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| Status |
Public on May 13, 2013 |
| Title |
NB Input 1 |
| Sample type |
SRA |
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| Source name |
Tonsillar Naïve B cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Tonsillar naive B cells
treatment: NA
chip antibody: none
purification: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker IgD
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously described (Ci et al., Blood, 2009). Briefly, 108 cells were fixed with 1% formaldehyde, lysed, and sonicated (Branson Sonicator; Branson) leading to a DNA average size of 200 bp. Five µg of antibodies were added to the precleared sample and incubated overnight at 4°C. The complexes were purified using protein-A beads (Roche) followed by elution from the beads and decrosslinking. DNA was purified using PCR purification columns (QIAGEN).
ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)
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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 |
genome build: hg18
Illumina Casava1.8 software used for basecalling.
RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.
FPKM were obtained using CuffLinks with upper-quartile and GC normalization
H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.
Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml)
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| Submission date |
Apr 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Matt Teater |
| E-mail(s) |
mrt2001@med.cornell.edu
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| Organization name |
Weill Cornell Medical College
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| Street address |
445 E 69th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platform ID |
GPL10999 |
| Series (1) |
| GSE45982 |
EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation |
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| Relations |
| BioSample |
SAMN02056240 |
| SRA |
SRX271845 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1129349_Sample_43_NB_Input_1.wig.gz |
210.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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