|
| Status |
Public on Aug 29, 2018 |
| Title |
microRNA-seq [Sample 4] |
| Sample type |
SRA |
| |
|
| Source name |
DBTRG-05MG
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: DBTRG-05MG
treatment: 1mM dbcAMP_24h
|
| Treatment protocol |
Samples 1-5 were the microRNA-seq data of DBTRG-05MG treated with dbcAMP at 0/6/12/24/48 hours. Sample 6-17 were the analysis of DBTRG-05MG cells treated with control-media, dbcAMP, miR-1275 mimics and combined dbcAMP and miR-1275 mimics on day3.
|
| Growth protocol |
The cells were cultured according to the guideline of ATCC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNA-seq for Sample 1-5: Total RNA was extracted using miRNeasy kit (QIAGEN) and was processed for reverse transcriptase with a miScript II RT kit and via qPCR using standard protocols. RNA-seq for Sample 6-17: Total RNA was isolated from cultured cell lines. Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR. The amplified library was sequenced.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
D4
micro-RNA
processed data file: miRNA_Time course of DBTRG treated with dbcAMP.txt
|
| Data processing |
We use Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC:RNA concentration, RIN value, 28S/18S and the fragment length distribution.
We use internal software SOAPnuke to filter reads.
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2 and then calculate gene expression level with RSEM.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: miRNA_Time course of DBTRG treated with dbcAMP.txt: Tab-delimited text file includes FPKM values for each Sample. D1 column represents the miRNA pattern of DBTRG treated with dbcAMP at 0h (FPKM); D2 column represents the miRNA pattern of DBTRG treated with dbcAMP at 6h (FPKM); D3 column represents the miRNA pattern of DBTRG treated with dbcAMP at 12h (FPKM); D4 column represents the miRNA pattern of DBTRG treated with dbcAMP at 24h (FPKM); D5 column represents the miRNA pattern of DBTRG treated with dbcAMP at 48h (FPKM).
Supplementary_files_format_and_content: RNA_dbcAMP_miR1275_DBTRG.txt: Tab-delimited text file includes FPKM values for each Sample. NC_1/NC_2/NC_3 were the DBTRG-05MG cells treated with control-media on day3 (FPKM); NC_db_1/NC_db_2/NC_db_3 were the DBTRG-05MG cells treated with dbcAMP on day3 (FPKM); X1275m_1/X1275m_2/X1275m_3 were the DBTRG-05MG cells treated with miR-1275 mimics on day3 (FPKM); and X1275m_db_1/X1275m_db_2/X1275m_db_3 were the DBTRG-05MG cells treated with combined dbcAMP and miR-1275 mimics on day3 (FPKM).
|
| |
|
| Submission date |
Aug 28, 2018 |
| Last update date |
Aug 29, 2018 |
| Contact name |
liu xincheng |
| E-mail(s) |
chaoyanglxc123@gmail.com
|
| Organization name |
sysu
|
| Street address |
zhongshan Road 74 Street
|
| City |
Guangzhou |
| ZIP/Postal code |
5100000 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE119161 |
Gene expression of DBTRG-05MG treated with dbcAMP or miR-1275 mimics |
|
| Relations |
| BioSample |
SAMN09929401 |
| SRA |
SRX4619146 |
