|
| Status |
Public on Mar 20, 2019 |
| Title |
REP1-K3AKO-S |
| Sample type |
SRA |
| |
|
| Source name |
HCT116_KDM3A KO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
genotype/variation: KDM3A knockout
culture condition: starvation; no-serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNASeq 5ug total RNA was used, and mRNA purification was performed using oligo-dT magnic beads(NEBNext PolyA mRAN magnetic isolation module # E7490). mRNA was fragmented and reverse transcript into 200-400bp dscDNA for library construction(NEB # E7525 # E6111).
Vazyme ND604 kit was used for RNASeq library construction. Brifely, about 10-100ng dscDNA was used as initiation for end repair and prepared for adaptor ligation. After adaptor ligation, PCR amplification with 8-13 cycles for each library and gel selection was used for library size selection and purification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNASeq raw data quality control by FastQC
RNASeq raw data clean performed by cutadapt
RNASeq data mapping to hg19 reference genome by tophat2 with at most 2 mismatch for each reads. Cuflinks was used for differential expression gene analysis,gene expression value with more than 2 fold change was defined differential expression genes.
Genome_build: hg19
Supplementary_files_format_and_content: txt format file for RNASeq gene expression level in each sample.
|
| |
|
| Submission date |
Jan 09, 2018 |
| Last update date |
Mar 20, 2019 |
| Contact name |
Pin-Ji Lei |
| E-mail(s) |
[email protected]
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Department of Radiation Oncology
|
| Lab |
Edwin L. Steele Laboratories
|
| Street address |
100 Blossom Street
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE108921 |
Gene Expression Profiling of WT and KDM3A Knocked out Cell |
| GSE108922 |
Genome-wide maps of chromatin state and Gene Expression Profiling in HCT116 cells |
|
| Relations |
| BioSample |
SAMN08330201 |
| SRA |
SRX3542400 |
