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| Status |
Public on Feb 02, 2024 |
| Title |
Hepatic stellate cells, Areg, sample 4 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
cell type: Hepatic Stellate Cells
genotype: C57BL/6 male
treatment: Areg (500 ng/mL)
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| Treatment protocol |
Quiescent hepatic stellate cells were isolated and cultured for 5 hours, then stimulated with recombinant mouse Areg (500 ng/mL) or control for 4 hours in starving media.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed with Trizol Reagent, and RNA was extracted using a Qiagen kit
Poly-A pull-down to enrich mRNAs from total RNA, then library construction using Illumina TruSeq chemistry
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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 |
Libraries were then sequenced using Illumina NovaSeq 6000, with multiplexed samples in each lane, which yields targeted number of paired-end 100bp reads for each sample
RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Mouse:GRCm38.p6) using kallisto (0.44.0).
Differentially expressed genes were assessed through DESeq2
Assembly: Ensembl v96, Mouse:GRCm38.p6
Supplementary files format and content: .tsv, abundance output from Kallisto that includes estimated counts, TPM, effective length for each transcript.
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| Submission date |
Jul 20, 2022 |
| Last update date |
Feb 02, 2024 |
| Contact name |
Nicholas Arpaia |
| E-mail(s) |
na2697@cumc.columbia.edu
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| Organization name |
Columbia University
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| Department |
Microbiology & Immunology
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| Street address |
701 West 168th Street
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE208705 |
Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis II |
| GSE208706 |
Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis |
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| Relations |
| BioSample |
SAMN29855399 |
| SRA |
SRX16368057 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6364804_NT146.tsv.gz |
1.6 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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