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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 10, 2017 |
| Title |
WT_mouse ES_RNA-seq 4 |
| Sample type |
SRA |
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| Source name |
WT_mouse ES cells
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| Organism |
Mus musculus |
| Characteristics |
strain: 129SVxC57/BL6
genotype/variation: wild type
cell type: embryonic stem cells (ES cells)
molecule subtype: rRNA-depleted RNA
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| Growth protocol |
Co-derived wild-type and Srap1 KO mouse ES cells were cultured on gelatin-coated plates in high-glucose DMEM containing 15% FBS, 1x non-essential amino acids, 2 mM L-glutamine, 100 mM beta-mercaptoethanol, 1x nucleosides (Millipore), 1000U/ml leukemia inhibitory factor (StemRD) and 2i (selective GSK3β & Mek 1/2 inhibitors; Millipore), 25 mg/ml L-ascorbic acid.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, total RNA was extracted from wild-type and Srap1 KO mouse ES cells using the Zymo RNA Clean & Concentrator (Zymo Research), followed by rRNA depletion and cDNA preparation using the KAPA Stranded RNA-Seq Kit with RiboErase.
Library preparations were performed using the Kapa HyperPrep kit, followed by 12 cycles of PCR amplification with Kapa HiFi HotStart polymerase.
Amplified libraries were pooled, purified twice with 0.9X Ampure XP beads and analyzed on the Illumina HiSeq2000 or NextSeq500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
For RNA-seq, ChIP-seq and DIP-seq, raw reads were trimmed to remove adapters and low-quality reads using Trim Galore (v0.3.5).
Bowtie (v0.12.8) was used to obtain reads mapped uniquely to the mouse genome (mm9). ChIP and DIP peak candidates were identified with MACS (v2.1.1)using input as the control data set.
To remove nonspecific signals, IgG samples were processed similarly and their normalized read density (RPKM) values were subtracted from modification-specific peaks.
For RNA-seq, Cufflinks (v 2.2.1.0) was used to assemble transcripts, estimate their abundances and test for differential transcript expression.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM
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| Submission date |
Jun 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Douglas Edmund Feldman |
| E-mail(s) |
defeldma@usc.edu
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| Organization name |
USC Keck School of Medicine
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| Department |
Pathology
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| Lab |
HMR 212
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| Street address |
2011 Zonal Avenue
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE81222 |
Erasure of Tet-oxidized 5-methylcytosine by a SRAP nuclease |
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| Relations |
| BioSample |
SAMN05256991 |
| SRA |
SRX1852006 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2203819_RNA_WT-4.txt.gz |
252.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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