GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3304485 Query DataSets for GSM3304485
Status Public on Jan 08, 2019
Title POOL1__pMPRA1__input_DNA
Sample type SRA
Source name plasmid DNA
Organism synthetic construct
Characteristics sample type: plasmid DNA
Treatment protocol K562 cells were transiently transfected for 48 hours with a ratio of 1:1 with Xtreme Gene HP (Roche), HeLa and HepG2 both with 3:1 Xtreme Gene HP according to the manufacturer protocol. 4x10e6 K562 cells in 6 cm dish, 1.6x10e6 HeLa or HepG2 cells in 10 cm dish were seeded 12-16 hours prior to the transfection. Cells were counted before the transfection and per 1 x 10e6 cells, 5 µg oligopool were transfected. Media was not changed and transfection efficiency was microscopically determined by GFP expression 48 hours post transfection.
Extracted molecule genomic DNA
Extraction protocol RNA from transiently transfected K562, HeLa, and HepG2 was precipitated by phenol-chloroform extraction according to standard protocols. DNase treatment (Worthington) was followed by cDNA synthesis with SuperScript III First-Strand Synthesis System (Invitrogen).
cDNA was subject to library amplification and libraries were cleaned up with AMPure beads (0.6x, 1.6x, 1.0x).
plasmid sequencing and RNA-seq
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Data processing We used cutadapt to remove adapters from the raw reads and trim bases with a Phred score < 20.
We then counted barcodes if they exactly matched an 11-bp barcode in the design index as well as the constant upstream 6 bp.
All scripts used for subsequent data analysis of processed files can be found at
Genome_build: hg19
Supplementary_files_format_and_content: Barcode sequence and count per replicate
Submission date Jul 24, 2018
Last update date Jan 08, 2019
Contact name Martha L. Bulyk
Organization name Brigham and Women's Hospital
Department Division of Genetics
Lab Bulyk Lab
Street address 77 Avenue Louis Pasteur, Rm 468
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL19604
Series (1)
GSE117594 High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity
BioSample SAMN09709469
SRA SRX4452455

Supplementary file Size Download File type/resource
GSM3304485_POOL1_pMPRA1_input_DNA_COUNTS.txt.gz 619.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap