|
| Status |
Public on Mar 16, 2021 |
| Title |
KO.1 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
ccdc26 status: KO.1
genotype: CCDC26 -/-
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
At harvesting time, total RNA was extracted from cultured cells using RNeasy Mini Kit (Qiagen, Germany), treated with Amplification Grade DNase I (sigma) to remove genomic DNA and quantified by NanoDrop. The quality of RNA was checked using Agilent's Tapestation.
RNA libraries were prepared for sequencing using standard Illumina protocols using TruSeq® Stranded mRNA Library Prep Kit for NeoPrep™
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat v2.0.9 with parameters -p 8 -q 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) and differential expression were calculated against ensemble gene annotations using cuffdiff program with default options and masking repeats.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and differential expression calculation
|
| |
|
| Submission date |
Oct 16, 2017 |
| Last update date |
Mar 16, 2021 |
| Contact name |
Aditi Kanhere |
| E-mail(s) |
a.kanhere@liverpool.ac.uk
|
| Organization name |
University of Liverpool
|
| Lab |
Kanhere Lab
|
| Street address |
Institute of Systems, Molecular and Integrative Biology
|
| City |
Liverpool |
| ZIP/Postal code |
L69 3GE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE105029 |
A long intergenic non-coding RNA regulates nuclear localization of DNA methyl transferase-1 |
|
| Relations |
| BioSample |
SAMN07790048 |
| SRA |
SRX3288544 |
