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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 06, 2011 |
| Title |
Round-spermatids_Kcro |
| Sample type |
SRA |
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| Source name |
Round spermatids
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| Organism |
Mus musculus |
| Characteristics |
cell type: Round spermatids
antibody: pan anti-lysine crotonylation antibody
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq for histone Kcr or Kac was carried out as previously described with 500 μg IMR90 chromatin (or 100 μg of fractionated germ cells chromatin) and 5 μg pan anti-Kcr or anti-Kac antibody (Hawkins et al., 2010). ChIP-seq libraries for sequencing were prepared following Illumina protocols (Illumina, San Diego, CA) with minor modifications. Libraries for input samples were generated using 20 ng corresponding input chromatin. Briefly, ChIPed DNA was first blunted with END-IT DNA repair kit (Epicenter Biotechnology, Madison, WI) and then incubated with Klenow (exo-) (New England Biolabs, MA) and dATP to generate single base 3′-dA overhang. Illumina sequencing adaptor was then ligated to the resulting DNA, and followed by size selection (180-400bp) from a 8% acrylamide gel. This size-selection step was repeated after PCR amplification with DNA primers supplied by Illumina. Libraries were sequenced using Illumina GAII or HiSeq machine as per manufacturer's protocols.
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
RS_Kcro
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| Data processing |
Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline. Reads were mapped to human hg18 (for IMR90 data) or mouse mm9 (for sperm cell data) genome build with a bowtie software package. Total mapped tags were paired down to unique, monoclonal tags. These are tags that mapped to one location in the genome and each sequence is represented once.
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| Submission date |
Oct 06, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Fulai Jin |
| E-mail(s) |
[email protected]
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| Phone |
2163681811
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| Organization name |
Case Western Reserve University
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| Lab |
Fulai Jin
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| Street address |
10900 Euclid Avenue
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| City |
Cleveland |
| State/province |
OH - OHIO |
| ZIP/Postal code |
44106 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE32663 |
Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification |
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| Relations |
| SRA |
SRX099897 |
| BioSample |
SAMN00737736 |
| Named Annotation |
GSM810678_RS.Kcro.monoclonal.bed.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM810678_RS.Kcro.monoclonal.bed.gz |
514.6 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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