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| Status |
Public on Oct 15, 2011 |
| Title |
Whole genome shotgun bisulfite sequencing of the H1 mesendoderm cell line; methylC-seq_h1-mesendoderm_r1b |
| Sample type |
SRA |
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| Source name |
H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); methylC-seq_h1-mesendoderm_r1b
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| Organism |
Homo sapiens |
| Characteristics |
sample alias: h1_mesendoderm_r1
sample common name: H1 BMP4 Derived Mesendoderm Cultured Cells
molecule: genomic DNA
disease: None
biomaterial_provider: Thomson Laboratory
biomaterial_type: Cell Line
line: H1
lineage: NA
differentiation_stage: embryonic stem cell differentiated into mesendoderm cells
differentiation_method: H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium
passage: 20
medium: TeSR
Sex: Male
batch: Replicate 1
experiment_type: DNA Methylation
extraction_protocol: Qiagen DNeasy mini kit, performed as per manufacturer's instructions
extraction_protocol_type_of_sonicator: Covaris S2
extraction_protocol_sonication_cycles: Standard fragment express, 6 cycles
dna_preparation_initial_dna_qnty: 5 µg
dna_preparation_fragment_size_range: 100-150
dna_preparation_adaptor_sequence: A: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B: 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT
dna_preparation_adaptor_ligation_protocol: 16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)
dna_preparation_post-ligation_fragment_size_selection: Two rounds of purification with AMPure XP beads (Agencourt)
bisulfite_conversion_protocol: Invitrogen MethylCode
bisulfite_conversion_percent: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample
library_generation_pcr_template_conc: One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction
library_generation_pcr_polymerase_type: Stratagene Pfu Turbo Cx
library_generation_pcr_thermocycling_program: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min
library_generation_pcr_number_cycles: 4
library_generation_pcr_f_primer_sequence: 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
library_generation_pcr_r_primer_sequence: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
library_generation_pcr_primer_conc: 25 µM
library_generation_pcr_product_isolation_protocol: Two rounds of purification with AMPure XP beads (Agencourt)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Five µg of genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 100-150 bp, followed by end repair and addition of a 3' A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 µl 10X PfuTurbo reaction buffer, 31 µM dNTPs, 1 µl Primer 1, 1 µl Primer 2 (50 µl final). The thermocycling parameters were: 95C 2 min, 98C 30 sec, then 4-8 cycles of 98C 15 sec, 60C 30 sec and 72C 4 min, ending with one 72C 10 min step. The reaction products were purified using AMPure XP beads (two rounds). Up to three separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to three independent libraries from the same biological sample.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
sample_term_id: NTR_0000856
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 and Activin A
Library name: methylC-seq_h1_mesendoderm_r1b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10255
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
****************
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| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM818004_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1_mesendoderm_r1b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-mesendoderm_r1b.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library methylC-seq_h1_mesendoderm_r1b were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12975
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HBDM BS 1b
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1b EA Release 7
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 231,518,888
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.42
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 33
**********************************************************************
ANALYSIS FILE NAME: GSM818004_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-mesendoderm_r1a-methylC-seq_h1-mesendoderm_r1b-methylC-seq_h1_mesendoderm_r2a-methylC-seq_h1_mesendoderm_r2b.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12976
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HBDM BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Combined Libraries EA Release 7
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 898,944,318
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.44
SPECIAL NOTE: generated from combined data in GSM818003, GSM818004, GSM818005, GSM818006 (thus .wig files on these records are identical)
**********************************************************************
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| Submission date |
Oct 14, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
UCSD AND SALK |
| Organization name |
University of California, San Diego
|
| Street address |
Health Sciences Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92092 |
| Country |
USA |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
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| Relations |
| SRA |
SRX101207 |
| BioSample |
SAMN00739304 |
| Named Annotation |
GSM818004_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1_mesendoderm_r1b.wig.gz |
| Named Annotation |
GSM818004_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.combined.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM818004_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.combined.wig.gz |
210.9 Mb |
(ftp)(http) |
WIG |
| GSM818004_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1_mesendoderm_r1b.wig.gz |
151.2 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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