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| Status |
Public on Feb 25, 2021 |
| Title |
REC-1 cells, G8 |
| Sample type |
SRA |
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| Source name |
Mantle cell lymphoma cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: B cells
cell line: REC-1
treatment: 400 nM ibrutinib for 48 h
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| Treatment protocol |
Ibrutinib (Selleck Chemicals, Absource Diagnostics, Munich, Germany), dissolved in DMSO, was added to the 48 h sample at seeding and after 42 h to the 6 h sample reaching a final concentration of 400 nM, Ctr was untreated.
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| Growth protocol |
3 x 10e6 REC-1 cells grew for 48 h in 5 ml RPMI1640 medium (supplemented with 10% heat-inactivated fetal bovine serum and 2 mmol/l L-Glutamine)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and were washed with phosphate-buffered saline (PBS), stained with propidium iodide (2 µg/ml), and 30,000 cells were sorted by FACS (ARIA III, BD Biosciences, San Jose, CA, US) to exclude possible cell debris, apoptotic cells, and doublets. After counting of the cells using trypan blue staining, they were loaded into the 10x Genomics Chromium (10x Genomics, Pleasanton, CA, US).
To generate the libraries, the Chromium Single Cell 3’ Kit v2 Chemistry was applied and all steps were performed following the standard 10x Genomics protocol. For the quantification of the libraries a QubitTM 3.0 Fluometer (Thermo Fisher) was utilized and a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent Technologies, Waldbronn, Germany) was used for quality check. The reads were sequenced to a length of 50 bp in paired-end format on a S1 flowcell with a Novaseq 6000 (Ilumina, San Diego, CA, US).
scRNA-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Rep2_48h
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| Data processing |
The Cell Ranger software (version 3.0.1) offered by 10x Genomics was used to analyze the data.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix
h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
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| Submission date |
Nov 27, 2020 |
| Last update date |
Feb 26, 2021 |
| Contact name |
Antoine-Emmanuel Saliba |
| E-mail(s) |
emmanuel.saliba@helmholtz-hzi.de
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| Phone |
+49-931-31-81341
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| Organization name |
Helmholtz Institute for RNA-based Infection Research
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| Street address |
Josef-Schneider-Straße 2 / D15
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| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE162234 |
Time-resolved single cell transcriptomics of an ibrutinib-treated mantle cell lymphoma cell line |
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| Relations |
| BioSample |
SAMN16939887 |
| SRA |
SRX9597504 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4947355_G8_filtered_feature_bc_matrix.tar.gz |
32.6 Mb |
(ftp)(http) |
TAR |
| GSM4947355_G8_molecule_info.h5 |
379.2 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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