title: WCE_G1Ebmp_r1_101201_2

city: Boston

first: Teresa

middle: Venezia

last: Bowman

address: One Blackfan Circle, 7th floor

institute: Children's Hospital Boston

description: Chromatin IP against G1E BMP SMAD1

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build (hg18) using Eland.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 10bp bins. Counts were normalized to reads per million, and bins with at least 0.5 reads per million are shown.

source_name: Input ChIP-Seq in mouse G1E treated with BMP

growth_protocol: G1E cells were maintained in IMDM medium plus 15% heat-inactivated fetal calf serum (Hyclone SH30071.01) in the presence of 2% P/S, 2 U/mL Epo, 50ng/ml mouse SCF (R&D 455-MC-010), and 124 X 10-4 monothioglycerol (Sigma M6145) as previously described (Tsang et al., Cell 1997). Erythroid differentiation was induced with 10-7 M Î²-estradiol for 24hrs both in G1ER and in G1E cells as a control.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: During the last two hours of estradiol treatment, rhBMP4 was added to the cultures at a final concentration of 25ng/ml and cells were harvested for chromatin immunoprecipitation.

value: Erthyroid Progenitor (G1E)

tag: antibody catalog number

value: None WCE


title: Gata1_G1ERbmp_r1_100914_4

status: Public on Oct 07 2011

type: SRA

state: MA

country: USA

description: Chromatin IP against BMP GIER GATA1

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Gata1 ChIP-Seq in mouse G1ER treated with BIO

growth_protocol: G1ER cells were maintained in IMDM medium plus 15% heat-inactivated fetal calf serum (Hyclone SH30071.01) in the presence of 2% P/S, 2 U/mL Epo, 50ng/ml mouse SCF (R&D 455-MC-010), and 124 X 10-4 monothioglycerol (Sigma M6145) as previously described (Tsang et al., Cell 1997). Erythroid differentiation was induced with 10-7 M Î²-estradiol for 24hrs both in G1ER and in G1E cells as a control.

treatment_protocol: During the last two hours of estradiol treatment, cells were serum-starved for 24 hrs and stimulated for 2hrs with 25ng/Î¼l recombinant human BMP4 (R&D 314-BP-010).

tag: cell type

value: Erthyroid Progenitor (G1ER)

tag: chip antibody

value: Santa Cruz SC-265


title: Gata2_G1Ebmp_r1_101201_3

description: Chromatin IP against G1E BMP SMAD1

source_name: Gata2 ChIP-Seq in mouse G1E treated with BMP

value: Santa Cruz SC-9008


title: Smad1_G1Ebmp_r1_100914_6

description: Chromatin IP against G1E BMP SMAD1

source_name: Smad1 ChIP-Seq in mouse G1E treated with BMP

treatment_protocol: During the last two hours of estradiol treatment, cells were serum-starved for 24 hrs and stimulated for 2hrs with 25ng/ml recombinant human BMP4 (R&D 314-BP-010).

value: Santa Cruz SC-7965


title: Smad1_G1ERbmp_r1_100914_5

description: Chromatin IP against BMP G1ER SMAD1

source_name: Smad1 ChIP-Seq in mouse G1ER treated with BMP


title: WCE_G1ERbio_r1_100914_1

description: Chromatin IP against BIO G1ER INPUT

source_name: Input ChIP-Seq in mouse G1ER treated with BIO

treatment_protocol: During the last two hours of estradiol treatment, cells were stimulated for 4hrs with 5Î¼M BIO dissolved in DMSO and were harvested for chromatin immunoprecipitation.


title: GATA1 ChIP-seq K562

description: GATA1 ChIP-seq in K562 cells

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using Eland.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 10bp bins. Counts were normalized to reads per million, and bins with at least 0.5-1 reads per million are shown.

organism: Homo sapiens

tag: cell line

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: Input ChIP-Seq K562-C/EBPA bmp4

description: Input ChIP-Seq in K562-C/EBPA treated with bmp4

value: WCE


title: GATA2 ChIP-seq K562

description: GATA2 ChIP-seq in K562 cells


title: SMAD1 ChIP-Seq K562-C/EBPA bmp4

description: SMAD1 ChIP-Seq in K562-C/EBPA treated with bmp4


title: CEBPA ChIP-Seq K562-C/EBPA bmp4

description: CEBPA ChIP-Seq in K562-C/EBPA treated with bmp4

value: CEBPA


title: ECC1_standard_rep1

status: Public on Oct 10 2011

city: Huntsville

first: Jason

last: Gertz

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

description: RNA-seq from poly(A) selected mRNA

library_source: transcriptomic

data_processing: To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters: --phred64-quals -n 2 -k 1 -m 10 â-best.  The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.

molecule: total RNA

growth_protocol: The human endometrial Â cancer cell line ECC-1 was grown in RPMI-1640 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone) and 1% penicillin-streptomycin (Invitrogen).

extract_protocol: Library construction protocols are indicated in the characteristics: Protocol

tag: protocol

value: Standard RNA-seq

tag: mrna input

value: 50 ng


title: WCE_U937dmso_r1_100505_3

description: Input ChIP-Seq in U937 treated with DMSO

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build (hg18) using Eland.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 10bp bins. Counts were normalized to reads per million, and bins with at least 0.5-1 reads per million are shown.

source_name: Input ChIP-Seq U937 DMSO

growth_protocol: U937 cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI-1640 media with 10% Fetal Bovine Serum by the National Cell Culture Center(NCCC). For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.


title: WCE_U937bio_r1_100709_6

description: Input ChIP-Seq in U937 treated with BIO

source_name: Input ChIP-Seq U937 BIO


title: ggo br M 1

status: Public on Oct 13 2011

city: Lausanne

first: Henrik

last: Kaessmann

address: Génopode

department: Center For Integrative Genomics

country: Switzerland

institute: University of Lausanne

description:
sample name: Matze_br
Paired-end libraries, 101bp run

data_processing: for processed data, please refer to the original publication

molecule: polyA RNA

organism: Gorilla gorilla

source_name: Brain, prefrontal cortex

extract_protocol: Total RNA was extracted using the Trizol (Invitrogen) procedure or RNAeasy/RNAeasy Lipid/miRNeasy (Qiagen) column purification kits as indicated. RNA quality was assessed using an Agilent 2100 Bioanalyzer. Sequencing libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer's instructions. Briefly, polyadenylated RNA was isolated using a poly-dT bead procedure and then chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded cDNA were repaired. After 3'-end adenylation of these products, Illumina Paired-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were run on gels; 250-300 bp fragments were excised and then PCR-amplified (15 cycles). After column-purification, qualities of the resulting libraries were assessed using Agilent 2100 Bioanalyzers. Potential influences on RNA sequencing results due to different experimenters preparing the libraries were ruled out on the basis of RNA- Seq data comparisons of replicate libraries prepared by the different experimenters (i.e., expression levels derived from replicate libraries were highly correlated: rho > 0.99). The RNA-Seq libraries were each sequenced with 76 (101) cycles in at least one lane of the Illumina Genome Analyzer IIx platform according to the manufacturer's specifications. Technical replicates (i.e., sequencing the same library on different machines) were performed to rule out potential biases during the sequencing step (i.e., expression levels between technical replicates were highly correlated: rho > 0.98). After sequencing, we processed the fluorophore intensity files with the Ibis base caller (version 1.11), in addition to applying the standard Illumina base calling algorithms. As illustrated in Supplementary Note Table 1 and Supplementary Note Figure 1 for a small subset of samples, we found that Ibis significantly increased the number of usable reads and drastically reduced the error rate. This improvement was more pronounced for the sequencing runs processed with early versions of the Illumina pipeline, but remained noticeable even for the latest Illumina release (GA pipeline 1.60). All subsequent analyses were performed on the Ibis-called reads.

