|
| Status |
Public on Apr 30, 2024 |
| Title |
P.troglodytes iPSC mono-ribosomal fraction biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
C305
|
| Organism |
Pan troglodytes |
| Characteristics |
cell line: C305
cell type: iPSC
fraction: mono-ribosomal fraction
|
| Treatment protocol |
not applicable
|
| Growth protocol |
C305 cells were cultured on matrigel in mTeSR, Eip-8919-1A and Jos-C31 were cultured on vitronectin in Essential 8 media
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Frac-seq experiments were performed as previously published (Sterne-Weiler et al. 2013) using human, chimpanzee, and orangutan iPSC lines, with modification to the number of fractions collected. Cytosolic extracts from cell lines/tissues are fractionated by sucrose gradient centrifugation. We collected the total cytosolic lysate, the monoribosomal fraction (80s), as well as light (P2-4), medium (P5-8), and heavy (P9+) polyribosomal fractions.
polyA+ selected RNA from each fraction and individually barcoded libraries using the Bioo NEXTflex Directional RNASeq kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
cips_mono_jd942
chimpanzee_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv
|
| Data processing |
mapping to hg38/panTro6/ponAbe3 with STAR (v 2.7)
repeatmasking with bowtie2
identification of unannotated transcripts with Stringtie
identification and quantification of pairwise alternative splicing events with in house python scripts (junctionCounts)
Assembly: hg38, panTro6, ponAbe3
Supplementary files format and content: *_splice_lib_events.gtf - tab delimited file in GTF format containing all identified splice events for each cell line
Supplementary files format and content: all_species_junctioncounts_restricted.tsv - tab delimited file containing pairwise splicing events (between all combinations of cell lines), the number of reads supporting the isoforms and the percent spliced in (PSI) value
Supplementary files format and content: all_distances.tsv - tab delimited file containing multiple distance metrics computed between pair wise splicing events
Supplementary files format and content: all_dpsi.tsv - tab delimited file containing delta PSI values for all events contained in all_species_junctioncounts_restricted.tsv
Supplementary files format and content: all_ddpsi.tsv - tab delimited file containing delta delta PSI values for all events contained in all_species_junctioncounts_restricted.tsv
|
| |
|
| Submission date |
Apr 24, 2023 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Jeremy Sanford |
| E-mail(s) |
jsanfor2@ucsc.edu
|
| Organization name |
University of California, Santa Cruz
|
| Street address |
1156 High St
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL23423 |
| Series (1) |
| GSE230441 |
Isoform-specific translational control is evolutionarily conserved in primates |
|
| Relations |
| BioSample |
SAMN34355967 |
| SRA |
SRX20087080 |
