|
| Status |
Public on May 16, 2016 |
| Title |
FL-HSPC LKO_infected experiment_1 (LKO in shHOXA7gene_exp.diff) |
| Sample type |
SRA |
| |
|
| Source name |
FL-HSPC LKO_infected
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human fetal liver, CD34+CD38-CD90+CD45+
cell type: fetal liver-hematopoietic stem/progenitor cell (FL-HSPC)
infected with: emtpy lentiviral vector (LKO)
|
| Treatment protocol |
Cells were infected with VSV-g pseudotyped lentivirus encoding shRNA and puromicin resistance and selected with puromycin and sorting
|
| Growth protocol |
Cells in culture were cultured at 37C and 5% CO2 in alpha-MEM (Invitrogen), 20% FBS (Hyclone), 2 mM L-glutamine and 1% penicillin/streptomycin (10,000 U/ml, Invitrogen) supplemented with SCF (25 ug/ml, Peprotech), Flt-3 (25 ug/ml, Peprotech) and TPO (25 ug/ml, Peprotech)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from sorted cells using RNeasy Mini Kit (QIAGEN), according to manufacturer's instructions.
Ovation Rna-seq system System v2 (Nugen), followed by KAPA LTP Library Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
LKO_1
|
| Data processing |
Alignment: TopHat v2.0.14
parameters --no-coverage-search -M -T -x 1
Coverage file: Genomecov, Bedtools
parameters -bg -split –ibam
Abundance estimations: Cufflinks v2.2.1
parameters --compatible-hits-norm -N -u --GTF gencode.v19.annotation.gtf
Merging assemblies: Cuffmerge
Differential expression: Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: output of cuffdiff (text file .diff); Please note that the '#NAME' is the program output for log2 value of 0.
|
| |
|
| Submission date |
Jan 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hanna Katri Annikki Mikkola |
| E-mail(s) |
hmikkola@mcdb.ucla.edu
|
| Organization name |
University of California, Los Angeles
|
| Department |
Molecular, Cell and Developmental Biology
|
| Lab |
Mikkola Lab
|
| Street address |
621 Charles E Young Drive South, 2204, Mailbox 160606
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90092 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE76683 |
RNA-seq expression data from FL-HSPCs after HOXA7 knockdown |
| GSE76685 |
Medial HOXA gene expression is a landmark for the definitive haematopoietic fate and a prerequisite for human HSC function |
|
| Relations |
| BioSample |
SAMN04395229 |
| SRA |
SRX1526337 |
