me1 C646 rep2

status: Public on Jan 03 2012

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against H3K4me1 in C646 treated cells- ChIPSeq replicate 2

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

source_name: Embryonic stem cells

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

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

tag: chip antibody

value: Abcam

tag: chip antibody catalog number

value: V6.5 embryonic stem cells

tag: drug

tag: concentration

tag: time

tag: replicate


title: H3K4me1 C646 rep1

description: Chromatin IP against H3K4me1 in C646 treated cells- ChIPSeq replicate 1

tag: chip antibody manufacturer


title: SLX-4111.666.s_2

description:
Chromatin IP against ER
G8


title: H3K4me1 rep2

description: H3K4me1 in DMSO treated cells- replicate 1 ChIPSeq

value: DMSO


title: H3K27ac C646 rep2

description: Chromatin IP against H3K27ac in C646 treated cells- ChIPSeq replicate 2


title: H3K27ac rep2

description: Chromatin IP against H3K427ac in DMSO treated cells- ChIPSeq replicate 1


title: SLX-4107.665.s_6

description:
Chromatin IP against ER
G7


title: H3K27ac rep1

description: Chromatin IP against H3K27ac- ChIPSeq replicate 2


title: H3K4me1 rep1

description: Chromatin IP against H3K4me1 in DMSO treated cells- ChIPSeq replicate 2


title: CoREST_ChipSeq

description: Chromatin IP against CoREST

value: CoREST


title: WCE-DMSO-t48_ChipSeq

description: Chromatin IP against WCE-DMSO-t48

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
See Supplemental Information of associated manuscript for details regarding generation of WIGs.

source_name: ZHBTc4 ES cells

growth_protocol: ZHBTc4 Oct4 shutdown inducible cells were grown on irradiated MEFs and split onto gelatin coated dishes for 2 passages in mES media.

value: Embryonic stem cells

tag: duration of treatment

value: 48 hr

value: dox


title: H3K4me1_DMSO_48HR_ChipSeq

description: Chromatin IP against H3K4me1

growth_protocol: ZHBTc4 Oct4 shutdown inducible cells were grown on irradiated MEFs and split onto gelatin coated dishes for 2 passages in mES media. Oct4 shutdown was induced by addition of 2ug doxycycline for 48hours

tag: antibody catalog number

value: Abcam AB8895

tag: antibody lot number

tag: cell type


title: H3K4me1_DMS0_0HR_ChipSeq

description: Chromatin IP against H3K4me1


title: H3K4me1_TCP_48HR_ChipSeq

description: Chromatin IP against H3K4me1

growth_protocol: ZHBTc4 Oct4 shutdown inducible cells were grown on irradiated MEFs and split onto gelatin coated dishes for 2 passages in mES media. Oct4 shutdown was induced by addition of 2ug doxycycline for 48 hours.

value: TCP


title: WCE-DMSO-t0_ChipSeq

description: Chromatin IP against WCE-DMSO-t0


title: mES_Mi-2b

description: Chromatin IP against Mi2-b

source_name: Embyonic stem cells

value: Abcam AB72418


title: untransduced

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing: Sequence reads were obtained using the Illumina Genome Analyzer IIx. Reads were aligned to human genome (hg18) using BWA. Peaks are called using in-house developed R package peakSig.

source_name: untransduced

growth_protocol: Primary myoblasts grown in F-10 nutrient media, 20% FBS, 1% Pen/Strep, 10 ng/ml bFGF and 1 µM Dexamethasone.

extract_protocol: Standard Illumina ChIP-seq sample prep kit protocol with two modifications: (1) DNA fragments ranging from 150 to 300 bp were selected at the gel-selection step; (2) 21 cycles of PCR were performed at the PCR amplification step instead of 18.

value: Combined anti-DUX4 C-terminus rabbit polyclonal antibodies MO488 and MO490

value: human myoblasts


title: mES_REST

description: Chromatin IP against REST (replicate 2)

value: REST

value: Upstate 07-574


title: HDAC2 mES biological replicate

description: Chromatin IP against HDAC2

value: Abcam AB7029


title: H3K27ac C646 rep1

description: Chromatin IP against H3K27ac in C646 treated cells- ChIPSeq replicate 1


title: lenti-DUX4-fl

value: Combined anti-DUX4 C-terminus rabbit polyclonal antibodies MO488 and MO489

tag: treatment

value: myoblasts transduced with lentivirus carrying DUX4


title: ChIP-Seq for Lsd1 in mES cells

description: Chromatin IP against Lsd1

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

value: Abcam AB17721


title: mES_LSD1

description: Chromatin IP against LSD1 (replicate 3)

value: V6.5 embryonic stem cells


title: HDAC1 mES biological replicate

description: Chromatin IP against HDAC1

value: Abcam AB7028


title: WCE-TCP-48_ChipSeq

description: Chromatin IP against WCE-TCP-48


title: HDAC1 mES_ChipSeq

description: Chromatin IP against HDAC1 mES


title: Ago 2 immunoprecipitated RNA extracted from HHV-6 infected Sup-T-1 cells

status: Public on Jan 01 2012

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

data_processing:
Counts: Raw reads were trimmed using either the R/Bioconductor package ShortRead (Sup-T-1-HHV-6B-counts.txt) or the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit, Ago2-HHV-6B-counts.txt) and selected according to their final size (exclusion of reads shorter than 15 nt). Remaining sequences with counts included.
Bed: Small RNA reads were mapped to the Z29 strain of HHV-6B (RefSeq NC_000898.1) and the human genome (UCSC hg19) using Nexalign (http://genome.gsc.riken.jp/osc/english/software/src/nexalign-1.3.5.tgz) by permitting up to 2 mismatches. Only alignments of reads specific to the virus or having 0 or strictly less mismatches on the pathogen than on the host genome are reported.

