title: Gro-seq-siBcataninsiSATB1

description:
Nascent RNA sequencing
Gro-seq in rat GC pituitary cells transfected with siRNA specific against JMJD6 (Qiagen)

data_processing:
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the rn4 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.

extract_protocol:
GC cells were in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5min on ice and harvested. Cells were first re-suspended and lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol). The resultant nuclei were washed once again with 10 ml lysis buffer and then re-suspended in 100ml of freezing buffer (50mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).
For run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase In, 1% sarkosyl, 500mM ATP, GTP, and Br-UTP, 2mM CTP) and incubated for 5 min at 30°C. The nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Invitogen) following manufacturer’s instructions. NRO-RNA was then subjected to base hydrolysis on ice for 40 min and followed by treatment with DNase I and antarctic phosphatase. To purify the Br-UTP labeled nascent RNA, the NRO-RNA was immunoprecipitated with an anti-BrdU agarose beads (Santa Cruz Biotech) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween-20) for 1h at 4°C while rotating.  To repair the end, the immunoprecipitated BrU-RNA was re-suspended in 50mL reaction (43mL DEPC water, 5.2mL T4 PNK buffer, 1mL SUPERase In and 1mL T4 PNK (New England BioLabs)) and incubated at 37°C for 1h. RNA was then extracted, precipitated using acidic phenol-chloroform (Ambion) and subjected to poly-A tailing reaction by using poly-A polymerase (New England BioLabs) for 30 min at 37°C. Subsequently, reverse transcription was performed using oNTI223- primers (5’- pGATCGTCGGACTGTAGAACTCT; CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’) where the p indicates 5’ phosphorylation, ‘;’ indicates the abasic dSpacer furan and VN indicates degenerate nucleotides. Specifically, tailed RNA (8.0mL) was subjected to reverse transcription using superscript III (Invitrogen), after which the cDNA products were separated on a 10% polyacrylamide TBE-urea gel. The extended first-strand product (100-500bp) was excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1 (New England BioLabs). Re-linearized single strand cDNA (sscDNA) was separated in a 10% polyacrylamide TBE gel as described above and the product of needed size was excised (~170-400bp) for gel extraction. Finally, sscDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB) according to the manufacturer’s instructions. Primers oNTI200 (5’-CAAGCAGAAGACGGCATA-3’) and oNTI201 (5’- AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG-3’) were used to generate DNAs for deep sequencing.

tag: transfection

value: siRNA specific against JMJD6 (Qiagen)


title: Cdk8_mES_r1_ChipSeq

status: Public on Aug 03 2014

type: SRA

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description:
Chromatin IP against Cdk8_mES_r1
08082012_C12E8ACXX_2.GAGTGG

library_source: genomic

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 (human); mm8 (mouse)
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

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

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

tag: chip antibody

tag: antibody catalog number

value: Santa Cruz SC-1521

tag: cell type

value: V6.5 embryonic stem cells


title: Sox2GFP_K27Ac_ChipSeq

description:
Chromatin IP against Sox2GFP_K27Ac
04252013_D24CWACXX_3.GCCAAT

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For samples MEF_WCE_ChipSeq, MEF_K27Ac_ChipSeq, 13F_WCE_ChipSeq, Sox2GFP_WCE_ChipSeq, 13F-K27Ac_ChipSeq, and Sox2GFP_K27Ac_ChipSeq reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
For samples AD-12-Med1-Skeletal_ChipSeq and AD-1-WCE-astrocytes_ChipSeq reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 (human); mm8 (mouse)
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Neural Progenitors

growth_protocol: Jaenisch lab- John Cassady

tag: chip-seq antibody

value: Abcam AB4729

tag: cll type

value: Sox2-GFP primary


title: Total mRNA of Cd25pos Mast Cells (rep 1)

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

library_source: transcriptomic

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and a mean distance between pairs (-r) of 120bp
Transcripts abundances were quantified and differentially expressed genes were called using Cufflinks 2.0.2 (PMID: 20436464), using default parameters and -N -u arguments
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM), *.diff list the statistics for differential expression among Cd25plus and Cd25minus (refer to http://cufflinks.cbcb.umd.edu/manual.html for details)

molecule: total RNA

growth_protocol: Primary murine mast cells were differentiated from bone marrow of C57BL/6 mice as previously described (PMID: 20827536) and cultured in the presence of IL-3 as survival factor. Briefly, bone marrow cells were isolated from femurs and tibias of 6-12 weeks old C57BL/6 mice and differentiated in IMDM complete medium until they were homogeneously mast cells (>95% Kit+ FcepsilonRIalpha+ at surface staining) (IMDM complete medium: Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% (v/v) heat-inactivated fetal bovine serum, 2 mM L-glutamine, 100 U/mL penicillin, 100 mg/mL streptomycin, 0.1 mM nonessential amino acids, and 50 mM beta-mercaptoethanol, recombinant murine IL-3). After 5 weeks of differentiation, bone marrow-derived mast cells (BMMCs) from two independent cultures underwent surface staining for CD25 expression and were FACS-sorted in CD25pos and CD25neg populations. After sorting, the CD25neg population was > 99% pure, and the CD25pos was 86-96% pure.

extract_protocol: Total RNA was extracted immediately after sorting and subjected to library preparation under Standard Illumina Protocol.

tag: strain

value: Primary bone marrow-derived mast cells (BMMCs)

tag: cell stage

value: 5th day of differentiation

tag: cell subpopulation

value: FACS-sorted CD25pos cells


title: Chipseq-H2K4me2

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

description: H3K4me2 ChIP-seq in rat GC pituitary cells

data_processing:
Basecalls performed using CASAVA version 1.4
reads were aligned to the rn4 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.

organism: Rattus norvegicus

source_name: rat GC pituitary cells

growth_protocol: GC cells are grown in Untraculture medium containing 5% FBS

extract_protocol:
For ChIP-seq, fixation was stopped by adding Glycine (0.125M) and incubating for 5 min at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300–500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4°C, followed by incubation with protein G magnetic beads (Invitrogen) for an additional 2 h. After washing and elution, the protein–DNA complex was reversed by heating at 65°C overnight. For samples fixed with glutaraldehyde, proteinase K (0.3mg/ml) (Ambion) was added during de-crosslinking. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) ;
the libraries were constructed following Illumina’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: siRNA and overexpression experiments in GC cells were performed using Neon system (Invitrogen). Conditions of 2 pulses of 1150 V with 30ms spacing were used. 100 nM siRNA and 3ug of DNA were used per 3x106 cells. Knockdown was repeated after 48h to obtain optimal depletion of the protein, verified by Western blotting.

