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GEO help: Mouse over screen elements for information. |
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Status |
Public on Sep 02, 2022 |
Title |
CCD-18Co cells, TGF-beta, CTRL siRNA, biol rep 2 |
Sample type |
SRA |
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Source name |
CCD-18Co
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Organism |
Homo sapiens |
Characteristics |
cell line: CCD-18Co cell type: Colon fibroblast cell line genotype: CTRL siRNA treatment: TGF-beta
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Treatment protocol |
At day 1, CCD18-Co cells were seeded to be 60%- 70% confluent at the day of transfection. At day 2, 10nM siRNA ZNF281 (Silencer™ pre-designed siRNA, Ambion) or Silencer™ Select Negative Control No. 1 siRNA (Ambion) were transfected using Lipofectamine RNAiMAX Reagent (Life Technologies), following manufacturer’s protocol. At day 3, the medium was replaced with low-serum starvation medium (MEM complemented with 0.5% FBS, penicillin/streptomycine, 2mM L-glutamine, 1mM Sodium pyruvate). At day 4, TGF-β1 (10,ng/mL) was added to low-serum starvation medium for 24h.
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Growth protocol |
CCD18-Co cells were grown in MEM (S-51416C, Sigma) supplemented with 10% FBS, penicillin/streptomycin, 2mM L-glutamine, 1mM Sodium pyruvate
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Extracted molecule |
total RNA |
Extraction protocol |
1x10^6 cells were lysed in 300ul of Trizol and RNA was purified using Direct-zol™ RNA MiniPrep Kit (Zymo Research), following manufacturer’s protocol. TruSeq stranded total RNA with Ribo-Zero
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 550 |
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Data processing |
TopHat2 alignment to hg38, gencode v31 GTF file. Other options:--library-type fr-firststrand Htseq-count, command line options: -f bam -s reverse -m intersection-strict --secondary-alignments=ignore –supplementary-alignments=ignore Assembly: hg38, gencode v31 Supplementary files format and content: read counts at gene level, as assessed by htseq-count
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Submission date |
May 26, 2022 |
Last update date |
Sep 04, 2022 |
Contact name |
valerio fulci |
Organization name |
Università i Roma "La Sapienza"
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Department |
Dipartimento di Medicina Molecolare
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Street address |
Vle regina Elena, 324
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City |
Roma |
ZIP/Postal code |
00161 |
Country |
Italy |
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Platform ID |
GPL21697 |
Series (1) |
GSE204868 |
Role of ZNF281 in intestinal fibroblast activation: new insights in IBD-related fibrosis |
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Relations |
BioSample |
SAMN28679713 |
SRA |
SRX15470174 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6199150_6_htseq_count_out.txt.gz |
230.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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