organism: Human betaherpesvirus 6B

growth_protocol: Sup-T-1 cells (CRL-1942; ATCC) were maintained in RPMI-1640 medium containing 7% fetal bovine serum (FBS). 3x105 cells/mL were infected with HHV-6B (a strain that is routinely used for immunofluorescent-based antibody detection in the laboratory) by co-cultivation of uninfected Sup-T-1 cells with infected cells at a ratio of 1:1000.

extract_protocol: RNA was extracted from HHV-6B infected (7 days post infection) Sup-T-1 cells using Tri-reagent (MRC, Inc) as per manufacturer’s instructions. Small RNA cloning was conducted from 30 μg of total RNA as previously described (Pfeffer, S. 2007. Identification of virally encoded microRNAs. Methods Enzymol. 427:51-63), except that PCR products were not concatemerized, and instead sent directly for large-scale sequencing. Similarly, for deep-sequencing of small RNAs incorporated into Ago2-containing RISC complexes, a small RNA library was performed from hAgo2-IP of Sup-T-1 cells infected with HHV-6B at 4 days post infection.

treatment_protocol: For the RISC-immunoprecipitation, 1x108 cells were used for each replicate and washed twice in PBS before lysis in 10 mL of lysis buffer, containing 25 mM Tris HCl pH 7.5, 150 mM KCl, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, and complete protease inhibitor (Roche). DTT and protease inhibitors were always prepared freshly and added immediately before use. Lysates were incubated for 30 min at 4°C and cleared by centrifugation at 20,000 g for 30 min at 4°C. Total RNA was prepared from 100 µL of cell lysates using the miRNeasy kit (Qiagen) following the manufacturer’s instructions. Ago2-immunoprecipitation was performed as previously described (16). Briefly, 6 µg of purified monoclonal hAgo2- antibody (α-hAgo2; 11A9) or control monoclonal BrdU-antibody (Abcam) was added to 5 mL of RPMI-medium and incubated with 30 µL of Protein-G-Sepharose beads (GE Healthcare) in Pierce centrifuge columns (Thermo Scientific) under constant rotation at 4°C overnight. Columns were drained by gravity flow and washed once with the lysis buffer. Beads were subsequently incubated with 5 mL of cell lysates for 2.5 h under constant rotation at 4°C. After incubation, the beads were washed four times with IP wash buffer (300 mM NaCl, 50 mM Tris HCl pH 7.5, 5 mM MgCl2, 0.1% NP-40, 1 mM NaF) and once with PBS to remove residual detergents. RNA was recovered from the beads by adding 700 µL of Qiazol to the columns. After 5 min, the Qiazol lysates were collected from the columns. This step was repeated once and the Qiazol lysates were combined. RNA was prepared using the miRNeasy kit (Qiagen) according to the manufacturer's instructions. RNA samples were eluted in 30 µL H2O and stored at -80°C until subjected to further analyses.

tag: specific-host

value: Homo sapiens

tag: host cell line

value: Sup-T-1 (CRL-1942; ATCC)

tag: host cell type

value: T lymphocyte

tag: antibody for ip


title: Total RNA extracted from HHV-6 infected Sup-T-1 cells


title: CS ZT12 rep2 polyA

city: Philadelphia

first: Michael

last: Hughes

state: PA

address: 421 Curie Bvd, Brb 835

institute: UPenn

data_processing: RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25"

organism: Drosophila melanogaster

source_name: CS ZT12 polyA

growth_protocol: 3-5 day old adult female flies were maintained on standard food and housed at 25 degrees in a 12hr:12hr light:dark environment.

extract_protocol: total RNA was purified using the PicoPure kit from MDS; RNA amplification and rRNA depletion was performed using the RiboAmp kit from MDS (polyA) and Ovation RNAseq kit from NuGEN (non polyA).  Fragmentation, cDNA synthesis, and adaptor ligation was performed using standard protocols.

treatment_protocol: brains were manually dissected in PBS at ZT0, ZT6, ZT12, and ZT18

tag: genotype

value: wild-type

tag: genetic background

value: Canton S

tag: time point

tag: tissue

value: brain

tag: amplification

value: MDS (polyA)

tag: paired or single-end

value: single (1x75)

tag: mean insert size

value: 75 bp


title: Per ZT12 rep1 polyA

source_name: Per ZT12 polyA

value: yw, per0


title: Per ZT12 rep2 polyA


title: Per ZT0 rep2 polyA

source_name: Per ZT0 polyA


title: Mi-2 v6.5_ChipSeq

description: Chromatin IP against Mi-2b (replicate 2)

tag: chip antibody

value: Abcam AB72418


title: HDAC2 mES_ChipSeq

description: Chromatin IP against HDAC2 mES

value: Abcam AB7029


title: Per ZT12 rep1 non-polyA

source_name: Per ZT12 non-polyA

value: Nugen (non polyA)

value: paired (2x100)