tag: gender

value: Female (note:this sample was originally provided as a "male" sample to us and therefore labeled this way in the Brawand et al. paper and original GEO submission; however, detailed data analyses carried out in the meantime clearly show that this sample stems from a female individual)

tag: age

value: 51 years

tag: extraction

value: RNeasy

tag: rin

tag: tissue source

value: Zoo Frankfurt, Germany


title: CEBPA_U937dmso_r1_100505_5

description: CEBPA ChIP-Seq in U937 treated with DMSO

source_name: CEBPA ChIP-Seq U937 DMSO

treatment_protocol: DMSO control

value: Santa Cruz SC-9314


title: SMAD1_U937bmp4_r1_100608_1

description: SMAD1 ChIP-Seq in U937 treated with BMP4

source_name: SMAD1 ChIP-Seq U937 BMP4

value: Santa Cruz SC-6031


title: TCF7L2_U937bio_r1_100505_7

description: TCF7L2 ChIP-seq in U937 treated with BIO

source_name: TCF7L2 ChIP-seq U937 BIO

treatment_protocol: Cells were stimulated for 2hrs with 5Î¼M BIO dissolved in DMSO.

value: Santa Cruz SC-8631


title: WCE_U937bmp4_r1_100608_3

description: Input ChIP-Seq in U937 treated with BIO

value: None WCE


title: WCE_U937bio_r1_100608_5

description: Input ChIP-Seq in U937 treated with BIO


title: WCE_U937bio_r1_100505_6

description: Input ChIP-Seq in U937 treated with BIO


title: WCE_U937bio_r1_100709_4

description: Input ChIP-Seq in U937 treated with BIO


title: CEBPA_U937bio_r1_100709_5

description: CEBPA ChIP-Seq in U937 treated with BIO

source_name: CEBPA ChIP-Seq U937 BIO


title: WCE_K562bmp4_r1_100608_1

description: Input ChIP-Seq in K562 cells treated with BMP

source_name: Input ChIP-Seq K562 BIO

growth_protocol: K562 cells were maintained in IMDM medium (Invitrogen 12440) with 10% Fetal Bovine serum, 2ÂµM Glutamine, 100 U/mL penicillin and 100 Âµg/mL streptomycin (1% P/S). Cells were split 1:10 every 2-3 days. Prior to stimulation, cells were serum starved in IMDM medium with 2ÂµM Glutamine, 1% P/S for 24hrs at a concentration of 106cells/ml.

treatment_protocol: Cells were stimulated with 5ÂµM BIO dissolved in DMSO for 4hrs.


title: TCF7L2_K562bio_r2_Childrens

description: TCF7L2 ChIP-seq in K562 cells treated with BIO

source_name: TCF7L2 ChIP-seq K562 BIO


title: WCE_K562bio_r1_100106_5

description: Input ChIP-Seq in K562 cells treated with BIO

source_name: Input ChIP-Seq K562

treatment_protocol: 5ÂµM BIO (GSK3 inhibitor IX - Calbiochem 361550)


title: TCF7L2_K562bio_r1_100106_7


title: SMAD1_K562campk_r1_110323_2

description: SMAD1 ChIP-Seq in K562 cells treated with dorso

source_name: SMAD1 ChIP-Seq K562 dorso

treatment_protocol: Cells were treated with 20ÂµM dorsomorphin (Calbiochem AMPK inhibitor, Compound C 171260) for 2hrs


title: SMAD1_K562bmp4_r1_100608_2

description: SMAD1 ChIP-Seq in K562 cells treated with BMP4

source_name: SMAD1 ChIP-Seq K562 bmp4


title: GATA2_K562bio_r1_110325_5

description: GATA2 ChIP-seq in K562 cells treated with BIO

source_name: GATA2 ChIP-seq K562 BIO

treatment_protocol: 25ng/ml recombinant human BMP4 (R&D 314-BP-010) for 2hrs


title: GATA1_K562bmp_r1_110325_4

description: GATA1 ChIP-seq in K562 cells treated with BMP

source_name: GATA1 ChIP-seq K562 BMP


title: GATA1_K562bio_r1_110325_6

description: GATA1 ChIP-seq in K562 cells treated with BIO

source_name: GATA1 ChIP-seq K562 BIO


title: Input E2 rep1

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

country: France

institute: IGBMC

data_processing: Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

source_name: H3396 cells

growth_protocol: H3396 cells were maintained in RPMI 1640 supplemented with 10 mM HEPES, 10% fetal bovine serum (FBS), and antibiotics.

extract_protocol: ChIP assays were performed according to standard protocols

treatment_protocol: Before 1h of estrogen or ethanol treatment, H3396 cells were cultured in charcol stripped medium for 72h

value: H3396 cells

tag: treatment

value: estrogen


title: CARM1 E2

description: Chromatin IP against CARM1

tag: comment

value: In house Rabbit polyclonal:aa. 595-608

tag: chip antibody manufacturer

value: In house


title: CARM1 EtOH

description: Chromatin IP against CARM1

value: ethanol


title: PolII EtOH

description: Chromatin IP against Polymerase II

value: In house Mouse:7C2 Clone

value: PolII 7C2 clone


title: WCE_CD34prog_bio_r1_101201_1

description: Input ChIP-seq in CD34+ progenitors treated with BIO

source_name: Input ChIP-seq CD34+ progenitors BIO

growth_protocol: CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were obtained from the Yale Center of Excellence in Molecular Hematology. The cells were maintained and differentiated as previously described (Sankaran et al., 2008). Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with 1X CC100 cytokine mix (Stem Cell Technologies Inc.) and 2% P/S for a total of 6 days.

treatment_protocol: At day 6 cells were stimulated for 2hrs with 5ÂµM of BIO and harvested for performing chromatin immunoprecipitation.

value: Hematopoietic Stem & Progenitor Cells

value: WCE


title: PolII E2

description: Chromatin IP against Polymerase II


title: WCE_CD34eryth_bmp_r2_101105_2

description: Input ChIP-Seq CD34 erythroid BMP

source_name: Input ChIP-Seq CD34 erythroid BMP

growth_protocol: CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were obtained from the Yale Center of Excellence in Molecular Hematology. The cells were maintained and differentiated as previously described (Sankaran et al., 2008). Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with 1X CC100 cytokine mix (Stem Cell Technologies Inc.) and 2% P/S for a total of 6 days.  For studying the binding in differentiated cells after  day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 uM dexamethasone, and 1 uM Î²-estradiol), at a density of 0.5â1 X 106 cells/ml till harvesting. At day 5 of differentiation cells reached the proerythroblast cells were stimulated for 2hrs with rhBMP4 at a final concentration of 25ng/Âµl and harvested for performing chromatin immunoprecipitation.

