title: [E-MTAB-308] Zebrafish adult male body mRNA 3' end

description: Provider: SANGER

source_name: Zebrafish adult male body mRNA 3' end

value: fertilization

value: whole fish without head or testis


title: cells.H3K27me3.input

status: Public on Dec 02 2010

type: SRA

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Input DNA.

library_source: genomic

data_processing: Alignment: Sequence reads were mapped to the mouse mm9 genome using Bowtie (PMID: 19261174; Illumina pipeline version 1.3). All reads that map uniquely to the genome with two or fewer mismatches were retained.

molecule: genomic DNA

organism: Mus musculus

source_name: Cells isolated from the spleen of leukemic blasts-injected mice, input

growth_protocol: Leukemic blasts were isolated from APL transgenic mice and intravenously injected (1 x 10^6 cells) into syngeneic recipient mice to induce secondary leukemias (Minucci, S. et al. Blood 100, 2989-2995 (2002)) and establish a massive splenomegaly.

extract_protocol:
Chromatin preparation: Rehydrated formaldehyde-fixed and paraffin-embedded (FFPE) spleen sections (tissue) and APL leukemic cells isolated from spleens and cross-linked ex vivo (cells) were incubated in 0.5 ml permeabilization buffer (1xTBS; 0.5% Tween20; 1mM PMSF; 10 ug/ml RNAse A) for 30 min at RT in a rotating platform. After centrifugation at 18,000g for 5 min at +4Â°C, samples were resuspended in 200 ul digestion buffer (50mM Tris-HCl, pH 7.4; 0,32M sucrose; 4mM MgCl2; 1mM CaCl2; 0.1mM PMSF). FFPE-derived samples were partially fragmented through mild sonication, 3 times x 30 sec at 50W using a Labsonic L sonicator (B. Braun Biotech International) and then digested for 1 min at 37Â°C with micrococcal nuclease (USB - N.70196Y) at the final concentration of 1U/10ug of chromatin (based on spectrophotometric optical density measured at 260 nm). After centrifugation at 18,000g for 5 min at +4Â°C, samples were resuspended in 200 ul sonication buffer (1xTBS; 0.1% SDS; 1 mM Na2EDTA pH 8.0) and further fragmented 3 times x 30 sec (in ice-cold bath) either at 100W (FFPE samples) or 50W (Cells). After centrifugation at 8,000g for 5 min at RT, the first supernatant was collected (volume of approximately 170 ul). The pellets were washed once with 50 ul sonication buffer, vortexed for 5 sec, centrifuged again to obtain the second supernatant (to reach a final volume of approximately 220 ul).

Chromatin immunoprecipitation assay (PAT-ChIP and Cells-ChIP): Chromatin was quantitated fluorimetrically by Qubit Invitrogen, according to the manufacturer's instructions.  Immunoselection of chromatin was carried out in ChIP buffer (30mM Tris-HCl, pH 7.4; 50mM NaCl; 5mM Na2EDTA; 0.1mM PMSF) in a final volume of 300 ul, using 260-600 ng of chromatin for each assay (dependent on either the amount of chromatin extracted from FFPE samples in each experiment and the number of ChIP assays to perform) and incubated 16 hr at +4Â°C in a rotating platform with the desired antibody (Active Motif rabbit anti-histone H3 trimethyl Lys4 pAb or Upstate rabbit anti-trimethyl-histone H3 (Lys27) pAb) at a previously determined optimal amount. 40ul of 50% v/v slurry rec-Protein G-Sepharose 4B Conjugate (preincubated 16 hours at +4Â°C with 1mg/ml of BSA in ChIP buffer - Zymed) were added to each ChIP assay and incubated for 3 hr at +4Â°C. After centrifugation at 2,000g, for 5 min at +4Â°C, pellets were washed sequentially with 10 ml of washing buffer A (50mM Tris-HCl, pH 7.4; 1% TritonX-100; 50mM NaCl; 5mM Na2EDTA; 0.1mM PMSF), 10 ml of washing buffer B (50mM Tris-HCl, pH 7.4; 1% TritonX-100; 100mM NaCl; 5mM Na2EDTA; 0.1mM PMSF), and 10 ml of washing buffer C (50mM Tris-HCl, pH 7.4; 1% TritonX-100; 150mM NaCl; 5mM Na2EDTA; 0.1mM PMSF). Elution was carried out by adding 200ul of elution buffer (1xTE/1%SDS) and incubating for 30 min at RT in a rotating platform. After centrifugation at 1,200g for 5 min at RT, the supernatant was saved and the elution repeated to obtain a final volume of 400ul (bound fraction).

DNA isolation: Decrosslinking was performed through an overnight incubation at 65Â°C in elution buffer/0.2M NaCl followed by a digestion with 80ug/ml proteinase K (3hr at +45Â°C). DNA was isolated by sequential extractions with one-third volume of phenol:chloroform (1:1), one volume of phenol:chloroform (1:1), one volume of chloroform and performing a centrifugation at 6,000g for 10 min at RT between each step of extraction. DNA was precipitated adding 1/10th volume of 5M sodium acetate, pH 5.2, 20ug of linear poly-acrylamide (LPA), 2.5 volumes of 100% ethanol (overnight at -20Â°C). After centrifugation at 3,000g for 30 min at +4Â°C, DNA pellets were washed once in 1 ml of ice-cold 70% ethanol solution, centrifuged, air dried and resuspended in 50ul of TE buffer (stored at -20Â°C).

Tagged libraries were produced according to Illumina's instructions from 7-10 nanograms of the bound and the input DNA, and as described by Schweiger, M.R. et al. Plos One 5, e5548 (2009).

treatment_protocol: None.

tag: strain

tag: tissue

value: spleen

tag: sample type

value: cells

tag: antibody


title: tissue.H3K27me3.input

description: Input DNA.

source_name: Spleen FFPE sections of leukemic blasts-injected mice, input

value: tissue


title: tissue.H3K27me3.IP

description: Chromatin IP against H3K27me3.

data_processing:
Alignment: Sequence reads were mapped to the mouse mm9 genome using Bowtie (PMID: 19261174; Illumina pipeline version 1.3). All reads that map uniquely to the genome with two or fewer mismatches were retained.

Peaks: Analyses were performed using MACS (PMID: 18798982) with a p-value threshold of 10^-5, a bandwith of 300bp and the mfold parameter set to 16. All ChIPs were normalized against the corresponding input DNA. The peaks are in the *peaks.bed files.

source_name: Spleen FFPE sections of leukemic blasts-injected mice, H3K27me3 ChIP

tag: antibody vendor

value: Upstate

tag: antibody catalog #

tag: antibody lot #


title: cells.H3K4me3.IP.rep2

description: Chromatin IP against H3K4me3.

source_name: Cells isolated from the spleen of leukemic blasts-injected mice, H3K4me3 ChIP

value: Active Motif


title: [E-MTAB-223] TAM_CTCF_ChIP_lane1

status: Public on Dec 04 2010

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

description: Performer: CRUK-CRI

data_processing: scanning | The Eland software (Illumina) was used to align reads against the hg18 reference genome. The first 32 bases were aligned allowing a maximum of 2 mismatches. Reads aligning to multiple locations were discarded. The remaining un-aligned reads were shortened by 3 bases at the 3' end and the procedure repeated until the remaining aligned sequences were 23 bases long.

organism: Homo sapiens

growth_protocol: grow | RPMI 1640 medium por DMEM supplemented with 10% inactivated FBS, l-glutamine and PEST at 37C with 5% CO2.

extract_protocol:
immunoprecipitate | Antibodies were from Santa Cruz Biotechnology (sc-543), abcam (ab5089 and ab23738) and Millipore (07-729) and ChIP was performed using 10e7-10e8 cells per reaction. Briefly, crosslinking of protein and DNA was done in room temperature for 10 minutes with serum free media containing 0,37 % formaldehyde. Cells were scraped and washed in PBS before treatment of cell lysis buffer with protease inhibitors on ice. Pelleted nuclei were resuspeded in RIPA buffer and a BioRuptor (Diagenode) was used to sonicate DNA. ChIP was performed with 10 micrograms of antibody. ChIP DNA was gel fractionated and amplified to create two size libraries corresponding to insert sizes of 200-300 bp. For DNase I hypersensitivity was performed as previously described (Eeckhoute et al., 2006). Digested DNA was run on a gel and the digested material (between 200bp and 500bp in size). For all ChIPs washing was done six times with RIPA buffer and once with TE-buffer and DNA-protein complexes were eluted from beads twice with 200 microlitres of 0.1 M NaHCO3 and 1 % SDS and treated with RNAseA at 65C for 6 hours and Proteinase K at 45C over night. Chromatin was amplified with Solexa protocol chromatin amplification.
sequencing | Sequencing was carried out by the genomic service of Cambridge Research Institute-CRUK using the Illumina genome analyzer II

tag: material type

tag: cellline

tag: Sex

value: female

tag: diseasestate

value: breast cancer

tag: chip antibody

value: CTCF


title: cells.H3K27me3.IP

description: Chromatin IP against H3K27me3.