title: Per ZT18 rep2 non-polyA

source_name: Per ZT18 non-polyA


title: Per ZT6 rep2 non-polyA

source_name: Per ZT6 non-polyA


title: CS ZT12 rep1 polyA


title: CS ZT0 rep2 polyA

source_name: CS ZT0 polyA


title: CS ZT18 rep2 non-polyA

source_name: CS ZT18 non-polyA


title: Per ZT0 rep1 non-polyA

source_name: Per ZT0 non-polyA


title: Per ZT12 rep2 non-polyA


title: Per ZT0 rep1 polyA


title: Per ZT0 rep2 non-polyA


title: Per ZT6 rep1 non-polyA


title: CS ZT0 rep1 polyA


title: CS ZT6 rep2 non-polyA

source_name: CS ZT6 non-polyA


title: CS ZT0 rep1 non-polyA

source_name: CS ZT0 non-polyA


title: CS ZT0 rep2 non-polyA


title: CS ZT12 rep1 non-polyA

source_name: CS ZT12 non-polyA


title: CS ZT6 rep1 non-polyA


title: CS ZT18 rep1 non-polyA


title: CS ZT12 rep2 non-polyA


title: Per ZT18 rep1 non-polyA


title: mRNASeq_ZS97

city: wuhan

first: Chen

last: Li

state: hubei

address: shizishan street

institute: National Key laboratory of crop genetic improvement, Huazhong Agricultural University

description:
ZS
Instrument model: Illumina HiSeq 2000 model

data_processing:
All clean tags were mapped to the reference sequences  (O. sativa version 6.1; ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_6.1/all.dir/all.cDNA) using MAQ software (Li et al., 2008) and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags) (t Hoen et al., 2008; Morrissy et al., 2009).
The significance of digital gene expression was determined using a published statistical model as descried previously (Audic and Claverie, 1997). The significance of gene expression difference was judged by using "FDR≤0.001 and the absolute value of log2Ratio≥1" (Reiner, 2003) as the threshold.
Processed data files are the comparisons of gene expression difference in all genes (DiffGeneExp.txt) and list of differentially expressed genes (DiffGeneExpFilter.txt) of pairs of samples.

organism: Oryza sativa

source_name: seedling

growth_protocol: Rice seeds were germinated and the seedlings were grown on 1/2 MS medium under a 15h/light at 30 °C and 9h/dark cycle at 25 °C for 15 days.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. The digital expression analysis was performed by Beijing Genomics Institute using the following standardized procedure: The main reagents and supplies are Illumina Gene Expression Sample Prep Kit and Illumina Sequencing Chip (flowcell), and the main instruments are Illumina Cluster Station and Illumina HiSeq™ 2000 System. Six µg of total RNA were to purify mRNA by using oligo(dT) magnetic beads, and the mRNAs were used to synthesize the first and second-strand cDNA using oligo(dT) as primer. The bead-bound cDNAs were subsequently digested with restriction enzyme NlaIII, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to oligo(dT) beads were washed away and the Illumina adaptor 1 was ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites. It cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 was ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form a tag library. After 15 cycles of linear PCR amplification, 95bp fragments were purified by 6% TBE PAGE Gel electrophoresis. After denaturation, the single-chain molecules were fixed onto the Illumina Sequencing Chip (flowcell). Each molecule grows into a single-molecule cluster sequencing template through in situ amplification. Then four types of nucleotides which are labeled by four colors were added, and sequencing was performed with the method of sequencing by synthesis (SBS). Each tunnel generated millions of raw reads with sequencing length of 35bp.

value: 15 days old seedling

tag: cultivar

value: Zhenshan 97


title: mRNASeq_SY63

description:
SY
Instrument model: Illumina HiSeq 2000 model

value: Shanyou 63


title: mRNASeq_HDT1 RNAi in SY63

description:
FR
Instrument model: Illumina HiSeq 2000 model

tag: genotype/variation

value: OsHDT1 inactivation


title: mRNASeq_overexpression HDT1 in SY63

description:
FV
Instrument model: Illumina HiSeq 2000 model

value: OsHDT1 overexpression


title: mRNASeq_MH63

description:
MH
Instrument model: Illumina HiSeq 2000 model

value: Minghui 63


title: wildtype MILI IP testes

city: Cold Spring Harbor

first: Felix

last: Muerdter

state: New York

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratories

description:
small RNA
19-33 nt

data_processing:
The 3' linker (CTGTAGGCACCATCAATTC) was clipped from the sequences, which are then collapsed.
Clipping: fastx_clipper
Part of FASTX Toolkit 0.0.14 by A. Gordon (gordon@cshl.edu)
Collapsing: fastx_collapser
Part of FASTX Toolkit 0.0.14 by A. Gordon (gordon@cshl.edu)

source_name: wildtype MILI IP testes

extract_protocol: RNA was isolated from total ovaries and Piwi protein immunoprecipitates with Trizol, then separated with PAGE to obtain a small RNA fraction ranging from 19 to 33 nt. Adapters for Solexa sequencing were ligated, then the ligated product amplified by RT-PCR. The PCR product is gel-purified for sequencing.

value: testes

tag: strain

tag: antibody

tag: antibody vendor

value: non-commercial published in Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ. 2007b. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316:744-747.; Vagin VV, Wohlschlegel J, Qu J, Jonsson Z, Huang X, Chuma S, Girard A, Sachidanandam R, Hannon GJ, Aravin AA. 2009. Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes Dev 23:1749-1762.


