|
| Status |
Public on Jan 31, 2024 |
| Title |
REH shSTAT3_3 |
| Sample type |
SRA |
| |
|
| Source name |
REH
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: REH
treatment: shSTAT3 transduced REH
|
| Treatment protocol |
REH cells were transduced with either scramble control or STAT3 specific shRNA, via lentiviral particles. Transduced cells were selected with puromycin for 3 days and then Dead Cell Removal was performed prior to total RNA extraction.
|
| Growth protocol |
REH cells (B precursor ALL cell line) (DSMZ, Braunschweig, Germany) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 100 units/ml penicillin and 100 ug/ml streptomycin at 37°C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy Plus Mini Kit according to manufacturers instructions
Indexed RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA v2 protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
All tools in the analysis were invoked through the Galaxy Project for NGS analysis, as follows:
Fastq was demultiplexed and generated using Illumina bcl2fastq v2.19 before pre-processing (trimmomatic) to remove adapter read-through and poor quality sequences.
Pre-processed data were then aligned to the genome (UCSC hg38) with Bowtie 2 and deduplicated using Picard.
Reads-per-transcript were counted by FeatureCounts, before differential expresson analysis by SARTools, a DESeq2 wrapper.
hg38
Genome_build: tab-delimited text file including average count values for each sample.
|
| |
|
| Submission date |
Jul 02, 2021 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Luca Gasparoli |
| E-mail(s) |
lucagasparoli@gmail.com
|
| Organization name |
UCL Great Ormond Institute of Child Health
|
| Department |
Developmental Biology and Cancer
|
| Street address |
30 Guilford Street, Location 1B
|
| City |
London |
| ZIP/Postal code |
WC1N 1EH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE179332 |
Gene expression changes in REH following STAT3 inhibition by shRNA |
|
| Relations |
| BioSample |
SAMN20010649 |
| SRA |
SRX11335529 |
