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| Status |
Public on Apr 18, 2016 |
| Title |
ESC1 whole chromatin rep1 16U MNase |
| Sample type |
SRA |
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| Source name |
J1 ESC
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| Organism |
Mus musculus |
| Characteristics |
cell type: J1 ESC
mnase concentration (u): 16
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
s2 MNase-seq:
Cells were grown in Schneider?s medium supplemented with 10% heat inactivated FBS at 28C. For fixation, 107 S2 cells were pelleted and rinsed twice in PBS. Cells were crosslinked in 1.1% formaldehyde in PBS for 10 minutes at room temperature, tumbling end over end in a volume of 10 mL. After addition of 50 uL of 2.5M glycine, the cells were tumbled at room temperature for 2 minutes to quench the reaction. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, the cell pellet was resuspended in PBS with 0.1% Triton-X100 (PBS-TX). Digestion of 106 cells per titration point took place in a volume of 400uL PBS-TX supplemented with 1mM CaCl2. Either 1.5U, 6.25U, 25U, or 100U of MNase (Worthington Biochemical) were added to pre-warmed cells and incubated at 37C for 3 minutes. Digestion was halted by moving to ice and adding 10 uL of 250 mM EDTA, 250 mM EGTA. Prior to DNA clean-up, the digestions were adjusted to 0.5% SDS and 10 mM Tris pH 8. For DNA cleanup, digestions were incubated with RNase (Roche) for 30 minutes at 37C, with proteinase K (Roche) for 60 minutes at 55C, and incubated at 65C for 60 minutes to reverse crosslinks. This was followed by phenol-chloroform extraction and ethanol precipitation. For size selection, digestion products in a volume of 100 uL of water were incubated for 5 minutes at room temperature with 60uL of Agencourt AMPure XP beads (Beckman Coulter). After bead separation, the supernatant was moved to a new tube and 120uL of new bead suspension was added. DNA was eluted from these beads and used as input into the library preparation protocol described in Bowman et al. (BMC Genomics 2013). For histone ChIP, after halting the MNase digestion, adding EDTA/EGTA, and adding SDS, 135 uL was removed from the 400 uL digestion as an input fraction and kept overnight at 4C. The remainder of each digestion was split in half (135uL each). Each chromatin aliquot was independently adjusted to ChIP buffer conditions in a volume of 500 uL (10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.5% sarkosyl, 1% Triton X-100, and 1X COMPLETE protease inhibitors (Roche)). After adding 1 mL additional ChIP buffer to each chromatin aliquot (total volume of 1.5ml), this was tumbled end over end for 10 min at 4C and then subjected to a high-speed spin in a microcentrifuge for 10 min at 4C. Supernatant was taken to a new tube for precipitation. 2 uL of antibody was added to each tube (histone H3 ChIP, ab1791, Abcam).
s2 ChIP-seq:
After halting the MNase digestion, adding EDTA/EGTA, and adding SDS, 135 uL was removed from the 400 uL digestion as an input fraction and kept overnight at 4C. The remainder of each digestion was split in half (135uL each). Each chromatin aliquot was independently adjusted to ChIP buffer conditions in a volume of 500 uL (10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.5% sarkosyl, 1% Triton X-100, and 1X COMPLETE protease inhibitors (Roche)). After adding 1 mL additional ChIP buffer to each chromatin aliquot (total volume of 1.5ml), this was tumbled end over end for 10 min at 4C and then subjected to a high-speed spin in a microcentrifuge for 10 min at 4C. Supernatant was taken to a new tube for precipitation. 2 uL of antibody was added to each tube (histone H3 ChIP, ab1791, Abcam; histone H4 ChIP, ab10158, Abcam).
