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| Status |
Public on Dec 31, 2020 |
| Title |
6C2 cells, cell sample s1, Total RNAseq |
| Sample type |
SRA |
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| Source name |
6C2 cell
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| Organism |
Gallus gallus |
| Characteristics |
cell line: chicken erythroleukemia line 6C2
cell cycle: Cycling cells
developmental stage: cells arrested at the erythroid colony-forming unit stage of hematopoietic development
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| Treatment protocol |
N/A
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from 6C2 cells were isolated using RNeasy plus mini kit (Qiagen) following manufacturer's instruction. DNase digestion was performed (Promega) to remove any genomic DNA in the purified RNA.
SOLiD Total RNA-Seq kit was used to prepare whole transcriptome libraries. RNA quality and integrity was assessed using the RNA pico Kit and 2000 Bioanalyzer (Agilent technologies). 4-6 ug of Total RNA was subjected to rRibosomal depletion (RiboMinus eukaryote system v2, Life technologies) followed by RNAse III fragmentation, adaptor hybridization and reverse transcription. Reversed transcribed DNA was size selected and PCR amplified. Libraries were sequenced in a multiplex manner, pooling two libraries per lane.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
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| Data processing |
XSQ files generated from SOLiD machine were mapped on reference genome gal3 using LifeScope v2.5.1 software
Whole.transcriptome.pe workflow of LifeScope was used with 2 mismatch penalty settings
Adaptor and barcode sequences were removed
Read counts and rpkm were aligned to RefSeq genes from the WUGSC 2.1/galGal3 Assembly using the WT count module of LifeScope v2.5.1
Genome_build: galGal3
Supplementary_files_format_and_content: TEXT, ensembl gene ID, chr, strand, start, end, count, length, RPKM, gene symbol
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| Submission date |
Nov 26, 2019 |
| Last update date |
Jan 16, 2023 |
| Contact name |
James Ronald Davie |
| E-mail(s) |
jim.davie@umanitoba.ca
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| Phone |
2042723174
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| Organization name |
University of Manitoba
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| Department |
Biochemistry and Medical Genetics
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| Street address |
745 Bannatyne Avenue, RM 333A
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| City |
Winnipeg |
| State/province |
Manitoba |
| ZIP/Postal code |
R3E 0J9 |
| Country |
Canada |
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| Platform ID |
GPL21224 |
| Series (2) |
| GSE141014 |
Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes [RNA-seq] |
| GSE141015 |
Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes |
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| Relations |
| BioSample |
SAMN13387618 |
| SRA |
SRX7217436 |
| 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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