|
| Status |
Public on May 05, 2019 |
| Title |
GFP1 |
| Sample type |
SRA |
| |
|
| Source name |
Immortalized T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell types: Jurkat
treatment: Control virus
|
| Treatment protocol |
Jurkat cells (1.0 x 105/well) were cultured in 48-well plate overnight. Then cells were incubated with medium containing lentiviral particles (multiplicity of infection (MOI) =10) and 5 mg/ml polybrene (Sigma-Aldrich), and were centrifuged for 99 mins at 500 g at 30 oC. Four to five days post-infection, GFP positive cells were purified via a FACS Aria cell sorter III (BD Biosciences) with purities typically greater than 95%. The analyzing & sorting gates were restricted to the living cells as determined by the forward and side scatter properties.
|
| Growth protocol |
All cells were cultured in RPMI-1640 medium (Hyclone) supplemented with 10% heat-inactivated fetal bovine serum (FBS, BI), 100 U/ml penicillin and 100 mg/ml streptomycin (Beyotime) at 37 °C in a humidified incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was extracted with the Total RNA Kit II (OMEGA).
Library construction and sequencing was performed on a BGISEQ-500 by Beijing Genomics Institution (BGI) in Wuhan, China. Oligo (dT) magnetic beads are used to select mRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Raw reads are filtered to clean reads as follows: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (we define the low quality base to be the base whose sequencing quality is no more than 5).
Clean reads are mapped to reference using HISAT/Bowtie2 tool.
Quantifications of gene expression were performed using RSEM.
Differential expressions between two groups with three independent replicates were compared via Deseq.
Genome_build: hg19
|
| |
|
| Submission date |
Nov 05, 2018 |
| Last update date |
May 05, 2019 |
| Contact name |
Jun Wang |
| E-mail(s) |
jwang79@suda.edu.cn
|
| Organization name |
Soochow University
|
| Street address |
199 Ren-Ai Rd, Suzhou University,, Suzhou Industrial Park,
|
| City |
Suzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
215123 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE122191 |
Transcriptome analysis in Jurkat cell with sufficient and deficient ZBTB24 expressions |
|
| Relations |
| BioSample |
SAMN10380633 |
| SRA |
SRX4980506 |
