|
| Status |
Public on Mar 01, 2020 |
| Title |
HD12 |
| Sample type |
SRA |
| |
|
| Source name |
primary purified circulating tumor cells
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: primary human sample
cell type: purified circulating tumor cells
patient diagnosis: healthy donor
|
| Treatment protocol |
CTCs were purified from whole blood utilizing the CTC-iChip as described in the publication
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA isolation was performed using the AllPrep kit (Qiagen) including the optional on column DNAse treatment (Qiagen) per manufacturer's protocol.
To generate libraries for total RNA sequencing the Illumina Smarter Stranded Total RNA-Seq kit v2 (Cat No#634413) was used according to the manufacturer's instructions. Pooled libraries were sequenced on an Illumina NextSeq 500 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
HLD_F43.4.18.16
|
| Data processing |
Reads aligned to HG38
Deduplicated BAM files used with HTSeq-Count to create count tables
Data was analyzed with DESeq2 for differential expresison analysis
Genome_build: GRCH38
Supplementary_files_format_and_content: Raw and normalized read counts in Text format
|
| |
|
| Submission date |
Jan 30, 2020 |
| Last update date |
Mar 01, 2020 |
| Contact name |
David T Ting |
| E-mail(s) |
dting1@partners.org
|
| Phone |
617-726-0337
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Cancer Center
|
| Lab |
Ting Lab
|
| Street address |
149 E 13th street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE144561 |
Pancreatic Circulating Tumour Cell Profiling Identifies LIN28B as a Metastasis Driver and Drug Target |
|
| Relations |
| BioSample |
SAMN13948150 |
| SRA |
SRX7652750 |
