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| Status |
Public on Dec 26, 2018 |
| Title |
X3D_BC |
| Sample type |
SRA |
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| Source name |
Retina
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Mouse retinal progenitor cells
treatment: bFGF and CHIR99021
time course: 3day
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| Treatment protocol |
The mouse retinal progenitor cells culture with or without bFGF,CHIR99021
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| Growth protocol |
mouse retinal progenitor cells cultured with or without bFGF and CHIR99021 after 1,3,5,7 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent and extracted with phenol:chloroform:isoamyl alcohol.
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature.We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
SOAPnuke used for filtering with parameters -l 15 -q 0.2 -n 0.1
RNA-seq reads mapped to Mus musculus whole genome using BOWTIE2 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments Per Kilobase per Million mapped fragments of library size (FPKM) were calculated using RSEM with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: text files include FPKM values for each Sample.
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| Submission date |
Jul 10, 2018 |
| Last update date |
Dec 26, 2018 |
| Contact name |
Qingjian Ou |
| E-mail(s) |
vip@ouqingjian.com
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| Organization name |
Tongji University
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| Department |
Medical
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| Lab |
LCVS
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| Street address |
Siping Rd
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE116840 |
Transcriptomic analysis of normal mouse retinal and conditional medium cultured retinal progenitor cells |
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| Relations |
| BioSample |
SAMN09635546 |
| SRA |
SRX4372611 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3262694_X3D_BC.gene.fpkm.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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