value: rat GC pituitary cells

tag: chip antibody vendor

value: Millipore 07-030


title: Total mRNA of Cd25pos Mast Cells (rep 2)


title: Total mRNA of Cd25minus Mast Cells (rep 2)

value: FACS-sorted CD25neg cells


title: Total mRNA of Cd25minus Mast Cells (rep 1)


title: Gro-seq-siCTL

description:
Nascent RNA sequencing
Gro-seq in rat GC pituitary cells transfected with control siRNA

value: control siRNA


title: RPE-CTCF_ChipSeq

description:
Chromatin IP against RPE-CTCF
05042013_D269BACXX_7.CAGATC

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For samples RPE-WCE(2)_ChipSeq, RPE-H3K27ac_ChipSeq, RPE-WCE(3)_ChipSeq, RPE-CTCF_ChipSeq, RPE-E2F4_ChipSeq, RPE-POLII_ChipSeq, and ZNF92_Abgent_AT4646a_ChipSeq reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
For samples AD-3-WCE-Retina_ChipSeq reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

organism: Homo sapiens

source_name: Retinal pigment cells, science cell

growth_protocol: sciencell epithelial media

value: CTCF

value: Upstate 07-729

value: Retinal pigment cells #6540


title: Chipseq-BLRP-Bcatenin

description: BLRP-Bcatenin ChIP-seq in rat GC pituitary cells

value: BLRP-Bcatenin

value: Streptavidin beads


title: 13F-K27Ac_ChipSeq

description:
Chromatin IP against 13F-K27Ac
04252013_D24CWACXX_3.CAGATC

value: iNPC-derived from fibroblasts-clone 13F


title: Chipseq-matrin3

description: Matrin3 ChIP-seq in rat GC pituitary cells


title: Chipseq-HA-Pit1wt

description: HA-Pit1wild type ChIP-seq in rat GC pituitary cells


title: Sox2GFP_WCE_ChipSeq

description:
Chromatin IP against Sox2GFP_WCE
04252013_D24CWACXX_2.TTAGGC

value: None WCE


title: 13F_WCE_ChipSeq

description:
Chromatin IP against 13F_WCE
04252013_D24CWACXX_2.TGACCA


title: MEF_K27Ac_ChipSeq

description:
Chromatin IP against MEF_K27Ac
04252013_D24CWACXX_3.ACTTGA

source_name: Mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts were grown in DMEM with 10% FBS.

value: MEF


title: MEF_WCE_ChipSeq

description:
Chromatin IP against MEF_WCE
04252013_D24CWACXX_2.ACAGTG


title: PG0198_A01

status: Public on Aug 02 2014

city: Tokyo

first: Shurei

last: Sugita

address: 7-3-1, Hongo, Bunkyo-ku

department: Sensory & Motor System Medicine

country: Japan

institute: The University of Tokyo

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7
peaks were called using MACS version 1.4.2 with the following setting: ChIP gsize(2700000000) mfold (7,30).
Genome_build: hg19
Supplementary_files_format_and_content: PG0198_A01_annotation.xlsx: annotation data of enrich area with neighborhood gene information. Three bed files were generated for UCSC genome browser. Each file represented the site of enrich area (*region.bed), depth of sequencing (*depth.bed), mapping information of unique hit sequence (*read_uniq.bed).

source_name: SW1353 cells

growth_protocol: SW1353 cells transfected with FLAG-tagged HES1 by in DMEM with 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
All protocols for TruSeq ChIP Sample Preparation Guide Rev. A (Illmina)

tag: cell line

value: Human chodrogenic cells

tag: transfected with

value: FLAG-tagged HES1

tag: passage

tag: chip-antibody

value: Anti-FLAG M2 Affinity Antibody

value: SIGMA

tag: chip-antibody cat. #

tag: chip-antibody lot #


title: Chipseq-H3K27ac

description: H3K27ac ChIP-seq in rat GC pituitary cells


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r1); Sample_GH278A_2/GH278A_2_NoIndex_L004_R1_001.fastq.gz

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
Library strategy: TAB-Seq
Library name: GH278_L4.2013_07_31
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19721
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); 2013_07_31_FISH_SR_Q33_A/fastq/Project_GH/Sample_GH278A_2/GH278A_2_NoIndex_L004_R1_001.fastq.gz

extract_protocol: Library construction protocol: See http://www.nature.com/nprot/journal/v7/n12/full/nprot.2012.137.html

tag: sra sample accession

tag: disease

value: Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: embryonic stem cell differentiated into mesendoderm cells

value: H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium

tag: medium

value: TeSR

tag: Sex

value: Male

tag: batch

value: Replicate 1

value: DNA Methylation

value: Covaris

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.

value: Standard Illumina adaptor sequence

value: TruSeq

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)

value: not measured

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq

value: undiluted Illumina TruSeq kit PCR primers

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r1); Sample_GH278_2/GH278_2_NoIndex_L002_R1_001.fastq.gz

description:
sample_term_id: NTR_0000856
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH278_L2.2013_07_31
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19719
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); 2013_07_31_FISH_SR_Q33_A/fastq/Project_GH/Sample_GH278_2/GH278_2_NoIndex_L002_R1_001.fastq.gz

value: Thomson Laboratory

value: Cell Line


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r1); Sample_GH278B_2/GH278B_2_NoIndex_L007_R1_001.fastq.gz

description:
sample_term_id: NTR_0000856
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH278_L7.2013_07_31
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19709
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); 2013_07_31_FISH_SR_Q33_A/fastq/Project_GH/Sample_GH278B_2/GH278B_2_NoIndex_L007_R1_001.fastq.gz

value: embryonic stem cell differentiated into mesendoderm cells

value: H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r1); Sample_GH278B_1/GH278B_1_NoIndex_L006_R1_001.fastq.gz

description:
sample_term_id: NTR_0000856
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH278B_L6.2013_07_31
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19723
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); 2013_07_31_FISH_SR_Q33_A/fastq/Project_GH/Sample_GH278B_1/GH278B_1_NoIndex_L006_R1_001.fastq.gz

value: TeSR

value: Male


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r1); Sample_GH278_1/GH278_1_NoIndex_L001_R1_001.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH278_L1.2013_07_31
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19718
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); 2013_07_31_FISH_SR_Q33_A/fastq/Project_GH/Sample_GH278_1/GH278_1_NoIndex_L001_R1_001.fastq.gz

value: Replicate 1

value: DNA Methylation


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r1); 2013_08_07_FISH_SR_Q33_A/fastq/GH278B.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH278B.2013_08_07
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19717
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); 2013_08_07_FISH_SR_Q33_A/fastq/GH278B.fastq.gz

value: Covaris

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r1); Sample_GH278A_1/GH278A_1_NoIndex_L003_R1_001.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH278A_L3.2013_07_31
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19720
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); 2013_07_31_FISH_SR_Q33_A/fastq/Project_GH/Sample_GH278A_1/GH278A_1_NoIndex_L003_R1_001.fastq.gz

value: Standard Illumina adaptor sequence

value: TruSeq


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r1); 2013_08_07_FISH_SR_Q33_A/fastq/GH278A.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH278A.2013_08_07
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19706
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); 2013_08_07_FISH_SR_Q33_A/fastq/GH278A.fastq.gz

