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| Status |
Public on Nov 17, 2014 |
| Title |
CJ7 wt RNA |
| Sample type |
SRA |
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| Source name |
ES cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: CJ7
cell type: ES cells
background: 129/S
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| Growth protocol |
ESCs were plated with irradiated murine embryonic fibroblasts (MEFs) and grown under typical ESC conditions on gelatinized tissue culture plates. Briefly, cells were grown in Knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibitory factor (LIF), non-essential amino acids, L-glutamine, and penicillin/streptomycin as previously described (Boyer et al., 2006). Before collection or in vitro differentiation, cells were briefly plated on non-gelatinized tissue culture plates to remove MEFs.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol according to manufacturer’s instructions, including optional step in protocol. RNA quality was determined by Agilent Bioanalyzer. RNA-seq libraries were prepared as previously described (Wamstad et al., 2012). A final round of size selection by Agencourt AMPure XP beads was performed to remove small fragments such as primers. Sequencing was run on either an Illumina GA-2 or Hi-Seq (barcoded). .
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
prepared and sequenced with ST20; use as wt control for batch normalization.
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| Data processing |
Illumina Offline BaseCaller1.9.3 software used for basecalling.
Bowtie v. 0.12.7, Tophat v1.3.2 and Cufflinks v 1.2.1 and Cuffdiff were utilized to determine the expression levels of genes (Trapnell et al., 2012), using a NCBIN37, ENSEMBL-based annotation and flags -p 4, -r 170, --segment-length 20 --segment-mismatches 1 --solexa1.3-quals --no-novel-juncs
Cufflinks was guided using the same annotation as Tophat with flags -b -u -p 6
Genome_build: mm9 (iGenome)
Supplementary_files_format_and_content: Txt file containing a table of RPKM values for each sample described in the study
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| Submission date |
Dec 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Laurie A Boyer |
| E-mail(s) |
lboyer@mit.edu
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| Phone |
617 324-3335
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| Organization name |
Massachusetts Institute of Technology
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| Department |
Biology
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| Lab |
Boyer
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| Street address |
77 Massachusetts Avenue
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE53506 |
PRC2 coordinates lineage fidelity and DNA methylation during ESC differentiation (RNA-Seq) |
| GSE53508 |
PRC2 coordinates lineage fidelity and DNA methylation during ESC differentiation |
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| Relations |
| BioSample |
SAMN02469230 |
| SRA |
SRX396329 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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