value: Pro-erythroblasts


title: WCE_CD34prog_bio_r1_100826_6


title: WCE_CD34prog_bio_r2_101105_5


title: WCE_CD34eryth_bio_r2_101103_5

description: Input ChIP-Seq CD34 erythroid BIO

source_name: Input ChIP-Seq CD34 erythroid BIO

treatment_protocol: At day 5 of differentiation cells reached the proerythroblast cells were stimulated for 2hrs with 5ÂµM BIO (GSK3 inhibitor IX - Calbiochem 361550)and harvested for performing chromatin immunoprecipitation.


title: WCE_CD34prog_bmp_r1_101201_7

description: Input ChIP-seq in CD34+ progenitors treated with BMP

source_name: Input ChIP-seq CD34+ progenitors BMP

treatment_protocol: At day 6 cells were stimulated for 2hrs with rhBMP4 at a final concentration of 25ng/Âµl and harvested for performing chromatin immunoprecipitation.


title: WCE_K562bio_r1_100608_2


title: WCE_CD34eryth_bmp_r1_100922_3

description: Input ChIP-Seq in CD34 erythroid treated with BMP

treatment_protocol: At day 5 of differentiation cells reached the proerythroblast cells were stimulated for 2hrs with rhBMP4 at a final concentration of 25ng/Âµl and harvested for performing chromatin immunoprecipitation.


title: mml lv M 1

description: sample name: 565

organism: Macaca mulatta

source_name: Liver

value: Male

value: 8 years

value: Standard

value: Macaque facility in Souzhou, China


title: H3K18ac EtOH

description: Chromatin IP against H3K18ac

value: Abcam:H3K18ac (ab1191)

value: Abcam

tag: chip antibody catalog #


title: ERa EtOH

description: Chromatin IP against Estrogen receptor alpha

value: Santa Cruz:ERa (HC20)

value: ERa

value: Santa Cruz


title: H3K18ac E2

description: Chromatin IP against H3K18ac

value: H3396 cells

value: estrogen


title: H3-4ac E2

description: Chromatin IP against Total H3 and H4 acetylated

value: In house Rabbit polyclonal:Total H3/H4 acetylated

value: H3/H4 acetylated

value: In house


title: CBPR2151m EtOH

description: Chromatin IP against CBPR2151m

value: ethanol

value: In house Rabbit polyclonal:peptide AGVP(Rme2a)PGVPC

value: CBPR2151m peptide AGVP(Rme2a)PGVPC


title: CBPR2151m E2

description: Chromatin IP against CBPR2151m


title: WCE_CD34eryth_bio_r1_101103_4

description: Input ChIP-Seq in CD34 erythroid treated with BIO

growth_protocol: CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were obtained from the Yale Center of Excellence in Molecular Hematology. The cells were differentiated as previously described (Sankaran et al., 2008). Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with 1X CC100 cytokine mix (Stem Cell Technologies Inc.) and 2% P/S for a total of 6 days. For studying the binding in differentiated cells after  day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 uM dexamethasone, and 1 uM Î²-estradiol), at a density of 0.5â1 X 106 cells/ml till harvesting. At day 5 of differentiation cells reached the proerythroblast stage of erythroid differentiation. At this day cells were stimulated for 2hrs with rhBMP4 at a final concentration of 25ng/Âµl and harvested for performing chromatin immunoprecipitation.

value: Pro-erythroblasts

value: WCE

tag: antibody catalog number

value: None WCE


title: ERa E2


title: TCF7L2_CD34prog_bio_r2_101105_4

description: TCF7L2 ChIP-seq in CD34 progenitors treated with BIO

source_name: TCF7L2 ChIP-seq CD34 progenitors BIO

tag: cell type

value: Hematopoietic Stem & Progenitor Cells

value: Santa Cruz SC-8631


title: GATA2_K562bmp_r1_110325_3

description: GATA2 ChIP-seq in K562 cells treated with BMP

source_name: GATA2 ChIP-seq K562 BMP

tag: chip antibody

value: Santa Cruz SC-9008


title: TCF7L2_CD34prog_bio_r1_100826_7


title: CBPR768m EtOH

description: Chromatin IP against CBPR768m

tag: cell line

value: In house Rabbit polyclonal:peptide ISPS(Rme2a)MPQPC

value: CBPR768m peptide ISPS(Rme2a)MPQPC


title: RAC3 E2

description: Chromatin IP against RAC3

value: Santa Cruz:RAC3 (M397)

value: Santa Cruz


title: CBPR768m E2

description: Chromatin IP against CBPR768m

value: H3396 cells

value: estrogen


title: SMAD1_CD34prog_bmp_r2_101105_3

description: SMAD1 ChIP-seq in CD34+ progenitors treated with BMP

source_name: SMAD1 ChIP-seq CD34+ progenitors BMP

value: Santa Cruz SC-7965


title: CBPR742m E2

description: Chromatin IP against CBPR742m

value: In house Rabbit polyclonal:peptide MGP(Rme2a)AASPMC

value: peptide MGP(Rme2a)AASPMC

value: In house


title: SMAD1_CD34prog_bmp_r1_100901_1


title: SMAD1_CD34eryth_bmp_r2_101103_7

description: SMAD1 ChIP-seq in CD34 ertyhroid treated with BMP

source_name: SMAD1 ChIP-seq CD34 ertyhroid BMP

growth_protocol: CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were obtained from the Yale Center of Excellence in Molecular Hematology. The cells were maintained and differentiated as previously described (Sankaran et al., 2008). Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with 1X CC100 cytokine mix (Stem Cell Technologies Inc.) and 2% P/S for a total of 6 days. For studying the binding in differentiated cells after  day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 uM dexamethasone, and 1 uM Î²-estradiol), at a density of 0.5â1 X 106 cells/ml till harvesting.


title: SMAD1_CD34eryth_bmp_r1_100922_5


title: CBP EtOH

description: Chromatin IP against CBP

value: ethanol

value: Santa Cruz:CBP (A22)

value: CBP


title: CBP E2

description: Chromatin IP against CBP


title: GATA1_CD34eryth_bmp_r1_100922_4

description: GATA1 ChIP-seq in CD34 erythroid treated with BMP

source_name: GATA1 ChIP-seq CD34 erythroid BMP

growth_protocol: CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were obtained from the Yale Center of Excellence in Molecular Hematology. The cells were maintained and differentiated as previously described (Sankaran et al., 2008). Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with 1X CC100 cytokine mix (Stem Cell Technologies Inc.) and 2% P/S for a total of 6 days. At day 6 cells were stimulated for 2hrs with rhBMP4 at a final concentration of 25ng/Âµl or 5ÂµM of BIO as indicated and harvested for performing chromatin immunoprecipitation. For studying the binding in differentiated cells after  day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 uM dexamethasone, and 1 uM Î²-estradiol), at a density of 0.5â1 X 106 cells/ml till harvesting. At day 5 of differentiation cells reached the proerythroblast cells were stimulated for 2hrs with rhBMP4 at a final concentration of 25ng/Âµl and harvested for performing chromatin immunoprecipitation.

