|
| Status |
Public on Dec 31, 2019 |
| Title |
JARC-2 |
| Sample type |
SRA |
| |
|
| Source name |
JAR cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: JAR
tissue: Human Choriocarcinoma
|
| Treatment protocol |
Treatment with Cyclopamine 20μM for 24h
|
| Growth protocol |
Human JAR cells were grown in RPMI 1640 medium supplemented with 10% FBS at 37°C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
bcl2fastq software were used for basecalling.
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).The steps are: 1) trim Smart-seq2 public primer sequence from the Reads; 2) remove the contaminated reads for adapters; 3) remove the low quality reads; and 4) remove the reads whose N base more than 5% for total bases.
Sequenced reads were mapped to hg38 using Bowtie2 v2.2.3 software.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0. and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Trapnell, C. et al., Nat. Biotechnol, 2010.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Apr 26, 2019 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Yibin Pan |
| E-mail(s) |
11018158@zju.edu.cn
|
| Phone |
13958102579
|
| Organization name |
Sir Run Run Shaw Hospital
|
| Street address |
3 East Qingchun Road,
|
| City |
Hangzhou |
| ZIP/Postal code |
310020 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE130367 |
Sonic Hedgehog inhibitor cyclopamine effect on JAR cells |
|
| Relations |
| BioSample |
SAMN11514817 |
| SRA |
SRX5757572 |
