|
| Status |
Public on Mar 31, 2016 |
| Title |
control sample #18 TU |
| Sample type |
SRA |
| |
|
| Source name |
lymphoblastoid cell line HG3
|
| Organism |
Homo sapiens |
| Characteristics |
strain: HG3
cell line: lymphoblastoid cell line HG3
sample type: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using an RNeasy Plus Mini kit (Qiagen). The RNA integrity and concentration was determined on a Bioanalyzer instrument (Agilent) using an RNA 6000 Nano kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
control sample #18 TU
|
| Data processing |
The reads were aligned to the human genome hg19 assembly (https://genome.ucsc.edu) using Tophat2 software (version 2.0.4)
The FPKM summary and statistical tests were performed using the Cufflinks tool (version 2.2.1)
The RNAseq read count quantification was performed using the HTSeq tool (version 0.6.1)
To identify the gene expression differences between the three pairs of HG3 pools, DESeq2 software was used. (Love, Huber et al. 2014)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each Sample.
|
| |
|
| Submission date |
Dec 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
L. H. |
| Organization name |
Uppsala University
|
| Street address |
Dag Hammarskjölds Väg 20
|
| City |
Uppsala |
| ZIP/Postal code |
751 85 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE75844 |
Transposon mutagenesis reveals fludarabine-resistance mechanisms in chronic lymphocytic leukemia |
|
| Relations |
| BioSample |
SAMN04327455 |
| SRA |
SRX1472495 |