title: wildtype MIWI IP testes

description:
small RNA
19-33 nt

source_name: wildtype MIWI IP testes


title: R37, MILI IP, testes

description:
small RNA
19-33 nt

source_name: R37, MILI IP, testes

value: R37 (B6xSJL)


title: R37, total RNA, testes, 19-33 nt

description:
small RNA
19-33 nt

source_name: R37, total RNA, testes, 19-33 nt


title: R37, MIWI IP, testes

description:
small RNA
19-33 nt

source_name: R37, MIWI IP, testes


title: R13, total RNA, testes, 19-33 nt

description:
small RNA
19-33 nt

source_name: R13, total RNA, testes, 19-33 nt

value: R13 (B6xSJL)


title: R13, MIWI IP, testes

description:
small RNA
19-33 nt

source_name: R13, MIWI IP, testes


title: AA3

city: Jefferson

first: Zhiguang Li

state: AR

address: HFT130, 3900 NCTR Road

department: Division of Genetic an Reproductive Toxicology

institute: National Center for Toxicological Research

data_processing: We used the miRanalyzer webserver [16] for the detection of known microRNAs (http://www.mirbase.org/). The required input in read/count format was generated by means of the provided groupReads.pl perl script. In both analysis steps, (i) conversion of fq.gz to read/count and (ii) the microRNA expression profiling we used the default parameters of the programs. To detect differentially expressed genes we proceeded as following: (i) download all Ensembl transcripts in fasta format (RGSC3.4), (ii) align the reads with Bowtie [17] using a seed alignment of 18 nt and allowing 1 mismatch. Initially we retain the best 10 alignments (--best --strata) performing a seed extension to find the best alignment(s) as described in the miRanalyzer paper. Finally we accept the alignments if equal or less than 9 best alignments (after the seed extension) exist. (iii) calculate the read count for each reference sequence (Ensembl transcript). Note that by doing so, a read with multiple mappings will contribute to the total read count of several transcripts. Another way would be to distribute the read count equally over the multiple mapped transcripts (dividing the read count of an ambiguously mapped read by the number of mappings). However, this would lead to non-integer read counts which might cause that we cannot use DESeq in the same way for mRNA and microRNA. Moreover, we are interested in differentially expressed mRNA and therefore the effect of the multiple mapping treatments will cancel out between the two conditions.We used the DESeq bioconductor package (http://www.ncbi.nlm.nih.gov/pubmed/20979621) to detect differentially expressed microRNA and mRNA. miRanalyzer incorporates a differential expression module which is based on DESeq. For the mRNA sequencing data, we built an expression matrix with the raw read counts of all transcripts and conditions that is the input for DESeq.

organism: Rattus norvegicus

source_name: AA treated

extract_protocol: The small RNA library construction and deep sequencing was carried out at University of Texas Southwestern Medical Center Microarray Core Facility. Samples were prepared using illumina small RNA sample Prep kit with the small RNA v1.5 sample preparation guide.  Approximately 10 µg of total RNA was used for small RNA library construction. The v1.5 sRNA 3’ and SRA 5’ adaptors (Illumina, USA) were added to both ends of the small RNA. The 3’ and 5’ Ligated RNAs were used as templates for reverse transcription followed by PCR amplification.  The enriched cDNA constructs were loaded to 6% TBE PAGE gel and the bands containing the 22-30 nt RNA fragments (93-100 nt in length with both adapters) were cut and purified. The concentrations of the libraries were determined using a NanoDrop ND-1000 Spectrophotometer and the size and purity were determined using an Agilent 2100 Bioanalyzer in combination with the Agilent DNA 1000 Kit. The purified DNA was used directly for cluster generation and sequence analysis using the Illumina Genome Analyzer II(Illumina, San Diego, CA, USA) according to the manufacturer's instructions (36 cycle single read cluster kit v4 and sequence kit v4).  The image files generated by the sequencer were then processed to produce digital-quality data. After masking of the adaptor sequences and removal of contaminated reads, clean reads were processed for computational analysis.

treatment_protocol: The treatment schedule was based on the previous carcinogenicity study (Mengs et al. 1982).  Groups of four 6 week-old male Big Blue rats were treated with AA as its sodium salt at 10.0 mg/kg body weight by gavage (4 ml/kg body weight) 5 times a week for 12 weeks.  The rats that were treated with 0.9% sodium chloride on the same schedule were used as control.  All animals were sacrificed 1 day after the last treatment.  The kidneys were isolated, frozen quickly in liquid nitrogen and stored at −80 ◦C.  The rats were obtained from Taconic Laboratories (Germantown, NY) through a purchase from Stratagene (La Jolla, CA).  Aristolochic acid (AA) was purchased from Sigma (St. Louis, MO).  The purity of AA was 96% and included 40% of AAI and 56% of AAII.  The recommendations set forth by the NCTR Institutional Animal Care and Use Committee were followed for the handling, maintenance, treatment and sacrifice of the rats.

