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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 02, 2020 |
| Title |
total_RNA_MCM2_2A_mESC rep2 |
| Sample type |
SRA |
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| Source name |
mESC
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| Organism |
Mus musculus |
| Characteristics |
genotype: MCM2_2A
experiments: total_RNA
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| Growth protocol |
Mouse E14 ES cells (a gift from Dr. Tom Fazzio, University of Massachusetts Medical School, Worcester, MA) were cultured in DMEM (Corning) medium supplemented with 15% (vol/vol) fetal bovine serum (FBS), 1% penicillin/streptomycin (Invitrogen), 1 mM sodium pyruvate (Cellgro), 2 mM L-glutamine (Cellgro), 1% MEM non-essential amino acids (Invitrogen), 55 µM β-Mercaptoethanol (Sigma), 10 ng/mL mouse leukemia inhibitory factor (mLIF) on gelatin-coated dishes in a 37°C incubator with a humidified, 5% CO2 atmosphere. Yeast cells were synchronized and cultured following the standard protocol (Dunham et al., 2015).
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| Extracted molecule |
total RNA |
| Extraction protocol |
eSPAN in yeast was performed exactly as previously described (Yu et al., 2014). Total RNA samples were purified the same as for RT-PCR. OK-seq was performed as previously described with some modifications (Petryk et al., 2016).
RNA-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. For eSPAN libraries, the supernatants were purified with ChIP DNA concentrator columns and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.
RNA-Seq, ChIP-Seq, CUT&TAG, OK-Seq, eSPAN
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
CUT&TAG, OK-Seq and eSPAN reads were mapped using bowtie2. RNA-Seq reads were mapped using STAR.
Read count on gene body or promoters were calculated by FeatureCount.
Differential genes and log fold change were calculated by DEseq2
Read coverage in each bin was calculated using the R package of Rsamtools. Histone bias was computed from trimmed, mapped, unique reads in each bin as Bias=(W-C)/(W+C), where W and C are the number of reads mapped on Crick and Watson strand in each bin, respectively.
Genome_build: For mouse, reads were mapped to mm10. For yeast, reads were mapped to saccer3.
Supplementary_files_format_and_content: bw files, the score represents reads coverage at each genomic position. Read coverage on plus strand, minus strand and total were calculated seperately.
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| Submission date |
Jan 03, 2020 |
| Last update date |
Sep 02, 2020 |
| Contact name |
zhiguo zhang |
| Organization name |
Columbia University
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| Department |
Pediatric and Genetics and Development
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| Lab |
Irving Cancer Research Center
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| Street address |
1130 St. Nicholas Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE142996 |
DNA polymerase α interacts with H3-H4 and facilitates the transfer to parental histones to lagging strand |
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| Relations |
| BioSample |
SAMN13718036 |
| SRA |
SRX7496380 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4247626_LZM065_MCM2_2A_total_RNA.cntTable.txt.gz |
227.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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