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| Status |
Public on Jul 15, 2013 |
| Title |
K562 |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell line: K562
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| Growth protocol |
K562 cells were culture in the culture flask containing RPMI 1640 medium (Gibco) supplied with 10% fetal bovine serum (Hylone) and penicillin (100 U/ml)-streptomycin (0.1 mg/ml) (Invitrogen, Carlsbad, CA).
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| Extracted molecule |
total RNA |
| Extraction protocol |
SOLiD RNA-seq with Invitrogen ribominus kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
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| Description |
chronic myelogenous leukemia (CML)
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| Data processing |
Human genome (release 55) from Ensembl database was used as reference to do read mapping. We also constructed an Exon–exon Junction Database for reads mapping with randomly combination of 49 bp sequences near each exonic junction points. We first mapped the full length 50 bp reads to the ribosomal RNA database to wipe off the disturbance of remnants of rRNA. The left data were then aligned with Human genome and exon junction database for annotation, with the allowance of five mismatches, and then the last 5 bp were cut off from unmapped tags for the next matching with chromosome and exon junction database (allowing five mismatches) to increase annotation rate of raw data. We repeated this step until remained length of the reads was 25bp and reduced the number of mismatches gradually from five to two. Finally, after these six steps, tags with matching information were collected for subsequent gene expression analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated according to Mortazavi A, et al., Nature methods, 2008.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for K562
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| Submission date |
Jul 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
yadong yang |
| E-mail(s) |
yangyd@big.ac.cn
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| Organization name |
Beijing Institute of Genomics
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| Street address |
No.1-104 Beichen West Road, Chaoyang
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL9442 |
| Series (1) |
| GSE39374 |
Transcriptomes of K562 cell line |
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| Relations |
| SRA |
SRX170364 |
| BioSample |
SAMN01091989 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM967005_K562.txt.gz |
203.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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