esc and npc MNase-seq:
J1 ESCs (ESC1) and E14-derived ESCs (ESC2) were maintained on mitomycin-C inactivated embryonic fibroblast feeder layers in DMEM supplemented with 15% fetal bovine serum (Hyclone) and 1000U/ml of leukemia inhibitory factor (EMD Millipore). ESC cultures were depleted of feeder cells prior to use in experiments. Neural progenitors (NPC1) were derived by in vitro differentiation from J1 ESC and maintained using previously described methods38. Embryonic NPCs (NPC2) were isolated from the brains of E13.5 embryos and maintained on poly-l-ornithine coated plates in DMEM:F12 containing B-27 and N-2 supplements (Gibco) and EGF+FGF-2 (10ng/ml). One million Cells were cross-linked at room temperature for 10 minutes with 1% formaldehyde and cross-linking stopped by the addition of 125mM glycine. Nuclei were isolated and MNase digestion performed on either 200,000 or 250,000 nuclei per reaction. Digestions were performed using 64U, 16U, 4U or 1U MNase (Worthington) in 10mM Tris pH 7.4, 15mM NaCl, 60mM KCl, 1mM CaCl2 for 10 minutes (250,000 nuclei reactions) or 15 minutes (200,000 nuclei reactions) at 25C. Reactions were stopped with EDTA/EGTA and 0.5% SDS and 125mM NaCl added to the samples. RNase A and proteinase K treatment along with cross-link reversal at 65C were performed. DNA was purified by phenol-chloroform extraction and column purification. MNase digestion was evaluated and the recovered DNA from 1 -64U MNase digested samples was used to generate sequencing libraries
k562 Mnase-seq:
Human K562 cells were grown in Iscove's Modified Dulbecco's Medium supplemented with 10% heat inactivated FBS at 37C. Human cells were expanded to yield approximately 4 million cells/reaction and cross-linked with 1.1% formaldehyde for 10 minutes at room temperature. Cells were lysed and nuclei were isolated using a sucrose cushion and treated with a range of 18 MNase concentrations in buffer containing 10mM Tris pH 7.4, 15mM NaCl, 60mM KCl and protease inhibitors for 15 minutes at room temperature. EDTA and EGTA were added to stop the digestion. Cross-link reversal was performed at 65 degrees C for 16 hours followed by RNase treatment for 30 minutes at 37 degrees C, followed by the addition of SDS to a final concentration of 1% and proteinase K digestion overnight, at 55C. DNA was purified by phenol- chloroform extraction and ethanol precipitation. Ampure SPRI beads (Beckman Coulter) were used in a double size selection with ratios of 0.7X and 1.7X to obtain a range of fragment sizes from approximately 100 bp to 1000 bp.
s2 RNA-seq:
10^7 Drosophila S2 cells were harvested on ice, washed in cold PBS and their RNA was extracted using the RNeasy Kit (Qiagen) with on column DNAse digestion according to the manufacturer?s protocol. Ribosomal RNA was depleted from the total RNA (5ug) by using the RiboZero gold magnetic kit (Epicentre/Illumina) according to manufacturer?s instructions. cDNA was generated with the TruSeq non?stranded kit (Illumina) according to manufacturer?s instructions
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
processed data file:
esc1.Pooled_WholeChromatin.ReplicateSet_bin500.bedGraph.gz;
esc1.MACC_WholeChromatin.ReplicateSet_bin500.bedGraph.gz
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| Data processing |
Mnase-seq and ChIP-seq: The sequenced paired-end reads were mapped to dm3, hg19, and mm9 genomes in the cases of D. melanogaster, H. sapiens and M. musculus data respectively using Bowtie aligner v. 0.12.939. Only uniquely mapped reads with no more than two mismatches were retained. The reads with the insert sizes less than 50 bp or larger than 500 bp were filtered out. Genomic positions with the numbers of mapped tags above the significance threshold of z-score = 7 were identified as anomalous, and the tags mapped to such positions were discarded. Read frequencies were computed in 300-bp non-overlapping bins in the case of fly data and in 500-bp bins in the case of human data for each titration point independently. The read frequencies were normalized by the corresponding library sizes to represent values per one million of mapped reads. To facilitate the comparison of the results between different genomes, the frequencies were additionally scaled by the factors representing ratios between the corresponding genome size and 100 Mb, similarly to the approach described in Kasinathan et al. (Nat Methods 2014).
RNA-seq: Tags were aligned using Tophat software package with default parameters. RNA-Seq tag frequencies were normalized for GC-content using bioconductor package EDASeq and then the expression estimates for each gene were obtained using bioconductor package DESeq.
Genome_build: dm3, mm9 and hg19
Supplementary_files_format_and_content: bedGraph files representing either tag occupancy profiles normalized to library sizes or MNase accessibility (MACC) profiles
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| Submission date |
Mar 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Tolstorukov |
| E-mail(s) |
tolstorukov@molbio.mgh.harvard.edu
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| Organization name |
Massachusetts General Hospital
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| Department |
Molecular Biology
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| Street address |
185 Cambridge Street
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE78984 |
MNase titration reveals differences between nucleosome occupancy and chromatin accessibility |
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| Relations |
| BioSample |
SAMN04538243 |
| SRA |
SRX1619273 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2083107_esc1.mnase_16U_WholeChromatin.r1_bin500.bedGraph.gz |
30.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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