source_name: Cells isolated from the spleen of leukemic blasts-injected mice, H3K27me3 ChIP


title: [E-MTAB-308] Zebrafish adult ovary mRNA 3' end

description: Provider: SANGER

library_source: transcriptomic

data_processing: processed data not provided

molecule: total RNA

organism: Danio rerio

source_name: Zebrafish adult ovary mRNA 3' end

growth_protocol: grow | Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at -70 C.

extract_protocol:
nucleic_acid_extraction | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions. Pellets were resuspended RNase-free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments).
specified_biomaterial_action | 20 µg of total RNA was fragmented using RNA Fragmentation Reagent (Ambion) for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl.   RNA was annealed to the oligo stBPM1polyT22 (biotin-GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN) and bound to streptavidin  magnetic beads.   After washing by pull down on a magnet, the bound RNA was reverse transcribed with SuperScript II (Invitrogen) and a second strand synthesised with DNA polymerase I (Promega) and RNase H (NEB).   After further washing, the double strand cDNA was released from the beads with BpmI (NEB).   The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturerÕs protocol with a fragment size of 250 to 300 bp.
scanning | Base calling was performed using Illumina pipeline 1.3 (Bustard 1.3.4) with phred quality scores at 64 levels using Illumina pipeline 1.3 (Gerald).    There were 152 cycles of sequencing with 2 reads per cluster, a forward read starting at base 1 and a reverse read starting at base 77.
sequencing | Sequencing was performed using the Illumina Genome Analyzer II

tag: strainorline

value: Tuebingen

tag: age

tag: initialtimepoint

tag: developmentalstage

value: adult

tag: organismpart

value: ovary


title: [E-MTAB-223] FoxA1_ChIP_T47D_full_media

description: Performer: CRUK-CRI


title: Heatshock_Day1_wt

city: New Haven

first: Frank

middle: J

last: Slack

state: CT

address: 266 Whitney Ave

department: MCDB

country: USA

institute: Yale University

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

organism: Caenorhabditis elegans

source_name: Day 1 wild-type young adult with heat shock treatment

growth_protocol: Wild-type N2 hermaphrodites were maintained for a few generations without starvation at 20 °C to collect embryos. After embryos were harvested, they were incubated at 20 °C without a food source in M9 buffer for 24 hrs with rotation to arrest their growth at the L1 stage. Synchronized animals were exposed to each stress when they were Day 0 young adult (day X represents days post-L4 molt). As for L1 arrest sample, embryos were prepared in a similar manner but incubated without food for 48 hrs.

extract_protocol: Total RNAs were prepared using the mirVana miRNA Isolation kit (Ambion), and 10 μg of total RNAs were used for cDNA library preparation for small RNAs using the DGE-Small RNA Sample Prep Kit ver. 1.0 (Illumina) according to the manufacturers' instructions.

treatment_protocol: Wild-type N2 young adults were exposed to each stress during Day 0 stage (day X represents days post-L4 molt), 6 hrs at 32 °C for heat shock treatment and 12 hrs for PA14 exposure. RNAs were purified from Day 1 stage animals just after stress treatment together with the untreated control. As for L1 arrest sample, prepared embryos were incubated without a food source in M9 buffer for 48 hrs, and then used for RNAs preparation.

tag: strain

value: wild-type N2_hermaphrodites

tag: developmental stage

value: Day1 post-L4 molt

tag: growth condition

value: 20 °C

tag: stress conditions

value: heat shock at 32 °C for 6 hrs


title: L1_arrest

source_name: wild-type L1 arrest

value: developmentally arrested L1

value: L1s without food for 48 hrs


title: shLuc.1309;ROSA-rtTA (-dox)

status: Public on Dec 01 2010

city: New York

first: Colin

middle: Dean

last: Malone

state: NY

address: NYUMC, Skirball Institute, 540 1st Ave, 4-10

department: Skirball Institute - Developmental Genetics

institute: NYU Medical Center

description: small RNA sequencing

data_processing: The 36nt long Illumina reads were stripped of the 3’ linker and the resulting small RNA sequences were mapped to the Release 9 genome. Only reads matching the mouse genome 100% were used for further analysis. For annotation, we used UCSC for non-coding RNAs and transposons/repeats (repeat masker tracks) and the most recent miRNA catalog. To control for sequencing depth, small RNA counts were normalized to the same total number after subtracting those matching abundant cellular RNAs such as rRNAs and tRNAs.

source_name: mouse embryonic fibroblasts (MEFs)

growth_protocol: 24 degrees C

extract_protocol: Trizol/Phenol Cholorofom extractions


title: shLuc.1309;ROSA-rtTA (+dox)

description: small RNA sequencing


title: tissue.H3K4me3.input

description: Input DNA.

tag: tissue

value: spleen

tag: sample type

tag: antibody


title: shLuc.1309 (+dox)

description: small RNA sequencing


title: shLuc.1309 (-dox)

description: small RNA sequencing


title: Control_Day1_wt

source_name: Day 1 wild-type young adult, untreated control

value: no stress treatment


title: PA14_Day1_wt

source_name: Day 1 wild-type young adult with PA14 exposure

value: PA14 exposure for 12 hrs


title: mRNA-Seq on dcl1-5 early globular embryos

city: Cambridge

first: Michael

middle: D

last: Nodine

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description:
polyA RNA
normalized dcl1 readNum (reads per million genome-matching reads in dcl1 library)

data_processing:
After removing adaptor sequences, sequences were mapped to the Arabidopsis thaliana genome (TAIR9 assembly) using the Bowtie short read aligner allowing up to two mismatches within a 25 nt ‘seed’ sequence and retaining reads mapping uniquely to the genome. Since the Arcuturus RiboAmp HS Plus kit generates amplified RNAs in the antisense orientation, reads were counted as matching TAIR9 annotated genes if they overlapped the antisense strand. To normalize for differences in library size, the number of reads matching each gene was divided by the total number of million genome-matching reads for each library.
Number of reads per million genome-matching reads overlapping indicated gene

organism: Arabidopsis thaliana

source_name: dcl1-5 embryos

growth_protocol: Plants were grown at 20° – 24° C in a growth room with a 16 hour light/8 hour dark cycle.

extract_protocol:
30 wild-type (Col-0) and 30 dcl1-5 early globular embryos were hand-dissected in water, immediately transferred to 30 ul of RNAlater (Ambion), incubated at 60° C with 500 ul TRIzol Reagent (Invitrogen) for 30 minutes, and then purified according to the TRIzol Reagent protocol for RNA isolation from small quantities of tissue (Invitrogen).
Two rounds of linear amplification of poly(A) RNA were performed using the Arcturus RiboAmp HS Plus kit (Molecular Devices). Strand-specific mRNA-Seq libraries were generated as previously described (Drinnenberg et al., Science, 2009).

value: embryos

value: early globular


title: cells.H3K4me3.input

description: Input DNA.

value: cells


title: [E-MTAB-305] heart RNA

description: Provider: TRON

source_name: heart RNA

extract_protocol:
nucleic_acid_extraction | We purchased total RNA from Ambion (Austin, USA). Each tissue samples was pooled from multiple donors. Librarys were prepared as in Armour CD, Castle JC, Chen R, Babak T, Loerch P, et al. (2009) Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nat Methods 6: 647-649.
sequencing | We generated an average of 50 million sequence reads per tissue using an Illumina GA-II sequencer, with sequence lengths of 36 nt (adipose, hypothalamus, liver) and 50 nt (colon, heart, kidney, lung, ovary, skeletal muscle, spleen, testes). We trimmed reads to a common length of 28 nt to avoid aligning sequenced amplification primers.

tag: material type

value: heart


title: tissue.H3K4me3.IP.rep1

description: Chromatin IP against H3K4me3.

source_name: Spleen FFPE sections of leukemic blasts-injected mice, H3K4me3 ChIP

value: tissue

tag: antibody vendor

value: Active Motif

tag: antibody catalog #

tag: antibody lot #


title: cells.H3K4me3.IP.rep1

description: Chromatin IP against H3K4me3.


title: tissue.H3K4me3.IP.rep2

description: Chromatin IP against H3K4me3.


title: mRNA-Seq on wild-type early globular embryos

description:
polyA RNA
normalized wild-type readNum (reads per million genome-matching reads in wild-type library)

source_name: Col-0 embryos


title: Adult_mRNA

city: Ithaca

first: Jacob

last: Crawford

address: 3130 Comstock Hall Cornell University

department: Entomology

institute: Cornell University

data_processing: Illumina CASAVA pipeline 1.6

organism: Anopheles funestus

source_name: Adult female carcass

extract_protocol: Total RNA extracted with Trizol under liquid Nitrogen.  Fragmented mRNA converted into cDNA with random primers.  Paired-end library preparation performed per Illumina specifications.  Fragments size selected to give an average insert size of 250bp.

value: CNRFP, Burkina Faso

value: whole organism

tag: gender

value: female


title: YY1

status: Public on Nov 30 2010

city: Duarte

first: Dustin

middle: E

last: Schones

state: CA

address: 1500 E Duarte Rd.

institute: City of Hope

description: Chromatin IP against YY1.

data_processing: Sequence reads were obtained and mapped to the human hg18 (NCBI Build 36; March 2006) genome using the Illumina Genome Analyzer Pipeline.  All reads aligning with two or fewer mismatches were retained for further analysis. Peak detection was performed with the SICER algorithm (http://home.gwu.edu/~wpeng/Software.htm).

