|
| Status |
Public on Aug 03, 2020 |
| Title |
Hs_H1_BG97_3D_d11_ctrl_Riboseq_replicate1_5 |
| Sample type |
SRA |
| |
|
| Source name |
Unmodified hESCs were differentiated to the PP2 stage
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1 ES cells
cell type: ES-derived late pancreatic progenitor cells
genotype: WT
library: ribosome-protected
|
| Treatment protocol |
Definitive endoderm and pancreatic progenitor stage cells were collected, and RNA was extracted for RNA-seq library preparation.
|
| Growth protocol |
Pancreatic differentiation was performed as previously described (Rezania et al., 2012; Rezania et al., 2014), with minor modifications. Cells were grown either as a monolayer (RNA-seq of lncRNA KO hESC-derived tissues and corresponding WT controls) , or in suspension culture (Ribo-seq and matched RNA-seq).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using either Trizol or the QIAGEN RNeasy Mini Kit. For cell fractionation experiments, the Paris Kit (Thermo Fisher Scientific) was used.
Libraries were prepared according to Illumina's (TruSeq Stranded Total RNA Library Prep Gold; TruSeq Stranded mRNA Library Prep; TruSeq Ribo Profile (Mammalian) or Roche's (KAPA mRNA HyperPrep Kit) instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
hs_pan_002_bg_Ri_S11_L008
processed data file: 3d_pp2_riboseq_rpkm.txt
|
| Data processing |
Reads were aligned to hg38 using STAR (v2.5.3b) with the following parameters: --twopassMode Basic --outFilterMismatchNmax 6 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 3 --outFilterType BySJout --seedSearchStartLmax 50.
Reads per kilobase of transcript, per million mapped reads (RPKM) were calculated with Cufflinks (v2.2.1)
Count tables for differential gene expression analysis with DESeq2 (v1.10.1) were generated with htseq-count from the HTSeq Python library.
Genome_build: hg38
Supplementary_files_format_and_content: gene expression data table in text format
|
| |
|
| Submission date |
Feb 03, 2020 |
| Last update date |
Aug 03, 2020 |
| Contact name |
Maike Sander |
| E-mail(s) |
masander@ucsd.edu
|
| Organization name |
UC San Diego
|
| Street address |
2880 Torrey Pines Scenic Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE144682 |
The role of long noncoding RNAs during pancreas development |
|
| Relations |
| BioSample |
SAMN13975844 |
| SRA |
SRX7666678 |
