|
Status |
Public on Jun 27, 2019 |
Title |
TAGATA: HCC1806_Palbociclib_3.16 |
Sample type |
SRA |
|
|
Source name |
HCC1806
|
Organism |
Homo sapiens |
Characteristics |
cell type: HCC1806 breast cancer cell line cell line: HCC1806 drug treatment: Palbociclib concentration (um): 3.16 time (hours): 6
|
Treatment protocol |
24 hours after seeding cells, CDK4/6 inhibitors were added. Cells were lysed in the plates after 6 hours.
|
Growth protocol |
Cells were plated at densitieis ranging from 500 to 2000 cells per well in a 384-well plate and allowed to adhere for 24 hours
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using TCL lysis buffer, samples were using universal adapters, barcodes, unique molecular identifiers, and a template switching reverse transcriptase. Libraries were prepared using Nextera DNA kit (Illumina). Digitial gene expression (DGE)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 550 |
|
|
Description |
well: F10 barcode: TAGATA HCC1806_Palbociclib_3.16
|
Data processing |
barcode and Unique moelcular identifiers (UMIs) were identified for all reads and reads not within one edit distance of a well known barcode were discarded surviving reads were quasialigned using RapMap. Reads per well were counted using UMI's, duplicate UMIs were discarded. Mutimapped reads were weighted by the number of transcirpts they aligned to Reads counts were collapsed to gene counts by adding all counts for each transcript of a gene. Genome_build: GRch38 Supplementary_files_format_and_content: .csv file of counts for all gene identifiers that mapped to a mRNA across all 335 samples
|
|
|
Submission date |
Jan 16, 2019 |
Last update date |
Jun 27, 2019 |
Contact name |
Kartik Subramanian |
E-mail(s) |
kartik_subramanian@hms.harvard.edu
|
Organization name |
Harvard Medical School
|
Street address |
200 Longwood Avenue
|
City |
Boston |
ZIP/Postal code |
02115 |
Country |
USA |
|
|
Platform ID |
GPL21697 |
Series (1) |
GSE125215 |
Digital gene expression (DGE) based transcript profiling of CDK inhibitors |
|
Relations |
BioSample |
SAMN10760327 |
SRA |
SRX5255668 |