|
| Status |
Public on Nov 06, 2024 |
| Title |
control for PAF1 data HEL RNA-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEL cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: shCtrl
|
| Growth protocol |
Human cells HEL were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR. Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.
ssRNAseq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
HEL.shCtrl_and_shPaf1.read_count_table.txt
|
| Data processing |
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
Read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq in human cells and mm10 for RNA-seq in mouse.
Supplementary_files_format_and_content: Tab-delimited text files include read/fragment count values of genes for each sample.
|
| |
|
| Submission date |
Nov 08, 2021 |
| Last update date |
Nov 06, 2024 |
| Contact name |
Aiwei Wu |
| E-mail(s) |
aiwei.wu@sjtu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University
|
| Department |
School of Life Sciences and Biotechnology
|
| Lab |
Ming Yu
|
| Street address |
800 Dongchuan Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE188415 |
The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [RNA-seq] |
| GSE188417 |
The PAF1 Complex Regulates Transcriptional Termination and Reinitiation |
|
| Relations |
| BioSample |
SAMN22984493 |
| SRA |
SRX13057084 |
