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Status |
Public on Apr 02, 2020 |
Title |
HeLa_CENP-C_IP |
Sample type |
SRA |
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Source name |
HeLa cells
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Organism |
Homo sapiens |
Characteristics |
cell line: HeLa chip antibody: Anti-CENP-C (MBL international, PD030)
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Growth protocol |
Human cell line HeLa were grown in DMEM (Invitrogen/ThermoFisher Cat #11965) supplemented with 10% FBS and 1X penicillin and streptomycin cocktail.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Libraries were constructed with the PacBio Standard Seq (v3) protocol. After cells were grown to ~80% confluency, they were harvested as described here (Bui et al 2012; Bui et al 2017), but with a few modifications. In short, cells were harvested, washed with PBS and PBS containing 0.1% Tween 20 (Sigma-Aldrich cat #P7949). Nuclei were released with TM2 (20 mM Tris-HCl, pH 8.0; 2 mM MgCl2; 0.5 mM PMSF) with 0.5% Nonidet P-40 (Sigma-Aldrich cat #74385). Afterwards, nuclei were washed with TM2 and dissolved in a total volume of 2 mL of 0.1 M TE (10 mM Tris-HCl, pH 8.0; 0.2 mM EDTA, 100 mM NaCl). Subsequently, chromatin was digested for 6 minutes with 0.25 U MNase (Sigma-Aldrich cat #N3755-500UN) and supplemented with 1.5 mM CaCl2. MNase reaction was quenched with 10 mM EGTA. All centrifugations were done at 1000 rpm at 4ºC. The cell or nuclei pellet was only tapped once to facilitate breaking them up. Supernatant was removed, and chromatin extracted overnight in low salt solution (0.5X PBS; 0.1 mM EGTA supplemented with a protease inhibitor cocktail (Roche cat #05056489001) N-ChIP chromatin bound to Protein G Sepharose beads (GE Healthcare cat #17-0618-02) were washed twice with ice cold 0.5X PBS and spun down for 1 minute at 4ºC at 800 rpm. The samples were used to prepare libraries for PacBio single-molecule sequencing as described in manufacturer’s protocol (PacBio, Menlo Park, CA). Libraries were produced and loaded on ZMW chip either by diffusion or following size selection of the inserts (> 1000 bp) for all four samples.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
PacBio RS II |
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Data processing |
Circular Consensus Sequence (CCS) reads in fastq format were filtered to remove PacBio internal control (MG551957.1) by alignment with Bowtie v2.3.4 Filtered reads were converted to fasta, and sequence composition was examined using an in-house perl script. Alignments to alpha-satellite subunits and HORs were performed with Bowtie v2.3.4 in sensitive-local mode Genome_build: hg19 Supplementary_files_format_and_content: TXT files include sequence composition information (mono and dinucleotide counts) for IP samples
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Submission date |
Apr 04, 2019 |
Last update date |
Apr 03, 2020 |
Contact name |
David Sturgill |
E-mail(s) |
davidsturgill@mail.nih.gov
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Phone |
240-760-6725
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Organization name |
NIH
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Department |
NCI
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Lab |
LRBGE
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Street address |
Building 41, Rm B622
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City |
Bethesda |
State/province |
MARYLAND |
ZIP/Postal code |
20892 |
Country |
USA |
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Platform ID |
GPL21311 |
Series (1) |
GSE129351 |
Octameric nucleosomes are present within the inner kinetochore of human centromeres |
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Relations |
BioSample |
SAMN11347521 |
SRA |
SRX5644010 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3711474_CENP-C_ccs_filtered_sequence_comp.txt.gz |
264.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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