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| Status |
Public on Sep 25, 2020 |
| Title |
MDCKII DENND5A-KD1 2D-D4 RNA-seq |
| Sample type |
SRA |
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| Source name |
MDCKII cells
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| Organism |
Canis lupus familiaris |
| Characteristics |
cell line: MDCKII
genotype: DENND5A-KD
culturing time: day 4
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| Growth protocol |
MDCKII cells were maintained in Eagle’s minimal essential medium with 5% fetal bovine serum, 10 mM HEPES, 2 mM glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin; For 3D cultures, cells were grown on top of matrigel. For 2D cultures, cells were seeded on transwell inserts grown until over-confluence. The cells for seeding were regarded as day0 samples.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cysts grown for 24h, 3, 5, 8, 14 days, cells for seeding (day 0) and over-confluent cells were collected and RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen)
RNA-seq libraries were constructed using KAPA Stranded mRNA-Seq Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Read pairs were aligned to the dog reference genome canFam3 with HISAT v2.1.0.
Cufflinks v2.2.1 was used to quantify gene expression in FPKM, guided by canine gene annotation CanFam3.1.84 downloaded from UCSC genome browser
Genome_build: canFam3
Supplementary_files_format_and_content: Tab-delimited files with expression values in FPKM for each sample
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| Submission date |
Apr 15, 2019 |
| Last update date |
Sep 25, 2020 |
| Contact name |
Shaying Zhao |
| E-mail(s) |
szhao@uga.edu
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| Organization name |
University of Georgia
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| Lab |
Shaying Zhao
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| Street address |
B304B Life Sciences, 120 Green Street
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| City |
ATHENS |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL21400 |
| Series (2) |
| GSE129823 |
RNA-seq for MDCKII 3D and 2D epithelial morphogenesis. |
| GSE129824 |
ATAC-seq and RNA-seq for MDCKII 3D and 2D epithelial morphogenesis |
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| Relations |
| BioSample |
SAMN11418779 |
| SRA |
SRX5685934 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3722672_2-1-D4-FPKM.txt.gz |
199.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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