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| Status |
Public on Nov 01, 2018 |
| Title |
BeWo IN-3 |
| Sample type |
SRA |
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| Source name |
choriocarcinoma cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: BeWo
cell type: choriocarcinoma cells
transfected with: hsa-miR-371a-5p inhibitor
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| Treatment protocol |
Cells were plated in 24-well plates the day before transfection and grown to 70-80% confluence. Cells were then transfected with 150 nM hsa-miR-371a-5p, hsa-miR-518a-3p or control inhibitor by using Lipofectamine 3000 (Invitrogen) according to the manufacturer’s instructions.At 36 h post transfection, cells were washed three times with PBS and harvested.
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| Growth protocol |
BeWo, JAR and JEG-3 cells were maintained in Dulbecco's modified Eagle's medium (DMEM, Invitrogen, NY, USA) in T25 flasks supplemented with 10% fetal bovine serum (FBS, Invitrogen) at 37°C.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany).RNA integrity was analyzed by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Beckman Coulter, Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Qiagen).
Libraries were prepared according to the Whole Transcriptome Sequencing Protocol (ShanghaiBio Corporation, Shanghai, China). Steps briefly included the followings: mRNA purification with RNA Purification Beads, mRNA fragmentation, synthesis of the first strand cDNA, synthesis of the second strand cDNA, end repair, 3' end adenylation, adapters ligation, PCR amplification,library quality control.Libraries were sequenced on the HiSeq X Ten (Illumina, San Diego, CA, USA) following the manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
C2_FPKM
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| Data processing |
Base calling performed using Illumina Real Time Analysis (RTA).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HG38 whole genome with Hisat2 (version:2.0.4).
Fragments Per Kilobase of exon per Megabase (FPKM) were calculated using edgeR-DESeq2.
Genome_build: HG38
Supplementary_files_format_and_content: FPKM and count values for each Sample
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| Submission date |
Nov 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiuru zhao |
| Organization name |
International Peace Maternity and Child Health Hospital Affiliated to Shanghai Jiao Tong University School of Medicine
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| Department |
Pathology and Bio-Bank
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| Street address |
Hengshan Road 910#
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| City |
Shanghai |
| ZIP/Postal code |
200030 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE106394 |
Hsa-miR-371a-5p and hsa-miR-518a-3p regulated genes in choriocarcinoma cells |
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| Relations |
| BioSample |
SAMN07962232 |
| SRA |
SRX3349260 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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