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)

value: not measured


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r1); Sample_GH278A_3/GH278A_3_NoIndex_L005_R1_001.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH278A_L5.2013_07_31
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19722
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); 2013_07_31_FISH_SR_Q33_A/fastq/Project_GH/Sample_GH278A_3/GH278A_3_NoIndex_L005_R1_001.fastq.gz

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r1); 2013_08_07_FISH_SR_Q33_A/fastq/GH278.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH278.2013_08_07
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19707
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); 2013_08_07_FISH_SR_Q33_A/fastq/GH278.fastq.gz

value: undiluted Illumina TruSeq kit PCR primers

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r2); 2013_02_01_FISH_SR_flowcell-B/GH266.fastq.gz

description:
sample_term_id: NTR_0000856
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH266_IDX_6.2013_02_01
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19740
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10253
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 2 (r2); 2013_02_01_FISH_SR_flowcell-B/fastq_files/GH266.fastq.gz

value: Thomson Laboratory

value: Cell Line

value: Replicate 2


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r2); 2013_04_24_FISH_SR_flowcell-A/lane7_6.fastq.bz2

description:
sample_term_id: NTR_0000856
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH266B_L7.2013_04_24
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19783
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10253
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 2 (r2); 2013_04_24_FISH_SR_flowcell-A/fastq_files/lane7_6.fastq.bz2

value: embryonic stem cell differentiated into mesendoderm cells

value: H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium

value: TeSR


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r2); 2013_03_26_ChIP_SR_flowcell-B/lane7.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH266B_L7.2013_03_26
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19726
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10253
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 2 (r2); 2013_03_26_ChIP_SR_flowcell-B/fastq_files/lane7.fastq.bz2

value: Male

value: DNA Methylation


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r2); 2013_03_20_FISH_SR_flowcell-B/lane4.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH266A_L4.2013_03_20
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19759
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10253
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 2 (r2); 2013_03_20_FISH_SR_flowcell-B/fastq_files/lane4.fastq.bz2

value: Covaris

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r2); 2013_03_27_ChIP_SR_flowcell-A/lane7.fastq.bz2

description:
sample_term_id: NTR_0000856
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH265B_L7.2013_03_27
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19733
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10253
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 2 (r2); 2013_03_27_ChIP_SR_flowcell-A/fastq_files/lane7.fastq.bz2

value: Standard Illumina adaptor sequence

value: TruSeq


title: TAB-Seq: H1 Cell Line treated with BMP4 (r2); 2013_03_27_ChIP_SR_flowcell-A/lane6.fastq.bz2

description:
sample_term_id: UBERON_0000088
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH265B_L6.2013_03_27
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19732
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3378
****************
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: H1 Cell Line treated with BMP4, biological replicate 2 (r2); 2013_03_27_ChIP_SR_flowcell-A/fastq_files/lane6.fastq.bz2

value: embryonic stem cell differentiated by treatment with BMP4

value: H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days

value: 25, including 10 passages in TeSR

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)

value: not measured


title: TAB-Seq: H1 Cell Line treated with BMP4 (r2); 2013_02_01_FISH_SR_flowcell-B/GH265.fastq.gz

description:
sample_term_id: UBERON_0000088
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH265_IDX_5.2013_02_01
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19741
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3378
****************
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: H1 Cell Line treated with BMP4, biological replicate 2 (r2); 2013_02_01_FISH_SR_flowcell-B/fastq_files/GH265.fastq.gz

value: Thomson Laboratory

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq

value: undiluted Illumina TruSeq kit PCR primers

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r2); 2013_03_27_ChIP_SR_flowcell-A/lane1.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH266A_L1.2013_03_27
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19727
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10253
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 2 (r2); 2013_03_27_ChIP_SR_flowcell-A/fastq_files/lane1.fastq.bz2

value: Cell Line

value: embryonic stem cell differentiated into mesendoderm cells

value: H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium

value: TeSR

value: Replicate 2


title: TAB-Seq: H1 Cell Line treated with BMP4 (r2); 2013_03_20_FISH_SR_flowcell-B/lane7.fastq.bz2

description:
sample_term_id: UBERON_0000088
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH265B_L7.2013_03_20
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19762
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3378
****************
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: H1 Cell Line treated with BMP4, biological replicate 2 (r2); 2013_03_20_FISH_SR_flowcell-B/fastq_files/lane7.fastq.bz2

value: Male

value: DNA Methylation

value: Covaris

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.

value: Standard Illumina adaptor sequence


title: TAB-Seq: H1 Cell Line treated with BMP4 (r2); 2013_03_20_FISH_SR_flowcell-B/lane3.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH265A_L3.2013_03_20
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19758
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3378
****************
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: H1 Cell Line treated with BMP4, biological replicate 2 (r2); 2013_03_20_FISH_SR_flowcell-B/fastq_files/lane3.fastq.bz2

value: embryonic stem cell differentiated by treatment with BMP4

value: H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days

value: 25, including 10 passages in TeSR

value: TruSeq

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)


title: TAB-Seq: H1 Cell Line treated with BMP4 (r2); 2013_03_26_ChIP_SR_flowcell-B/lane5.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH265A_L5.2013_03_26
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19738
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3378
****************
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: H1 Cell Line treated with BMP4, biological replicate 2 (r2); 2013_03_26_ChIP_SR_flowcell-B/fastq_files/lane5.fastq.bz2

value: Thomson Laboratory

value: not measured

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq

value: undiluted Illumina TruSeq kit PCR primers


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r2); 2013_03_27_ChIP_SR_flowcell-A/lane5.fastq.bz2

description:
sample_term_id: CL_0000047
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH264B_L5.2013_03_27
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19731
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6200
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 2 (r2); 2013_03_27_ChIP_SR_flowcell-A/fastq_files/lane5.fastq.bz2

value: Cell Line

value: embryonic stem cell differentiated into neural progenitor cells

value: H1 cells were differentiated by culturing in insulin, SB, Noggin

value: TeSR

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r2); 2013_02_01_FISH_SR_flowcell-B/GH264.fastq.gz

description:
sample_term_id: CL_0000047
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH264_IDX_4.2013_02_01
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19742
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6200
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 2 (r2); 2013_02_01_FISH_SR_flowcell-B/fastq_files/GH264.fastq.gz

