|
| Status |
Public on Apr 13, 2024 |
| Title |
NPC_IMP1_KD_biological_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
hIPSC_derived NPC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hIPSC_derived NPC
cell type: Neuronal progenitor
genotype: si_IMP1
treatment: Neuronal differentiation protocol
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
NPC and neurons were washed with PBS 1X and harvested by centrifugation. Total RNA was extracted using Maxwell RSC simplyRNA cells kit including DNase treatment in the Maxwell RSC instrument following manufacturer’s instructions. RNA concentration and the 260/280 ratio were assessed using Nanodro
Poly(A)+ selected reverse stranded RNA sequencing libraries were prepared from total RNA using KAPA mRNA HyperPrep Library kit for Illumina® kit, with 200 ng of total RNA as input
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw mRNA sequencing reads were trimmed using TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore),
Quality was evaluated using FastQC 0.11.7, (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Rreads were aligned to GRCh38.p13 human genome using splice-aware aligner STAR v2.6.1 40 with default parameters.
Aligned reads were quantified using --quantMode (TranscriptomeSAM GeneCounts) function.
Differential gene expression was measured using DESeq2 41 using STAR count matrix as an input (DESeqDataSetFromMatrix function).
Assembly: GRCh38.p13 human genome
Supplementary files format and content: raw count table from Deseq2
|
| |
|
| Submission date |
May 23, 2022 |
| Last update date |
Apr 13, 2024 |
| Contact name |
Pierre Klein |
| E-mail(s) |
klein.pierre1@gmail.com
|
| Organization name |
University College London
|
| Department |
Institute of Structural and Molecular Biology
|
| Street address |
Gower Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6XA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE203568 |
m6a methylation drives IMP1 regulation during human neuronal differentiation [RNA-seq] |
| GSE203571 |
m6a methylation drives IMP1 regulation during human neuronal differentiation. |
|
| Relations |
| BioSample |
SAMN28595621 |
| SRA |
SRX15412446 |
