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| Status |
Public on Aug 19, 2024 |
| Title |
HEPG2 ERCC spike-in |
| Sample type |
SRA |
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| Source name |
ERCC
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| Organism |
synthetic construct |
| Characteristics |
tissue: ERCC
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
1% dilution of ERCC RNA Spike-In Mix (4456740, ThermoFisher)
Sample was processed into a short read library using the TruSeq Stranded mRNA Sample Prep Kit from Illumina, Inc (Cat#: 20020594). The fragmented mRNA was reverse transcribed to cDNA using random primers. This was followed by second stranded cDNA synthesis. The library preparation processes of mono-adenylation, adapter ligation and amplification were performed following the manual provided by the manufacturer. The quantity and quality of the libraries were assessed in a manner similar to that described for whole genome DNA library preparation. The procedure of 150 cycle paired-end sequencing on the Illumina NextSeq550 followed per the manufacturer’s guidelines.
Illumina short-read RNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
The raw RNA-seq data were pre-processed by FastQC and Trimmomatic for quality control and trimming.
Then the reads were aligned to ERCC reference genome by STAR aligner
Transcript counts were collected based on the alignment and the count per million (CPM) was calculated for transcript quantification.
BCFtools were applied on the aligned file to call the variant sites.
Assembly: ERCC
Supplementary files format and content: Illumina.HepG2_ERCC_S1.STAR.ReadsPerGene.out.tab: transcript count file in TAB format
Supplementary files format and content: Illumina.mpileup.txt: BCFtool variant calling file in TXT format
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| Submission date |
Nov 02, 2023 |
| Last update date |
Aug 19, 2024 |
| Contact name |
Shuchang Liu |
| E-mail(s) |
shl96@pitt.edu
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| Organization name |
University of Pittsburgh
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| Street address |
203 Lothrop Street
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
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| Platform ID |
GPL27609 |
| Series (2) |
| GSE246832 |
Set2: ERCC bulk short-read RNA-seq by Illumina NextSeq platform |
| GSE246838 |
Utility analyses of AVITI sequencing platforms |
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| Relations |
| BioSample |
SAMN38080308 |
| SRA |
SRX22339319 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7879929_Illumina.HepG2_ERCC_S1.STAR.ReadsPerGene.out.tab.gz |
893 b |
(ftp)(http) |
TAB |
| GSM7879929_Illumina.mpileup.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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