|
| Status |
Public on Oct 25, 2012 |
| Title |
IMR90_H1.5KD |
| Sample type |
SRA |
| |
|
| Source name |
IMR90 human lung fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
passages: 7-9
transfection: siRNA targeting H1.5
|
| Treatment protocol |
Control siRNAs or iRNAs targeting H1.5 (MU-012049-00) were purchased from Dharmacon. 1.5 µg of siRNAs were transfected to 2x106 cells by using Lipofectamine RNAiMAX (Invitrogen Cat # 13778075). Cells were collected 48 hours after transfection.
|
| Growth protocol |
IMR90 human primary lung embryo fibroblasts (purchased from ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO2. Growing cells with 50~70% confluence were used for further assay.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted by using TriZol reagent (Invitrogen).
5 µg of total RNA from control knockdown and H1.5 knockdown IMR90 fibroblasts were used to prepare libraries for mRNA-seq by using mRNA-seq Sample Preparation Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA-seq
|
| Data processing |
Unique sequences were aligned to human genome reference HG19 by using TopHat-1.3.2 (default setting). Reads per kb per million reads (RPKM) of each RefSeq genes were calculated for expression comparison.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files containing RPKM for each refseq genes
|
| |
|
| Submission date |
Oct 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jing-Yu Li |
| E-mail(s) |
jingyuli@mednet.ucla.edu
|
| Organization name |
University of California, Los Angeles
|
| Street address |
615 Charles E. Young Dr. South BSRB 357
|
| City |
Los Angeles |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE41761 |
Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation |
|
| Relations |
| SRA |
SRX201224 |
| BioSample |
SAMN01780172 |
