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| Status |
Public on Feb 13, 2019 |
| Title |
EL4 |
| Sample type |
SRA |
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| Source name |
thymocyte
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
cell line: EL4
cell type: thymoma
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| Growth protocol |
EL4 or MC38 (1 × 10^6 cells/well/6 well plate) were cultured for 24 h in RPMI1640 supplemented with 10%FBS.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy Mini Kit Plus (Qiagen, Valencia, CA, USA).
Libraries were prepared for sequencing using library creation kits (TruSeq Stranded mRNA sample prep kit, Illumina, San Diego, CA, USA)
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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 |
Samples were sequenced using Illumina HiSeq2500 instrument with paired-end 2 x 125-bp cycle
Base calls were performed on CASAVA 1.8.2. pipeline
Quality check for sequence reads using FastQC
Pre-processing of sequence reads using Trimmomatic version 0.36 with LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 as command option. Fastq reads were generated using BCL2FASTQ Conversion Software1.8.4; First line begins with a '@' character and is followed by a sequence identifier. Second line represent raw nucleotide sequence letters. The last line encodes the quality values for the sequence.
Mapping of sequence reads using TopHat version 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: only bam files were generated to compare the allele imbalance among samples and available as SRA records.
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| Submission date |
Feb 11, 2019 |
| Last update date |
Feb 13, 2019 |
| Contact name |
Ranmaru Shimoda |
| E-mail(s) |
shimoda@rhelixa.com
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| Phone |
+818043368250
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| Organization name |
Rhelixa, Inc.
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| Street address |
3F Yayoi Bldg., 3-7-4 Iwamotocho
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| City |
Chiyoda |
| State/province |
Tokyo |
| ZIP/Postal code |
101-0032 |
| Country |
Japan |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE126280 |
Allele imbalance in Reps1 and Adpgk |
| GSE126281 |
Type I Interferon Delivery by iPSC-Derived Myeloid Cells Elicits Antitumor Immunity via XCR1+ Dendritic Cells |
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| Relations |
| BioSample |
SAMN10911790 |
| SRA |
SRX5360314 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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