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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 24, 2013 |
| Title |
TMK4_MEF8_WT |
| Sample type |
SRA |
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| Source name |
TMK4_ChIPseq
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J/N
genotype/variation: homozygously constitutively null for H3f3b
cell type: mouse embryonic fibroblasts (MEF)
passages: passage 7, replicate 2
chip-antibody: H3K9Ac
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| Growth protocol |
Frozen cells thawed at passage 5 and grown to passage 7 on 15 cm tissue culture treated plates in DMEM high glucose with L-glutamine and non-essential amino acids. Harvest at passage 7 yielded approximately 2 x 10^6 cells per line.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq: MEF cells were trypsinized, washed, then crosslinked with 1% formaldehyde for 10 minutes, and quenched with a final volume of 0.125M glycine. Cells were washed 3 times in cold PBS, flash-frozen, and stored at -80C. Yield was approximately 2 x 10^6 cells per MEF line. Chromatin immunoprecipitation was performed exactly as described in O'Geen et al. 2011 (PMID: 21913086) with the following modifications: Nuclear pellet was flash frozen in liquid nitrogen after incubation in 100ul nuclear lysis buffer, and thawed on ice to aid disruption of nuclei before sonication. Chromatin was sonicated on a Diagenode Bioruptor in 1.5 ml Eppendorf tubes in a volume of 100 ul nuclear lysis buffer to a fragment size between 100-200 base pairs. ChIP assays were performed using H3K9Ac (Upstate # 06-942, lot number 31636) and H3K4Tm3 (Millipore # 04-475, lot number NG1680351) antibodies. Antibodies were collected with 20 ul magnetic protein G beads, and washed as described. After reversing the crosslinks, samples were purified and eluted in 2 x 10 ul elution buffer using the Qiagen MinElute PCR purification kit.
Libraries were prepared on the library automation system from IntegenX (Apollo324) using the PrepX™ DNA Library Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using the bwa aligner (http://bio-bwa.sourceforge.net/).
Peaks: Peak detection was performed Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) using the input DNA as a control.
Genome Build:
libACH3MEF8.bed: mm9
ACH3_MEF8_peaks.gff: mm9
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| Submission date |
Jan 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Henriette O'Geen |
| Organization name |
UC Davis
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| Street address |
1 Shields Avenue
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE34546 |
Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development |
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| Relations |
| SRA |
SRX116588 |
| BioSample |
SAMN00774079 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM863804.bed.gz |
91.3 Mb |
(ftp)(http) |
BED |
| GSM863804.gff.gz |
200.2 Kb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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