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| Status |
Public on Aug 01, 2022 |
| Title |
HFL, palbo, bin2, rep4 |
| Sample type |
SRA |
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| Source name |
HFL, palbo, bin2
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| Organisms |
Drosophila melanogaster; Homo sapiens |
| Characteristics |
human cell type: Human lung fibroblasts (HLF)
cell status: arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor)
sorted cells: bin 2 = small cells.
fly spike-in: S2 cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Direct-zolTM RNA Microprep Kit (Zymo Research)
mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490). The NEBNext Ultra II RNA Library Prep Kit for Illumina® (NEB, #E7775) was then used to prepare libraries for paired-end (2x150 bp) Illumina sequencing (Novogene)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
HFL_palbo_bin2_rep4
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 2 = small cells.
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| Data processing |
read alignment, RNA-seq data: STAR-2.5.3a
bigWig file generation: custom code
Assembly: hg38 + dm6
Supplementary files format and content: The files are bigWig, but their content is a bedGraph file; bedGraph of read coverage, normalized to RPM.
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| Submission date |
Jul 17, 2022 |
| Last update date |
Aug 01, 2022 |
| Contact name |
Georgi Kolev Marinov |
| Organization name |
STANFORD UNIVERSITY
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| Department |
Genetics
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| Street address |
279 Campus Drive West, Beckman Center, B-257A/259
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5101 |
| Country |
USA |
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| Platform ID |
GPL29805 |
| Series (1) |
| GSE208348 |
Increasing cell size remodels the proteome and promotes senescence |
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| Relations |
| BioSample |
SAMN29787318 |
| SRA |
SRX16311780 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6341667_HFL_palbo_bin2_rep4.hg38.bigWig |
140.5 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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