 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 02, 2022 |
| Title |
CCD-18Co cells, TGF-beta, ZNF281 siRNA, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
CCD-18Co
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CCD-18Co
cell type: Colon fibroblast cell line
genotype: ZNF281 siRNA
treatment: TGF-beta
|
| 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.
|
| Growth protocol |
CCD18-Co cells were grown in MEM (S-51416C, Sigma) supplemented with 10% FBS, penicillin/streptomycin, 2mM L-glutamine, 1mM Sodium pyruvate
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| 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
|
| |
|
| Submission date |
May 26, 2022 |
| Last update date |
Sep 04, 2022 |
| Contact name |
valerio fulci |
| Organization name |
Università i Roma "La Sapienza"
|
| Department |
Dipartimento di Medicina Molecolare
|
| Street address |
Vle regina Elena, 324
|
| City |
Roma |
| ZIP/Postal code |
00161 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE204868 |
Role of ZNF281 in intestinal fibroblast activation: new insights in IBD-related fibrosis |
|
| Relations |
| BioSample |
SAMN28679715 |
| SRA |
SRX15470172 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6199148_4_htseq_count_out.txt.gz |
230.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
