|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jun 14, 2021 |
Title |
HEK293 si-Control DMSO rep2 |
Sample type |
SRA |
|
|
Source name |
HEK293 cells
|
Organism |
Homo sapiens |
Characteristics |
si-rna knockdown: si-Control treatment: DMSO for 4 h
|
Extracted molecule |
total RNA |
Extraction protocol |
RNase I footprinting, ribosome pelleting, TRIZOL extraction of riboseom-protected mRNA fragments Preadenylated linker ligation, reverse transcription, cDNA circularization, rRNA depeletion, PCR amplification
|
|
|
Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Library strategy: Ribo-seq Basecalling with Illumina NCS software (2.2.0) 3' adaptor sequence of each read was trimmed by FastX-toolkit. Reads mapped to four rRNA sequences (RNA5S1, RNA5-8SN5, RNA18SN5, and RNA28SN5) by HISAT2 (2.0.3) were eliminated. The remaining reads were aligned to the transcript variant with the longest coding sequence (CDS) of each human gene using HISAT2 (2.0.3). Multi-mapped reads were discarded, and only reads with the size ranging from 18 to 34 nt were utilized. Genome_build: hg38 Supplementary_files_format_and_content: Text file; Column-1: 5'end position of read on Xbp1 (nt), Column-2: Read count, and Column-3: Read per million total reads (RPM).
|
|
|
Submission date |
May 04, 2021 |
Last update date |
Jun 14, 2021 |
Contact name |
Jae Seok YOON |
Organization name |
Cystic Fibrosis Foundation
|
Department |
CFFT Lab
|
Street address |
44 Hartwell Avenue
|
City |
Lexington |
State/province |
MA |
ZIP/Postal code |
02421 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE173852 |
A role for the ribosome-associated complex in activation of the IRE1 branch of UPR |
|
Relations |
BioSample |
SAMN19014971 |
SRA |
SRX10773162 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5281837_si-Control_DMSO_rep2.txt.gz |
5.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|