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| Status |
Public on Jul 26, 2022 |
| Title |
8861_hpNPC_H3K27Ac |
| Sample type |
SRA |
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| Source name |
PT Rep 3 (8861 line)
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| Organism |
Pan troglodytes |
| Characteristics |
cell type: Hippocampal_Intermediate_Progenitors_Day5
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Barcoded libraries were made with NEB ULTRA II DNA Library Prep Kit for Illumina, and sequenced on Illumina NovaSeq6000, producing 100x100 PE reads or the NextSeq500 producing 80x80 PE reads
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Jul 25, 2022 |
| Last update date |
Aug 05, 2022 |
| Contact name |
Marco Trizzino |
| E-mail(s) |
m.trizzino@imperial.ac.uk
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| Phone |
07521215018
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| Organization name |
Imperial College London
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| Department |
Life Sciences
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| Street address |
Imperial College Road
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| City |
London |
| State/province |
UK |
| ZIP/Postal code |
SW7 2AZ |
| Country |
United Kingdom |
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| Platform ID |
GPL30573 |
| Series (1) |
| GSE189347 |
Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors |
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| Relations |
| BioSample |
SAMN29939343 |
| SRA |
SRX16655195 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6384043_8861_hpNPC_Tbr2_MT237_mem_srt_q10_rmdup_normalized.bw |
68.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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