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| Status |
Public on Aug 30, 2023 |
| Title |
Duck-EF 2020-02 High P5 [C34] |
| Sample type |
SRA |
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| Source name |
embryonic fibroblasts P5
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| Organism |
Anas platyrhynchos |
| Characteristics |
cell type: embryonic fibroblasts P5
Sex: male
medium: DMEM/10percent FBS
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| Growth protocol |
Embryonic fibroblast cells were isolated from eggs incubated for ~10 days at 38.5 °C to reach stage HH36. Embryos were then treated by resection of head and neck, limb, skin and fat deposit, and internal developing organs. The remained trunk portion was trypsinized at 37°C, followed by neutralization and centrifugation to obtain digested cell pellet. Cell pellet was resuspended with DMEM/10%FBS and seeded in DMEM/10%FBS or DMEM/F12/10%FBS for expansion.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using commercial reagents (TRIzol, Invitrogen) from each sample of avian embryonic fibroblast cells at the fifth passage (P5).
5ug of RNA from each fibroblast sample was used for nAnTi-CAGE and polyA RNAseq libraries preparation and subsequent sequencing using the Illumina HiSeq2500 platform (K. K. DNAForm, Yokohama, Japan)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
C34
Duck_CAGE.xlsx
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| Data processing |
Quality of sequenced CAGE reads was checked by using FastQC v0.11.5 and then trimmed with fastx_trimmer -Q33 -l 75 (FASTX Toolkit 0.0.14). Moirai removeN script was applied to remove reads with “N” nucleotides. CAGE reads matching to adapters or rRNA (Moirai defined rRNA for galGal3) were removed with Trimmomatic-0.38 and RNAdust 1.06, respectively.
Trimmed CAGE reads were aligned with BWA 0.7.10-r789 and unmapped reads realigned with Hisat2 v2.1.0
Alignments were processed into CTSS (CAGE transcription start sites) and CAGE peaks with PromoterPipeline (https://github.com/Population-Transcriptomics/C1-CAGE-preview) with default threshold of at least 10 TPM (tags per million) in one of the samples.
CAGE peaks were associated with nearby transcripts located on the same strand by using ChIPseeker v1.32.0 package for R.
Quality of sequenced RNAseq reads was checked by using FastQC v0.11.5 and then trimmed with Trimmomatic-0.38
Trimmed RNAseq reads were aligned to reference genome assemblies by using Hisat2 v2.1.0, counted with HTSeq v2.0.1, and normalized by library size and exon length in edgeR v3.42.2.
Assembly: galGal6 (GCF_000002315.6)
Assembly: Coturnix_japonica_2.1 (GCF_001577835.2)
Assembly: MGAL_WU_HG_1.0 (GCA_905368555.1)
Assembly: GT_SO_6221 (http://gigadb.org/dataset/100559)
Assembly: ZJU1.0 (GCF_015476345.1)
Assembly: bTaeGut2.pat.W.v2 (GCF_008822105.2)
Assembly: ZJU1.0 (GCA_016128335.1)
Supplementary files format and content: xlsx files with CAGE peaks coordinates, TSS position, associated genes, tag per million normalized counts
Supplementary files format and content: xlsx files with RNAseq raw and FPKM counts
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| Submission date |
Jun 30, 2023 |
| Last update date |
Aug 30, 2023 |
| Contact name |
Ruslan Deviatiiarov |
| E-mail(s) |
ruselusalbus@gmail.com
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| Phone |
+79196948678
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| Organization name |
Kazan Federal University
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| Department |
Institute of Fundamental Medicine and Biology
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| Lab |
Extreme Biology
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| Street address |
Paris Commune, 9
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| City |
Kazan |
| State/province |
Tatarstan |
| ZIP/Postal code |
420021 |
| Country |
Russia |
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| Platform ID |
GPL22591 |
| Series (1) |
| GSE213253 |
Dosage compensation of Z sex chromosome genes in avian fibroblast cells |
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| Relations |
| BioSample |
SAMN36094265 |
| SRA |
SRX20836915 |
| 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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