 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 30, 2014 |
| Title |
LncHSC-1-KD RNA-Seq (II) |
| Sample type |
SRA |
| |
|
| Source name |
KSL cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Murine bone marrow KSL cells transduced with KD retrovirus
cell surface marker: c-Kit+Sca-1+Lin-GFP+
strain: C57BL/6
genotype/variation: LncHSC-1-KD
|
| Treatment protocol |
PolyA selection
|
| Growth protocol |
Sca-1+ cells from 5-FU injected mice were isolated and transduced with retrovirus. After in vitro culture for two days in transduction medium, containing Stempro 34 (Gibco, Carlsbad, CA), nutrient supplement, penicillin/streptomycin, L-glutamine (2mM), mSCF (10ng/ml; R&D Systems Minneapolis, MN) and mTPO (100ng/ml; R&D Systems), KSL-GFP+ cells were sorted for RNA-seq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extract RNA using Qiagen Rneasy Micro kit.
Tru-Seq RNA sample prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Knockdown LncRNA LncHSC-1
|
| Data processing |
RUM to make alignments; Customized script to count fragments on gene; DESEQ to do differential expression test;
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated text file for gene's count and fpkm for each sample
|
| |
|
| Submission date |
Jan 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
deqiang sun |
| E-mail(s) |
dsun@tamu.edu
|
| Phone |
(713) 677-7439
|
| Organization name |
Texas A&M University
|
| Street address |
2121 W Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE53928 |
Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function (RNA-Seq) |
| GSE63277 |
Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function |
|
| Relations |
| BioSample |
SAMN02580189 |
| SRA |
SRX424001 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1303701_LncHSC-1.tsv.gz |
665.1 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
