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| Status |
Public on Sep 04, 2021 |
| Title |
GRA415A105 |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Homo sapiens |
| Characteristics |
patient id: 75
subgroup: TB Drug Resistance
group: PTB
days_from_att: 354
days_from_att_categ: [315,374]
subgroup_att: TB Drug Resistance
response_group: weaker
gender: M
smear_results: Negative
culture_result: Positive
igra: Pos
resistance: H, E
ethnicity: Central Europe (Poland)
birth_place: Foreign Born
age: 41
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| Treatment protocol |
NA
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| Growth protocol |
NA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated, from blood from tuberculosis progressors and Treatment reponse cohorts, and IGRA-ve healthy controls simultaneously, from 1ml whole blood using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit . Globin RNA was depleted from the total RNA (1.5–2 μg) using the human GLOBINclear kit.
Samples (200 ng) with an RQS > 6 were used to prepare a cDNA library using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). The tagged libraries were sized and quantitated in duplicate (Agilent TapeStation system) using D1000 ScreenTape and reagents (Agilent), normalised, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (100 bp) per sample
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
TB Drug Resistance
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| Data processing |
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long.The filtered reads were aligned to the Homo sapiens genome Ensembl GRCh38 (release 95) using HISAT2 v2.1.0 with default settings and RF rna-strandedness. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness
Raw readcounts were processed using the bioconductor package DESeq2 v.1.12.4 in R v.3.5.1 and normalized using the DESeq method to remove the library-specific artefacts. Genes with 5 read counts or more in at least 12 samples were considered and normalized with variance stabilizing transformation to obtain normalized log2 gene expression values.
Genome_build: Ensembl GRCh38 (release 95)
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.
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| Submission date |
Sep 08, 2020 |
| Last update date |
Sep 04, 2021 |
| Contact name |
Anne OGarra |
| E-mail(s) |
Anne.OGarra@crick.ac.uk
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| Organization name |
Francis Crick Insititue
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| Lab |
IMMUNOREGULATION AND INFECTION LABORATORY
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| Street address |
1 Midland Road
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| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE157657 |
Blood transcriptomics for diagnosis, risk, and treatment monitoring in tuberculosis reveal the evolution and resolution of TB disease: Does one signature capture all? |
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| Relations |
| BioSample |
SAMN16081496 |
| SRA |
SRX9092864 |
| 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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