|
| Status |
Public on Sep 02, 2021 |
| Title |
DL3A193_rnaseq |
| Sample type |
SRA |
| |
|
| Source name |
CD19+ B cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lymph node
disease state: diffuse large B cell lymphoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with a Qiagen RNeasy kit.
rRNA-depleted (Ribo-Zero) libraries were prepared using TruSeq RNA Sample kits with indexed adaptors.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
bcl2fastq (v1.8.4) was used to demultiplex and convert base call files into FASTQ files.
Read quantification was performed by salmon (v0.14.1) to gencode.v31lift37 annotations with the -validateMappings and -seqBias parameters.
Differential gene expression analyses and normalized gene-level counts were generated with DESeq2 (v1.26.0).
Genome_build: hg19
Supplementary_files_format_and_content: Raw transcript counts as quantified by salmon (v0.14.1) using gencode.v31lift37 annotations. Contains transcriptID, Length, effectiveLength, TPM, and NumReads columns.
|
| |
|
| Submission date |
Feb 24, 2020 |
| Last update date |
Sep 02, 2021 |
| Contact name |
Jared Andrews |
| E-mail(s) |
jared.andrews@stjude.org
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Developmental Neurobiology
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE145842 |
Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers (RNA-seq) |
| GSE145848 |
Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers |
|
| Relations |
| BioSample |
SAMN14175873 |
| SRA |
SRX7796004 |
