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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 29, 2018 |
| Title |
MAX8 |
| Sample type |
SRA |
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| Source name |
blastocyst
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| Organism |
Rattus norvegicus |
| Characteristics |
cell type: XENP
strain: WKY
passages: 11, 12
gender: Female
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| Growth protocol |
Mouse pXEN and rat XENP cells were cultured essentially as previously described (Lo Nigro et al., 2012).
Mouse XEN cells were cultured on mouse embryo fibroblasts in 20% FBS as previously described (Kunath et al., 2005).
Mouse ES cells were cultured in 15% FBS and supplied with LIF and '2i' as previously described (Czechanski et al., 2014).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA). Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2500 (101 cycles PE lane).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
Quality controlled FASTQ files were alignment to Mus musculus UCSC mm10 reference genome sequence (or Rattus norvegicus UCSC rn6 sequence) using the STAR (version 2.5.1) aligner software. To measure differential gene expression, DESeq2 was used.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Mus musculus UCSC mm10; Rattus norvegicus UCSC rn6
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample
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| Submission date |
Oct 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Young Gyu Chai |
| E-mail(s) |
ygchai@hanyang.ac.kr
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| Phone |
+82-31-400-5513
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| Organization name |
Hanyang Univ.
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| Department |
Molecualr & Life Science
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| Street address |
55 Hanyangdaehak-ro
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| City |
Ansan |
| State/province |
Gyeonggi-do |
| ZIP/Postal code |
15588 |
| Country |
South Korea |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE106158 |
Comparative gene expression profiling of mouse pXEN, XEN, ES, and rat XENP cells |
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| Relations |
| BioSample |
SAMN07834131 |
| SRA |
SRX3325626 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2830593_r-MAX8.ReadsPerGene.out.tab.gz |
95.0 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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