|
| Status |
Public on Mar 22, 2022 |
| Title |
Patient 13 Co-culture |
| Sample type |
SRA |
| |
|
| Source name |
CLL Cells
|
| Organism |
Homo sapiens |
| Characteristics |
condition: CLL on CD40L Fibroblast Co-culture
patient source: 13
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Micro Kit
NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Processed data column name: TB215
|
| Data processing |
Sequenced reads were trimmed for adaptor sequences and for quality (minimum 20) using trim-galore v0.6.5.
Trimmed reads were mapped separately to the mouse GRCm39 genome and the human GRCh38 genome using HISAT2 generating separate bam files
Human reads in each sample were identified by analysing the mouse and human bam files for each sample using the R package XenofilteR v1.6
Human reads in the XenofilteR output were quantified against human GRCh38 transcripts using kallisto quant
kallisto quantifications were converted to gene level by tximport, then normalised and analysed for differential expression using DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file. Matrix table with raw gene counts for every gene and every sample, generated by tximport
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
Aug 31, 2022 |
| Contact name |
Chris Pepper |
| E-mail(s) |
[email protected]
|
| Phone |
+ 44 (0)1273 678644
|
| Organization name |
University of Sussex
|
| Department |
Brighton and Sussex Medical School
|
| Street address |
Falmer
|
| City |
BRIGHTON |
| ZIP/Postal code |
BN1 9PX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE198455 |
Elucidation of focal adhesion kinase as a modulator of migration and invasion and as a potential therapeutic target in chronic lymphocytic leukemia (RNA-Seq II) |
| GSE198456 |
Elucidation of focal adhesion kinase as a modulator of migration and invasion and as a potential therapeutic target in chronic lymphocytic leukemia |
|
| Relations |
| BioSample |
SAMN26584177 |
| SRA |
SRX14439420 |
