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| Status |
Public on Nov 23, 2022 |
| Title |
p63.KO rep2 |
| Sample type |
SRA |
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| Source name |
ITGB4-hi with KO of p63
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| Organism |
Homo sapiens |
| Characteristics |
parental line: SUM159
subline: ITGB4-hi
cell type: mammary carcinoma cells
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| Treatment protocol |
CRISPR was used to generated the various KO lines and a non-targeting sgRNA (NT) was used as a control.
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| Growth protocol |
RNA was isolated from cells grown under standard tissue culture conditions
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated with a modified Trizol protocol. Libraries were prepared for RNA-Seq using KAPA Biosystems KAPA mRNA HyperPrep Kit, according to manufacturer’s directions. Briefly, total RNA (0.1-1 ug) is enriched for polyadenylated sequences using oligo-dT magnetic bead capture. The enriched mRNA fraction is then fragmented, and first-strand cDNA is generated using random primers. Strand specificity is achieved during second-strand cDNA synthesis by replacing dTTP with dUTP, which quenches the second strand during amplification. The resulting cDNA is A-Tailed and ligated with indexed adapters. Finally, the library is amplified using a DNA Polymerase which cannot incorporate past dUTPs, effectively quenching the second strand during PCR.
KAPAHyperPrepmRNA
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The 40-nt long single-end reads had very good quality as checked with FastQC. Reads were mapped with STAR 2.5.4b to hg38 version of human genome using the “sjdbOverhang” parameter set to 39, and the annotation file from ENSEMBL GRCh38.90. At least 79% of reads were uniquely mapped, corresponding to at least 22 millions uniquely mapped reads. The samples were stranded, and counts for the 2nd read strand aligned with RNA were used for calculating the number of counts per gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file with raw gene counts for every gene
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| Submission date |
Apr 07, 2021 |
| Last update date |
Nov 23, 2022 |
| Contact name |
Arthur W. Lambert |
| Organization name |
Whitehead Institute
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| Lab |
Robert A. Weinberg
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| Street address |
455 Main street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE171629 |
ΔNp63/p73 drive metastatic colonization by controlling a regenerative epithelial stem cell program in quasi-mesenchymal cancer stem cells |
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| Relations |
| BioSample |
SAMN18647075 |
| SRA |
SRX10531641 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5229520_p63.KO.2_counts.txt.gz |
242.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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