|
| Status |
Public on Jul 01, 2017 |
| Title |
HG03729 |
| Sample type |
SRA |
| |
|
| Source name |
EB virus transformation cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Lymphocyte
cell line: HG03729
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=HG03729
|
| Growth protocol |
Recover cell lines from the liquid nitrogen by thawing a vial rapidly in a 37 degree centigrade water bath. Re-suspend the entire contents of the vial in fresh culture medium. Cell culture in the T25 tissue culture flask with 10 ml medium (85%RPMI 1640+15% fetal bovine serum) in the 37 degree centigrade incubator (5% CO2) for 4 to 5 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each cell with TRIzol Reagent (Invitrogen, Life Technologies, USA), then was treated with DNase I (Invitrogen, Life Technologies, Waltham, MA)
mRNA enrichment with Oligo(dT)25 Dynabeads twice and purified with Dynabeads® mRNA Purification Kit (Invitrogen, No. 61006). The eluted mRNA was fragmented with Fragmentation Buffer Mix at 94 degree centigrade for 10min. Reverse transcription was performed with RT Buffer Mix and RT Enzyme Mix and followed by the double strand cDNA (dscDNA) synthesis with Second Strand Buffer Mix and Second Strand Enzyme Mix. End repairing, adaptor (with barcode) ligation and PCR amplification were performed after dscDNA purification. Then the purified double stranded PCR products were heat denatured to single strand and circularized with Splint Oligo Mix and Ligation Enzyme. The single strand circle DNA (ssCirc DNA) library was rolling circle amplified to make DNA nanoball (DNB) and load into the patterned nanoarray
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
BGseq-500
|
| Data processing |
Base calling was done via Zebra Call from BGIseq-500
Read pairs with low quality in either read were filtered out (10% bases with N or 50% bases with Q5)
Alignment was performed against RefSeq by bowtie2 (version 2.2.5) with parameters as: -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200
FPKM values of each gene for each sample was measured via RSEM (version v1.2.12) with parameters as: --paired-end -p 8
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene in each sample
|
| |
|
| Submission date |
Jan 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Zirui DONG |
| E-mail(s) |
elvisdong@link.cuhk.edu.hk
|
| Organization name |
The Chinese University of Hong Kong
|
| Department |
Dept. of Obstetrics and Gynaecology
|
| Street address |
Shatin, N.T.
|
| City |
Hong Kong |
| ZIP/Postal code |
999077 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE94043 |
RNA-seq from four balanced translocation carriers in 1000 Genomes Project |
|
| Relations |
| BioSample |
SAMN06266631 |
| SRA |
SRX2600707 |