tag: gender

value: Male

tag: age

value: 6 weeks

value: Fisher 344

tag: genetics

value: Big Blue Transgenic

value: liver


title: D. melanogaster, lacZ containing transgene insertion in X-TAS, ovaries, 19-28nt

description:
small RNA
19-28 nt

value: ovaries


title: AA4


title: D. melanogaster, GFP insertion into the flamenco locus, ovaries, 19-28nt

description:
small RNA
19-28 nt


title: D. melanogaster, GFP insertion into the TJ locus, ovaries, 19-28nt

description:
small RNA
19-28 nt


title: R13, MILI IP, testes

description:
small RNA
19-33 nt

source_name: R13, MILI IP, testes


title: AA1


title: CTL1

source_name: sodium chloride treated


title: Ty1 insertions in diploid yeast

city: Baltimore

first: Sarah

last: Wheelan

address: 550 N. Broadway

department: Oncology

institute: Johns Hopkins University School of Medicine

data_processing:
flowcell62_lanedip.filter.R.clones.sequences; genome build: S288c, SGD 2/2009
We considered only those Illumina reads that started with the Ty1 LTR, allowing one “N” mismatch. After trimming sequence not derived from the yeast genome, the reads were aligned to the yeast genome using Bowtie (Langmead et al, 2009), using a seed of 20bp. Only uniquely and perfectly mapping reads were retained; reads mapping to identical genomic positions were counted only once to avoid biases due to PCR or other amplification artifacts.

source_name: yeast cells

growth_protocol: The strain used for the sequencing experiment was BY348 (MATα his3Δ200 ura3-167 GAL+) containing plasmid pJEF2365. pJEF2365 is a derivative of pVIT41 (Lauermann et al, 1997) with a higher performing 2 micron origin fragment derived from pJEF1562 (Monokian et al, 1994). The Ty1 element in this plasmid is tagged with a sequence called ssb (Fig. 1A). The media used were YPD, SC–Ura containing either 2% glucose (glu), 2% galactose, (gal) or 1% raffinose (raf), and SC+ 5-Foa (fluoro-orotic acid).  Media were prepared as described (Rose et al, 1990, Smith et al, 1997).

extract_protocol: Twelve individual colonies of strain BY348 were grown on SC–Ura glucose plates grown at 30˚C. These were used as the starting material for 96 independent galactose inductions to minimize jackpot effects. The colonies were picked into 5 mL SC–Ura 1% Raf and grown at 30˚C overnight. For each of the 12 cultures, corresponding to one column of a 96-deep well plate, the following were added to each well: a sterile 3 mm glass bead, 200 µL of the above inoculum and 1 mL SC–Ura gal. The plate was covered with Air Pore tape and grown at 22˚C at 240 rpm for 48 hours in a refrigerated air shaker. 1150 µL were removed from each well and replaced with 1150 µL of YPD and grown at 30˚C overnight with shaking to allow plasmid loss.  1150 µL were removed from each well and replaced with 1150 µL of SC + 1 mg/mL 5-Foa medium and grown overnight with shaking to select for plasmid free cells.  The 8 cultures in each column were pooled to make a DNA preparation as described (Boeke et al, 1985).  The DNA was then extracted three times with phenol/chloroform/isoamyl alcohol, and ethanol precipitated. Custom Illumina adapters were ordered as duplexes from IDT (top strand oligonucleotide;, 5’-pTAGTCCCTTAAGCGGAG-NH2; bottom strand oligonucleotide, 5’-GTAATACGACTCACTATAGGGCTCCGCTTAAGGGAC).  2 µG gDNA was digested to completion with 60 U MseI and 120 U BglII in a 100 µL reaction overnight and purified on a QiaQuick column (Qiagen).  MseI-compatible adaptors were ligated overnight at 16˚C and heat inactivated at 70˚ for 15 min. Custom Illumina adapters were ordered as duplexes from IDT (top strand oligonucleotide;, 5’-pTAGTCCCTTAAGCGGAG-NH2; bottom strand oligonucleotide, 5’-GTAATACGACTCACTATAGGGCTCCGCTTAAGGGAC).  2 µG gDNA was digested to completion with 60 U MseI and 120 U BglII in a 100 µL reaction overnight and purified on a QiaQuick column (Qiagen).  MseI-compatible adaptors were ligated overnight at 16˚C and heat inactivated at 70˚ for 15 min.

tag: tip-seq

value: Ty1 flanking regions

tag: cell type

value: diploid


title: AA2


title: Ty1 insertions in haploid yeast

data_processing:
flowcell36_lane7_filter.clones.sequences; genome build: S288c, SGD 2/2009
We considered only those Illumina reads that started with the Ty1 LTR, allowing one “N” mismatch. After trimming sequence not derived from the yeast genome, the reads were aligned to the yeast genome using Bowtie (Langmead et al, 2009), using a seed of 20bp. Only uniquely and perfectly mapping reads were retained; reads mapping to identical genomic positions were counted only once to avoid biases due to PCR or other amplification artifacts.

value: haploid

tag: genotype

value: BY348 (MATα his3Δ200 ura3-167 GAL+) containing plasmid pJEF2365


title: CTL2


title: CTL4


title: CTL3


title: Paradoxus Rep 2

status: Public on Dec 31 2011

city: Chestnut Hill

first: Gabor

last: Marth

address: 140 Commonwealth Ave

institute: Boston College

description: ribosome-depleted RNA from S. paradoxus

data_processing: S. cerevisiae build  is sacCer2. S. paradoxus, S. mikatae, and S. bayanus annotations are from Kellis et al. (2003). Read counts included in "all aligned reads" include reads that align to multiple positions in the genome.  "Uniquely aligned reads" aligned unambiguously to one position.

