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| Status |
Public on Jun 14, 2021 |
| Title |
HEK293 si-Hsp70L1_si-Pelo Thapsigargin rep2 |
| Sample type |
SRA |
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| Source name |
HEK293 cells
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| Organism |
Homo sapiens |
| Characteristics |
si-rna knockdown: si-Hsp70L1 and si-Pelo
treatment: Thapsigargin for 4 h
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| 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
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| 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).
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| Submission date |
May 04, 2021 |
| Last update date |
Jun 14, 2021 |
| Contact name |
Jae Seok YOON |
| Organization name |
Cystic Fibrosis Foundation
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| Department |
CFFT Lab
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| Street address |
44 Hartwell Avenue
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| City |
Lexington |
| State/province |
MA |
| ZIP/Postal code |
02421 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE173852 |
A role for the ribosome-associated complex in activation of the IRE1 branch of UPR |
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| Relations |
| BioSample |
SAMN19014957 |
| SRA |
SRX10773176 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5281851_si-Hsp70L1_si-Pelo_Thapsigargin_rep2.txt.gz |
6.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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