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| Status |
Public on Mar 05, 2021 |
| Title |
colostrum fed immediately after birth rep4 |
| Sample type |
SRA |
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| Source name |
Ileum
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| Organism |
Bos taurus |
| Characteristics |
tissue: Ileum
developmental stage: newborn
age: 51 h of age
feeding strategy: colostrum fed immediately after birth
tissue: Ileum
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were collected after dissection of calves, flash frozen on liquid nitrogen, and RNA was harvested using a mirVana total RNA Isolation Kit (Ambion, Carlsbad, CA, USA).
TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA, USA) was used with 100 ng of total RNA for the construction of sequencing libraries.The RNA libraries were prepared using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
all_counts_ileum.txt
4133_1
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Filtered reads were aligned to the reference bovine genome (UMD 3.1) using Tophat 2.1.1.
The BAM alignment files generated from Tophat were sorted using Samtools (v1.4) and converted to SAM files.
The SAM files were analyzed using HTSeq-count to obtain gene read counts based on the annotation from ENSEMBL bovine genes.
Genome_build: UMD3.1
Supplementary_files_format_and_content: a text file includes raw counts number for each sample
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| Submission date |
Apr 18, 2018 |
| Last update date |
Mar 05, 2021 |
| Contact name |
Yang Song |
| E-mail(s) |
ysong3@ualberta.ca
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| Phone |
7807100997
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| Organization name |
University of Alberta
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| Department |
AFNS
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| Street address |
8515,112st, NW, #1208
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| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G1K7 |
| Country |
Canada |
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| Platform ID |
GPL23295 |
| Series (1) |
| GSE113331 |
Delayed colostrum feeding influences ileum transcriptome profile in neonatal calves |
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| Relations |
| BioSample |
SAMN08948927 |
| SRA |
SRX3961910 |
| 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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