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| Status |
Public on Mar 16, 2020 |
| Title |
074 |
| Sample type |
SRA |
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| Source name |
fecal sample
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| Organism |
Homo sapiens |
| Characteristics |
phenotype: obese
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extractedfrom fecal samples using the ZR Soil/Fecal RNA MicroPrep (Zymo Research) and RNeasy Mini Kit (Qiagen).
Libraries were prepared following the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Quality filtering with Trimmomatic, remotion of adapters and ambiguous bases.
rRNA depletion with Ribopicker.
Alignment to the human genome and transcriptome (GRCh_snp_tran) with HISAT2
Non-human sequences were assembled using Trinity
Abundance of expression was determined by FPKM was used for the normalization of sequencing depth and transcripts length, considerating only the transctipts with FPKM>1
Supplementary_files_format_and_content: normalized abundance measurements RSEM
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| Submission date |
Jan 06, 2020 |
| Last update date |
Mar 16, 2020 |
| Contact name |
Fernanda Cornejo |
| E-mail(s) |
[email protected]
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| Organization name |
Instituto de Biotecnología UNAM
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| Street address |
Av Universidad 2001
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| City |
Cuernavaca |
| ZIP/Postal code |
62100 |
| Country |
Mexico |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE143207 |
Defining the Secrebiome: the expressed secretome of the gut microbiome and its role in obese Mexican children |
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| Relations |
| BioSample |
SAMN13810091 |
| SRA |
SRX7528783 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4252143_obese_rep2_RSEM.genes.results.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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