value: Male

value: Replicate 2

value: DNA Methylation

value: Covaris

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r2); 2013_03_20_FISH_SR_flowcell-B/lane6.fastq.bz2

description:
sample_term_id: CL_0000047
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH264B_L6.2013_03_20
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19761
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6200
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 2 (r2); 2013_03_20_FISH_SR_flowcell-B/fastq_files/lane6.fastq.bz2

value: Standard Illumina adaptor sequence

value: TruSeq


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r2); 2013_03_27_ChIP_SR_flowcell-A/lane4.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH264B_L4.2013_03_27
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19730
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6200
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 2 (r2); 2013_03_27_ChIP_SR_flowcell-A/fastq_files/lane4.fastq.bz2

value: Thomson Laboratory

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r2); 2013_03_26_ChIP_SR_flowcell-B/lane4.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH264A_L4.2013_03_26
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19737
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6200
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 2 (r2); 2013_03_26_ChIP_SR_flowcell-B/fastq_files/lane4.fastq.bz2

value: not measured

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r2); 2013_02_01_FISH_SR_flowcell-B/GH263.fastq.gz

description:
sample_term_id: EFO_0000586
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH263_IDX_2.2013_02_01
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19743
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11128
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 2 (r2); 2013_02_01_FISH_SR_flowcell-B/fastq_files/GH263.fastq.gz

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

value: standard Illumina TruSeq

value: undiluted Illumina TruSeq kit PCR primers


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r2); 2013_03_26_ChIP_SR_flowcell-B/lane3.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH264A_L3.2013_03_26
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19736
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6200
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 2 (r2); 2013_03_26_ChIP_SR_flowcell-B/fastq_files/lane3.fastq.bz2

value: Cell Line

value: embryonic stem cell differentiated into neural progenitor cells

value: H1 cells were differentiated by culturing in insulin, SB, Noggin

value: TeSR

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r2); 2013_03_20_FISH_SR_flowcell-B/lane5.fastq.bz2

description:
sample_term_id: EFO_0000586
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH263B_L5.2013_03_20
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19760
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11128
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 2 (r2); 2013_03_20_FISH_SR_flowcell-B/fastq_files/lane5.fastq.bz2

value: Male

value: Replicate 2

value: DNA Methylation

value: Covaris

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r2); 2013_03_27_ChIP_SR_flowcell-A/lane3.fastq.bz2

description:
sample_term_id: EFO_0000586
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH263B_L3.2013_03_27
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19729
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11128
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 2 (r2); 2013_03_27_ChIP_SR_flowcell-A/fastq_files/lane3.fastq.bz2

value: Thomson Laboratory

value: Standard Illumina adaptor sequence

value: TruSeq

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)

value: not measured


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r2); 2013_04_24_FISH_SR_flowcell-A/lane5_2.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH263B_L5.2013_04_24
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19724
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11128
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 2 (r2); 2013_04_24_FISH_SR_flowcell-A/fastq_files/lane5_2.fastq.bz2

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq


title: TAB-Seq: H1 Cell Line treated with BMP4 (r2); 2013_03_26_ChIP_SR_flowcell-B/lane6.fastq.bz2

description:
sample_term_id: UBERON_0000088
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH265A_L6.2013_03_26
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19755
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3378
****************
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: H1 Cell Line treated with BMP4, biological replicate 2 (r2); 2013_03_26_ChIP_SR_flowcell-B/fastq_files/lane6.fastq.bz2

value: Cell Line

value: embryonic stem cell differentiated by treatment with BMP4

value: H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days

value: 25, including 10 passages in TeSR

value: TeSR

value: undiluted Illumina TruSeq kit PCR primers


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r2); 2013_03_20_FISH_SR_flowcell-B/lane1.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH263A_L1.2013_03_20
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19756
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11128
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 2 (r2); 2013_03_20_FISH_SR_flowcell-B/fastq_files/lane1.fastq.bz2

value: Male

value: Replicate 2

value: DNA Methylation

value: Covaris

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r2); 2013_03_26_ChIP_SR_flowcell-B/lane1.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH263A_L1.2013_03_26
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19734
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11128
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 2 (r2); 2013_03_26_ChIP_SR_flowcell-B/fastq_files/lane1.fastq.bz2

value: Thomson Laboratory

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: Standard Illumina adaptor sequence

value: TruSeq

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)

value: not measured


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r2); 2013_04_24_FISH_SR_flowcell-A/lane6_6.fastq.bz2

description:
sample_term_id: NTR_0000856
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH266B_L6.2013_04_24
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19725
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10253
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 2 (r2); 2013_04_24_FISH_SR_flowcell-A/fastq_files/lane6_6.fastq.bz2

value: Cell Line

value: embryonic stem cell differentiated into mesendoderm cells

value: H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq


title: TAB-Seq: H1 cell line treated with BMP4 and Activin A (r2); 2013_03_27_ChIP_SR_flowcell-A/lane2.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH266A_L2.2013_03_27
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19728
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10253
****************
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: H1 cell line treated with BMP4 and Activin A biological replicate 2 (r2); 2013_03_27_ChIP_SR_flowcell-A/fastq_files/lane2.fastq.bz2

value: TeSR

value: Male

value: undiluted Illumina TruSeq kit PCR primers


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r2); 2013_03_26_ChIP_SR_flowcell-B/lane2.fastq.bz2

description:
sample_term_id: EFO_0000586
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH263A_L2.2013_03_26
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19735
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11128
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 2 (r2); 2013_03_26_ChIP_SR_flowcell-B/fastq_files/lane2.fastq.bz2

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

value: Replicate 2

value: DNA Methylation

value: Covaris


title: Young rep3

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

description: MeDIP library for the paired-end sequencing in 50 bp read length

data_processing:
Raw sequencing data were processed by Illumina base-calling pipeline. After filtering the low quality reads, the MeDIP-seq data were aligned to the UCSC pig reference genome (Sscrofa9.2) using SOAP2 (Version 2.21). The paired-end mapped reads were defined as fragments (BED file) that were used in further analysis.
Genome_build: Sscrofa9.2
Supplementary_files_format_and_content: The processed data is BED file, which contains chromsome, fragment start site and fragment end site

organism: Sus scrofa

source_name: LDM: longissimus dorsi muscle

growth_protocol: pigs aged 7 years old (MA) and 0.5 year old (Young)