value: Pro-erythroblasts

value: Santa Cruz SC-265


title: WCE_CD34eryth_bio_r1_101201_4

description: Input ChIP-Seq CD34 erythroid BIO

value: WCE

value: None WCE


title: GATA1_CD34eryth_bio_r2_101103_7

description: GATA1 ChIP-seq in CD34 erythroid treated with BIO

source_name: GATA1 ChIP-seq CD34 erythroid BIO

growth_protocol: CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were obtained from the Yale Center of Excellence in Molecular Hematology. The cells were maintained and differentiated as previously described (Sankaran et al., 2008). Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with 1X CC100 cytokine mix (Stem Cell Technologies Inc.) and 2% P/S for a total of 6 days. For studying the binding in differentiated cells after  day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 uM dexamethasone, and 1 uM Î²-estradiol), at a density of 0.5â1 X 106 cells/ml till harvesting. At day 5 of differentiation cells reached the proerythroblast stage of erythroid differentiation.


title: H3K4me1 ChIP-seq K562 bmp4

description: H3K4me1 ChIP-seq in K562 cells treated with BMP

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Truseq Genomic DNA protocol. Fragmented DNA were ligated to Illumina Truseq adapters and size selected between 200 and 400bp using the SPRIWorks system and subjected to 18 cycles of PCR using oligos provided by Illumina. Amplified libraries were purified using Ampure XP beads to remove linker prior to sequencing.

tag: chip antibody vendor


title: iPS1-C3 day 10

status: Public on Oct 06 2011

city: bronx

first: Mingyan

last: Lin

state: ny

address: 1300 Morris Park Avenue

institute: Albert Einstein college of medicine

description: amplified cDNA (The average fragment length : 250bp,  the standard deviation : 50bp)

data_processing: iPS cell and neuron RNA-Seq reads were separately aligned to the human genome (GRCh37/hg19) using the software TopHat (version 1.2.0).

source_name: neurons

growth_protocol: Stem cell lines were maintained on irradiated mouse embryonic fibroblasts (MEFs) in hES medium consisting of knockout (KO)-DMEM, 1mM pen/strep, 1 mM Gluta-MAX, 1X nonessential amino acids (NEAA), 55 μM β-mercaptoethanol (β-ME) (Gibco, Carlsbad, CA), 10% Knockout (KO) serum replacement (Invitrogen, Carlsbad, CA), 10% plasmanate (Talecris Biotherapeutics, Research Triangle Park, NC), and 10 ng/ml FGF2 (R&D Systems Inc., Minneapolis, MN).

extract_protocol: Total RNA (25 ng) was converted to cDNA using the NuGEN Ovation RNA-Seq System according to the manufacturer's protocol (NuGEN, San Carlos, CA, USA). The protocol employs a single primer isothermal amplification (SPIA) method to amplify RNA target into double stranded cDNA under standardized conditions that markedly deplete rRNA without preselecting mRNA. cDNA was then used for Illumina sequencing library preparation using Encore NGS Library System I. NuGEN-amplified double-stranded cDNA was fragmented into ,300 base pair (bp) using a Covaris-S2 system. DNA fragments (200 ng) were then end-repaired to generate blunt ends with 59 phosphatase and 39 hydroxyls and adapters were ligated for paired end sequencing on Illumina HiSeq 2000. The average fragment length is 250bp and the standard deviation is 50bp.

treatment_protocol: To support glutamatergic differentiation, adherent colonies were treated on day 10 with WNT3A (100ng/ml) (R&D Systems, Minneapolis, MN) in neural induction medium. Cells were fed every other day for 2 weeks. On day 25, medium was changed to neuronal differentiation medium, which consists of Neurobasal medium, 1X N2 supplement, 2X B27, 0.1 mM NEAA, supplemented with cAMP (1 μM), BDNF, GDNF, and IGF1 (10 ng/ml each, PeproTech, Rocky Hill, NJ). The concentration of WNT3A was reduced to 10ng/ml.

value: hiPSCs-derived neurons

tag: passages

tag: clone


title: Spermatocyte_pan-lysine-acetylation

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

data_processing: Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline. Reads were mapped to human hg18 (for IMR90 data) or mouse mm9 (for sperm cell data) genome build with a bowtie software package. Total mapped tags were paired down to unique, monoclonal tags. These are tags that mapped to one location in the genome and each sequence is represented once.

source_name: Spermatocyte

extract_protocol:
ChIP-seq for histone Kcr or Kac was carried out as previously described with 500 μg IMR90 chromatin (or 100 μg of fractionated germ cells chromatin) and 5 μg pan anti-Kcr or anti-Kac antibody (Hawkins et al., 2010). ChIP-seq libraries for sequencing were prepared following Illumina protocols (Illumina, San Diego, CA) with minor modifications. Libraries for input samples were generated using 20 ng corresponding input chromatin. Briefly, ChIPed DNA was first blunted with END-IT DNA repair kit (Epicenter Biotechnology, Madison, WI) and then incubated with Klenow (exo-) (New England Biolabs, MA) and dATP to generate single base 3′-dA overhang. Illumina sequencing adaptor was then ligated to the resulting DNA, and followed by size selection (180-400bp) from a 8% acrylamide gel. This size-selection step was repeated after PCR amplification with DNA primers supplied by Illumina. Libraries were sequenced using Illumina GAII or HiSeq machine as per manufacturer's protocols.
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

value: Spermatocyte

tag: antibody

value: pan anti-lysine acetylation antibody


title: Round-spermatids_pan-lysine-acetylation

source_name: Round spermatids

value: Round spermatids


title: Round-spermatids_input


title: PolII_ChIPSeq_rep2

city: Davis

first: Chung-Il

last: An

state: CA

address: One Shields Ave.

institute: University of California, Davis

description: Chromatin IP against Pol II

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (NCBI37/mm9) genome using Bowtie (version 0.12.5) (http://bowtie-bio.sourceforge.net/index.shtml). All reads mapping with two or fewer mismatches were retained.
Peaks: Peak calling was performed with SISSRs (version 1.4) (http://sissrs.rajajothi.com/)

source_name: primary myotubes

growth_protocol: Primary myoblasts isolated from wild type mouse fetal (E18.5) limb muscle were cultured in differentiation medium (DMEM + 2% horse serum) for 48 hours to induce myotubes.

extract_protocol: DNA Imprint Chromatin Immunoprecipitation Kit (vender: Sigma-Aldrich) includes all necessary reagents for isolating genomic DNA in addition to those for ChIP. Immunoprecipitated Immunoprecipitated material was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 18-cycles of PCR and size selected (300-600 bp) followed by single end sequencing on an Illumina Genome Analyzer II.

