|
| Status |
Public on Oct 11, 2016 |
| Title |
single cell RNAseq tumor B cells [1350A03_Tumor_A03] |
| Sample type |
SRA |
| |
|
| Source name |
1350A03_Tumor_A03
|
| Organism |
Homo sapiens |
| Characteristics |
condition: Tumor
patient_id: patient_1
cell type: B cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Live CD45+ and CD19+ cells were sorted in 2ul of Qiagen TCL buffer in 96-well plates
SmartSeq2 protocol with modifications (Trombetta et al., 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were mapped to the human gemome (hg19) by Bowtie/Tophat using the Broad pipeline.
Only single cell samples with at least 100.000 paired-end reads and a minimum of 20% aligning to the genome were retained for further analysis.
FeatureCounts was used to count features based on the Gencode v19 transcriptome annotation.
Only features detected in at least 10 single cell samples were used and further refinement of high quality samples was based on feature complexity, read distribution and number of features detected.
DESeq2 was used with raw counts to estimate differential expression between tumor and normal cells.
Counts were normalized according to their library size and displayed as log2(normalized counts + 1).
Genome_build: hg19
Supplementary_files_format_and_content: fcount_primary_output: matrix of raw feature counts
|
| |
|
| Submission date |
Jul 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ruben Dries |
| E-mail(s) |
rubendries@gmail.com
|
| Organization name |
DFCI
|
| Department |
Computational Biology
|
| Lab |
Longwood Center
|
| Street address |
360 Longwood Ave
|
| City |
Boston |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE84789 |
Single-cell profiling of non small cell lung cancer associated B-cells. |
| GSE84799 |
Multi-parametric profiling of non-small cell lung cancers reveals distinct immunophenotypes |
|
| Relations |
| BioSample |
SAMN05438829 |
| SRA |
SRX1975024 |