extract_protocol:
DNA of each collected tissue was extracted using DNeasy Blood & Tissue Kit (Qiagen)
Each MeDIP library was subjected to the paired-end sequencing using Illumina HiSeq 2000 and in 50 bp read length. Five µg original DNA was isolated using E.Z.N.A.® HP Tissue DNA Midi Kit (OMEGA) and was sonicated to ~ 100 – 500 bp fragments with a Bioruptor sonicator (Diagenode). Then libraries were constructed using the Illumina Paired-End protocol consisting of end repair, <A> base addition and adaptor ligation steps, and were performed using Illumina’s Paired-End DNA Sample Prep kit following the manufacturer’s instructions. Adaptor-ligated DNA was immunoprecipitated by monoclonal anti-methylcytidine antibody. The specificity of the enrichment were confirmed by qPCR using SYBR green mastermix (Applied Biosystems) and primers for positive and negative internal control DNA of non-human samples were supplied in the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode). Cycling of qPCR validation was  95℃ 5 min, followed by 40 cycles 95℃ 15 s and 60℃ 1 min. The enriched fragments with methylation and 10% input DNA were purified on ZYMO DNA Clean & Concentrator-5 columns following the manufacturer’s instructions. DNA was eluted in 30 µl buffer EB and its concentration was measured. Enriched fragments was amplified by adaptor-mediated PCR in a final reaction volume of 50 µl consisting of 23 µl purified DNA, 25 µl Phusion DNA polymerase mix (NEB) and 2µl PCR primers. Amplification consisted of 94℃ 30 s, 10 cycles of 94℃ 30s, 60℃ 30 s, 72℃ 30 s then prolong with 5 min at 72℃ and products could be hold at 4℃. Amplifications quality and quantity were evaluated by Agilent 2100 Analyzer DNA 1000 chips purified by 2% agarose gel and eluted in 15 µl buffer EB. Ultra-high-throughput 50 bp pair-end sequencing was carried out using the Illumina HiSeq 2000 according to manufacturer instructions. Raw sequencing data were processed by Illumina base-calling pipeline.

tag: breed

value: Jinhua pig

tag: gender

value: female

tag: age

value: 0.5 years old


title: TAB-Seq: H1 Cell Line treated with BMP4 (r1); 2012_12_13_ChIP_SR_flowcell-A/GH259.fastq.gz

description:
sample_term_id: UBERON_0000088
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH259_IDX5.2012_12_13
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19708
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3377
****************
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: H1 Cell Line treated with BMP4, biological replicate 1 (r1); 2012_12_13_ChIP_SR_flowcell-A/fastq_files/GH259.fastq.gz

value: Thomson Laboratory

value: embryonic stem cell differentiated by treatment with BMP4

value: H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days

value: 27, including 16 passages in TeSR

value: Replicate 1

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.

value: Standard Illumina adaptor sequence

value: TruSeq

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)

value: not measured

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: TAB-Seq: H1 Cell Line treated with BMP4 (r1); 2013_02_15_FISH_SR_flowcell-B/lane5.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH259A_L5.2013_02_15
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19749
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3377
****************
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: H1 Cell Line treated with BMP4, biological replicate 1 (r1); 2013_02_15_FISH_SR_flowcell-B/fastq_files/lane5.fastq.bz2

value: Cell Line

value: TeSR

value: Male

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq

value: undiluted Illumina TruSeq kit PCR primers


title: TAB-Seq: H1 Cell Line treated with BMP4 (r1); 2013_01_24_ChIP_SR_flowcell-A/UCSD_C16BPACXX_3.fastq.gz

description:
sample_term_id: UBERON_0000088
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH259A_L3.2013_01_24
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19746
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3377
****************
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: H1 Cell Line treated with BMP4, biological replicate 1 (r1); 2013_01_24_ChIP_SR_flowcell-A/fastq_files/UCSD_C16BPACXX_3.fastq.gz

value: Thomson Laboratory

value: DNA Methylation

value: Covaris


title: TAB-Seq: H1 Cell Line treated with BMP4 (r1); 2013_02_15_FISH_SR_flowcell-B/lane6.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH259A_L6.2013_02_15
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19748
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3377
****************
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: H1 Cell Line treated with BMP4, biological replicate 1 (r1); 2013_02_15_FISH_SR_flowcell-B/fastq_files/lane6.fastq.bz2

value: embryonic stem cell differentiated by treatment with BMP4

value: H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days

value: 27, including 16 passages in TeSR


title: Young rep2

value: Jinhua pig

value: female

value: 0.5 years old


title: Young rep1


title: TAB-Seq: H1 Cell Line treated with BMP4 (r1); 2013_02_22_FISH_SR_flowcell-B/lane5.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH259B_L5.2013_02_22
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19752
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3377
****************
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: H1 Cell Line treated with BMP4, biological replicate 1 (r1); 2013_02_22_FISH_SR_flowcell-B/fastq_files/lane5.fastq.gz

value: Replicate 1

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.

value: Standard Illumina adaptor sequence

value: TruSeq

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)

value: not measured


title: TAB-Seq: H1 Cell Line treated with BMP4 (r1); 2013_01_24_ChIP_SR_flowcell-A/UCSD_C16BPACXX_6.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH259B_L6.2013_01_24
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19744
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3377
****************
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: H1 Cell Line treated with BMP4, biological replicate 1 (r1); 2013_01_24_ChIP_SR_flowcell-A/fastq_files/UCSD_C16BPACXX_6.fastq.gz

value: Cell Line

value: TeSR

value: Male

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: MA rep3

value: 7 years old


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r2); 2013_03_20_FISH_SR_flowcell-B/lane2.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH264A_L2.2013_03_20
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19757
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6200
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 2 (r2); 2013_03_20_FISH_SR_flowcell-B/fastq_files/lane2.fastq.bz2

value: Thomson Laboratory

value: embryonic stem cell differentiated into neural progenitor cells

value: H1 cells were differentiated by culturing in insulin, SB, Noggin

value: Replicate 2

value: DNA Methylation

value: Covaris

value: undiluted Illumina TruSeq kit PCR primers


title: MA rep2

value: Jinhua pig

value: female


title: MA rep1


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r1); 2013_02_15_FISH_SR_flowcell-B/lane4.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH258A_L4.2013_02_15
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19750
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6199
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 1 (r1); 2013_02_15_FISH_SR_flowcell-B/fastq_files/lane4.fastq.bz2

value: Replicate 1

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.

value: Standard Illumina adaptor sequence

value: TruSeq

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)

value: not measured


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r1); 2013_02_22_FISH_SR_flowcell-B/lane2.fastq.gz

description:
sample_term_id: CL_0000047
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH258B_L2.2013_02_22
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19763
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6199
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 1 (r1); 2013_02_22_FISH_SR_flowcell-B/fastq_files/lane2.fastq.gz

value: Cell Line

value: TeSR

value: Male

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r1); 2012_12_13_ChIP_SR_flowcell-A/GH258.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH258_IDX4.2012_12_13
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19739
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6199
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 1 (r1); 2012_12_13_ChIP_SR_flowcell-A/fastq_files/GH258.fastq.gz

value: Thomson Laboratory

value: embryonic stem cell differentiated into neural progenitor cells

value: H1 cells were differentiated by culturing in insulin, SB, Noggin

value: DNA Methylation


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r1); UCSD_C16BPACXX_2.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH258A_L2.2013_01_24
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19747
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6199
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 1 (r1); 2013_01_24_ChIP_SR_flowcell-A/fastq_files/UCSD_C16BPACXX_2.fastq.gz

value: Covaris

value: undiluted Illumina TruSeq kit PCR primers


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r1); 2012_12_13_ChIP_SR_flowcell-A/GH257.fastq.gz

description:
sample_term_id: EFO_0000586
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH257_IDX2.2012_12_13
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19716
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11127
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 1 (r1); 2012_12_13_ChIP_SR_flowcell-A/fastq_files/GH257.fastq.gz