tag: strain

value: myotubes induced from wild type mouse fetal (E18.5) primary myoblasts

value: Pol II

tag: antibody vender

value: Abcam

tag: antibody lot/batch#

value: no record

tag: antibody catalog#


title: InputDNA_ChIPSeq_rep2

description: Input DNA


title: Spermatocyte_input


title: InputDNA_ChIPSeq_rep1

description: Input DNA


title: Sox6_ChIPSeq_rep2

description: Chromatin IP against Sox6


title: Sox6_ChIPSeq_rep1

description: Chromatin IP against Sox6


title: IMR90_Kcro

source_name: fetal lung fibroblast IMR90 cell line

value: fetal lung fibroblast

value: pan anti-lysine crotonylation antibody


title: hippocampus 6h following ECS replicate 2

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description: Small RNA sequence data

data_processing: The processed data files contain adapter-trimmed and grouped reads. 3' adapter sequences were trimmed using custom perl scripts and and inserts longer than 18 nt were use in the subsequent analysis.

source_name: size fractionated RNA from mouse hippocampus following ECS

extract_protocol:
Total RNA was prepared from tissue using Trizol and size fractionated by PAGE collecting the ~18-24nt range.  RNA was cloned using Illumina DGE small RNA kit with provided primers.
Illumuna DGE small RNA kit

treatment_protocol: Electroconvulsive shock

tag: tissue

value: hippocampus

tag: time

value: 6 hr


title: GATA1_CD34eryth_bmp_r2_101105_1


title: GATA2_CD34prog_bmp_r1_101201_1

description: GATA2 ChIP-seq in CD34+ progenitors treated with BMP

source_name: GATA2 ChIP-seq CD34+ progenitors BMP

value: Hematopoietic Stem & Progenitor Cells

value: Santa Cruz SC-9008


title: hippocampus 1h following ECS replicate 2

description: Small RNA sequence data

value: 1 hr


title: hippocampus 3h following ECS replicate 2

description: Small RNA sequence data

value: 3 hr


title: IMR90_pan-lysine-acetylation


title: H3K4me1 ChIP-seq K562 BIO

description: H3K4me1 ChIP-seq in K562 cells treated with BIO

value: Santa Cruz

tag: chip antibody cat. #


title: hippocampus 24h following ECS replicate 2

description: Small RNA sequence data

value: 24 hr


title: hippocampus 0.5h following ECS replicate 2

description: Small RNA sequence data


title: Untreated mouse hippocampus replicate 2

description: Small RNA sequence data

source_name: size fractionated RNA from mouse hippocampus before ECS

value: 0 hr


title: GATA1_CD34eryth_bio_r1_101103_6

value: Pro-erythroblasts

value: Santa Cruz SC-265


title: IMR90_input


title: H3-T7 (new) H4 tail delete generation 3

city: Jerusalem

first: Assaf

last: Weiner

address: Givat Ram

department: Computer Science

country: Israel

institute: The Hebrew University of Jerusalem

data_processing: Mapped Reads: Unique reads were mapped to the yeast genome (S288C_reference_genome_R61-1-1_20080605; 05-Jun-2008) with minimal errors (as described in Yassour et al. PNAS, 2009 (PMID 19208812)).

organism: Saccharomyces cerevisiae

source_name: H3-T7, H4 tail deletion, generation 3

growth_protocol: For tag switch experiments, yeast cells were grown overnight in YPD in the presence of Hygromycin B (200 μg/mL, Invitrogen). The cells were then diluted 1:10 into fresh YPD and incubated for 30–36 h. Recombination was induced by the addition of 1 μM β-estradiol (E-8875, Sigma-Aldrich). Subsequently, cells were diluted 1:25 in fresh YPD media to release the cells back into the cell cycle and kept in log phase by 1:2 dilutions into fresh media after each population doubling. Samples were taken after 1, 3, and 6 cell divisions or after 5 hours of G2/M arrest. The number of population doublings was determined by microscopy and OD. G2/M arrest was induced by addition of 15 μg/ml Nocodazole (Sigma-Aldrich) and confirmed by FACS analysis.

extract_protocol: The majority of obtained fragments was around 150bp, as determined on a 2% TAE agarose gel stained with ethidium bromide. The isolated chromatin of the equivalent of 3x10^8 cells was immunoprecipitated overnight at 4°C using magnetic Dynabeads (Invitrogen), which were previously incubated with antibody O/N at 4°C.

treatment_protocol: ChIP was performed as described previously (PMID 20018668) with the following modifications. All steps were done at 4°C unless otherwise indicated. Following cell lysis by bead beating, the insoluble chromatin of 1x10^9 cells was washed, resuspended in 400 μl FA lysis buffer (50 mM HEPESKOH [pH 7.6], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), and sheared using a Bioruptor (Diagenode) for 6 minutes with 30 seconds intervals at high. The 16 soluble fraction was diluted three fold in buffer 15mM Tris-HCl pH 7.4, 50mM NaCl, 1.5mM CaCl2, 5mM β-meracptoethanol, 5mM MgCl2,  after which 25 units of micrococcal nuclease (MNase; Worthington) were added. The digestion reaction was incubated 20 minutes at 37°C and stopped by the addition of 10mM EDTA and 10mM EGTA, and tubes were placed on ice.

tag: genotype

value: H4 tail deletion

tag: epitope tag

tag: histone h3

value: new

tag: sampling time

value: after 3 cell divisions


title: CEBPA ChIP-Seq U937 bmp4

description: CEBPA ChIP-Seq in U937 treated with BMP4

tag: chip antibody

value: CEBPA


title: H3-HA (old) H4 tail delete generation 3

source_name: H3-HA, H4 tail deletion, generation 3

value: HA

value: old


title: hippocampus 24h following ECS replicate 1

description: Small RNA sequence data

value: hippocampus


title: hippocampus 6h following ECS replicate 1

description: Small RNA sequence data

value: 6 hr


title: PolII_ChIPSeq_rep1

description: Chromatin IP against Pol II

tag: cell type

value: myotubes induced from wild type mouse fetal (E18.5) primary myoblasts

value: Pol II

value: Abcam

value: no record


title: hippocampus 3h following ECS replicate 1

description: Small RNA sequence data

value: 3 hr


title: hippocampus 0.5h following ECS replicate 1

description: Small RNA sequence data


title: Untreated mouse hippocampus replicate 1

description: Small RNA sequence data


title: H3-HA (old) cac1 deletion generation 3

source_name: H3-HA, cac1 deletion, generation 3

value: cac1 deletion


title: H3-T7 (new) generation 1

source_name: H3-T7, wt, generation 1

value: wt

value: at 1 cell division


title: H3-HA (old) generation 1

source_name: H3-HA, wt, generation 1


title: H3-T7 (new) in G2/M

value: after 5 hrs of G2/M arrest


title: H3-HA (old) in G2/M

source_name: H3-HA, wt, G2/M


title: H3-HA (old) generation 0

source_name: H3-HA, wt, generation 0

value: before release from arrest


title: H3-T7 (new) generation 0

source_name: H3-T7, wt, generation 0

value: new


title: Spermatocyte_Kcro

value: Spermatocyte

value: pan anti-lysine crotonylation antibody


title: H3-T7 (new) top1 deletion generation 3

source_name: H3-T7, top1 deletion, generation 3

value: top1 deletion

value: after 3 cell divisions


title: Round-spermatids_Kcro

value: Round spermatids


title: BJAB_shRFP

city: Frederick

first: Shalini

last: Oberdoerffer

state: MD

address: 1050 Boyles Street

institute: National Cancer Institute

description: RNA-seq

data_processing:
Illumina software pipeline was used for primary analyses (Basecalls were done using Illumina RTA 1.8 for GAIIx run generating 35 bp reads). Alignments towards the human genome (assembly hg19) were done using Bowtie.
The exon inclusion levels were computed using the Mixture of Isoforms program (Katz et al. Nat Methods 2010); the data are linked as a supplementary file to Series record.

