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| Status |
Public on Sep 25, 2020 |
| Title |
HCEC 1CT_APC KD-3 |
| Sample type |
SRA |
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| Source name |
Colonic Epithelial Cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCEC
cell type: Human colonic epithelial progenitor cells
genotype: APC KD
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| Treatment protocol |
No Treatment
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| Growth protocol |
HCEC 1CT_WT and APC KD cells were routinely cultured in HCEC culture media (DMEM:M199=4:1) supplemented with EGF (20 ng/mL), hydrocortisone (1ug/mL), insulin (10 ug/mL), Sodium selenite (5nM), transferrin (2 ug/mL), and 2% FBS at 37°C in 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
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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 |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
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| Submission date |
Jun 16, 2020 |
| Last update date |
Sep 27, 2020 |
| Contact name |
Jeong-Ryeol Gong |
| E-mail(s) |
jrgong@kaist.ac.kr
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| Organization name |
KAIST
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| Lab |
SBIE
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| Street address |
291, Daehak-ro
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| City |
Yuseong-gu |
| State/province |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE152562 |
Transcriptomic analysis of APC knock down HCEC 1CT cells compared to the wild type HCEC 1CT cells. |
| GSE152746 |
APC knock down HCEC 1CT cells compared to the wild type HCEC 1CT cells |
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| Relations |
| BioSample |
SAMN15248472 |
| SRA |
SRX8554085 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4618279_ICT-A-3.txt.gz |
119.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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