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Sample GSM2310078 Query DataSets for GSM2310078
Status Public on Jan 27, 2017
Title #1-D20LKS
Sample type SRA
 
Source name ES-derived cells
Organism Mus musculus
Characteristics cell type: ES-derived hematopoietic progenitor cells
sorting strategy: Lin–Sca1–c-Kit+
Extracted molecule genomic DNA
Extraction protocol The genomic DNA of sorted cells were routinely extracted.
The sequences corresponding to each shRNA were PCR amplified using universal primers, digested with XhoI and EcoRI restriction enzymes, and gel purified. The purified fragments were then used for preparation of a sequencing library according to the Illumina Hi-seq kit instructions.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference sequences using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Supplementary_files_format_and_content: xlsx files include normalized reads of each shRNA
 
Submission date Sep 13, 2016
Last update date May 15, 2019
Contact name Tianxu Han
E-mail(s) tih028@ucsd.edu
Phone 858-4246-2918
Organization name UCSD
Lab Tariq Rana
Street address 9500 Gilman Dr
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL13112
Series (1)
GSE86898 A genome-wide RNAi screen identifies genes and networks governing hematopoietic stem cell development
Relations
BioSample SAMN05770367
SRA SRX2162578

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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