|
| Status |
Public on Apr 04, 2024 |
| Title |
Tx-mRNA-seq-HAP1-MZ-IFN-lib4-962021 |
| Sample type |
SRA |
| |
|
| Source name |
HAP1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HAP1
cell type: HAP1-MAZKO
treatment: IFNγ
treatment time_(hr): 24
|
| Growth protocol |
HAP1 control cells and MAZ KO cells are cultured in IMDM with 10% FBS and 1% Pen/Strep. K562 control cells and MAZ knocking down cells were grown in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, 10 mM HEPES (pH 7.3), and 1% penicillin-streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using an RNeasy mini Kit (Qiagen, 74104)
1 μg of the treated total RNA was used to prepare libraries with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, catalog no. E7490) and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB, catalog no.7760s) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bbtools-BBMap (v.38.76). The number of reads on each gene were counted with Subread (v.2.0.3). Read count data were analyzed with the R package DESeq2 (v.1.32.0).
Assembly: hg19
|
| |
|
| Submission date |
Oct 08, 2022 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Gary Felsenfeld |
| E-mail(s) |
txiao2015@gmail.com
|
| Organization name |
NIH
|
| Lab |
LMB
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE215080 |
The Myc-Associated Zinc Finger Protein (MAZ) controls STAT1-mediated antiviral response by reshaping epigenome [RNA-Seq] |
| GSE215083 |
The Myc-Associated Zinc Finger Protein (MAZ) controls STAT1-mediated antiviral response by reshaping epigenome |
|
| Relations |
| BioSample |
SAMN31215737 |
| SRA |
SRX17833979 |