source_name: B cells

growth_protocol: Cells were maintained in RPMI with 10% FBS and 1% L-glutatmine.

extract_protocol: Libraries were constructed from total RNA. Total RNA was isolated with the Qiagen RNeasy, according to the manufacturer's protocol.  Libraries were prepared according to Illumina's instructions accompanying the mRNA-Seq sample preparation kit (Part # 1004898 Rev.D). Briefly, the mRNA was purified from total RNA by Poly-A- selection. The mRNA was subjected to fragmentation using divalent cations under elevated temperature. cDNA synthesis was performed with fragmented RNA, and cDNA was end-repaired with 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, size selection was achieved by excising a band of 200±25 bp from an agarose gel to remove excess adapters. The gel 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 either uninfected, or infected with lentivirus encoding shRNA directed against CTCF or against RFP, as a control.

tag: cell line

value: Cell line derived from Burkitt's lymphoma

tag: passage

value: Multiple


title: BL41

description: RNA-seq


title: BJAB_shCTCF

description: RNA-seq


title: BL41_CTCF

description: Chromatin IP against CTCF

data_processing: Illumina software pipeline (Basecalls were done by using Illumina RTA 1.8 for GAIIx run.  Alignment was done by using Illumina  CASAVA_v1.7.0 pipelines) read length -> 36 bps for Chip-Seq data. The bed files are the MACS peaks and they are generated as follows: Illumina FastQ files were mapped to the human genome (hg19) using Bowtie (Langmead et al. Genome Biol 2009) requiring a unique match (using the '-m 1' flag). The aligned reads in SAM format were analzyed using the MACS peak caller (Zhang et a.l. Genome Biol 2008). MACS peak calling was run using the respective Rabbit Ig control sequencing data as background files for BJAB and BL41 CTCF ChIP-Seq data.

extract_protocol: Lysates were clarified from sonicated nuclei and chromatin complexes were isolated with antibody to CTCF (Millipore 07-729) or normal Rabbit Ig control (Cell signaling Technology 2729).  Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq sample preparation kit  (Part#11257047 Rev.A). 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, size selection was performed by excising a band of 200±25 bp from an agarose gel to remove excess adapters. The gel purified  DNA was PCR amplified with Illumina primers for 15 cycles and purified by MinElute PCR purification kit according to manufacturer's instruction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No treatment was performed.

value: CTCF

tag: chip antibody vendor

value: Millipore

tag: chip antibody catalog#

tag: chip antibody lot#


title: BL41_Rabbit

description: Chromatin IP against Rabbit IgG

value: Normal Rabbit IgG

value: Cell signaling Technology


title: BL41_shRFP

description: RNA-seq


title: H3-HA (old) top1 deletion generation 3

source_name: H3-HA, top1 deletion, generation 3

value: HA

value: old


title: BJAB_CTCF

description: Chromatin IP against CTCF


title: hippocampus 1h following ECS replicate 1

description: Small RNA sequence data

value: hippocampus

tag: strain

value: 1 hr


title: BJAB_Rabbit

description: Chromatin IP against Rabbit IgG


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me2 in BMP4 Mesendoderm Cells; renlab.H3K79me2.BMP4M.02.01

status: Public on Oct 04 2011

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me2 in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK169
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9776
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7808
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM807401_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K79me2.AK169.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.BMP4M.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me2 ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK169, 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.12423
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 81,186,481
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.287
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2598
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9952
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4042
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM807401_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K79me2.AK169.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.BMP4M.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me2 ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK169, 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.12496
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 6
BROWSER_TRACK_NAME: HBDM H3K79me2 69
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me2 Library AK169 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 81,186,481
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.287
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2598
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9952
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4042
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K79me2.BMP4M.02.01

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

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

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

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

value: Between 20 and 30

tag: medium

tag: Sex

value: Male

tag: batch

value: Histone H3K79me2

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Broad_ChipSeq_HepG2_H3K4me1

status: Public on Oct 05 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

value: immortalized cell line

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell description

value: hepatocellular carcinoma

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me1

tag: antibody

tag: antibody targetdescription

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

tag: antibody vendorname

value: abcam

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: controlid

tag: replicate

tag: softwareversion

value: Abcam

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: replicate description

value: tier 1


title: H3-T7 (new) cac1 deletion generation 3

source_name: H3-T7, cac1 deletion, generation 3

tag: genotype

value: cac1 deletion

tag: epitope tag

tag: histone h3

value: new

tag: sampling time

value: after 3 cell divisions


title: Broad_ChipSeq_HeLa-S3_H3K4me1

tag: line

tag: datatype

tag: datatype description

tag: cell lineage

value: ectoderm

tag: antibody antibodydescription


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in BMP4 Mesendoderm Cells; renlab.H3K79me1.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK138
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9767
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM807398_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K79me1.AK138.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.BMP4M.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK138, 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.12437
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 92,240,217
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.0155
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.027
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9669
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1436
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM807398_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K79me1.AK138.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.BMP4M.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK138, 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.12510
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 6
BROWSER_TRACK_NAME: HBDM H3K79me1 38
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK138 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 92,240,217
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.0155
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.027
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9669
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1436
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K79me1.BMP4M.01.01

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: lineage

value: Embryonic Stem Cell

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

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

tag: passage

value: Between 20 and 30

tag: medium

tag: Sex

value: Male

tag: batch

value: Histone H3K79me1

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H4K5ac in BMP4 Mesendoderm Cells; renlab.H4K5ac.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K5ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina Genome Analayzer IIx platform.
Library name: AK131
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9778
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing: Various levels of processed data files will be made available as this project proceeds.

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H4K5ac.BMP4M.01.01

value: H1 BMP4 Derived Mesendoderm Cultured Cells

value: Histone H4K5ac

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in BMP4 Mesendoderm Cells; renlab.H3K79me1.BMP4M.02.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK168
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9770
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7808
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM807399_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K79me1.AK168.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.BMP4M.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK168, 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.12374
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 80,158,210
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.0698
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.1231
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.937
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4081
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM807399_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K79me1.AK168.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.BMP4M.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK168, 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.12447
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 6
BROWSER_TRACK_NAME: HBDM H3K79me1 68
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK168 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 80,158,210
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.0698
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.1231
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.937
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4081
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K79me1.BMP4M.02.01

