|
| Status |
Public on Mar 11, 2021 |
| Title |
sh-E4F1_2 |
| Sample type |
SRA |
| |
|
| Source name |
U2OS expressing shRNA against E4F1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
knockdown: E4F1 shRNA
|
| Treatment protocol |
24h infection with shRNA + 48h puro selection
|
| Growth protocol |
U2OS in DMEM 10% FBS
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA RNA HyperPrep PolyA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the 6pb index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 26, based on Ensembl version 88
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
|
| |
|
| Submission date |
Feb 07, 2020 |
| Last update date |
Mar 11, 2021 |
| Contact name |
Guy Sauvageau |
| Organization name |
Institute for Research in Immunology and Cancer
|
| Street address |
2950, Chemin de Polytechnique
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3T 1J4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN14064664 |
| SRA |
SRX7693103 |
