 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 12, 2017 |
| Title |
C11B_Mel3.b |
| Sample type |
SRA |
| |
|
| Source name |
subcutaneous metastasis
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin (melanoma metastasis)
culture: melanoma short-term culture Ma-Mel-93
melanoma genetic conditions: BRAF wild type and NRAS G13R mutant
|
| Growth protocol |
melanoma short-term culture Ma-Mel-123
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single melanoma cells from short-term cultures were captured on an integrated fluidic circuit RNA-seq chip (Fluidigm, Hamburg, Germany) using the Fluidigm C1 system. Cells were loaded onto the chip at a concentration of 200 cells/μL and imaged by phase-contrast. Cell capture, cell lysis, reverse transcription, and cDNA amplification were performed on the chip as described (Camp et al., 2015).
Illumina libraries were constructed using the Illumina Nextera XT DNA Sample Preparation kit using the protocol supplied by Fluidigm. Ninety-six libraries were pooled (3 µL each) and purified with SPRI beads. Library concentration and size distribution were assessed on an Agilent Bioanalyzer and with Qubit dsDNA HS Assay kits and a Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Invitrogen, Darmstadt). Each cell was paired-end sequenced (100 base reads) on an Illumina HiSeq 2500 to a depth of 2–5 million reads and base-calling, adaptor trimming, and de-multiplexing were performed as described (Renaud et al., 2013; Renaud et al., 2015).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt
|
| Data processing |
Raw reads were processed using a custom script and aligned to a Bowtie2 (Langmead and Salzberg, 2012) indexed human genome (grch38 sourced from ENSEMBL) using TopHat (Trapnell et al., 2009) with default settings.
Transcript levels were quantified as fragments per kilobase of mapped reads (FPKM) generated by Cufflinks (Trapnell et al., 2010) using gencode protein coding genes (grch38 v22 Havana).
We excluded cells that did express neither of two housekeeping genes ACTB and GAPDH. 307 single cells remained for the transcriptome analysis.
Genome_build: grch38 sourced from ENSEMBL
Supplementary_files_format_and_content: FPKM values. The file GSE81383_data_melanoma_scRNAseq_BT_Mel.txt.gz contains the FPKM values for all samples. GSE81383_data_melanoma_scRNAseq_BT_2015-07-02.txt.gz contains the FPKM values for GSM2151479 - GSM2151570.
|
| |
|
| Submission date |
Jan 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Edith Willscher |
| E-mail(s) |
willscher@izbi.uni-leipzig.de
|
| Organization name |
IZBI
|
| Street address |
Haertelstraße 16-18
|
| City |
Leipzig |
| ZIP/Postal code |
04107 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE81383 |
Mapping heterogeneity in a patient-derived melanoma culture by single-cell RNA-seq |
|
| Relations |
| BioSample |
SAMN06218317 |
| SRA |
SRX2485565 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
