|
| Status |
Public on Jul 11, 2022 |
| Title |
H-CONT-2 |
| Sample type |
SRA |
| |
|
| Source name |
Scr control 2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HeLa cells (CCL2, ATCC)
treatment: Scr control
|
| Treatment protocol |
Mission plasmids encoding for two different shRNA against human ZIP11 and the control scrambled (Scr) construct with a puromycin resistance cassette ere used to tranduce HeLa cells. Stable cell lines were geenrated, and cells plated at 1x10^5 cells cm2 were allowed to proliferate for 48 h.
|
| Growth protocol |
HeLa cells obtained from American Type Culture Collection were cultured in DMEM media (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics (penicillin G/Streptomycin, Gibco) in a humidified atmosphere containing 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol was used to harvest total RNA from proliferating HeLa cells transduced with lentivirus for scr and ZIP11 shRNA
RNA libraries were prepared by the Beijing Genomics Institute (BGI) for sequencing on a BGISEQ-500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Basecalling performed by BGI
Sequenced reads were processed using the SOAPnuke software. Reads were trimmed for the adaptor sequence and filtered for low quality reads and stored in FASTQ format.
HISAT2 was used for genome mapping to GRCh38/hg38 after which a complete reference transcriptome was generated using StringTie, Cufflinks and CPC.
The SOAPnuke output was then mapped to the reference transcriptome using Bowtie2 and RSEM was used to calculate gene expression levels.
Differential gene expression was calculated using DESeq2
Assembly: GRCh38/hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
Jan 17, 2023 |
| Contact name |
Sabriya Syed |
| E-mail(s) |
[email protected]
|
| Phone |
5088567526
|
| Organization name |
University of Massachusetts Medical School
|
| Street address |
364 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE198411 |
Knockdown of ZIP11 impairs growth in HeLa cells. |
|
| Relations |
| BioSample |
SAMN26580176 |
| SRA |
SRX14437332 |