source_name: CD4+ T cells, YY1 ChIP

growth_protocol: Human CD4+ T cells were isolated as described in Barski et al., Cell 2007 (PMID 17512414).

extract_protocol: Prior to ChIP experiments, cells were cross-linked with formaldehyde and sonicated to obtain DNA fragments ranging in size from 150-200bp. Library preparation was performed as described in Barski et al., Cell 2007 (PMID 17512414).

tag: cell type

value: CD4+ T cells

value: rabbit anti-YY1 polyclonal

value: Abcam


title: HMGN1

description:
Chromatin IP against HMGN1.
Antibody to purified HMGN1 (Bustin et al. (1978) J. Bio. Chem. 253, 1694 (PMID 75209)) were prepared in rabbits and affinity purified on HMGN1-containing sepharose as described in Bustin (1989) Methods in Enzymol. 170, 214 (PMID 2770539).

source_name: CD4+ T cells, HMGN1 ChIP

value: rabbit anti-HMGN1


title: EcR_WPP-4-5h_GFP_INPUT_2

status: Public on Nov 24 2010

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

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

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

organism: Drosophila melanogaster

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No Treatment

tag: fly

value: transgenic


title: Liver_PR (illumina)

city: Shanghai

first: Wenchao

last: Hu

address: 320 Yueyang Road

department: Functional Genomics Group

country: China

institute: CAS-MPG Partner Institute for Computational Biology

description: 18-30nt RNA in PR stage

library_source: synthetic

data_processing: Alignments: Extracted 30 nt sequences from the 5’ends of Illumina sequence reads. After removing sequences with low complexity, they were aligned to the thirteen-lined ground squirrel genome by MegaBLAST, allowing only perfect match for at least 18 nts extending from the 5’end. Results (aligned with Squirrel, Ensembl release 49) are link to GSE19807 as a supplementary file.

organism: Urocitellus parryii

source_name: Liver total RNA, PR stage

extract_protocol: Liver tissue samples from 14 AGS were used in this study including 4 early aroused animals (EA), 4 late torpid animals (LT), and 6 post-reproductive animals (PRA) as non-hibernating animals. Total RNA from each tissue sample was extracted using TRizol (Invitrogen) according to the manufacturer's instructions. Total RNA quality was assessed by Bioanalyzer 2100 (Agilent). Total RNA of arctic ground squirrels from the same stage were mixed in the equal amount into three pooled samples: EA, LT, and PRA. About 10 ug total RNA from each pooled samples was loaded onto a denaturing 15% polyacrylamide gel. The nucleotides from 18 to 30 nts in length were excised, and RNA was eluted for four hours with 0.3M NaCl at room temperature. The small RNAs were recovered by ethanol precipitation. The small RNAs were then ligated sequentially to 5' and 3' RNA/DNA chimeric oligonucleotide adapters (TCGTATGCCGTCTTCTGCTTGT). Reverse transcription was preformed after ligation with adapters, followed by 15 cycles PCR amplification. The resulting PCR products were sequenced following the Solexa Genome Analysis User Guide (Illumina, USA) with no modifications.

treatment_protocol: S. parryii was trapped during July near Toolik Lake (68°N 149°W, elevation 809 m) and transported to the University of Alaska Fairbanks. Animals were housed at 20±2°C with a 16:8-h light:dark photoperiod and provided with Mazuri Rodent Chow and water ad libitum. Hibernating animals were implanted with temperature sensitive radio transmitters and maintained at a 4:20-h photoperiod. Tb was monitored for precise stage of torpor and arousal by an automated telemetry system that measures and records Tb every 10 min. Animals were allowed to go through at least 4 multi-day torpor bouts and were euthanized by decapitation on day 4 of a torpor bout. As a non-hibernating control (NHC), we used post-reproductive summer euthermic animals. NHC animals were deeply anesthetized with iso-flurane and decapitated. Liver tissue was rapidly dissected, frozen in liquid N2 and stored at -80°C. Frozen tissues were transported to Shanghai, China on dry ice.

value: liver

tag: stage

value: post-reproduction


title: Liver_LT (illumina)

description: 18-30nt RNA in LT stage

source_name: Liver total RNA, LT stage

value: late topor


title: EcR_WPP-4-5h_GFP_INPUT_1


title: 7T_W3L_GFP_INPUT_3


title: 7T_W3L_GFP_INPUT_1


title: 7T_W3L_GFP_INPUT_2


title: EcR_WPP-4-5h_GFP_ChIPSeq_1 and 2

tag: antibody name

value: GFP

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: IgG

description: Control for IP with IgG antibody.

source_name: CD4+ T cells, control ChIP

value: normal rabbit IgG

value: Santa Cruz


title: 7T_W3L_GFP_ChIPSeq_1, 2 and 3

tag: developmental stage


title: ATRX_Mouse_ES_ChIPseq

status: Public on Nov 29 2010

city: Oxford

first: Richard

last: Gibbons

state: Oxon

address: John Radcliffe Hospital,

department: MRC Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine

description:
ATRX ChIP DNA
Genomic Coordinates of Peak Calls

data_processing: High throughput sequencing: The human erythroid ChIP-seq Illumina library was generated for ATRX ChIP and input DNA as described elsewhere (Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., et al. (2007). Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4, 651-657.) except that 35bp reads were used. A total of 9,051,677 human ATRX ChIP reads and 18,232,783 input reads were generated . Reads were filtered to remove matches to the human ribosomal gene loci and were then mapped to the Hg18 (NCBI36) human genome build, without repeatmasking, using MAQ software (Li, H., Ruan, J., and Durbin, R. (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18, 1851-1858.  Lipps, H.J., and Rhodes, D. (2009). G-quadruplex structures: in vivo evidence and function. Trends Cell Biol 19, 414-422.  ). Short DNA sequencing reads were mapped using mapping quality scores. High quality alignments (MAQ quality score q > 13) were used with a maximum of 1 mismatched base per read; a unique filter was also used to reject reads which mapped to the genome more than 3 times. 2,265,081 ChIP reads and 9,823,950 input reads aligned to the genome. Peaks were called using SWEMBL 3.3 (http://www.ebi.ac.uk/~swilder/SWEMBL/) (Wilder, S Manuscript in preparation) using the input sequence as reference with an empirically determined input correction penalty (1.75).  For the mouse ES cell ATRX ChIP-seq 51bp reads were used. A total of 42,550,172 ATRX ChIP reads  and 11,116,559 input reads were generated . Reads were mapped to the mm9 (NCBI37) mouse genome build without repeatmasking using Bowtie (Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25.) with –best, -strata and m -1 parameters. A unique filter was used to discard reads which mapped to the genome more than once. 22,426,377 ChIP reads and 4,251,942 input reads aligned to the genome. Peaks were called using Seqmonk v0.9 with a contig probe generator and the input sequence as a reference.  For both mouse and human data, peaks within 1 kb of an adjacent peak were merged into one.

