|
| Status |
Public on Jan 01, 2018 |
| Title |
DOHH2 |
| Sample type |
SRA |
| |
|
| Source name |
DOHH2 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DOHH2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were centrifuged for 5 minutes at 1000 RPM, and supernatant was removed without disturbing the cell pellet. Cells were resuspended using 1000 uL of HGT Lysis buffer to maintain original concentration of 4 millions cells per 1000 uL. The lysis buffer cell suspension was placed in 95 degrees Celsius for fifteen (15) minutes. After allowing to cool at room temperature for ten (10) minutes, Proteinase K was added at 1/20 Lysis Buffer volume and samples were incubated at 50 for 180 minutes. Samples were run as singletons. Samples were plated initially at a concentration of 10000 cells per well (10000 cells/35 uL).
Samples submitted were individually barcoded and purified using AMPure XP beads and quantitated using KAPA Library Quantification kit. The library was sequenced at 4pM on an Illumina NextSeq using High Output, 75 cycle, v2 kit with two index reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sample 2
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt
|
| Data processing |
Illumina Casava1.7 software used for basecalling. Four fastq files per sample.
The HTG EdgeSeq Parser was used to align reads to the probe list to collate the data. Data are provided as raw counts data and median normalized.
Genome_build: hg38
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text file includes raw counts values.
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text file includes median normalized values.
|
| |
|
| Submission date |
Sep 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Francesco Bertoni |
| E-mail(s) |
francesco.bertoni@ior.usi.ch
|
| Phone |
+41 91 820 0367
|
| Organization name |
IOR
|
| Department |
Lymphoma & Genomics Research Program
|
| Street address |
Via V. Vela 6
|
| City |
Bellinzona |
| State/province |
Ticino |
| ZIP/Postal code |
6500 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE103934 |
Targeted RNA-Seq of Human Lymphoma Cell Line |
|
| Relations |
| BioSample |
SAMN07661061 |
| SRA |
SRX3194393 |
