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| Status |
Public on Oct 10, 2023 |
| Title |
COBLL1_C2 |
| Sample type |
SRA |
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| Source name |
MEL1 (INSGFP/W)
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MEL1 (INSGFP/W)
cell type: human embryonic stem cell
genotype: COBLL1 knockout
treatment: beta-cell differentiation
time: Day 24
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA of purified hESC-beta cells was harvested using the Absolutely RNA Nanoprep kit (Agilent Technologies, Santa Clara, CA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
We aligned the raw reads to the GRCh38 genome assembly using STAR v2.73a (Dobin et al. 2013) with default parameters.
We quantified expression levels of Gencode v19 genes (Ensembl release 103) using QoRTs v1.3.6, (Hartley & Mullikin 2015).
Finally, we generated a raw read count matrix of gene by library.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include read counts per gene per sample
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| Submission date |
Mar 31, 2023 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Shuibing Chen |
| E-mail(s) |
shuibing.chen@gmail.com
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| Phone |
2127465431
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| Organization name |
Weill Cornell Medical College
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| Department |
Surgery
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| Street address |
A 827B, 1300 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE228662 |
Functional interrogation of twenty Type 2 Diabetes-associated genes using isogenic hESC-derived β-like cells [RNA-Seq] |
| GSE228665 |
Functional interrogation of twenty Type 2 Diabetes-associated genes using isogenic hESC-derived β-like cells |
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| Relations |
| BioSample |
SAMN34031203 |
| SRA |
SRX19839220 |
| 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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