|
| Status |
Public on Aug 05, 2018 |
| Title |
CHD3-KO_3 |
| Sample type |
SRA |
| |
|
| Source name |
HAP1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Male Chronic Myelogenous Leukemia (CML) cell line derived from KBM-7
cell line: HAP1
genotype/variation: CHD3 knock out cell line
|
| Treatment protocol |
No treatment
|
| Growth protocol |
HAP1 cells were cultivated in IMDM (ThermoFisher Scientific) supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptamycin
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNeasy Mini kit (Qiagen, 74104)
TruSeq stranded RNA library prep, poly(A) selection (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Crisper-Cas9 generated cell lines
|
| Data processing |
Basecalls were performed using RTA v2.7.7, demultiplexing and conversion to FASTQ format was done using bcl2fastq v2.18.0.12.
Low quality reads and adaptors were trimmed/removed using Trimmomatic v0.36
Illumina spike-in PhiX were removed using BBMap v37.4
Cleaned reads were aligned to Homo sapiens GRCh38 ensembl release 90 using Tophat2 v2.1.1 with ‘--library-type fr-firststrand --no-mixed --no-novel-juncs' as parameters
Differential expression was calculated using cuffdiff in cufflinks suite v2.2.1 and viewed using the R package cummeRbund v2.16.
Genome_build: GRCh38 release 90
Supplementary_files_format_and_content: Replicate FPKM table from cummeRbund
|
| |
|
| Submission date |
Feb 28, 2018 |
| Last update date |
Aug 05, 2018 |
| Contact name |
Roza Berhanu Lemma |
| E-mail(s) |
r.b.lemma@ibv.uio.no
|
| Phone |
+4740975997
|
| Organization name |
University of Oslo
|
| Department |
Department of Biosciences
|
| Lab |
Odd Stokke Gabrielsen
|
| Street address |
Blindernveien 31
|
| City |
Oslo |
| ZIP/Postal code |
0371 |
| Country |
Norway |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE111272 |
Global transcriptome analysis of HAP1 cells |
|
| Relations |
| BioSample |
SAMN08623906 |
| SRA |
SRX3752214 |