source_name: Mouse Embryonic Stem Cells

extract_protocol: Protocol:  Chromatin Immunoprecipitation coupled with Microarray Analysis (ChIP-chIP):    I. Dynabead Preparation    -Make PBS/BSA   -For each ChIP reaction. Wash 100ul of beads 3-4 times with PBS BSA (5mg/ml)  -Transfer beads to a 500ul PCR tube.  -For ATRX antibody binding, Add 200ul ATRX H300, 22ul 50mg/ml BSA, 4ul ssDNA (Invitrogen 10mg/ml)  -For NoAb Rxn. Add 222ul PBS BSA 4ul ssDNA  -Incubate 3-4 hrs on roller at 4 oC  -Wash 4 times in PBS BSA  -Resuspend in 100ul PBSBSA and add 4ul (40ug) ssDNA      For each preclear reaction    -Take 100ul of Dynabeads  -Wash 3-4 times with 1ml PBS BSA (5mg/ml freshly prepared)  -Add 100ul of PBS BSA(5ug/ul)  -Add 4ul ssDNA (10ug/ul)  -Incubate at 4oC on roller with antibody binding reactions  -Use 100ul for each preclearing reaction         II. Cell cross-linking:     Need 4oC PBS, Formaldehyde, EGS 1M glycine, Trypan blue, gilsons, timer 1.5ml tubes, calculator,  A. Suspension Cells:    1. Make up EGS (Pierce 21565) stock fresh: 0.046g EGS in 200ul DMSO for 500mM stock  2. Chill PBS  3. Wash twice in PBS and resuspend in 20mls PBS (Important as FCS inhibits EGS)  4. Count cells  5. Use 3x107 – 5x107 cells for each ChIP reaction  6. Add EGS (it will form a white PPT which disperses afer a second) to 2mM and incubate at room temperature of 45 mins with occasional mixing. (80ul per 20mls of PBS).  7. Add formaldehyde solution to 1% for 20mins (526ul /20mls. 4 x 131.5ul)  8. Add 1/8 volume of 1M glycine to tubes to quench formaldehyde.(2.5ml glycine / 20ml PBS).  9. Spin cells at 1k for 5 min at 4oC. Make up protease inhibitors and add to lysis buffers.  10.Wash twice with 20ml 4oC PBS      III. Cell sonication (keep all steps on ice):  Note: Add protease inhibitors to all lysis buffers before use. If using a protease inhibitor cocktail tablet from Complete, dissolve one tablet in 2 ml water for 25X solution. Store aliquots at -20oC.    1. Resuspend each tube of cells in 10 ml of lysis buffer I. Rock at 4oC for 10 min, and then spin at 2k in a table-top centrifuge for 2 min at 4oC.   2. Resuspend each tube of cells in 5-10 ml of lysis buffer 2. Pellet nuclei in table-top centrifuge by spinning at 2.5k for 2 min at 4oC.  3. Resuspend the pellet in each tube in 3 ml lysis buffer 3. (Retain the buffer for step 6)  4. Sonicate the suspension in 15ml corning blue top tubes. 2mls per tube. Use the Bioruptor at high power for 20mins (4x5mins). After each 5 minute pulse, replenish the ice.  5. Add 1/10 volume of 10% Triton X-100. Transfer to 1.5 ml centrifuge tubes. Spin out debris at 14k for 10 min at 4oC. The lysate contains the fragmented DNA.  6. Save pellet for western analysis and take 50ul lysate for western analysis  7. Transfer lysate to 15 ml conical tube, adjusting the volume to 3 ml using lysis buffer 3.  8. Save 50µl of cell lysate from each sample as input. Save 50ul to assess sonication efficiency.    IV. Chromatin immunoprecipitation:   -Add 100ul of the preclearing beads from step I to the 3mls of chromatin lysate  -Preclear on roller at 4 oC for 1 hour  -Precipitate beads from chromatin using magnet and remove chromatin to new 3ml tubes  -Add the washed antibody bound beads from step 1  -Incubate overnight on roller at 4 oC      V. Washing, eluting, and reverse cross-linking:  Note: Carry steps 1-3 in the cold room and all wash solution must be ice cold.  1. Transfer lysates from the 3 ml tubes to a 1.5ml tube.  2. Wash the IPs 5 times with 1 ml wash buffer (be sure to add protease inhibitors to the wash buffer). Use the magnetic stand to precipitate the beads.   3. Wash once with 1 ml cold PBS. Aspirate residual PBS.  4. Add 250µl of elution buffer. Elute on a roller at room temperature for 15 minutes.  5. Add 250ul more of elution buffer to beads, vortex, precipitate and combine with previous round of elution.  6. Take 50ul of eluate for western blot analysis  7. PPT beads and remove eluate to a new tube. Add 20ul 5M NaCl and incubate at 65oC for 4 hours.  Thaw input, make up to 500ul with elution buffer, add 20ul 5M NaCl and incubate for 4hrs at 65oC.      VI. RNase, Proteinase K, Phenol/Chloroform, EtOH PPT:  Remove beads. Then add 20ul of 1M Tris pH6.5, 10ul 0.5M EDTA, 2ul 10mg/mg Proteinase K. Incubate for 1hrs at 45°C.    Phenol chloroform and EtOH PPT with 20ug of carrier glycogen. Resuspend in 21ul sigma water. Use low volume to give the option of labelling for ChIP on Chip. For real time PCR, use 1/12 ul per reaction      Solutions    PBS BSA 5mg/ml  For 50mls: 5mls 10XPBS, 250mg BSA Fraction V, Filter sterilise. Make up fresh every time.    Lysis Buffer 1 (100 ml):        100mM HEPES  140mM NaCl  1mM EDTA  10% Glycerol  0.5% NP40  0.25% Triton X    Lysis Buffer 2 (100 ml):   200mM NaCl  1mM EDTA  0.5mM EGTA  10mM Tris pH 8    Lysis Buffer 3 (100 ml):   1mM EDTA  0.5mM EGTA  1mMTris-HCl pH8  100mM NaCl  0.1% Na DOC  0.5% N-lauroyl Sarcosine    Wash buffer (RIPA Buffer, 100 ml):   50mM Hepes, pH 7.6  1mM EDTA  0.7% Na DOC  1% NP40  500mM LiCl

value: Mouse Embryonic Stem Cells

tag: strain

value: ATRX H300 (Santa Cruz Biotechnology, batch G0105)

tag: cell passage


title: E0-8h_D_KW3-D-D2_ChIPSeq_1 and 2


title: ATRX_Human_Erythroid_CHIPseq

source_name: Human Cultured Primary Erythroblasts

growth_protocol: Basic Protocol 1: Preparation of Peripheral Blood Mononuclear Cells for Erythroid Cultures    Cultures can be initiated with cells derived from a whole unit of blood obtained from normal donors (or polycythemic patients undergoing phlebotomy). The starting material, i.e., the “buffy-coat” fraction, is readily available, since it is routinely separated and discarded by the blood bank during preparation of packed red blood cells (RBC) and platelet-rich plasma. Anemic patients commonly show high frequencies of erythroid progenitors; cultures from anemic patients (e.g., thalassemia, sickle cell anemia) are usually initiated with cells derived from ~20 ml peripheral blood.   Materials        *        Peripheral blood or buffy coat fraction      *        Phosphate-buffered saline (PBS), pH 7.4 (appendix 2A)      *        Ficoll-Hypaque (density = 1.077 g/ml)        *        15- or 50-ml centrifuge tubes      *        Centrifuge       1.     Dilute peripheral blood or the buffy coat fraction 1:1 (v/v) with PBS. Gently layer on top of a layer of Ficoll-Hypaque such that the Ficoll-Hypaque layer constitutes one-third of the total volume.    Depending on the blood volume, use either 15- or 50-ml tubes.    For convenience, tubes (available from Sigma) containing a special grid that separates the blood from the Ficoll can be used.   2.     Centrifuge 20 min at 400 × g, at room temperature. Do not apply the brake.   3.     Aspirate off the top layer (consisting of plasma and platelets), collect the interphase layer of mononuclear cells with a pipet, and transfer to a 50-ml tube.   4.     Add 40 ml PBS, mix, then centrifuge 5 min at 160 × g, room temperature. Aspirate the supernatant, then resuspend the pellet in the residual buffer by tapping.   5.     Add 40 ml PBS, mix, then centrifuge 5 min at 100 × g, room temperature, and aspirate the supernatant. Repeat this procedure for an additional wash.    Use low-speed centrifugation in order to remove residual platelets.    All procedures should be performed at room temperature. If the blood cannot be processed on the same day, leave overnight at room temperature.    In experiments where Hb content is measured, special care has to be taken to avoid contamination by mature RBC that originated from the processed blood. This does not usually present a problem when normal blood is processed, but may occur with blood derived from patients, e.g., with thalassemia. The contaminating RBCs can be of patient origin and/or derived from transfused blood. In both cases, they may interfere with measurement of the Hb produced in vitro. When the interphase layer is heavily contaminated with RBC, the latter cells should be removed by osmotic hemolysis (see Support Protocol 6) prior to culturing. When only slightly contaminated, the mononuclear cells may be cultured without hemolysis; RBC tend to lyse and disappear during culture. Alternatively, they may be removed by Percoll separation at the second phase of the culture (see Support Protocol 7).  [Top of Page]     Basic Protocol 2: Erythroid Cell Culture Procedure    The culture procedure is divided into two phases. The first is an EPO-independent phase in which peripheral blood mononuclear cells are isolated (described in Basic Protocol 1) and cultured in the presence of a combination of growth factors, but in the absence of EPO. During this phase, early erythroid-committed progenitors, called burst-forming units erythroid (BFUe), proliferate and differentiate into colony-forming unit erythroid (CFUe)–like progenitors. In the second phase, these cells, cultured in an EPO-supplemented medium, continue to proliferate and mature into orthochromatic normoblasts and enucleated erythrocytes.   Materials        *        Complete MEM medium (see recipe)      *        Preselected FBS (see recipe); do not heat-inactivate      *        50 mg/ml cyclosporin A (Sandoz)      *        Conditioned medium from 5637 human bladder carcinoma cell line (see recipe)      *        Mononuclear cells, washed (see Basic Protocol 1)      *        10% (w/v) deionized BSA (see recipe)      *        2-mercaptoethanol (Sigma)      *        4 mg/ml dexamethasone sodium phosphate (Elkin-Sinn Pharmaceuticals, Cherry Hill N.J.)      *        Human holo-transferrin (Sigma)      *        Human recombinant stem cell factor (CytoLab Ltd.; http://www.cytolab.com/)      *        Human recombinant erythropoietin (EPO; Ortho Pharmaceutical)        *        25- or 75-cm2 tissue culture flasks       1.     Prepare Phase I medium by adding the following ingredients to complete MEM medium:        *        10% (v/v) preselected FBS (not heat-inactivated)      *        1 µg/ml cyclosporin A (add from 50 mg/ml stock)      *        10% (v/v) conditioned medium from 5637 human bladder carcinoma cell line.     2a.     For cells obtained from peripheral blood (10 to 20 ml): Plate the washed mononuclear cells in Phase I medium in 25-cm2 flasks at a culture volume equivalent to the original volume of blood.   2b.     In the case of cells obtained from a whole blood unit (400 to 500 ml): Plate the washed mononuclear cells in Phase I medium in two 75-cm2 flasks at a culture volume of 80 to 100 ml.   3.     Incubate the cultures at 37°C in a humidified, 5% CO2 incubator for 5 to 7 days.    Full humidification is achieved by leaving a tray with water standing at the bottom of the incubator.   4.     After the 5- to 7-day incubation in phase I, shake the cultures and harvest the nonadherent cells (do not trypsinize).   5.     Centrifuge the cells 5 min at 160 × g, room temperature, and aspirate the supernatant. Fill the tube with complete MEM, centrifuge 5 min at 160 × g, room temperature, and aspirate the supernatant. Repeat for a second wash.   6.     Prepare Phase II medium by adding the following ingredients to complete MEM medium:        *        30% (v/v) preselected FBS (not heat-inactivated)      *        1% (w/v) deionized BSA (add from 10% w/v stock)      *        10–5 M 2-mercaptoethanol      *        10–6 dexamethasone (add from 4 mg/ml stock)      *        0.3 mg/ml human holo-transferrin      *        10 ng/ml human recombinant stem cell factor      *        1 U/ml human erythropoietin (EPO).     7.     Plate cells in the original volume of phase II medium (as in step 2a or 2b according to the original blood volume) and incubate up to 14 days at 37°C in a humidified, 5% CO2, incubator.

