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| Status |
Public on Jul 04, 2017 |
| Title |
FLC_1 (HSF6) |
| Sample type |
SRA |
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| Source name |
human embryonic stem cells, induction
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HSF6
cell type: ES-derived human follicle-like cells
gender: female
days: after differentiation, day 11
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| Extracted molecule |
total RNA |
| Extraction protocol |
Each sample was picked out from the plate and lysed in 1ml TRIzol reagent (Invitrogen, 15596026). A total amount of 125ng RNA of each sample was used for RNA-seq according to Guo, F. et al. NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, E7370) was used for the construction of sequencing library.
Sequencing library was prepared according to the protocol of NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, E7370).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
polyA RNA
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| Data processing |
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were firstly trimmed to remove low qulifty bases and the adapter sequences.
Secondly, the cleaned reads were aligned to the human hg19 reference by using Tophat (v.2.0.12) according to Trapnell et al., 2009.
Thirdly, the transcripts were assembled by using Cufflinks (v2.2.1) with default parameters.
Forthly, the ranscription levels (FPKM, fragments per kilobase of transcript per million mapped reads) of annotated genes were quantified by using Cufflinks (v2.2.1) according to Trapnell et al., 2010.
Genome_build: hg19
Supplementary_files_format_and_content: processed data files are txt files. FPKM values of RefSeq genes are included
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| Submission date |
Apr 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kehkooi Kee |
| E-mail(s) |
seagullkk@163.com
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| Phone |
+86-10-62794200
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| Organization name |
Tsinghua University
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| Department |
Basic Medical Sciences
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| Street address |
Room D110, Medical Science Building, School of Medicine, Tsinghua University
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE97388 |
In vitro differentiation of human embryonic stem cells into ovarian follicle-like cells |
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| Relations |
| BioSample |
SAMN06681553 |
| SRA |
SRX2705212 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2563696_FLC_1_HSF6_FPKM.txt.gz |
129.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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