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

value: Replicate 1

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r1); 2013_01_24_ChIP_SR_flowcell-A/UCSD_C16BPACXX_4.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH257B_L4.2013_01_24
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19714
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11127
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 1 (r1); 2013_01_24_ChIP_SR_flowcell-A/fastq_files/UCSD_C16BPACXX_4.fastq.gz

value: Cell Line

value: Standard Illumina adaptor sequence

value: TruSeq

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)

value: not measured


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r1); 2013_02_22_FISH_SR_flowcell-B/lane1.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH257B_L1.2013_02_22
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19713
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11127
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 1 (r1); 2013_02_22_FISH_SR_flowcell-B/fastq_files/lane1.fastq.gz

value: Male

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r1); 2013_01_24_ChIP_SR_flowcell-A/UCSD_C16BPACXX_1.fastq.gz

description:
Library strategy: TAB-Seq
Library name: GH257A_L1.2013_01_24
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19710
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11127
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 1 (r1); 2013_01_24_ChIP_SR_flowcell-A/fastq_files/UCSD_C16BPACXX_1.fastq.gz

value: Thomson Laboratory

value: DNA Methylation


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r1); 2013_02_15_FISH_SR_flowcell-B/lane2.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH257A_L2.2013_02_15
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19712
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11127
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 1 (r1); 2013_02_15_FISH_SR_flowcell-B/fastq_files/lane2.fastq.bz2

value: Covaris

value: undiluted Illumina TruSeq kit PCR primers


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r1); 2013_02_15_FISH_SR_flowcell-B/lane1.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH257A_L1.2013_02_15
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19711
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11127
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 1 (r1); 2013_02_15_FISH_SR_flowcell-B/fastq_files/lane1.fastq.bz2

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r1); 2013_02_22_FISH_SR_flowcell-B/lane3.fastq.gz

description:
sample_term_id: CL_0000047
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH258B_L3.2013_02_22
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19754
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6199
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 1 (r1); 2013_02_22_FISH_SR_flowcell-B/fastq_files/lane3.fastq.gz

value: embryonic stem cell differentiated into neural progenitor cells

value: H1 cells were differentiated by culturing in insulin, SB, Noggin

value: TeSR

value: Replicate 1


title: 10023X9_normal_RNA

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

description: rRNA subtracted, total RNA mapped to RefSeq transcripts

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Fastq files were trimmed for adapter sequence and low-quality reads were filtered using the FASTX- Toolkit
Fastq files were mapped against these RefSeq protein-coding transcripts using bowtie alignment parameters: –v 2 –a –best – strata.
The 5’ end of mapped reads were assigned to their transcript position rejecting mapped reads with more than 1 mismatch in their bowtie alignment.
Genome_build: Human RefSeq fasta sequences were retrieved from the UCSC genome browser (Hg19 assembly, RefSeq Genes table downloaded Apr. 2013) using the sequence retrieval and formatting options for 5’ UTR, CDS, 3’ UTR exons as one record per transcript.
Supplementary_files_format_and_content: Tab-delimited text files include reads per million mapped reads (RPM) values and a calcualted translation efficiency for the 1000 most abundant (by RNA mass) transcripts detected.

source_name: skeletal muscle

growth_protocol: Tissue homogenates were prepared from 40 frozen ten-micron sections of muscle biopsy obtained from a patient with an NM_004006:c.40_41delGA mutation and a normal control.

extract_protocol:
Sections were lysed by 20 passages through a 26 gauge needle after addition of 500 μl of ice-cold 20 mM Tris*Cl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100 and 100 μg / ml cycloheximide (Sigma).  For RNA-Seq, 100 μl of lysate was added to 300 μl of TriZOL LS reagent (Life Technologies) and total RNA was extracted according to the manufacturer’s specifications. For RPF-Seq, 6 μl of RNase I (100 U/ μl, Ambion) and 3 μl of Turbo DNase (2 U/ μl, Ambion) was added to 250 μl of lysate and incubated at room temperature with gentle agitation.  After 90 min., 750 μl of TriZOL LS reagent was added and ribonuclease-resistant RNA fragments were isolated by extraction.  RNA fragments were electrophoresed on a denaturing 15% polyacrylamide TBE-urea gel (Life Technologies, EC68852BOX). The gel region containing 26-38 nucleotide size RNA fragments was excised and RNA isolated by passive elution. Gel-purified RNA fragments were treated with 5 units of Antarctic Phosphatase (5 U/ μl NEB) in the presence of 40 units of RNase Inhibitor (40 U/ μl, Ambion) for 30 min. at 37oC, followed by 5 min. at 65oC to deactivate the enzyme.  Fragments were then treated with 20 units of T4 polynucleotide kinase (10 U/ μl NEB) for 60 min. at 37oC and purified using RNeasy MinElute columns (Qiagen) according to the manufacturer’s recommendations for small RNA.
RPF-Seq libraries were built using the TruSeq Small RNA Sample Preparation Kit (Illumina) according to the manufacturer’s specifications, using Superscript II (Invitrogen).  After PCR to enrich for ligated fragments, the final gel purification was eliminated and instead the amplified library samples were cleaned using 50 μl of AMPure XP magnetic beads (Agencourt) according to the manufacturer’s specifications.   For RNA-Seq libraries, 4 μg of TRIzol-extracted total RNA from each sample was depleted for rRNA using Ribo-Zero rRNA Removal Kit Human/Mouse/Rat (Epicentre).  The rRNA-depleted total RNA was then processed using the TruSeq RNA Sample Preparation v2 Kit (Illumina) according to the manufacturer’s specifications using Superscript II (Invitrogen).

tag: tissue

value: skeletal muscle

tag: genotype/variation

value: normal control


title: 10023X8_c.40_41del_RNA

value: c.40_41delGA dystrophin mutation


title: 9962X9_normal_RPF

description: ribosome-protected fragments mapped to RefSeq transcripts


title: 9962X8_c.40_41del_RPF


title: Leaf_MACE

status: Public on Aug 01 2014

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

country: Germany

institute: University Medicine Greifswald

description: Massive Analysis of cDNA ends (MACE)

data_processing:
FastQC preprocessing
Filtering for sequences shorter than 14bp
MACE reads were aligned using SSAHA2 via the pipeline CRACPipe; kmer 14, skip 1
Data were weighted concerning equal hits and filtered for mapping with a max. of 1 insertion, deletion or mismatches
Genome_build: http://plants.ensembl.org ; ITAG2.3
Supplementary_files_format_and_content: comma separated files (csv) representing the Transcript per million (TPM) for the mRNAs.

