|
| Status |
Public on Jun 25, 2020 |
| Title |
human unselected 80S 1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T cells
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: no
cell line: HEK293T
protocol: RNA 80S footprint
|
| Treatment protocol |
incubation of the cell culture with 0.3 % w/v formaldehyde for 5 min in a cold room
|
| Growth protocol |
3.5 Mio cell seeded into one Ø 15 cm dish, 48 h growth, around 80 % confluency at harvest; growth at 37ºC, 5 % CO2, in DMEM + 10% FBS (20 ml per dish)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
in-plate cell lysis with detergent, RNase I digestion to generate ribosomal footprints, 40S/80S separation (followed by Co-IP if indicated), hot acid phenol RNA extraction
according to Ingolia et al., 2010, Methods Enzymol (different RNA fragment size selection, different set of rRNA depletion oligos)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Raw data were originally paired-end but only read 1 was analysed and is provided here.
|
| Data processing |
Library strategy: TCP-seq
Illumina CASAVA 1.8 for base calling
adapter trimming (fastx_clipper of FASTX Toolkit 0.0.13), filtering by alignment to rRNA (bowtie 1.2.2) and ncRNA, tRNA (bowtie2 2.2.6)
alignment to transcriptome Ensembl GRCh38.80 and genome GRCh38 with TopHat 2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: human_metagene_FP5end_AUG_-80+30_FPlength.ods; counts of footprint 5’ ends positioned from -80 nt to +30 nt relative to the AUG start codon (over rows) respecting the footprint length (18 – 98 nt over columns)
Supplementary_files_format_and_content: human_metagene_FP5end_STOP_-80+30_FPlength.ods; counts of footprint 5’ ends positioned from -80 nt to +30 nt relative to the STOP codon (over rows) respecting the footprint length (18 – 98 nt over columns)
Supplementary_files_format_and_content: human_metagene_coverage_CAP_-40+40.csv; footprint coverage from -40 nt to +40 nt relative to the transcript start
Supplementary_files_format_and_content: human_genewise_FPcount_transcript_area.csv; footprint count per transcript area
Supplementary_files_format_and_content: human_genewise_mean_CI_FP5end_FP3end_AUG_-50+50.ods; distribution (mean and 95 percentiles) of footprint 5’end and 3’end positions relative to the AUG start codon of start codon associated footprints without 5’extension (footprint 5’end from -12 to -14 nt)
Supplementary_files_format_and_content: human_coverage_ATF4_ENST00000396680_-50.csv; coverage for the 5’UTR and the beginning of the CDS for ATF4 (starting at -50 nt from the transcript start)
|
| |
|
| Submission date |
Oct 20, 2019 |
| Last update date |
Jun 25, 2020 |
| Contact name |
Susan Wagner |
| E-mail(s) |
[email protected]
|
| Organization name |
Australian National University
|
| Department |
The John Curtin School of Medical Research
|
| Lab |
RNA Biology - Preiss Group
|
| Street address |
131 Garran Road
|
| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE139131 |
Selective Translation Complex Profiling in yeast and human Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes [Human] |
| GSE139132 |
Selective Translation Complex Profiling in yeast and human Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes |
|
| Relations |
| BioSample |
SAMN13065526 |
| SRA |
SRX7026378 |
