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Sample GSM8229187 Query DataSets for GSM8229187
Status Public on Jul 31, 2024
Title PT1|001|Full.ROI
Sample type other
 
Source name liver_biopsy,HBV_HIV_coninfectio
Organism Homo sapiens
Characteristics dsp_sample_id: DSP-1012340089901-B-D03
slide_name: 21549290
estimated_immune: 0%
estimated_hbv: 0%
patient_id: PT1
numeric.estimated.immune: 0
numeric.estimated.hbv: 0
Treatment protocol N.a.
Growth protocol n.a.
Extracted molecule other
Extraction protocol n.a.
Label n.a.
Label protocol Tissue sections were loaded into the GeoMx platform and scanned for an immunofluorescent signal. A geometric strategy was employed for selection of regions of interest (ROIs) which were segmented on the basis of HBsAg staining and presence of immune cell infiltrate
 
Hybridization protocol n.a.
Scan protocol n.a.
Description HBV_HIV_coninfectio
Data processing Quality control checks and data analysis were performed in the GeoMx DSP Data Analysis suite. All regions of interest (ROI) had acceptable sequencing quality metrics after examination of the raw, trimmed, stitched, aligned and deduplicated reads, and the sequencing saturation (>60%). An expression value per gene target per ROI was generated in GeoMx DSP Analysis Suite through the compilation of multiple probes, within the NanoString GeoMx Human Whole Transcriptome Atlas probe mix, for each transcript. The manufacturer’s recommended threshold for the detection of genes in referred to as the Limit of Quantification (LOQ); the LOQ is 2 geometric standard deviations above the geometric mean. The AOI from PT2, PT1 and PT3 tissues were filtered to include only the genes detected over the LOQ in 3 or more AOI: 9672 genes. The data were then quantile normalised and the performance of the normalisation was assessed by the standardisation of housekeeping genes and distribution of total gene expression between ROI
 
Submission date Apr 24, 2024
Last update date Jul 31, 2024
Contact name Dimitra Peppa
Organization name University College London
Street address Pond Street
City London
ZIP/Postal code NW3 2PP
Country United Kingdom
 
Platform ID GPL30991
Series (1)
GSE265785 Characterization of HBV and co-infection with HDV and HIV through spatial transcriptomics

Data table header descriptions
ID_REF
VALUE DSP output of quality controled and normalised counts

Data table
ID_REF VALUE
A1BG 672.85
A1CF 99.24
A2M 603.04
A2ML1 9.25
A3GALT2 7.57
A4GALT 16.82
A4GNT 8.41
AAAS 19.34
AACS 10.09
AADAC 109.34
AADACL2 2.52
AADACL3 11.77
AADACL4 15.14
AADAT 42.05
AAGAB 15.14
AAK1 17.66
AAMDC 16.82
AAMP 50.46
AANAT 9.25
AAR2 7.57

Total number of rows: 18677

Table truncated, full table size 220 Kbytes.




Supplementary file Size Download File type/resource
GSM8229187_DSP-1012340089901-B-D03.dcc.gz 62.6 Kb (ftp)(http) DCC

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