value: Human Cultured Primary Erythroblasts


title: HP1-Abcam_Covance_INPUT_1


title: KW3-Trl-D2_INPUT_1


title: KW4-Hr39-D1_INPUT_1


title: Trem_ChIPSeq_1 and 2

source_name: Adult-Female

value: Adult-Female

value: Trem

value: Hawley Lab - Cathleen Lake


title: Liver_EA (illumina)

description: 18-30nt RNA in EA stage

source_name: Liver total RNA, EA stage

tag: tissue

value: early arousal


title: KW3-Trl-D2_ChIPSeq_1 and 2


title: HP1-Covance_ChIPSeq_1

value: Covance


title: KW4-Hr39-D1_ChIPSeq_1 and 2

value: iso1 (y; bw cn sp)


title: HP1-Abcam_ChIPSeq_1 and 2

value: Abcam


title: 15T_8-16_NW_GFP_ChIPSeq_1 and 2

value: transgenic


title: Trem_INPUT_1


title: ATRX_Human_Erythroid_Input

description: Input DNA

tag: antibody


title: 15T_8-16_NW_GFP_INPUT_1


title: macrophage_p65_LPS_ChIPSeq_1

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: Chromatin IP against p65 + LPS

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (July, 2007) 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 to create summary windows.
Peaks: Peak detection was performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).

source_name: primary bone marrow-derived macrophages

growth_protocol: Bone marrow was purified and differentiated in DMEM containing 20% fetal bovine serum, 30% L929 conditioned media, and antibiotics for 5 days, then re-plated in macrophage serum free media (Invitrogen) overnight.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the ChIP seq sample prep kit (IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were fixed with 2 mM disuccinimidyl glutarate for 30 minutes, then with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested.

value: primary bone marrow-derived macrophages

tag: treatment

value: 3 hr LPS stimulated macrophages

tag: donor age

value: 10 month old male

tag: chip antibody


title: macrophage_p65_LPS_ChIPSeq_2

description: Chromatin IP against p65 + LPS


title: macrophage_BCL6_LPS_ChIPSeq_2

description: Chromatin IP against BCL6 + LPS


title: macrophage_BCL6_LPS_ChIPSeq_1

description: Chromatin IP against BCL6 + LPS


title: macrophage_BCL6_ChIPSeq

description:
Chromatin IP against BCL6
processed data file (alignment): s_3_export.txt
processed data file (peaks): Bcl6_peaks.txt
raw data file: s_3_traces.srf

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (July 2007; mm9, NCBI Build 37) 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 to create summary windows.
Peaks: Peak detection was performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).

value: unstimulated macrophages


title: macrophage_IgG_ChIPSeq

description:
Chromatin IP against rabbit IgG
processed data file (alignment): s_1_export.txt
processed data file (peaks): s_1_peaks.txt
raw data file: s_1_traces.srf

value: IgG


title: macrophage_p65_ChIPSeq

description: Chromatin IP against p65 + LPS


title: macrophage_Pol_II_ChIPSeq

description:
Chromatin IP against Pol II
processed data file (alignment): s_2_export.txt
processed data file (peaks): s_2_peaks.txt
raw data file: s_2_traces.srf


title: macrophage_input_DNA

description:
Input control DNA
processed data file (alignment): s_4_export.txt
processed data file (peaks): s_4_peaks.txt
raw data file: s_4_traces.srf

value: n/a (input_DNA)


title: S2-DRSC-CG9412-RNAi-2

status: Public on Nov 20 2010

city: Farmington

first: Brenton

middle: R

last: Graveley

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

description:
dsRNA treatment: CG9412
read length: 76
library_source: RNA
library_selection: RT and size selection

data_processing: Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

growth_protocol: Schneider's medium + 10% heat-inactivated FCS

extract_protocol:
Oligo-dT selected, double stranded cDNA, Single Read Sequencing
TRIzol Dnase Rneasy

treatment_protocol: Cells were treated with dsRNA to the indicated gene

tag: cell line


title: S2-DRSC-CG9412-RNAi-1


title: S2-DRSC-CG8912-RNAi-2

description:
dsRNA treatment: CG8912
read length: 76
read length: 76
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG8749-RNAi-2

description:
dsRNA treatment: CG8749
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG8781-RNAi-1

description:
dsRNA treatment: CG8781
read length: 78
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG8781-RNAi-2


title: S2-DRSC-CG8636-RNAi-2

description:
dsRNA treatment: CG8636
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG8912-RNAi-1

description:
dsRNA treatment: CG8912
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG7971-RNAi-2

description:
dsRNA treatment: CG7971
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG6946-RNAi-2

description:
dsRNA treatment: CG6946
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG9983-RNAi-2

description:
dsRNA treatment: CG9983
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG8019_RNAi-1

description:
dsRNA treatment: CG8019
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG8749-RNAi-1


title: S2-DRSC-CG7437-RNAi-2

description:
dsRNA treatment: CG7437
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG8636-RNAi-1

description:
dsRNA treatment: CG8636
read length: 78
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG9373-RNAi-2

description:
dsRNA treatment: CG9373
read length: 76
read length: 80
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG6841_RNAi-1

description:
dsRNA treatment: CG6841
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG8019_RNAi-2


title: S2-DRSC-CG8241_RNAi-1

description:
dsRNA treatment: CG8241
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG6841_RNAi-2


title: S2-DRSC-CG6227_RNAi-2

description:
dsRNA treatment: CG6227
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG6227_RNAi-1


title: S2-DRSC-CG6203-RNAi-2

description:
dsRNA treatment: CG6203
read length: 76
library_source: RNA
library_selection: RT and size selection


title: smRNA_rdr6_2

status: Public on Nov 22 2010

first: Thomas

middle: James

last: Hardcastle

address: Downing Street

department: Plant Sciences

institute: University of Cambridge

description: library_source: Other

data_processing: Adaptor removal was performed with regexp matching. Only perfect matches to the nuclear Arabidopsis thaliana genome as defined by TAIR as identified by the 'patman' program were selected in the fasta files.

source_name: rdr6-15 knockout

extract_protocol: AGO1 immunoprecipitation, following which small RNA extraction by Trizol reagent following manufacturer's protocol

tag: ecotype

value: Whole aerial parts (leaf tissue)


title: smRNA_wt_1

description: library_source: Other

source_name: wildtype


title: smRNA_wt_2

description: library_source: Other


title: S2-DRSC-CG6203-RNAi-1


title: smRNA_rdr6_1

description: library_source: Other


title: S2-DRSC-CG5836-RNAi-2

description:
dsRNA treatment: CG5836
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG5655-RNAi-2

description:
dsRNA treatment: CG5655
read length: 76
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG6049-RNAi-2

description:
dsRNA treatment: CG6049
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG5442-RNAi-2

description:
dsRNA treatment: CG5442
read length: 76
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG5442_RNAi-1

description:
dsRNA treatment: CG5442
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG5821-RNAi-2

description:
dsRNA treatment: CG5821
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG5170-RNAi-1

description:
dsRNA treatment: CG5170
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG4878-RNAi-1

description:
dsRNA treatment: CG4878
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG4816_RNAi-1

description:
dsRNA treatment: CG4816
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG5170-RNAi-2


title: S2-DRSC-CG5099-RNAi-2

description:
dsRNA treatment: CG5099
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG4816_RNAi-2


title: S2-DRSC-CG4760_RNAi-1

description:
dsRNA treatment: CG4760
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG4262_RNAi-2

description:
dsRNA treatment: CG4262
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG4760_RNAi-2


title: S2-DRSC-CG4602-RNAi-2

description:
dsRNA treatment: CG4602
read length: 76
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG4262_RNAi-1


title: S2-DRSC-CG3584_RNAi-2

description:
dsRNA treatment: CG3584
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG6049-RNAi-1


title: S2-DRSC-CG3584_RNAi-1


title: S2-DRSC-CG3312_RNAi-1

description:
dsRNA treatment: CG3312
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG5422_RNAi-2

