|
| Status |
Public on Feb 21, 2015 |
| Title |
CLL0989_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
CLL primary B-cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissues: Blood
cell type: CD19+ B-cells
tissue: Tumor
|
| Growth protocol |
Primary B-cells were isolated from CLL using Dynal B-cell Isolation Kit (Invitrogen, Carlsbad, CA, USA); Normal B-cell samples were purchased from ALLCells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen AllPrep DNA/RNA/miRNA Universal Kit
RNA-seq libarary was prepared using Illumina TrueSeq mRNA library preparation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Transcriptome analysis by RNA-seq
|
| Data processing |
TopHat 2.0.8b [1] was used for mapping sequence reads to the human genome (hg19) with the parameter for Illumina stranded sequencing (--library-type fr-firststrand).
BedTools 2.16.2 [2] and bedGraphToBigWig generated stranded binary wiggle files after in-house scripts split reads mapped to each strand.
FeatureCounts 1.4.6 was used to compute the number of reads mapped to each gene and transcript. DESeq 1.10.1 [4] for differential expression analysis.
DESeq 1.10.1 was used for differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet contains FPKM values for each transcript in all samples.
|
| |
|
| Submission date |
Feb 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Huidong Shi |
| E-mail(s) |
[email protected]
|
| Phone |
706-721-6000
|
| Organization name |
Augusta University
|
| Department |
Georgia Cancer Center
|
| Lab |
2125 K
|
| Street address |
1120 15th Street, CN2138
|
| City |
Augusta |
| State/province |
GA |
| ZIP/Postal code |
30912 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE66117 |
Transcriptome analysis in chronic lymphocytic leukemia cells using RNA sequencing (RNA-seq) |
| GSE66167 |
Transcriptome analysis and Genome-wide DNA methylation maps in chronic lymphocytic leukemia cells determined by next-generation sequencing |
|
| Relations |
| BioSample |
SAMN03360465 |
| SRA |
SRX885264 |
