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Sample GSM3027634 Query DataSets for GSM3027634
Status Public on Aug 27, 2018
Title 1000_element_library_plasmid
Sample type SRA
 
Source name plasmid
Organism synthetic construct
Characteristics strain: NA
tissue: NA
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from the dissociated organoids using the QIAamp DNA Blood Maxi kit (#51194, Qiagen) and quantified using PicoGreen (P7589, Invitrogen) following the manufacturer’s instructions.
Illumina sequencing libraries were generated using PCR amplification with primers specific to the sequence of the genome of the lentiviral vector backbone. For each sample, 8 x 1 µg PCR reactions were performed in a volume of a 100µl each. For each reaction, a final concentration of 0.5 mM of each PCR primer (Integrated DNA Technologies), 0.5 mM dNTPs (#N8080261, Clontech) and 1x Titanium Taq and buffer (#639242, Clontech). The following conditions were used for PCR: 1x 98 °C for 5 min; 28x 95 °C for 15 s, 65 °C for 15 s, 72 °C for 30 s; 1x 72 °C for 5 min.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description 1000_element_library_plasmid
Data processing Library strategy: CRISPR screen
Basecalls performed using Illumina bcl2fastq version 2.17.1
Sequenced reads were trimmed to barcode/CRISPR sequence and aligned by bowtie version 1.0.1. For CRISPR reads, no mismatches were allowed during alignment. For barcode reads, two mismatches were allowed.
Read counts were summarized using custom python scripts
Genome_build: hg19
Supplementary_files_format_and_content: comma separated file with read counts
 
Submission date Feb 28, 2018
Last update date Apr 30, 2019
Contact name Frederic D Sigoillot
E-mail(s) frederic.sigoillot@novartis.com
Organization name Novartis Institutes for Biomedical Research
Department Chemical Biology and Therapeutics
Lab Data Science
Street address 181 Massachusetts Avenue
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL19604
Series (1)
GSE111269 A CRISPR loss-of-function Hepatic progenitor cells expansion screen in liver organoids
Relations
BioSample SAMN08623839
SRA SRX3751936

Supplementary file Size Download File type/resource
GSM3027634_1000_element_library_plasmid.csv.gz 11.1 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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