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Tomato plants (cv Moneymaker) were grown in a glasshouse under a 16/8h day/night cycle (24-20°C). Young leaves and anther from different developmental stages were collected from 8-week old plants for transcriptome analysis.

extract_protocol:
Total RNA was extracted using the NucleoSpin® RNA isolation kit (Macherey and Nagel) following the manufacturer’s instructions.
The mRNA was enriched by binding the poly-A-tail at the 3'-end and the last 500 bp were sequenced so that each transcript is represented by one read in the library

treatment_protocol: No treatment

value: Leaf

tag: cultivar

value: Moneymaker


title: Leaf_Heatstress_MACE

description: Massive Analysis of cDNA ends (MACE)

source_name: Heat stress

growth_protocol: Tomato plants (cv Moneymaker) were grown in a glasshouse under a 16/8h day/night cycle (24-20°C). Young leaves from different developmental stages were collected from 8-week old plants for transcroptome analysis.

treatment_protocol: Eight-week old tomato plants (Solanum lycopersicum cv Moneymaker) grown in a glasshouse under a 16/8h day/night cycle (24-20oC) were transferred to a growth chamber (120 μmol m-2 sec-1 light intensity) and exposed to heat stress conditions for 1 hour at 39oC and then allowed to recover at 24oC for 1.5 h.

tag: stress

value: Heat stress


title: Leaf Control_MACE

description: Massive Analysis of cDNA ends (MACE)

source_name: Control

value: Control


title: Anther_MACE

description: Massive Analysis of cDNA ends (MACE)

source_name: Anther

value: Anther


title: GEK46

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Brassica napus

source_name: mature seed

growth_protocol: B. napus (cultivar PFB-2, Embrapa) plants were grown in an open environment (30°S 51°W) from May to October 2010. Flowers were tagged upon opening and developing siliques from different plants were collected in the middle of a light cycle at 7, 14, 21, 28, 42 and 50 days after flower opening (DAF). The seeds were dissected from the siliques, immediately frozen in liquid nitrogen and stored at -80 °C.

extract_protocol: Total RNA was isolated from the seed material using Trizol (Invitrogen, CA, USA) according to the manufactures’ protocol, and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing. Two mRNA libraries were constructed, one from mature seeds (50 DAF) and one from an equivalent mixture of RNA from immature seeds at DAF stages 7-42, and they were sequenced by Illumina HiSeq2000. Briefly, the polyadenylated transcript sequencing (mRNA-seq) was performed using the following successive steps: Poli-A purification, cDNA synthesis using Poli-T primer shotgun to generate inserts of 500 nt, 3p and 5p adapters ligations, pre-amplification, colony generation and sequencing. The Illumina output data were sequence tags of 100 bases.

value: PFB-2, Embrapa

tag: sample type

value: single

tag: days after flower opening (daf)

value: seeds


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r1); 2013_02_15_FISH_SR_flowcell-B/lane3.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH258A_L3.2013_02_15
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19751
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6199
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 1 (r1); 2013_02_15_FISH_SR_flowcell-B/fastq_files/lane3.fastq.bz2

value: Thomson Laboratory

value: Cell Line

tag: passage

value: Male

value: DNA Methylation

value: Covaris

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.

value: Standard Illumina adaptor sequence

value: TruSeq

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)

value: not measured

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq

value: undiluted Illumina TruSeq kit PCR primers

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: TAB-Seq: H1 cell line differentiated into neural progenitor cells (r1); UCSD_C16BPACXX_5.fastq.gz

description:
sample_term_id: CL_0000047
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH258B_L5.2013_01_24
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19745
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6199
****************
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: H1 cell line differentiated into neural progenitor cells, biological replicate 1 (r1); 2013_01_24_ChIP_SR_flowcell-A/fastq_files/UCSD_C16BPACXX_5.fastq.gz

tag: sra sample accession

value: embryonic stem cell differentiated into neural progenitor cells

value: H1 cells were differentiated by culturing in insulin, SB, Noggin

value: TeSR

value: Replicate 1


title: Scc4-4 25°C  Mnase-Seq

city: London

first: Lidia

last: Lopez-Serra

address: 44 Lincoln's Inn Fields

department: Chromosome segregation

country: United Kingdom

institute: Canser Research UK

description: Genomic DNA obtained after digestion with MNase to isolate mono-nucleosomal DNA

data_processing:
Read alignment was performed using the Burrows-Wheeler Aligner, bwa (version 0.5.9-r16). If required, prior to alignment, the sacCer2 release of the budding yeast genome was modified to reflect genome alterations that were introduced for the experiment.
Discordantly mapped read-pairs were removed, leaving only those that were paired, had a maximum of 2 mismatches in any given read and an insert size between 140 and 170 bp.
Genome-wide wig files were generated by treating each pair of reads as a single fragment.
Genome_build: Saccharomyces cerevisiae genome (version sacCer2)
Supplementary_files_format_and_content: Genome-wide wig files were generated at 1bp resolution by treating each pair of reads as a single fragment, including the inferred insert portion. A total library size of 25 million read pairs was used to normalise the coverage for cross-sample comparison.

organism: Saccharomyces cerevisiae

source_name: Mono-nucleosomal DNA

growth_protocol: Cells were grown in YP + 2% Glucose to an OD600 of 0,4. Then the cells were incubated for two more hours at the indicated temperature.

extract_protocol:
Preparation of mono-nucleosomal DNA was performed as described (Lantermann et al. 2009) followed by high throughput sequencing on Illumina GAIIx and HiSeq 2500. Briefly, cells were grown under the specified conditions and then fixed with 1% formaldehyde. Spheroblasts were obtained and the chromatin digested with 30u/ml of Mnase (Fermentas) at 37°C for 20 minutes. The samples were then treated with RNase and Proteinase K to isolate the undigested, mono-nucleosomal DNA. The DNA was then size selected and purified in a 1.5% agarose gel and precipitated with ethanol.
Sequencing libraries were prepared according to the manufacturer's protocol (15005180 Rev. A and 15026486 Rev. B).

treatment_protocol: Cells were cross-linked with 1% Formaldehide for 30 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 10 minutes.

