 |
 |
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
 |