|
| Status |
Public on Jul 26, 2022 |
| Title |
chimp_d4_scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
PT Rep 3 (8861 line)
|
| Organism |
Pan troglodytes |
| Characteristics |
cell type: Hippocampal_Intermediate_Progenitors_Day3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were treated with hpIPC media (Yu et al 2014) in five wells representing each day of differentiation, with an additional untreated iPSC well. Six well from both species were collected on the same day and resuspened in 10%FBS prior to treatment with the Cell Multiplexing Oligos in accordance with the 10X Cell Multiplexing Oligos Protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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
scRNAseq data were mapped with cellranger using hg19 or panTro5 as appropriate, then analyzed in the R Package Seurat
ATAC-seq peaks were called with MACS2.
RNA-seq gene expression was quantified using Kallisto
For input bigwig was made with Deeptools
Assembly: 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, matrix + features + barcode files for scRNAseq
|
| |
|
| Submission date |
Jul 25, 2022 |
| Last update date |
Aug 05, 2022 |
| 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 |
GPL21121 |
| Series (1) |
| GSE189347 |
Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors |
|
| Relations |
| BioSample |
SAMN29939339 |
| SRA |
SRX16655199 |
