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| Status |
Public on Nov 28, 2013 |
| Title |
H3K4me3 marks of primed WIBR3 embryonic stem cells |
| Sample type |
SRA |
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| Source name |
hES Cells
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| Organism |
Homo sapiens |
| Characteristics |
chip antibody: anti-H3K4me3 (ab8580, Abcam)
cell line: WIBR3
cell type: hES Cells
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| Growth protocol |
Cells were grown on vitronectin+gelatin or MEF. Rock inhibitor was added 2-24 hours before splitting with trypsin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 40 × 106 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature), and then quenched with glycine (5 min at room temperature). Fixed cells were lysed in 50 mM HEPES KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4 °C (Roche), centrifuged at 950g for 10 min and resuspended in 0.2% SDS, 10 mM EDTA, 140 mM NaCl and 10 mM Tris-HCL. Cells were then fragmented with a Branson Sonifier (model S-450D) at −4 °C to size ranges between 200 and 800 bp, and precipitated by centrifugation. 10 μg of each antibody was pre-bound by incubating with Protein-G Dynabeads (Invitrogen100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 2 h at room temperature. Beads were added to the chromatin lysate, and then incubated overnight. Samples were washed 5 times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250 mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0 at 65 °C. Eluate was treated sequentially with RNase A (Roche) for 30 min and proteinase K (NEB) for 2 h, and then incubated at 65 °C for 4 h. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881)
140ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed twice on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 100ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 12 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer and KAPA HiFi matermix) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl). Approximately 5 picomoles of DNA library was then applied to each lane of the flow cell. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq2000 Analyzer following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to hg19 reference genome using bowtie version 1.0.0. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read (flags -a -m 1 --best --strata -v 1)
To rule out sequencing depth bias, the aligned sequences were down-sampled such that all samples had the same number of aligned reads. Human samples of the marks H3K4me3, H3K27me3, H3K4me1 and H3K27ac, as well as whole-cell extract, were down-sampled to include 3,750,000 aligned reads. H3K9me3 samples were down-sampled to 5,900,000 aligned reads.
Peaks were detected with MACS version 1.4.1, with whole-cell-extract used for control
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain enriched peaks detected by MACS version 1.4.1
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| Submission date |
Nov 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Noa Novershtern |
| E-mail(s) |
noa.novershtern@weizmann.ac.il
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| Organization name |
Weizmann Institute of Science
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| Department |
Molecular Genetics
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| Street address |
Weizmann Institute
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| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE52617 |
Derivation of novel human ground state naïve pluripotent stem cells [ChIP-seq; RRBS-seq] |
| GSE52824 |
Derivation of novel human ground state naïve pluripotent stem cells. |
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| Relations |
| BioSample |
SAMN02418952 |
| SRA |
SRX381334 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1272768_WIBR3_p_H3K4me3_peaks.bed.gz |
275.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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