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in BMP4 Mesendoderm Cells; renlab.H2AK5ac.BMP4M.02.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2AK5ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK170
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9586
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7808
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM807393_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2AK5ac.AK170.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.BMP4M.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2AK5ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK170, 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.12375
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 86,998,745
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0068
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0501
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.5765
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2496
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM807393_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2AK5ac.AK170.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.BMP4M.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2AK5ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK170, 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.12448
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 6
BROWSER_TRACK_NAME: HBDM H2AK5ac 70
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK170 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 86,998,745
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0068
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0501
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.5765
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2496
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H2AK5ac.BMP4M.02.01

value: genomic DNA

value: Histone H2AK5ac


title: Reference Epigenome: ChIP-Seq Analysis of H2BK5ac in BMP4 Mesendoderm Cells; renlab.H2BK5ac.BMP4M.02.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK5ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK171
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9763
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7808
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM807395_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK5ac.AK171.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.BMP4M.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK5ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK171, 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.12419
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 76,952,161
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.0546
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.095
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8959
IROC_PERCENTILE: 57
POISSON_SCORE: 0.2373
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM807395_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK5ac.AK171.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.BMP4M.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK5ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK171, 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.12492
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 6
BROWSER_TRACK_NAME: HBDM H2BK5ac 71
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK171 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 76,952,161
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.0546
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.095
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8959
IROC_PERCENTILE: 57
POISSON_SCORE: 0.2373
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H2BK5ac.BMP4M.02.01

value: James Thomson Laboratory

value: Cell Line

value: Histone H2BK5ac

value: Active Motif


title: BL41_shCTCF

description: RNA-seq

tag: cell line

value: Cell line derived from Burkitt's lymphoma

value: Multiple


title: Reference Epigenome: ChIP-Seq Analysis of H3T11ph in hESC H9 Cells; renlab.H3T11ph.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3T11ph in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK509
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9582
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6940
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM807403_UCSD.H9.H3T11ph.SK509.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3T11ph.hESC.H9.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3T11ph ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3T11ph ChIP-Seq on H9 Cell Line, Library SK509, 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.12436
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,179,386
NUMBER_OF_H3T11ph_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.02
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0632
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.7492
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1507
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM807403_UCSD.H9.H3T11ph.SK509.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3T11ph.hESC.H9.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3T11ph ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3T11ph ChIP-Seq read mappings from the H9 Cell Line, Library SK509, 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.12509
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 6
BROWSER_TRACK_NAME: H9 H3T11ph 09
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3T11ph Library SK509 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,179,386
NUMBER_OF_H3T11ph_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.02
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0632
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.7492
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1507
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3T11ph.hESC.H9.01.01

value: H9 Cell Line

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: mTeSER

value: Female

value: Histone H3T11ph


title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in BMP4 Mesendoderm Cells; renlab.H3K9ac.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina Genome Analayzer IIx platform.
Library name: AK128
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9774
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM807402_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K9ac.AK128.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.BMP4M.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK128, 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.12435
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,002,805
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.0777
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0962
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9928
IROC_PERCENTILE: 78
POISSON_SCORE: 0.1485
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

ANALYSIS FILE NAME: GSM807402_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K9ac.AK128.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.BMP4M.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK128, 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.12508
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 6
BROWSER_TRACK_NAME: HBDM H3K9ac 28
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK128 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,002,805
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.0777
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0962
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9928
IROC_PERCENTILE: 78
POISSON_SCORE: 0.1485
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K9ac.BMP4M.01.01

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

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

value: Between 20 and 30

value: Male

value: Histone H3K9ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: BJAB

description: RNA-seq

value: Cell line derived from Burkitt's lymphoma


title: Reference Epigenome: ChIP-Seq Analysis of H3K56ac in BMP4 Mesendoderm Cells; renlab.H3K56ac.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K56ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK174
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9765
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7808
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K56ac.BMP4M.01.01

value: H1 BMP4 Derived Mesendoderm Cultured Cells

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Histone H3K56ac

value: Upstate


title: Reference Epigenome: ChIP-Seq Analysis of H3K23me2 in hESC H9 Cells; renlab.H3K23me2.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23me2 in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK527
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9580
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6940
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM807396_UCSD.H9.H3K23me2.SK527.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23me2.hESC.H9.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K23me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23me2 ChIP-Seq on H9 Cell Line, Library SK527, 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.12416
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,105,459
NUMBER_OF_H3K23me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.1238
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.236
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9101
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3331
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM807396_UCSD.H9.H3K23me2.SK527.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23me2.hESC.H9.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K23me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23me2 ChIP-Seq read mappings from the H9 Cell Line, Library SK527, 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.12489
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 6
BROWSER_TRACK_NAME: H9 H3K23me2 27
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K23me2 Library SK527 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,105,459
NUMBER_OF_H3K23me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.1238
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.236
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9101
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3331
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K23me2.hESC.H9.02.01

value: H9 Cell Line

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: mTeSER

value: Female

value: Histone H3K23me2

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me2 in BMP4 Mesendoderm Cells; renlab.H3K79me2.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me2 in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK139
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9772
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K79me2.BMP4M.01.01

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

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

value: Between 20 and 30

value: Male

value: Histone H3K79me2

value: Biorupter

value: 500 micrograms

value: Active Motif


title: ActivatedBCell_AIDmm

status: Public on Oct 03 2011

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

description:
09-015_AIDmm
negative control ChIP from AID negative activated B cells

data_processing:
fastq: ***Raw data*** Image analysis, base calling, quality filtering:  Standard settings of GAPipeline 1.3+ using PhiX control; Fastq files contain full length reads (36nts) that passed the chastity filter. If necessary, quality scales were adjusted to phred64.
bedGraph: ***Peak finder results***.  Density of non-redundant alignments was determined in 100nt bins along the genome.  SICER 1.03 was used to detect regions of enrichment over a theoretical background model (e=0.00001).  BedGraph files show density in enriched regions only.

growth_protocol: CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech).  Following isolation, resting B cells were stimulated with LPS (50 mcg/ml) and IL-4 (2.5 ng/ml) for 72 hrs.

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37°C for 10 minutes followed by quenching with glycine and sonication. Chromatin fragments were then immunoprecipitated with the antibodies shown in the sample characteristics following standard protocols. Immunoprecipitates were processed following Illumina’s protocol and sequenced on a Genome Analyzer II.

tag: strain

tag: genotype/variation

value: AID-/-

tag: cell type

value: in vitro activated B cells

tag: chip target

value: AID

tag: chip antibody

value: Rabbit polyclonal described in Chaudhuri et al., Nature (2003)


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in BMP4 Mesendoderm Cells; renlab.H2AK5ac.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2AK5ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK126
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9578
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM807392_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2AK5ac.AK126.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.BMP4M.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2AK5ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK126, 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.12380
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,020,367
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.007
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0339
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.4802
IROC_PERCENTILE: 25
POISSON_SCORE: 0.174
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM807392_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2AK5ac.AK126.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.BMP4M.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2AK5ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK126, 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.12453
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 6
BROWSER_TRACK_NAME: HBDM H2AK5ac 26
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK126 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,020,367
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.007
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0339
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.4802
IROC_PERCENTILE: 25
POISSON_SCORE: 0.174
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H2AK5ac.BMP4M.01.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

tag: line

value: Embryonic Stem Cell

value: Histone H2AK5ac

value: magnetic anti-rabbit

value: 5 micrograms


title: tsb_total_RNA

status: Public on Oct 01 2011

city: Cambridge

first: Tsute

last: Chen

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

data_processing: Pileup forward: The Illumina sequence reads were mapped to the reference genome Porphyromonas gingivalis W83 (Accession No. NC_002950.2) using the software PerM allowing a maximum of two mismatches. Reads that did not align to the genome were trimmed from the 3' end, one base at a time, and the mapping-trimming process was repeated until the read was aligned or the trimmed length reached 24nt in length. Reads that were not aligned after being trimmed to 24-nt were discarded. The aligned results were separated into forward and reverse-complement groups and converted to the 'pileup' format by SAMtools. This process generated the reads that were mapped to the forward strand of the reference genome