description:
dsRNA treatment: CG5422
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG3312_RNAi-2


title: S2-DRSC-CG4878-RNAi-2


title: TM-1 fiber_10DPA_rep1

status: Public on Dec 03 2010

city: Wuhan

first: Xianlong

last: Zhang

address: No.1,Shizishan Street · Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

data_processing: To get high-quality total clean reads, low-quality reads, including 5' and 3' adapter contaminants, were removed from total reads. Unique clean reads (non-redundant total clean reads) were matched to the Rfam database (ftp://ftp.sanger.ac.uk/pub/databases/Rfam/9.0) with the short oligonucleotide analysis package (SOAP; http://soap.genomics.org.cn) [12]. rRNA, tRNA, snRNA, and snoRNA were identified and removed. Unique clean reads were mapped to plant miRNA sequences in miRBase Release 12.0 (http://microrna.sanger.ac.uk/seguence/index.html) [13] with SOAP to reveal the potential conserved miRNAs in our libraries. The TIGR cotton transcript assemblies (TAs) sequences (ftp://ftp.tigr.org/pub/data/plantta/Gossypium_hirsutum/) were used for BlastX at the NCBI non-redundant protein sequence library (E value: 10–5). Non-homologous TAs were considered to be non-coding TAs. By mapping clean unique reads to the non-coding TA sequences with SOAP, the unknown miRNA mapped reads were chosen for the prediction of candidate-novel pre-miRNAs by the MIREAP tool (https://sourceforge.net/projects/mireap/).

organism: Gossypium hirsutum

source_name: cotton fiber cells

growth_protocol: Gossypium barbadense cv. 3-79 and G. hirsutum cv. TM-1 plants were cultivated in an experimental field (Wuhan, Hubei, PR China) using normal farming practices.

extract_protocol: Fibers at 10 DPA were detached carefully from ovules and immediately immersed in liquid nitrogen. Total RNA was isolated from the collected tissues. The small RNA fraction was isolated from 15% denaturing polyacrylamide gel and then ligated to adaptors. The short RNA was converted to DNA by RT-PCR, and the DNA was sequenced on a Solexa machine (Illumina) in BGI-Shenzhen.

tag: cultivar

value: fiber

value: 10 days post-anthesis (DPA)


title: S2-DRSC-CG32423-RNAi-2

description:
dsRNA treatment: CG32423
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG33106-RNAi-1

description:
dsRNA treatment: CG33106
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG33106-RNAi-2


title: S2-DRSC-CG32423-RNAi-1

description:
dsRNA treatment: CG32423
read length: 78
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG31716-RNAi-1

description:
dsRNA treatment: CG31716
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG31716-RNAi-2


title: S2-DRSC-CG31000-RNAi-2

description:
dsRNA treatment: CG31000
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG30122-RNAi-2

description:
dsRNA treatment: CG30122
read length: 76
read length: 80
library_source: RNA
library_selection: RT and size selection


title: 3-79 fiber_10DPA_rep1

organism: Gossypium barbadense


title: S2-DRSC-CG16901-RNAi-2

description:
dsRNA treatment: CG16901
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG18350_RNAi-1

description:
dsRNA treatment: CG18350
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG17838-RNAi-2

description:
dsRNA treatment: CG17838
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG18426-RNAi-2

description:
dsRNA treatment: CG18426
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG18350_RNAi-2

description:
dsRNA treatment: CG18350
read length: 78
read length: 76
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG17136-RNAi-2

description:
dsRNA treatment: CG17136
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG16788-RNAi-2

description:
dsRNA treatment: CG16788
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG1646_RNAi-1

description:
dsRNA treatment: CG1646
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG1646_RNAi-2

description:
dsRNA treatment: CG1646
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG13425_RNAi-2

description:
dsRNA treatment: CG13425
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG11266-RNAi-1

description:
dsRNA treatment: CG11266
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG1101-RNAi-2

description:
dsRNA treatment: CG1101
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG11266-RNAi-2


title: S2-DRSC-CG10851-RNAi-2

description:
dsRNA treatment: CG10851
read length: 76
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG12749-RNAi-2

description:
dsRNA treatment: CG12749
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG10377_RNAi-2

description:
dsRNA treatment: CG10377
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG10328_RNAi-2

description:
dsRNA treatment: CG10328
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG1987-RNAi-2

description:
dsRNA treatment: CG1987
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG10328_RNAi-1


title: S2-DRSC-CG10203-RNAi-2

description:
dsRNA treatment: CG10203
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG10279_RNAi-1

description:
dsRNA treatment: CG10279
read length: 80
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG1559-RNAi-2

description:
dsRNA treatment: CG1559
read length: 76
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG10128-RNAi-2

description:
dsRNA treatment: CG10128
read length: 76
read length: 76
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG10279_RNAi-2

description:
dsRNA treatment: CG10279
read length: 80
read length: 80
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_Untreated_RNAi-32

description:
dsRNA treatment: Untreated
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_Untreated_RNAi-31

description:
dsRNA treatment: Untreated
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG16788-RNAi-1

description:
dsRNA treatment: CG16788
read length: 78
library_source: RNA
library_selection: RT and size selection


title: S2-DRSC-CG1101-RNAi-1


title: NHEK_CHIP_CTCF

status: Public on Nov 18 2010

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 5022 Genetic Medicine Building, CB#7264

department: Genetics

institute: UNC-Chapel Hill

description: Chromatin IP against CTCF

data_processing: Sequences from each experiment were aligned to the genome using Maq (Li et al., 2008) and those that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes). The resulting digital signal was converted to a continuous wiggle track using F-Seq (http://www.genome.duke.edu/labs/furey/software/fseq/) that employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Discrete sites (peaks) were identified from ChIP-seq using by setting a F-Seq score cutoff based on fitting these data to a gamma distribution and determining the threshold at a p-value of 0.05.

source_name: normal human epidermal keratinocytes

growth_protocol: Cells were grown according to the approved ENCODE cell culture protocols.Specific protocol descriptions can be found at http://genome.ucsc.edu/ENCODE/cellTypes.html.

extract_protocol:
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
To perform ChIP, proteins were cross-linked to DNA in vivo using 1% formaldehyde solution (Bhinge et al., 2007, ENCODE Project Consortium., 2007). Cross-linked chromatin was sheared by sonication and immunoprecipitated using a specific antibody against the protein of interest. After reversal of the cross-links, the immunoprecipitated DNA was used to identify the genomic location of transcription factor binding. This was accomplished by Solexa sequencing of the ends of the immunoprecipitated DNA (ChIP-seq), as well as labeling and hybridization of the immunoprecipitated DNA to NimbleGen Human ENCODE tiling arrays (1% of the genome) along with the input DNA as reference (ChIP-chip). The ENCODE array data were used to verify the accuracy of the sequencing data, and multiple independent growths (replicates) were compared to assess the reproducibility of the data

value: NHEK

value: rabbit polyclonal antibody

tag: vendor

value: Millipore

tag: cataog number

tag: lot number


title: K562_CHIP_CTCF

description: Chromatin IP against CTCF

source_name: chronic myeloid leukemia


title: H1_ES_CHIP_CTCF

description: Chromatin IP against CTCF

source_name: human embryonic stem cells


title: K562_DNASE

description: Dnase-seq

data_processing: Sequences from each experiment were aligned to the genome using Maq (Li et al., 2008) and those that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes). The resulting digital signal was converted to a continuous wiggle track using F-Seq (http://www.genome.duke.edu/labs/furey/software/fseq/) that employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Discrete sites (peaks) were identified from DNase-seq using by setting a F-Seq score cutoff based on fitting these data to a gamma distribution and determining the threshold at a p-value of 0.05.

extract_protocol:
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
DNaseI hypersensitive sites were isolated using methods called DNase-seq or DNase-chip (Boyle et al., 2008a, Crawford et al., 2006). Briefly, cells were lysed with NP40, and intact nuclei were digested with optimal levels of DNaseI enzyme. DNaseI digested ends were captured from three different DNase concentrations, and material was sequenced using Illumina (Solexa) sequencing. DNase-seq data were verified using material that was hybridized to NimbleGen Human ENCODE tiling arrays (1% of the genome). Multiple independent growths (replicates) were compared to verify the reproducibility of the data.


title: HUVEC_DNASE

description: Dnase-seq

source_name: umbilical vein endothelial cells

value: HUVEC


title: HelaS3_CHIP_CTCF

description: Chromatin IP against CTCF

source_name: cervical carcinoma


title: HelaS3_DNASE

description: Dnase-seq


title: S2-DRSC-CG10377_RNAi-1


title: GM18507_DNASE

description: Dnase-seq

source_name: lymphoblastoid cells

tag: individual


title: HNF4A ChIP-seq in differentiated cells

status: Public on Nov 17 2010

city: Piscataway

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

institute: Rutgers, the State University of New Jersey

description: chromatin IP against HNF4 in differentiated cells

data_processing: ChIP-Seq: ELAND mapping (hg18) + MACS for CDX2, HNF4, and GATA6 ChIP-Seq data. ELAND mapping (hg18) + NPS for H3K4me2 Mnase ChIP-Seq data.

