|
| Status |
Public on May 10, 2023 |
| Title |
TXN_IP_1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
cell type: Cervical cancer cells
rip antibody: anti-thioredoxin1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The Txn1-bound RNA was isolated from the immunoprecipitation of anti-Txn1 using Trizol (Invitrogen).
The cDNA libraries used the Illumina ScriptSeq™ v2 RNA-Seq Library Preparation Kit(Epicentre).The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 °C until used for sequencing.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina bcl2fastq software used for basecalling.
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of Txn1 on genome using “ABLIRC” strategy.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for each group.
|
| |
|
| Submission date |
Sep 02, 2022 |
| Last update date |
May 10, 2023 |
| Contact name |
Dong Chen |
| Organization name |
ABLife, Inc.
|
| Department |
Center for Genome Analysis
|
| Street address |
388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430075 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE212595 |
Thioredoxin1 binding metastasis-associated lung adenocarcinoma transcript 1 attenuates inflammation and apoptosis after intracerebral hemorrhage |
|
| Relations |
| BioSample |
SAMN30647114 |
| SRA |
SRX17407046 |