tag: strain

tag: genotype

value: MATa, scc4∆::HIS3, scc4-4::LEU2, Scc2-Ha6::HIS3


title: TAB-Seq: H1-Mesenchymal Stem Cell Line (r1); 2013_02_15_FISH_SR_flowcell-B/lane7.fastq.bz2

description:
Library strategy: TAB-Seq
Library name: GH257B_L7.2013_02_15
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19715
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11127
****************
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: H1-Mesenchymal Stem Cell Line, biological replicate 1 (r1); 2013_02_15_FISH_SR_flowcell-B/fastq_files/lane7.fastq.bz2

tag: disease

value: Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

value: Male


title: Scc4-4 37°C  Mnase-Seq


title: PR-SET7_LOBE replicate 1

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

data_processing:
Base calling was performed using software provided with the Ion Proton sequencer.
Sequenced reads were trimmed for adaptor sequence and mapped to mm9 whole genome using tophat 2.0.9 with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html)
Tags overlapping the Ensembl build 67 mouse exons were counted and filtered for artifacts as follows: if an annotated gene had up to five exons, tag presence was required in at least two exons. If an annotated gene had E >5 exons, tag presence was required in at least E/5 exons. The final gene counts were calculated as the sums of their exon tags. The counts table was normalized using EDASeq and analyzed for differential expression using DESeq. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited file containing normalized counts for each gene with length greater than 500bp and at least 1 read in at least 1 sample.

source_name: Liver

growth_protocol: Mice were maintained in grouped cages in a temperature-controlled, pathogen-free facility on a 12-hr light/dark cycle and fed by a standard chow diet (Altromin 1324; 19% protein, 5% fat) and water ad libitum

extract_protocol:
Approximately 20 µg of total RNAs were used for mRNA isolation using the Dynabeads® mRNA DIRECT™ Micro Kit (Life Technologies, Carlsbad, CA, USA)
The isolated mRNA was digested with RNaseIII, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA, USA). Samples were processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (Life Technologies, Carlsbad, CA, USA) and sequencing with the Ion PI™ Sequencing 200 Kit on Ion Proton PI™ chips (Life Technologies, Carlsbad, CA, USA) according to commercially available protocols.

value: 8 months

value: liver


title: PR-SET7_LOBE replicate 4


title: WT replicate 1

value: WT


title: WT replicate 2


title: PR-SET7_LOBE replicate 2


title: root

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

institute: University of Oxford

description: small RNA

data_processing:
As an initial quality filter, all reads containing Ns were discarded.
The adapter removal step was conducted using the UEA sRNA workbench [Stocks et al, 2012]. The 3' adapter sequence was identified using the first 6 nt. The HD component of the adapter (first 4 and last 4 nucleotides) was subsequently removed.
The reads were mapped full length, no mis-matches or gaps allowed to the reference Bamboo genome using PatMan [Prueffer et al, 2008]
The miRNAs were identified using the miRCat and miRprof tool within the UEA workbench.
The sRNA loci were identfied using CoLIde [Mohorianu et al, 2012]
The computational prediction of the targets was conducted using the plant target prediction tool within the UEA sRNA Workbench.
Phyllostachys heterocycla var. pubescens, ver 1.0
Genome_build: n/a
Supplementary_files_format_and_content: csv file containing the sRNA expression levels.

organism: Phyllostachys edulis

source_name: tissues from the pool of 15 plants

growth_protocol: The seeds were germinated in moist vermiculite. After germination, the plants were grown in the chamber with light strength of 100-200 μmol•m-2•s-1) and temperature 25℃ for about 2 months. Then the seedlings at 3-leaf stage  were transfered to the pots with turfy soil and grown at 25℃ under light strength of 100-200 μmol•m-2•s-1 for 3-4 months.

extract_protocol:
Trizol reagent was used for total RNA extraction and the low molecular weight RNA was isolated by using mirVana kit.
Script-miner small RNA library preparation kit was used for library construction and the high definition adapters were used

treatment_protocol: no special treatment

tag: developmental stage

value: 5-6 leaf stage

tag: tissue type

value: embryo-origin roots, airy roots and adventitious roots


title: leaf

description: small RNA

value: all leaves above ground


title: Sox2GFP_K27Ac_ChipSeq_GCCAAT

description:
Chromatin IP against Sox2GFP_K27Ac
barcode: GCCAAT

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Neural Progenitors

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

tag: chip antibody

tag: antibody catalog number

value: Abcam AB4729

tag: cell type

value: Sox2-GFP primary


title: Sox2GFP_WCE_ChipSeq_TTAGGC

description:
Chromatin IP against Sox2GFP_WCE
barcode: TTAGGC

value: None WCE


title: GEK47

source_name: developing seed

value: PFB-2, Embrapa

value: pooled

tag: tissue

value: seeds


title: 13F-K27Ac_ChipSeq_CAGATC

description:
Chromatin IP against 13F-K27Ac
barcode: CAGATC

value: iNPC-derived from fibroblasts-clone 13F


title: 13F_WCE_ChipSeq_TGACCA

description:
Chromatin IP against 13F_WCE
barcode: TGACCA


title: MEF_K27Ac_ChipSeq_ACTTGA

description:
Chromatin IP against MEF_K27Ac
barcode: ACTTGA

source_name: Mouse embryonic fibroblasts

value: MEF


title: PR-SET7_LOBE replicate 3

tag: age


title: SD_no_aminoacids_plus_His_Met_Leu

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

description: ribosome-protected RNA fragments

data_processing:
Library strategy: Ribo-seq
Barcode and adapter sequences are deleted
Only footprints longer than 22 nt are left for analysis.
alignment was done with Bowtie 0.12.7
first nucleotide of each read was removed before alignment.
duplicated gene pairs were combined in a single virtual "gene" record
Genome_build: Saccharomyces cerevisiae S288C genome, SGD release
Series supplementary file contents: 1) Expression_Table.txt contains quantitation of gene expression as rpkm values
Series supplementary file contents: 2) Ribosome_occupancy_plots.txt contants the footprint densities over ORFs. It can se used to quickly plot all the ribosome ocupancy graphs as was done in our manuscript.

source_name: cultured cell suspension

growth_protocol: YPD media, 30 °C

extract_protocol:
size fractionation
circ-ligation

treatment_protocol: To induce oxidative stress, cells were treated with 0.2 mM hydrogen peroxide. Concentrations of cycloheximide ranging from 1.56 to 10,000 ug/ml were used

tag: primer set

value: Set #2


title: MEF_WCE_ChipSeq_ACAGTG

description:
Chromatin IP against MEF_WCE
barcode: ACAGTG


title: SD_no_aminoacids

description: ribosome-protected RNA fragments

value: Set #1


title: edeine_noCHX

description: ribosome-protected RNA fragments