organism: Saccharomyces paradoxus NRRL Y-17217

source_name: Paradoxus

growth_protocol: Grown in complete media

extract_protocol: WT-Seq was performed according to a protocol/kit now available fromLife Technologies, with minor modifications that are included below. Briefly, 5–10 μg of RNA isolated from mouse cortical cultures was depleted of ribosomal RNAs using two rounds of Eukaryotic RiboMinus treatment (Life Technologies) with overnight ethanol precipitations for sample re-concentration. The removal of ribosomal RNAs was confirmed on a Bioanalyser Nano Chip (Agilent). A total of 500–1,000 ng of riboRNA-depleted total RNA was fragmented for 18 min at 95 °C in NEB buffer 3 followed by 30 minutes PNK treatment in the same buffer. Fragmentation was followed by size selection of ~50 to ~150 bp fragments using the flashPAGE denaturing PAGE-fractionator (Life Technologies) and ethanol precipitation overnight. The resulting RNA was directionally ligated, reverse-transcribed and RNaseH treated. After trial PCR to assess library quality and quantity, 30 μl cDNA was run on a native 6% PAGE gel. The 90–120-bp size window (corresponding to 50–80-bp RNA insert size) was cut from the gel, shredded and inserted directly into a 400 µl PCR reaction using standard WT-Seq kit components and submitted to 11–15 cycles of PCR. The PCR product was phenol-chloroform extracted, ethanol precipitated and re-suspended in 20 μl WT-Seq gel loading buffer. The resulting sample was run on a 6% native PAGE gel, and the 150–175-bp size range (corresponding to 60–85 bp) was cut from the gel, shredded, and extracted overnight in WT-Seq PAGE elution buffer. The resulting library was filtered through 0.45 μm spin filters (Life Technologies) to remove gel pieces and ethanol precipitated.


title: Cerevisiae Rep 2

description: ribosome-depleted RNA from S. cerevisiae

organism: Saccharomyces cerevisiae S288C

source_name: Cerevisiae

value: S288c wt (FY4xFY5).


title: Mikatae Rep 1

description: ribosome-depleted RNA from S. mikatae

organism: Saccharomyces mikatae IFO 1815

source_name: Mikatae


title: Cerevisiae Rep 1


title: Bayanus Rep 2

description: ribosome-depleted RNA from S. bayanus

organism: Saccharomyces uvarum CLIB 533

source_name: Bayanus


title: Mikatae Rep 2

description: ribosome-depleted RNA from S. mikatae


title: Wild-type PB insertions Rep #1

city: Collegeville

first: David

last: Mayhew

address: 1250 South Collegeville Road

department: Target Sciences, Computation Biology, R&D

institute: GlaxoSmithKline

description: Insertions of Wt PBase

data_processing:
Library strategy: Calling-Card
PBwt_rep1_insertions.txt; genome build: hg18
For Calling Card insertions: Paired reads were filtered by requiring the first bases to contain the end of the PB TR (to ensure specific amplification) on the first read, and a proper barcode and digestion site on the second read.  The non-genomic sequences were trimmed and the remaining sequence from each paired-end read was aligned to hg18 using bowtie with the options ‘--best --tryhard --minins 0 --maxins 1200’. Reads that could be uniquely aligned counted as an independent insertion for every position for every unique barcode at that position.  For ChIP-seq data: Model-based analysis of ChIP-seq (MACS) was used to generate the peaks file.  For RNA-seq data: reads were aligned to hg18 using Tophat and transcripts were quantified using Cufflinks.
bowtie version 0.12.7
MACS version 1.4.0alpha
cufflinks version 1.1.0

source_name: Wild-type PB insertions Rep #1

growth_protocol: Human colon adenocarcinoma cell line HCT116 (ATCC) was maintained in McCoy 5A Media Modified (Gibco) supplemented with 10% fetal bovine serum (Gibco). To select for PB transposition, G418 was added to the media to a final concentration 700 mg/ml. Cells were cultured at 37 oC in the presence of 5% CO2.

extract_protocol: Calling Card Illumina libraries were prepared by harvesting G418 resistant cells and extracting their genomic DNA. Each DNA sample was divided into three aliquots and digested with Taq1 or Csp61 or Msp1. Digested DNA was ligated overnight at 15°C in dilute solution (<10ng/ul) to encourage self-circularization. After ethanol precipitation, self-ligated DNA was resuspended in ddH2O and used as template in an inverse PCR. Primers that anneal to PB Donor sequence (OM8721 and OM8722) were used to amplify the genomic regions flanking PB integrations and the bar code within the transposon, as well as adding adapter sequences that allow the PCR products to be sequenced on the Illumina GA IIx analyzer. The PCR products were purified using the QIAquick PCR Purification Kit (Qiagen) and diluted to 10nM. For each sample, the same amount of PCR product from digestion with each restriction endonuclease was pooled and submitted for sequencing on the Illumina GAII.

