|
| Status |
Public on May 20, 2019 |
| Title |
CLL-01 COCULTURE |
| Sample type |
SRA |
| |
|
| Source name |
Primary CLL cells growing for 48h in coculture with EL08-1d1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
subject: patient 1
diagnosis: chronic lymphocytic leukemia (CLL)
cell type: CD19+CD5+ CLL CELLS
|
| Growth protocol |
Primary CLL cells were isolated from peripheral blood of 6 different patients and cultured with RPMI supplemented with 5% fetal calf serum. Adherend cells were cultured in MEM Alapha + GlutaMAX medium (Invitrogen) supplemented with 10% fetal calf serum (PAA, CoĢlbe, Germany), 10% horse Serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using the RNeasy Mini Kit (Qiagen). Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).
Libraries were prepared for sequencing using standard illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
2_BP_CNT
|
| Data processing |
Illumina Csava 1.8,2 software used for base-calling
merged fastaq packages of each sample were subject to adapter trimming using Trimmomatic 0.30 software tool. Trimmed sequences were aligned to the human genome 19 using aligner STAR
Sorted alignments were imported into StrandNGS (AvadisNGS)
For quantification of RNAs was used PartekGS
Genome_build: Hg19
Supplementary_files_format_and_content: excel file include raw data and RPKM for each samples, ratio, forld change and p-value
|
| |
|
| Submission date |
Jun 06, 2017 |
| Last update date |
May 20, 2019 |
| Contact name |
Ingo Ringshausen |
| E-mail(s) |
mm2084@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Street address |
Cambridge biomedical campus
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0AH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE99724 |
Gene expression activation in CLL mediated by MSCs contact |
|
| Relations |
| BioSample |
SAMN07198476 |
| SRA |
SRX2885658 |
