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Sample GSM3565466 Query DataSets for GSM3565466
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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