|
| Status |
Public on Mar 01, 2024 |
| Title |
K562 PABPC1-KD rep1 |
| Sample type |
SRA |
| |
|
| Source name |
K562 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
treatment: PABPC1 knockdown
|
| Treatment protocol |
K562 cells were maintaied in complete medium with the addition of 8 µg/ml (working concentration) polybrene and concentrated viral particles (shCtrl, shPABPC1) for 24 hours. Lentivirus infection medium system of K562 cells were replaced with fresh complete medium, and K562 cells were subjected to the following experiments after 48-72 hours of transfection.
|
| Growth protocol |
Human blast crisis CML cell line K562 was maintained in RPMI1640 supplemented with 10% FBS and 100 IU ml-1 penicillin and 100 μg ml-1 streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were collected and total RNA was harvested at third day after treatment using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Poly(A)+ RNA-seq after PABPC1 knockdown in K562 cell line
RNA-seq_Raw_gene_counts_matrix.txt
|
| Data processing |
(Sample 1-4) For RNA-seq: Reads were aligned to human genome using STAR with parameters " --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 " to retain uniquely mapped reads. FeatureCounts were used for calculating gene counts, and then normalized for transcript per million (TPM) using in-house scripts.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
(Sample 5-8) For eCLIP-seq: Raw reads with distinct inline barcodes were demultiplexed and the 10-mer random sequence was appended to the reads name in bam file. Cutadapt was used to trimming low quality reads and adapter sequence. Reads were aligned with the sequence of human repetitive elements in the RepBase database by STAR to remove the repetitive reads and obtain the cleaned reads. Cleaned reads were then mapped to human genome using STAR. Removing PCR duplicate reads based on sharing identical random sequence. Two biological replicates were merged by SAMtools. Peaks calling and downstream data analysis were performed by clipper. Peaks normalization by “Peak_input_normalization_wrapper.pl” tools. The eCLIP-seq peaks were filtered by P-value < 10e-6 and fold change > 2.5.
Assembly: GRCh38
Supplementary files format and content: peak text file, bw file
|
| |
|
| Submission date |
Mar 08, 2022 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Zhongyang Chen |
| E-mail(s) |
zhychen_96@126.com
|
| Organization name |
School of Basic Medicine, Peking Union Medical College (PUMC)
|
| Street address |
No.5, Dongdan Santiao, Dongcheng District
|
| City |
Beijing |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE198142 |
Selective translational control by PABPC1 phase separation regulates blast crisis and target therapy resistance of chronic myeloid leukemia |
|
| Relations |
| BioSample |
SAMN26526342 |
| SRA |
SRX14409614 |