source_name: differentiated Caco-2 cells

growth_protocol: for ChIP-seq experiments, Caco-2 cells were grown in 10% FBS DMEM and passaged frequently for subconfluent cells or fed every second day for post-confluent "differentiated" cells.  Cells were harvested at 50% confluence (proliferating) or 26 days post-confluent (differentiated)

extract_protocol: Libraries were constructed using 10 ng each of ChIP and input DNA from up to 3 pooled experiments were processed for deep sequencing according to manufacturer’s instructions (Illumina). Prior to sequencing, qPCR was used to verify that positive and negative control ChIP regions amplified in the linear range.

treatment_protocol: For transcription factor ChIP, cells were fixed in 1% formaldehyde for 10 minutes at 37 degrees, then washed with cold PBS and scraped into PBS, and resuspended in ChIP lysis buffer and immunoprecipitated and processed as described by Carroll, et al, 2005, PMID: 16009131 and as described in our current work. Antibodies used were CDX2 (Bethyl BL3194), GATA6 c-20 (Santa Cruz 7244), GATA6 h-92 (Santa Cruz 9055), HNF4α c-19 (Santa Cruz 6556) or HNF4α h-171 (Santa Cruz 8987).  For H3K4me2 ChIP, cells were collected in a digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, 5 mM Na butyrate, complete protease inhibitors) and treated with 0.2 U micrococcal nuclease (MNase, Sigma Aldrich) for 8 min at 37°C. The reaction was terminated by adding 5 mM EDTA in 10 mM Tris, pH7.6, and samples were dialyzed in chromatin RIPA buffer (10 mM Tris, pH7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na deoxycholate, 1% Triton X-100) before overnight IP at 4oC with Histone H3K27Ac (Abcam ab4729) or H3K4Me2 (Millipore 07-030) antibodies. IP material was subsequently handled as described below for conventional ChIP of sonicated genomic DNA.

tag: cell type

value: human intestinal cell line

value: HNF4A (Santa Cruz 8987 and Santa Cruz 6556)


title: HNF4A ChIP-seq in proliferating cells

description: chromatin IP against HNF4 in proliferating cells

source_name: proliferating Caco-2 cells


title: Caco2 cell input DNA

description: sonicated input DNA fragments


title: GATA6 ChIP-seq in proliferating cells

description: chromatin IP against GATA6 in proliferating cells

value: GATA6 (Santa Cruz 7244 and Santa Cruz 9055)


title: H3K4me2 in differentated cells

description: chromatin IP against H3K4me2 in differentiated cells

value: H3K4me2 (Millipore 07-030)


title: GATA6 ChIP-seq in differentiated cells

description: chromatin IP against GATA6 in differentiated cells


title: H3K4me2 in proliferating cells

description: chromatin IP against H3K4me2 in proliferating cells


title: CDX2 ChIP-seq in proliferating cells

description: chromatin IP against CDX2 in proliferating cells

value: CDX2 (Bethyl Labs BL3194)


title: HUVEC_CHIP_CTCF

description: Chromatin IP against CTCF


title: NHEK_DNASE

description: Dnase-seq


title: H1_ES_DNASE

description: Dnase-seq


title: NA19239: HapMap DNase Seq 7

status: Public on Nov 15 2010

middle: F

last: Degner

department: Human Genetics

description: Reads for one lane of Illumina GA flowcell for individual NA19239

data_processing: Read mapping: We used the raw sequencing reads, trimmed them to 20 bp (see DNase protocol), and mapped them on the human reference genome (hg18) using BWA (using the default settings). Then we ﬁltered out the reads with quality score < 10 or that mapped to more than one location in the genome. For reads obtained using the DNase-seq protocol, since their length is limited to 20bp, we further removed all reads that contained an insertion/deletion or that had more than one mismatch with respect to hg18. The aligned reads of multiple experimental replicates on the same cell-line type were combined into a single ﬁle for analysis.

growth_protocol: 37o in RPMI

extract_protocol: DNase seq protocol (Boyle et al. 2008) (see attached supplementary file: Duke_DNase_protocol.pdf)

value: lymphoblastoid cell line

tag: origin

value: Yoruba from Ibadan, Nigeria (YRI)


title: NA19239: HapMap DNase Seq 8


title: NA18507: HapMap DNase Seq 8

description: Reads for one lane of Illumina GA flowcell for individual NA18507


title: NA19239: HapMap DNase Seq 2


title: NA19239: HapMap DNase Seq 5


title: NA19239: HapMap DNase Seq 3


title: NA18507: HapMap DNase Seq 7


title: NA19239: HapMap DNase Seq 4


title: H3K27me3_K562_ChIP-seq_rep2

city: Palo Alto

first: Philip

last: Cayting

address: 1501 S California Ave

institute: Stanford University

description: Chromatin IP against H3K27me3

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome assembly hg18 (March, 2006) or hg19 (February, 2009) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks were called with Sole-Search (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi)

source_name: chronic myeloid leukemia cell line

growth_protocol: All cells were grown according to ENCODE standards (http://genomewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines)

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: harvest date

value: CST monoclonal rabbit rabbit anti-H3K27me3

tag: lot#


title: NA19239: HapMap DNase Seq 1


title: H3K4me3_K562_ChIP-seq_rep2

description: Chromatin IP against H3K4me3

value: CST monoclonal rabbit anti-H3K4me3


title: H3K27me3_K562_ChIP-seq_rep1

description: Chromatin IP against H3K27me3


title: CDX2 ChIP-seq in differentiated cells

description: chromatin IP against CDX2 in differentiated cells


title: input_genomic_rep1

status: Public on Nov 16 2010

city: Bethesda

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

description: Input DNA.

data_processing:
Alignment: Sequence reads were obtained and mapped to the human hg18 (March, 2006) genome using the Illumina Genome Analyzer Pipeline v 1.5. All quality-filtered reads mapping with two or fewer mismatches were retained.

Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).  Adjacent peaks separated by less than the half-width of the wider peak were merged.

source_name: HeLa cell culture, input

extract_protocol: DNA fragments from 200-500 bp were generated by sonication. p68 antibodies were incubated with Dynabeads G (Invitrogen) with rotation at room temperature for 20 mins. Chromatin preparations were then incubated with the complex of antibody-magnetic beads overnight at 4°C. Immune complexes were washed with low salt buffer, high salt buffer, LiCl buffer and TE buffer two times each.  We generated a ChIP-seq library by using the ChIP-seq kit from Illlumina (P/N: 1003473). Briefly, we used 20 ng of ChIP DNA or input DNA, repaired DNA ends to generate blunt-ended DNA and purified repaired DNA using the QIAGEN PCR purification kit (Cat. No: 28104). Then we added A bases to the blunt-ended DNA fragments using Klenow Fragment and purified DNA using the QIAGEN MinElute PCR purification kit (Cat. No: 28004). We ligated adapters to DNA fragments by incubating with T4 DNA ligase for 4 hrs at 16°C followed by 30 mins at room temperature. After that, we purified adaptor-ligated DNA fragments with the QIAGEN MinElute PCR purification kit. We did size selection by cutting the DNA fragments with sizes between 200-400bp from a 2% agarose gel and purified the DNA using a gel extraction kit (Cat. No: 28604). We performed 18 cycles of PCR with Illumina/Solexa primers 1.1 and 2.1, checked the fragment size of our amplified library on an agarose gel, and purified the remaining ChIP-seq library by gel purification to generate libraries for Solexa sequencing.

value: HeLa S3


title: NA18507: HapMap DNase Seq 6


title: p68_genomic_rep1

description: Chromatin IP against p68.

source_name: HeLa cell culture, p68 ChIP

tag: antibody vendor

value: abcam

tag: antibody catalog #

tag: antibody lot #


title: H3K4me3_K562_ChIP-seq_rep1

description: Chromatin IP against H3K4me3


title: NA18507: HapMap DNase Seq 4


title: NA18507: HapMap DNase Seq 3


title: ELK4_HeLa_ChIP-seq_rep1

description: Chromatin IP against ELK4 (Sap1a)

value: Santa Cruzi rabbit anti Sap-1a

value: Santa Cruz Biotechnology

tag: catalog#


title: NA18507: HapMap DNase Seq 5


title: NA18507: HapMap DNase Seq 2


title: TR4_HeLa_ChIP-seq_rep2

description: Chromatin IP against TR4

value: rabbit anti TR4 (JD Engel lab)


title: ELK4_HeLa_ChIP-seq_rep2

description: Chromatin IP against ELK4 (Sap1a)


