|
| Status |
Public on Nov 24, 2021 |
| Title |
40280_hpNPCd5_RNA |
| Sample type |
SRA |
| |
|
| Source name |
PT Rep 2 (40280 line)
|
| Organism |
Pan troglodytes |
| Characteristics |
cell type: Hippocampal_Intermediate_Progenitors_Day5
|
| Treatment protocol |
The stem cells were treated with a previously published media for differentiation into hippocampal intermediate progenitors (Yu et al 2014). This consists of 1:1 DMEM/F12 supplemented with N2, B27, Noggin, Cyclopamine, DKK-1 and SB43154 and PennStrep antibiotic. The cells were exposed to this media for five days prior to collection.
|
| Growth protocol |
The iPSC lines were expanded in feeder-free, serum-free mTeSR™1 medium (STEMCELL Technologies). Cells were passaged ~1:10 at 80% confluency using ReLeSR (STEMCELL Technologies) and small cell clusters (50–200 cells) were subsequently plated on tissue culture dishes coated overnight with Geltrex™ LDEV-Free hESC-qualified Reduced Growth Factor Basement Membrane Matrix (Fisher-Scientific).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research).
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® according to the manufacturer’s instructions (New England Biolabs). 1 μg of total RNA input was used for each library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ChIP-seq and ATAC-seq data were aligned to hg19 or panTro5 as appropriate using BWA-mem
RNA-seq data were analyzed with kallisto using hg19 or panTro5 as appropriate
ATAC-seq peaks were called with MACS2.
RNA-seq gene expression was quantified using Kallisto
For input bigwig was made with Deeptools
Genome_build: hg19 for Homo sapiens samples and panTro5 for Pan troglodytes samples.
Supplementary_files_format_and_content: peak text files (ChIP-seq, ATAC-seq), Kallisto quantification (spreadsheet) for RNA-seq. Bigwig for input of Chip-seq
|
| |
|
| Submission date |
Nov 22, 2021 |
| Last update date |
Nov 24, 2021 |
| Contact name |
Marco Trizzino |
| E-mail(s) |
m.trizzino@imperial.ac.uk
|
| Phone |
07521215018
|
| Organization name |
Imperial College London
|
| Department |
Life Sciences
|
| Street address |
Imperial College Road
|
| City |
London |
| State/province |
UK |
| ZIP/Postal code |
SW7 2AZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30573 |
| Series (1) |
| GSE189347 |
Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors |
|
| Relations |
| BioSample |
SAMN23390663 |
| SRA |
SRX13198196 |
