|
| Status |
Public on May 23, 2023 |
| Title |
Hybrid Retinal pigment epithelium, Hybrid2, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Hybrid2
|
| Organisms |
Pan troglodytes; Homo sapiens |
| Characteristics |
cell line: Hybrid2
cell type: Retinal pigment epithelium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy Mini Kit with on-column DNAse digestion (Qiagen)
Illumina TruSeq Stranded mRNA library prep kit (Illumina) & Illumina Stranded mRNA Prep (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNA29_RPE_Hyb2_total; RNA29_RPE_Hyb2_human; RNA29_RPE_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt
|
| Data processing |
Remove sequencing adapters with SeqPrep version 1.2
Map reads to GRCh38 and PanTro6 with STAR version 2.7.6a
Remove duplicate reads with Picard 2.23.8 with randomized discarding of duplicates
Remove reads which exhibit mapping bias with WASP (Hornet)
Count allele specific and total reads
Assembly: Human: GRCh38; Chimpanzee: PanTro6
Supplementary files format and content: Counts matrix with total and allele-specific raw read counts (rows are genes, there are 3 columns per sample: total, human and chimpanzee read counts)
Supplementary files format and content: matrix text files are provided for samples mapped on both the human and chimpanzee genomes
|
| |
|
| Submission date |
May 19, 2023 |
| Last update date |
May 23, 2023 |
| Contact name |
Hunter Fraser |
| Organization name |
Stanford University
|
| Street address |
327 Campus Drive
|
| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL27803 |
| Series (2) |
| GSE232948 |
Cell type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells [RNA-seq] |
| GSE232949 |
Cell type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells |
|
| Relations |
| BioSample |
SAMN35219123 |
| SRA |
SRX20447628 |
