|
| Status |
Public on Aug 22, 2022 |
| Title |
3seq_HeLa_DRB_R1 |
| Sample type |
SRA |
| |
|
| Source name |
3'seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
agent: DRB
time: 30 min
antibody: n/a
molecule subtype: nuclear RNA
|
| Treatment protocol |
Cells were treated with DMSO, DRB, or TNFα for the amount of time indicated in the sample's name.
|
| Growth protocol |
HeLa cells were maintained in DMEM with 10% fetal bovine serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nascent RNAs for mNET-seq were purified from Pol II IP products of solublilized chromatin. Nuclear RNAs were purified following cellular fractionation for 3'seq.
Libraries were prepared according to the protocol of TruSeq Small RNA Library Preparation Kit (Illumina) for mNET-seq. Libraries were prepared according to the protocol of NEBNext Fast DNA Library Prep Set for Ion Torrent (NEB) for 3'seq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Adapters were trimmed with Cutadapt v1.13
Mapping to the hg38 genome was performed with STAR v2.6.1d. For 3'seq, reads were mapped to the hg19 genome with Bowtie2.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.3.1
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
Bigwig files were generated with the Deeptools2 v2.5.0.1 bamCoverage tool
Genome_build: mNET-seq: hg38. 3'seq: hg19.
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples
|
| |
|
| Submission date |
Jun 10, 2021 |
| Last update date |
Aug 22, 2022 |
| Contact name |
Michael Tellier |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Leicester
|
| Department |
Department of Molecular and Cell Biology
|
| Lab |
Tellier Lab
|
| Street address |
Lancaster Road
|
| City |
Leicester |
| State/province |
Select State |
| ZIP/Postal code |
LE1 7HB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE176541 |
CDK9 and PP2A regulate RNA polymerase II transcription termination and coupled RNA maturation |
|
| Relations |
| BioSample |
SAMN19655570 |
| SRA |
SRX11111055 |