title: NA19239: HapMap DNase Seq 6


title: ELK1_HeLa_ChIP-seq_rep1

description: Chromatin IP against ELK1

value: Epitomics monoclonal rabbit anti ELK1


title: TR4_HeLa_ChIP-seq_rep1

description: Chromatin IP against TR4


title: NA18507: HapMap DNase Seq 1


title: TR4_GM_ChIP-seq_rep1

description: Chromatin IP against TR4

source_name: lymphoblastoid cell line


title: TR4_GM_ChIP-seq_rep2

description: Chromatin IP against TR4


title: TR4_HepG2_ChIP-seq_rep2

description: Chromatin IP against TR4

source_name: hepatocellular carcinoma


title: TR4_K562_ChIP-seq_rep2

description: Chromatin IP against TR4


title: TR4_K562_ChIP-seq_rep1

description: Chromatin IP against TR4


title: KAP1_K562_ChIP-seq_rep1

description: Chromatin IP against KAP1

value: abcam goat anti-KAP1

value: Abcam


title: KAP1_K562_ChIP-seq_rep2

description: Chromatin IP against KAP1


title: H3K9me3_K562_ChIP-seq_rep1

description: Chromatin IP against H3K9me3

value: CST rabbit anti-H3K9me3

value: Cell Signaling Technology


title: H3K9me3_K562_ChIP-seq_rep2

description: Chromatin IP against H3K9me3


title: TR4_HepG2_ChIP-seq_rep1a

description: Chromatin IP against TR4


title: SetDB1_K562_ChIP-seq_rep1

description: Chromatin IP against SetDB1

value: Proteintech group rabbit anti-SetDB1

value: Proteintech Group


title: SetDB1_K562_ChIP-seq_rep2

description: Chromatin IP against SetDB1


title: ZNF274_GM12878_ChIP-seq_rep1

description: Chromatin IP against ZNF274

source_name: lymphoblast cells

value: abnova mouse polyclonal anti-ZNF274

value: Abnova


title: ZNF274_GM12878_ChIP-seq_rep2

description: Chromatin IP against ZNF274


title: ZNF274_HelaS3_ChIP-seq_rep2

description: Chromatin IP against ZNF274


title: ZNF274_HelaS3_ChIP-seq_rep1

description: Chromatin IP against ZNF274


title: ZNF274_HepG2_ChIP-seq_rep2

description: Chromatin IP against ZNF274


title: ZNF274_K562_ChIP-seq_rep1

description: Chromatin IP against ZNF274


title: ZNF274_K562_ChIP-seq_rep2

description: Chromatin IP against ZNF274


title: ChIP-Seq analysis of H3K27me3 in human fetal heart cells; Lib:XZ:20100129:20--ChIP:XZ:20100125:20:fetal heart:H3K27me3

status: Public on Nov 12 2010

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100129:20--ChIP:XZ:20100125:20:fetal heart:H3K27me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3790
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3885
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621450_BI.Fetal_Heart.H3K27me3.UW_H-22727.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:20--ChIP:XZ:20100125:20:fetal heart:H3K27me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Heart Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Fetal Heart, Donor H-22727 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.4830
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0766
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1324
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9245
IROC_PERCENTILE: 58
POISSON_SCORE: 0.3855
POISSON_PERCENTILE: 27

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

ANALYSIS FILE NAME: GSM621450_BI.Fetal_Heart.H3K27me3.UW_H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:20--ChIP:XZ:20100125:20:fetal heart:H3K27me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Fetal Heart, Donor H-22727 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.5104
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: FH H3K27me3 27
BROWSER_TRACK_DESCRIPTION: BI Fetal Heart Histone H3K27me3 Donor H-22727 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0766
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1324
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9245
IROC_PERCENTILE: 58
POISSON_SCORE: 0.3855
POISSON_PERCENTILE: 27

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

source_name: Primary fetal heart tissue; Lib:XZ:20100129:20--ChIP:XZ:20100125:20:fetal heart:H3K27me3

extract_protocol: Library construction protocol: Single read - Illumina

value: surgery

tag: molecule

value: genomic DNA

tag: disease

value: Fetal heart

value: Unknown

value: Primary Tissue

value: heart

value: UW

value: 101 days

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: ChIP-Seq analysis of WCE in human Mobilized CD34 cells; Lib:RI:20100308:01--ChIP:MA:20100216:01:Mobilized CD34:WCE

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100308:01--ChIP:MA:20100216:01:Mobilized CD34:WCE/Lib:RI:20100308:04--ChIP:MA:20100216:04:Mobilized CD34:WCE/Lib:RI:20100309:13--ChIP:MA:20100216:01:Mobilized CD34:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3796
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3877
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621456_BI.Mobilized_CD34_Primary_Cells.Input.UW_RO_01480.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100308:01--ChIP:MA:20100216:01:Mobilized CD34:WCE-Lib:RI:20100308:04--ChIP:MA:20100216:04:Mobilized CD34:WCE-Lib:RI:20100309:13--ChIP:MA:20100216:01:Mobilized CD34:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mobilized CD34 Primary Cells, Donor RO 01480 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.4822
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0043
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.0022
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3194
POISSON_PERCENTILE: 81

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

ANALYSIS FILE NAME: GSM621456_BI.Mobilized_CD34_Primary_Cells.Input.UW_RO_01480.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100308:01--ChIP:MA:20100216:01:Mobilized CD34:WCE-Lib:RI:20100308:04--ChIP:MA:20100216:04:Mobilized CD34:WCE-Lib:RI:20100309:13--ChIP:MA:20100216:01:Mobilized CD34:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mobilized CD34 Primary Cells, Donor RO 01480 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.5096
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 Input 80
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells ChIP-Seq Input Donor RO 01480 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0043
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.0022
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3194
POISSON_PERCENTILE: 81

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

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100308:01--ChIP:MA:20100216:01:Mobilized CD34:WCE

tag: markers

value: Mobilized CD34

value: Primary Cell

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K36me3 in Mobilized CD34 cells; Lib:RI:20100308:10--ChIP:MA:20100216:10:Mobilized CD34:H3K36Me3

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100308:10--ChIP:MA:20100216:10:Mobilized CD34:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3799
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3877
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621459_BI.Mobilized_CD34_Primary_Cells.H3K36me3.UW_RO_01480.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100308:10--ChIP:MA:20100216:10:Mobilized CD34:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01480 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.4585
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1089
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.1771
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9266
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3754
POISSON_PERCENTILE: 15

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

ANALYSIS FILE NAME: GSM621459_BI.Mobilized_CD34_Primary_Cells.H3K36me3.UW_RO_01480.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100308:10--ChIP:MA:20100216:10:Mobilized CD34:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01480 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.4859
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 H3K36me3 80
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K36me3 Donor RO 01480 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1089
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.1771
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9266
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3754
POISSON_PERCENTILE: 15

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

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100308:10--ChIP:MA:20100216:10:Mobilized CD34:H3K36Me3

value: genomic DNA

value: Unknown

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of WCE in human hiPS-15b cells; Lib:MC:20100128:06--ChIP:MC:20100125:06:hiPS-15b:WCE

description:
sample_term_id: NTR_0001162
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100128:06--ChIP:MC:20100125:06:hiPS-15b:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3784
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3888
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621444_BI.iPS-15b.Input.Lib_MC_20100128_06--ChIP_MC_20100125_06_hiPS-15b_WCE.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100128:06--ChIP:MC:20100125:06:hiPS-15b:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-15b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS-15b Cell Line, Library Lib:MC:20100128:06--ChIP:MC:20100125:06:hiPS-15b:WCE 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.4806
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0056
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0085
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9773
IROC_PERCENTILE: 84
POISSON_SCORE: 0.2405
POISSON_PERCENTILE: 57

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

ANALYSIS FILE NAME: GSM621444_BI.iPS-15b.Input.Lib_MC_20100128_06--ChIP_MC_20100125_06_hiPS-15b_WCE.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100128:06--ChIP:MC:20100125:06:hiPS-15b:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-15b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS-15b Cell Line, Library Lib:MC:20100128:06--ChIP:MC:20100125:06:hiPS-15b:WCE 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.5080
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS15b Input CE
BROWSER_TRACK_DESCRIPTION: BI iPS-15b Cell Line ChIP-Seq Input Library Lib:MC:20100128:06--ChIP:MC:20100125:06:hiPS-15b:WCE EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0056
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0085
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9773
IROC_PERCENTILE: 84
POISSON_SCORE: 0.2405
POISSON_PERCENTILE: 57

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

tag: lineage

value: induced pluripotent cells

tag: medium

value: KSR

tag: passage

tag: line

tag: batch

value: Cell Line

value: undifferentiated

tag: Sex

value: Female

value: Harvard University


title: ChIP-Seq analysis of H3K4me1 in Mobilized CD34 cells; Lib:RI:20100524:09--ChIP:MA:20100517:09:Mobilized CD34:H3K4Me1

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100524:09--ChIP:MA:20100517:09:Mobilized CD34:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3791
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3881
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621451_BI.Mobilized_CD34_Primary_Cells.H3K4me1.UW_RO_01549.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:09--ChIP:MA:20100517:09:Mobilized CD34:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01549 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.4671
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.4931
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4797
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9991
IROC_PERCENTILE: 95
POISSON_SCORE: 0.5749
POISSON_PERCENTILE: 58

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

ANALYSIS FILE NAME: GSM621451_BI.Mobilized_CD34_Primary_Cells.H3K4me1.UW_RO_01549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:09--ChIP:MA:20100517:09:Mobilized CD34:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 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.4945
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 H3K4me1 49
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me1 Donor RO 01549 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.4931
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4797
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9991
IROC_PERCENTILE: 95
POISSON_SCORE: 0.5749
POISSON_PERCENTILE: 58

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

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100524:09--ChIP:MA:20100517:09:Mobilized CD34:H3K4Me1

value: Cauc

value: UW

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K4me1