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| Status |
Public on Jun 30, 2022 |
| Title |
AKATA |
| Sample type |
SRA |
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| Source name |
B cell lymphoma cell
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| Organism |
Homo sapiens |
| Characteristics |
cell line: AKATA
tissue: B cell lymphoma
cell type: EBV positive B cell lymphoma cell line
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from TW03-EV and TW03-Gal-9 cells were isolated using TRIzol reagent, and dissolved in RNase-free water.
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 3000 |
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| Data processing |
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.13 with parameters -p 8 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 -G hg19
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Counts and RPKMs for each Sample
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| Submission date |
Dec 02, 2020 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Jingxiao Xu |
| E-mail(s) |
xujx1@sysucc.org.cn
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| Phone |
17825845830
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| Organization name |
Sun Yet san university
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| Street address |
Dongfengdong Road 651
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| City |
Guangzhou |
| State/province |
Guangdong Province |
| ZIP/Postal code |
510000 |
| Country |
China |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE162516 |
Critical role of galectin-9 in EBV-driven transformation of human B-lymphocytes |
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| Relations |
| BioSample |
SAMN16981102 |
| SRA |
SRX9620198 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4953587_AKATA_positive_analysed.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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