organism: Porphyromonas gingivalis W83

source_name: P. gingivalis cells

growth_protocol: P. gingivalis strain W83 was routinely maintained on the blood agar plates BAPHK containing defibrinated sheep blood (5% v/v), hemin (1µg/ml), and vitK/menadione (0.5µg/ml), at 37°C in an anaerobic chamber containing 95% nitrogen and 5% carbon dioxide. Cells were cultured under the same conditions in three different media: i) BAPHK; ii) TSB: trypticase soy broth supplemented with hemin (1µg/ml) and vitK/menadione (0.5µg/ml); and iii) MIN: a chemically defined minimal liquid medium providing alpha-ketogluterate and bovine serum albumin (BSA) as the only protein sources. For BAPHK cultures, colonies grown on the plates for 48 hours were used. For liquid cultures, pre-warmed and pre-reduced medium was inoculated with an aliquot of overnight TSB culture so that the dilution rates were 1:100 and 2:100 for TSB and MIN, respectively. Liquid cultures were allowed to reach mid-log phase (OD550 0.4-0.5) prior to harvest.

extract_protocol: Lysis of pelleted cells was performed using the MasterPure RNA Purification Kit (Epicentre, Madison, WI, USA). The lysate was treated with Proteinase K at 65°C for 15 min and then filter purified applying the mirVana miRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the recommended protocol. To remove genomic DNA, the RNA extract was treated twice with Turbo DNase (Applied Biosystems/Ambion) at 37°C for 30 min, and purified again with the mirVana miRNA Isolation Kit. All samples were subjected to similar procedures except from the purifications steps where the mirVana filter based method was exchanged for MasterPure based RNA purification when preparing the MIN samples. The resulting total RNA samples were subject to partial removal of 16S and 23S RNAs applying the MICROBExpress Bacterial mRNA Enrichment Kit (Applied Biosystems/Ambion) and then fragmented with RNA Fragmentation Reagents (Applied Biosystems/Ambion) followed by ethanol precipitation. Antarctic Phosphatase (New England Biolabs, Cambridge, MA) was used, 5 U in a 20 ul reaction incubated at 37°C for 30 min, to remove 5' phosphate group from the RNA. Fragmented RNA was then subjected to size selection in a 15% Novex TBE-urea polyacrylamide gel (Invitrogen, Carlsbad, CA, USA), eluted, and ethanol precipitated prior to ligation of the 3' oligonucleotide adapter (5'-UCGUAUGCCGUCUUCUGCUUGUidT-3'). The adapter ligation was performed using T4 RNA ligase in 10% DMSO, incubated at 20°C for 6 hrs. The 3' adapter ligated RNA was purified on a 15% Novex TBE-urea polyacrylamide gel (Invitrogen), eluted, ethanol precipitated, and then phosphorylated in a 50 ul reaction containing 40 U T4 Polynucleotide Kinase (New England Biolabs) and 1 mM ATP (Epicentre) for 1h at 37°C. After phenol: chloroform purification and ethanol precipitation, the 5' oligonucleotide adapter (5'-GUUCAGAGUUCUACAGUCCGACGAUC-3') was ligated to the phosphorylated RNA under conditions similar to the 3' adapter ligation. The adapter ligated RNA was gel-purified and reverse transcribed using a primer specific to the 3' adapter (5'-CAAGCAGAAGACGGCATACGA-3') followed by PCR (15 cycles) using the reverse (5'-AATGATACGGCGACCACCGACAGGTTCAGAG TTCTACAGTCCGA-3') and forward (5'-CAAGCAGAAGACGGCATACGA-3') primers. The entire amplified product was size separated, ethanol precipitated, and dissolved in 10 ul resuspension buffer (Illumina) before the samples were subjected to sequencing.

value: TSB

tag: harvest time

value: mid-log phase


title: baphk_total_RNA

value: BAPHK

value: at 48 hours


title: GATA1 Replicate1

status: Public on Sep 30 2011

city: MADISON

first: Emery

middle: H

last: Bresnick

state: Wisconsin

address: 1111 Highland Avenue

department: Department of Cell and Regenerative Biology

institute: University of Wisconsin School of Medicine and Public Health

description: Chromatin IP against GATA1

data_processing: Sequence reads were aligned to the UCSC human genome assembly HG19 using the Eland pipeline (Illumina). Uniquely aligned sequences were used to identify GATA-1 occupancy peaks with Sole-search version 2 (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi). Peaks were called with an alpha value of 0.001 and an FDR of 0.0001 after merging two biological replicates together.

source_name: erythroblasts

growth_protocol: To differentiate erythroblasts from human peripheral blood mononuclear cells, fresh blood was collected in a heparin-containing tube, diluted with 2 to 4 volumes of PBS, and overlayed on Ficoll-Paque PLUS (GE Healthcare). Samples were centrifuged at 400 x g for 30 min at room temperature. The upper layer was removed, and mononuclear cells were washed twice with PBS. Mononuclear cells were cultured in StemSpan (STEMCELL Technologies) containing SCF (100 ng/ml), Flt3-L (33.3 ng/ml), IL-3 (13.3 ng/ml), BMP4 (13.3 ng/ml), EPO (2.67 U/ml) and 1 mM hydrocortisone (Sigma) for 7 days. Cells were then cultured in StemSpan with SCF (40 ng/ml), IGF-1 (40 ng/ml), IL-3 (13.3 ng/ml) BMP4 (13.3 ng/ml), EPO (3.3 U/ml) and hydrocortisone (1 mM) for another 7 days. Fresh medium was added every other day, and the cell density was maintained at ~3 x 105/ml. After 14 days, cells were collected by centrifugation at 2500 x g for 10 min, washed twice with PBS, and crosslinked with 1% formaldehyde in PBS for 10 min. The reaction was stopped by adding glycine at a final concentration of 125 mM. After 5 min, cells were washed twice with ice-cold PBS (Ca2+/Mg2+-free), collected by centrifugation at 2000 x g at 4°C and flash frozen in liquid nitrogen.

extract_protocol: ChIP assays were conducted with crosslinked human peripheral blood mononuclear cell-derived erythroblasts as described previously (O'Geen H et.al, 2010). Chromatin from 108 cells was incubated with 60 μl rabbit polyclonal anti-GATA-1 antibody. Following overnight incubation at 4°C, protein/DNA complexes were captured with 100 µl Staph-Seq (Sigma). After washing, crosslinks were reversed, DNA purified, and qPCR was used to confirm enrichment of target sequences in ChIP versus input samples. Libraries were created as described with minor modifications. Gel size selection of the 150-450 bp fraction was conducted after the adapter ligation step, followed by 18 amplification cycles. ChIP-seq libraries were analyzed with an Illumina GAIIx.

value: primary human PBMC derived erythroblasts

value: GATA1 made in-house