|
| Status |
Public on Oct 01, 2020 |
| Title |
5_BT-12_WT_1 |
| Sample type |
SRA |
| |
|
| Source name |
BT-12_WT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT-12
cell type: Atypical teratoid/rhabdoid tumor (AT/RT) cell line
primary tumor site: Posterior fossa
passage: 20-23
genotype/variation: WT
|
| Growth protocol |
BT-12 cells are grown in DMEM plus 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted from cell lines using TRIzol (Invitrogen, USA).
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 doublestrand 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. 6) Perform sequencing on prepared library. 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 doublestrand 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. 6) Perform sequencing on prepared library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
BT12-WT2
|
| Data processing |
RNA-seq reads were aligned to the human reference genome (hg19) using Tophat (v2.1.1; https://ccb.jhu.edu/software/tophat/index.shtml). gene models of Refgene were downloaded from the Illumina's iGenomes project (https://support.illumina.com/sequencing/sequencing_software/igenome.html). FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were generated using cufflinks (v2.2.1; http://cole-trapnell-lab.github.io/cufflinks/).
Genome_build: hg19
Supplementary_files_format_and_content: Assembled FPKM values across all samples generated by CummeRbund R package with the gct format
|
| |
|
| Submission date |
Oct 22, 2019 |
| Last update date |
Oct 01, 2020 |
| Contact name |
Filippo Giancotti |
| E-mail(s) |
[email protected]
|
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
Cancer Biology
|
| Lab |
Dr. Giancotti Lab
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE139262 |
Transcriptomic data of established human AT/RT cell lines BT-12. |
|
| Relations |
| BioSample |
SAMN13087481 |
| SRA |
SRX7036345 |
