|
| Status |
Public on Jun 20, 2016 |
| Title |
RANK-positive 4 |
| Sample type |
SRA |
| |
|
| Source name |
Normal human breast (wild-type)
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 4
tissue: fresh breast tissue
immunophenotype: luminal progenitor
cell population: RANK-positive
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS sorted cells were lysed for RNA preparation using the QIAGEN RNEasy plus micro-kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Image analysis was performed by the HiSeq Control Software (HCS) v2.2.38 and Real Time Analysis (RTA) v1.18.61. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Reads were aligned to the human genome by Rsubread version 1.16.1
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: hg19 (build 37.2)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapped to that gene
|
| |
|
| Submission date |
Jul 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
[email protected]
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE71203 |
Transcriptome analysis of RANK-positive and RANK-negative luminal progenitor subpopulations in the human breast |
|
| Relations |
| BioSample |
SAMN03892986 |
| SRA |
SRX1115353 |