tag: cell line


title: Wild-type PB insertions Rep #3

description: Insertions of Wt PBase

data_processing:
Library strategy: Calling-Card
PBwt_rep3_insertions.txt; genome build: hg18
For Calling Card insertions: Paired reads were filtered by requiring the first bases to contain the end of the PB TR (to ensure specific amplification) on the first read, and a proper barcode and digestion site on the second read.  The non-genomic sequences were trimmed and the remaining sequence from each paired-end read was aligned to hg18 using bowtie with the options ‘--best --tryhard --minins 0 --maxins 1200’. Reads that could be uniquely aligned counted as an independent insertion for every position for every unique barcode at that position.  For ChIP-seq data: Model-based analysis of ChIP-seq (MACS) was used to generate the peaks file.  For RNA-seq data: reads were aligned to hg18 using Tophat and transcripts were quantified using Cufflinks.
bowtie version 0.12.7
MACS version 1.4.0alpha
cufflinks version 1.1.0

source_name: Wild-type PB insertions Rep #3


title: RNA-seq - HCT116

description: HCT116 RNA-seq

data_processing:
HCT116_expression_hg18.txt; genome build: hg18
For Calling Card insertions: Paired reads were filtered by requiring the first bases to contain the end of the PB TR (to ensure specific amplification) on the first read, and a proper barcode and digestion site on the second read.  The non-genomic sequences were trimmed and the remaining sequence from each paired-end read was aligned to hg18 using bowtie with the options ‘--best --tryhard --minins 0 --maxins 1200’. Reads that could be uniquely aligned counted as an independent insertion for every position for every unique barcode at that position.  For ChIP-seq data: Model-based analysis of ChIP-seq (MACS) was used to generate the peaks file.  For RNA-seq data: reads were aligned to hg18 using Tophat and transcripts were quantified using Cufflinks.
bowtie version 0.12.7
MACS version 1.4.0alpha
cufflinks version 1.1.0

source_name: RNA-seq - HCT116


title: SP1 PB insertions Rep #2

description: Insertions of SP1-Pbase

data_processing:
Library strategy: Calling-Card
SP1_PB_rep2_insertions.txt; genome build: hg18
For Calling Card insertions: Paired reads were filtered by requiring the first bases to contain the end of the PB TR (to ensure specific amplification) on the first read, and a proper barcode and digestion site on the second read.  The non-genomic sequences were trimmed and the remaining sequence from each paired-end read was aligned to hg18 using bowtie with the options ‘--best --tryhard --minins 0 --maxins 1200’. Reads that could be uniquely aligned counted as an independent insertion for every position for every unique barcode at that position.  For ChIP-seq data: Model-based analysis of ChIP-seq (MACS) was used to generate the peaks file.  For RNA-seq data: reads were aligned to hg18 using Tophat and transcripts were quantified using Cufflinks.
bowtie version 0.12.7
MACS version 1.4.0alpha
cufflinks version 1.1.0

source_name: SP1 PB insertions Rep #2


title: Wild-type PB insertions Rep #2

description: Insertions of Wt PBase

data_processing:
Library strategy: Calling-Card
PBwt_rep2_insertions.txt; genome build: hg18
For Calling Card insertions: Paired reads were filtered by requiring the first bases to contain the end of the PB TR (to ensure specific amplification) on the first read, and a proper barcode and digestion site on the second read.  The non-genomic sequences were trimmed and the remaining sequence from each paired-end read was aligned to hg18 using bowtie with the options ‘--best --tryhard --minins 0 --maxins 1200’. Reads that could be uniquely aligned counted as an independent insertion for every position for every unique barcode at that position.  For ChIP-seq data: Model-based analysis of ChIP-seq (MACS) was used to generate the peaks file.  For RNA-seq data: reads were aligned to hg18 using Tophat and transcripts were quantified using Cufflinks.
bowtie version 0.12.7
MACS version 1.4.0alpha
cufflinks version 1.1.0

source_name: Wild-type PB insertions Rep #2


title: Paradoxus Rep 1

description: ribosome-depleted RNA from S. paradoxus


title: ChIP-Seq analysis of H3K4me1 in human hiPS-18a cells; DNA_Lib 346

status: Public on Dec 28 2011

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: NTR_0001165
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 346
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8718
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9471
****************
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: GSM773028_BI.iPS-18a.H3K4me1.DNA_Lib_346.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 346-DNA_Lib 346-DNA_Lib 346-DNA_Lib 346.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-18a Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the iPS-18a Cell Line, Library DNA_Lib 346, 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.10704
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,814,552
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.256
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.328
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9689
IROC_PERCENTILE: 50
POISSON_SCORE: 0.488
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773028_BI.iPS-18a.H3K4me1.DNA_Lib_346.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 346-DNA_Lib 346-DNA_Lib 346-DNA_Lib 346.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18a Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the iPS-18a Cell Line, Library DNA_Lib 346, 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.10968
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 5
BROWSER_TRACK_NAME: iPS18a H3K4me1 46
BROWSER_TRACK_DESCRIPTION: BI iPS-18a Cell Line Histone H3K4me1 Library DNA_Lib 346 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,814,552
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.256
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.328
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9689
IROC_PERCENTILE: 50
POISSON_SCORE: 0.488
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: induced pleuripotent 18a stem cell line; DNA_Lib 346

extract_protocol: Library construction protocol: Single read - Illumina

value: induced pluripotent stem cells

tag: sample alias

value: BioSam 173

tag: sample common name

value: iPS-18a Cell Line

tag: lineage

value: induced pluripotent cells

tag: medium

value: 10% KOSR (Invitrogen)

