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| Status |
Public on Mar 31, 2016 |
| Title |
WT-control (KD) rep1 |
| Sample type |
SRA |
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| Source name |
EML Cell Line
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| Organism |
Mus musculus |
| Characteristics |
cell line: EML
treatment: knockdown control
tissue: Bone marrow
cell type: Basophil
strain: BDF1
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| Growth protocol |
EML cells were maintained in medium containing stem cell factor (SCF). EML cells were grown in IMDM containing 20% FBS and SCF (200 ng/ml, PeproTech).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from TRIZOL (Invitrogen) or RNeasy RNA isolation kit (Qiagen).
Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3’ ends by Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina’s adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen). After purified twice, DNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Pusion PCR master mix (Thermo Scientific, Hudson, NH).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using Tophat-2.0.9 with parameters --bowtie1 --segment-length 21
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Cufflinks with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
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| Submission date |
Apr 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Tae-Young Roh |
| Organization name |
Ewha Womans University
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| Department |
Life Sciences
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| Lab |
Sysgem Genomics
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| Street address |
52 Ewhayeodae-gil, Seodaemun-gu
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| City |
Seoul |
| State/province |
--- Select One --- |
| ZIP/Postal code |
03760 |
| Country |
South Korea |
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| Platform ID |
GPL11002 |
| Series (1) |
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| Relations |
| BioSample |
SAMN02729211 |
| SRA |
SRX519915 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1370409_WT-KD_rep1.txt.gz |
385.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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