|
| Status |
Public on Aug 22, 2016 |
| Title |
SMARCB1_Null-B |
| Sample type |
SRA |
| |
|
| Source name |
HAP1 Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
passage: P12
mutation: SMARCB1 Null (CRISPR-2)
cell line: HAP1
|
| Growth protocol |
Cells were grown in IMDM medium supplemented with 10% FBS, 2mM L-Glutamine and 1x PenStrep. For RNAseq experiments cells were plated in 6 well plates. RNA was extratced when cells were 70% confluent.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were grown to 70% confluency and RNA was extracted using Trizol (Invitrogen).
Library preparation and sequencing was done in Stanford Functional Genomics Facility. In brief, KapaBiosystem Stranded mRNA kit was used for library preparation. Four uunique Illumina adapters (Bar Coded) for multiplexing were used
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQ files obtained from Stanford Functional Genomics Facility server were downloaded to desktop. These files were then uploaded to the Partek Flow Server
The raw data obtained was aligned, quantified and analyzed by using Partek Flow software, version 4.0, Partek Inc., St. Louis, MO, USA. Reads were aligned to human reference genome build hg19 using STAR Align and Quantify pipeline in Partek Flow. Differential gene expression (GSA) analysis was done using RPKM normalization.
Genome_build: hg19
Supplementary_files_format_and_content: This is an excel (xslx) file generated by Partek Flow software as explained above. The file has gene expression data for the samples compared to wildtype cells.
|
| |
|
| Submission date |
Nov 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Rajat Rohatgi |
| Organization name |
Stanford University School of Medicine
|
| Department |
Biochemistry
|
| Street address |
279 campus drive
|
| City |
stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE75515 |
Gene expression analysis of human haploid cells (HAP1) depleted of SMARCB1 and SMARCA4 |
|
| Relations |
| BioSample |
SAMN04302169 |
| SRA |
SRX1456276 |
