|
| Status |
Public on Mar 28, 2019 |
| Title |
E/M.2 |
| Sample type |
SRA |
| |
|
| Source name |
Epithelial/Mesenchymal hybrid derivatives of HMLER derived by FACS sorting for CDD4+ C104+ cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HMLER
cell state: Epithelial/Mesenchymal hybrid
genotype: wildtype
|
| Growth protocol |
All cells were grown in mammary epithelial growth medium (MEGM; Lonza)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNEasy plus kit
Libraries were prepared using the TruSeq stranded mRNA protocol as described in the kit (Illumina; Catalog # RS-122-2101) manual. Libraries were pooled together and sequenced on the HiSeq 2500 sequencer using the Standard sequencing protocols. Images analysis and base calling was done using the Standard Illumina pipeline, and then demultiplexed into fastq files
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 8 (Duplicate of Sample 2)
|
| Data processing |
RNASeq single-end reads from Illumina 1.5 encoding were aligned using TopHat (v 2.0.13) to the human genome (GRCh37) with Ensembl annotation (GRCh37.75) in gtf format: default parameters were used, except for base encoding. HTSeq-count was used to obtain counts with intersection-strict mode and strand=reverse.
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw counts from HTSeq-count
|
| |
|
| Submission date |
Aug 28, 2018 |
| Last update date |
Mar 29, 2019 |
| Contact name |
Cornelia Kroeger |
| E-mail(s) |
ckroeger@gmx.net
|
| Organization name |
Whitehead Institute
|
| Lab |
Weinberg
|
| Street address |
455 Main St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE119149 |
Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells |
|
| Relations |
| BioSample |
SAMN09928050 |
| SRA |
SRX4618908 |