tag: molecule

value: genomic DNA

tag: disease

value: presumed normal

tag: passage

tag: line

tag: batch

value: BioSAli 176

value: Cell Line

value: undifferentiated

tag: Sex

value: Unknown

value: Harvard

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Branson


title: ChIP-Seq analysis of H3K4me3 in human hiPS-18a cells; DNA_Lib 345

description:
sample_term_id: NTR_0001165
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 345
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8719
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9471
****************
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: GSM773029_BI.iPS-18a.H3K4me3.DNA_Lib_345.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 345-DNA_Lib 345-DNA_Lib 345-DNA_Lib 345.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-18a Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the iPS-18a Cell Line, Library DNA_Lib 345, 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.10622
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,897,728
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4568
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4694
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9994
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4969
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773029_BI.iPS-18a.H3K4me3.DNA_Lib_345.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 345-DNA_Lib 345-DNA_Lib 345-DNA_Lib 345.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18a Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the iPS-18a Cell Line, Library DNA_Lib 345, 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.10886
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 5
BROWSER_TRACK_NAME: iPS18a H3K4me3 45
BROWSER_TRACK_DESCRIPTION: BI iPS-18a Cell Line Histone H3K4me3 Library DNA_Lib 345 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,897,728
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4568
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4694
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9994
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4969
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: induced pleuripotent 18a stem cell line; DNA_Lib 345

value: induced pluripotent stem cells

value: BioSam 173

value: iPS-18a Cell Line

value: induced pluripotent cells

value: Millipore

value: Histone H3K4me3


title: SP1 PB insertions Rep #1

description: Insertions of SP1-Pbase

data_processing:
Library strategy: Calling-Card
SP1_PB_rep1_insertions.txt; genome build: hg18
For Calling Card insertions: Paired reads were filtered by requiring the first bases to contain the end of the PB TR (to ensure specific amplification) on the first read, and a proper barcode and digestion site on the second read.  The non-genomic sequences were trimmed and the remaining sequence from each paired-end read was aligned to hg18 using bowtie with the options ‘--best --tryhard --minins 0 --maxins 1200’. Reads that could be uniquely aligned counted as an independent insertion for every position for every unique barcode at that position.  For ChIP-seq data: Model-based analysis of ChIP-seq (MACS) was used to generate the peaks file.  For RNA-seq data: reads were aligned to hg18 using Tophat and transcripts were quantified using Cufflinks.
bowtie version 0.12.7
MACS version 1.4.0alpha
cufflinks version 1.1.0

source_name: SP1 PB insertions Rep #1


title: ChIP-Seq analysis of H3K9ac in human hiPS-18a cells; DNA_Lib 344

description:
sample_term_id: NTR_0001165
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 344
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8720
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9471
****************
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: GSM773030_BI.iPS-18a.H3K9ac.DNA_Lib_344.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 344-DNA_Lib 344-DNA_Lib 344-DNA_Lib 344.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-18a Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the iPS-18a Cell Line, Library DNA_Lib 344, 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.10623
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,443,334
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1753
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.2248
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9986
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2533
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773030_BI.iPS-18a.H3K9ac.DNA_Lib_344.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 344-DNA_Lib 344-DNA_Lib 344-DNA_Lib 344.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18a Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the iPS-18a Cell Line, Library DNA_Lib 344, 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.10887
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 5
BROWSER_TRACK_NAME: iPS18a H3K9ac 44
BROWSER_TRACK_DESCRIPTION: BI iPS-18a Cell Line Histone H3K9ac Library DNA_Lib 344 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,443,334
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1753
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.2248
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9986
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2533
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: induced pleuripotent 18a stem cell line; DNA_Lib 344

value: 10% KOSR (Invitrogen)

value: genomic DNA

value: presumed normal

value: BioSAli 176

value: Cell Line

value: undifferentiated

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K27ac in human hippocampus middle cells; DNA_Lib 585

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 585
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8710
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9441
****************
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: GSM773020_BI.Brain_Hippocampus_Middle.H3K27ac.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 585-DNA_Lib 585-DNA_Lib 585.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on Brain Hippocampus Middle, Donor 149, 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.10766
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,634,126
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.3083
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.353
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9864
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4862
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773020_BI.Brain_Hippocampus_Middle.H3K27ac.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 585-DNA_Lib 585-DNA_Lib 585.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 149, 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.11030
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 5
BROWSER_TRACK_NAME: BHM H3K27ac 49 85
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K27ac Donor 149 Library DNA_Lib 585 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,634,126
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.3083
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.353
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9864
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4862
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 585

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD evident at demise

value: Hippocampus Middle

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K27ac


title: SP1 ChIP-seq - HCT116

description: SP1 ChIP-seq

data_processing:
SP1_ChIPseq_peaks.bed; genome build: hg18
For Calling Card insertions: Paired reads were filtered by requiring the first bases to contain the end of the PB TR (to ensure specific amplification) on the first read, and a proper barcode and digestion site on the second read.  The non-genomic sequences were trimmed and the remaining sequence from each paired-end read was aligned to hg18 using bowtie with the options ‘--best --tryhard --minins 0 --maxins 1200’. Reads that could be uniquely aligned counted as an independent insertion for every position for every unique barcode at that position.  For ChIP-seq data: Model-based analysis of ChIP-seq (MACS) was used to generate the peaks file.  For RNA-seq data: reads were aligned to hg18 using Tophat and transcripts were quantified using Cufflinks.
bowtie version 0.12.7
MACS version 1.4.0alpha
cufflinks version 1.1.0

source_name: SP1 ChIP-seq - HCT116

tag: antibody

tag: antibody vendor

value: Active Motif

tag: antibody catalog number

tag: antibody lot number