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| Status |
Public on Jan 22, 2021 |
| Title |
4973_Nuclear RNA |
| Sample type |
SRA |
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| Source name |
Imortalized Lymphoblastoid cell line
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| Organism |
Pan troglodytes |
| Characteristics |
tissue: Imortalized Lymphocyte
Sex: M
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| Treatment protocol |
Cells were collected and pelleted at 200 g for 5 min at 4C, washed with cold PBS, then spun again the same way.
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| Growth protocol |
LCLs were grown in 20% FBS containing RPMI at 37 and 5% CO2. They were passagd 3 times, maintained at 8 X 10^5, and collected at concentration of 1 X 10^6.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The nuclear RNA was extracted using the first part of the nuclear isolation protocl from Mayer and Churchman. Once the sampes were pelleted in the nuclear wash buffer we resuspended in 700 ul of quizol lysis reagent and RNA isolation was complted using an miRNAEasy kit (Quiagen).
For each cell line we sampled both the total RNA in the cell, and the nucear RNA fraction through the ioslated nucleus.
3' RNA seq using Lexogen Rev. QuantSeq & RNA seq using Illumina TruSeq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Nuclear RNA
Chimpanzee individuals
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| Data processing |
Map 3' seq libraries to respective genome with STAR 3.30.1. Remove reads mapping to genomic regions with 6 A's in a row or 7 A's in the 10 bases upstream of read.
Merge all libraries and call PAS with in house scripts (available on github https://brimittleman.github.io/Comparative_APA/)
Use ucsc-liftover 377 to reciprocally lift PAS then assigned orthologous PAS to Refseq hg38 gene annotations.
Remove PAS used on average <5% in both human and chimpanzee nuclear libraries. Also remove PAS in genes with expession < 2 log2CPM in 8 individuals
bed files with hg39 and Pantro 6 genomic locations scores column is the mean usage of the PAS in the respective species Nuclear data, txt file with meta data for each PAS including column for PAS name (as used in bed file), gene, and genic location
Genome_build: human hg38, chimp Pantro6
Supplementary_files_format_and_content: PAS_doublefilter_either_ChimpCoordChimpUsage.sort.bed, bed file with Pantro6 coordinates and average chimpanzee usage
Supplementary_files_format_and_content: PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed, bed file with hg38 coordinates and average human usage
Supplementary_files_format_and_content: PAS_GeneLocation.txt, text file with PAS name, gene, and genic location
Supplementary_files_format_and_content: Supplemental_table1 - meta data for 3' sequencing libraries, column name explanations in second sheet
Supplementary_files_format_and_content: Supplemental_table2 - meta data for RNA sequencing libraries, column name explanations in second sheet
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| Submission date |
Jul 28, 2020 |
| Last update date |
Jan 22, 2021 |
| Contact name |
Yoav GiladLi |
| E-mail(s) |
gilad@uchicago.edu
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| Organization name |
University of Chicago
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| Department |
Section of Genetic Medicine
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| Lab |
Gilad
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| Street address |
920 e 58th St
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL21121 |
| Series (1) |
| GSE155245 |
Divergence in alternative polyadenylation between humans and chimpanzees contributes to gene regulatory differences between species |
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| Relations |
| BioSample |
SAMN15659610 |
| SRA |
SRX8837793 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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