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| Status |
Public on Jul 27, 2017 |
| Title |
a2i_ESC_4_XX_RNA-seq |
| Sample type |
SRA |
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| Source name |
ES cells
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| Organism |
Mus musculus |
| Characteristics |
passage: p3
strain: F1 (129X1/SvJ and C57BL6)
cell type: ES cells
gender: female
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy plus Mini Kit (QIAGEN) for RNA.
To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
RNA-seq
a2i-ESC #a4 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz
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| Data processing |
Libraries were sequenced on the HiSeq2500 (2 X 101 bp or 2×100 bp paired-end reads, illumina)
For RNA-seq analysis, the sequenced reads were mapped to the mouse reference genome (mm10) using tophat-2.1.0 11 with the GENCODE version M9 annotation gtf file and the aligner Bowtie2-2.2.5 6 after trimming adaptor sequences and low-quality bases by cutadapt-1.9.1 12. For allelic expression analysis of RNA-seq, the trimmed reads were also mapped to MSM genomes described as above, and the reads mapped to the same chromosome and positions of both B6 and MSM/Ms genomes with high mapping quality (MAPQ>=20) were used for further analyses. The expression level of each gene was calculated as reads per kilobase per million mapped reads (RPKM) by cufflinks-2.2.1
genome build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes RPKMs for each sample.
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| Submission date |
Dec 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yasuhiro Yamada |
| E-mail(s) |
yyamada@m.u-tokyo.ac.jp
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| Organization name |
University of Tokyo
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| Department |
Department of Molecular Pathology
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| Street address |
7-3-1 Hongo, Bunkyo-ku
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| City |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE84164 |
Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation |
| GSE84165 |
Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation |
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| Relations |
| BioSample |
SAMN06134270 |
| SRA |
SRX2416849 |
| 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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