|
| Status |
Public on Jun 19, 2024 |
| Title |
RNA_seq_siCDK12_OHT_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
U2OS
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
treatment: siCDK12_OHT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNeasy MinElute Spin columns from Qiagen according to the manufacturer and eluted in 14µl of RNase free water.
Libraries for RNA-Seq were prepared with the TruSeq RNA Sample Preparation Kits v2 (Illumina) following manufacturer instruction (except for skipping the first step of mRNA purification with poly-T oligo-attached magnetic beads)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing gene symbols/IDs, output of DESeq2 for each condition (siCDK12, OHT, siCDK12+OHT) vs control and raw and library-normalized counts
|
| |
|
| Submission date |
Jul 05, 2023 |
| Last update date |
Jun 19, 2024 |
| Contact name |
Stefano Campaner |
| E-mail(s) |
stefano.campaner@iit.it
|
| Organization name |
fondazione Istituto italiano di tecnologia
|
| Department |
Center for Genomic Science
|
| Lab |
Cancer Biology
|
| Street address |
Via adamello 16
|
| City |
Milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE236545 |
CDK12 prevents MYC-induced transcription-replication conflicts [RNA-seq] |
| GSE236553 |
CDK12 prevents MYC-induced transcription-replication conflicts |
|
| Relations |
| BioSample |
SAMN36313396 |
| SRA |
SRX20904118 |
