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| Status |
Public on Dec 28, 2022 |
| Title |
erythroblasts, WT-3 |
| Sample type |
SRA |
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| Source name |
erythroblasts
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
cell type: erythroblasts
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Isolation of erythroblasts was performed according to the manufacturer’s recommendations (130-049-901, Miltenyi Biotec), and RNA was harvested using Trizol reagent. Illumina VAHTS Universal V6 RNA-seq Library Prep Kit (NR604-01/02) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina 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 |
Illumina Casava software used for basecalling.
Remove adapter polluted reads. Remove low-quality reads. Remove reads which contain N higher than 5%.
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Dec 28, 2021 |
| Last update date |
Dec 28, 2022 |
| Contact name |
Lei Yang |
| E-mail(s) |
young210716@sina.com
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| Phone |
+8618752788543
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| Organization name |
Yangzhou University Medical College
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| Street address |
136 Jiangyang Road
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| City |
Yangzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
225009 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE192700 |
Aberrant Nrf2 activation delays erythroid maturation during chemotherapeutic drug-induced erythropoiesis |
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| Relations |
| BioSample |
SAMN24464432 |
| SRA |
SRX13521708 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5761264_WT-3.txt.gz |
210.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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