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GEO accession:
Series GSE234620
Query DataSets for GSE234620
Status
Public on Jun 14, 2023
Title
A contamination focused approach for optimizing the single-cell RNA-seq experiment
Organisms
Homo sapiens
;
Mus musculus
Experiment type
Expression profiling by high throughput sequencing
Summary
created metrics to measure quality of scRNA seq datasets
Overall design
compared contamination QC metrics and standard QC metrics on multiple experimental conditions
Contributor(s)
Lau K
,
Simmons A
,
Arceneaux D
Citation(s)
37496679
Submission date
Jun 09, 2023
Last update date
Aug 21, 2023
Contact name
Ken Lau
E-mail(s)
ken.s.lau@vanderbilt.edu
Phone
6159366859
Organization name
Vanderbilt University
Department
Cell and Developmental Biology
Street address
2215 Garland Ave. MRBIV10475
City
Nashville
State/province
TN
ZIP/Postal code
37232
Country
USA
Platforms (3)
GPL18573
Illumina NextSeq 500 (Homo sapiens)
GPL19057
Illumina NextSeq 500 (Mus musculus)
GPL24247
Illumina NovaSeq 6000 (Mus musculus)
Samples (28)
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More...
GSM7471989
4498-AS-1: Colagenase + DNaseS1 F1
GSM7471990
4498-AS-2: Cold Protease S2 F1 (CP on crypts)
GSM7471991
4498-AS-3: MACS (minced) S1 F1
GSM7471992
4498-AS-4: CP (minced) S2 F1
GSM7471993
4706-AS-1: S1 F1 MACS enzyme on crypts
GSM7471994
4812-YX-1: All Cell S1 200c:50 Dil
GSM7471995
4812-YX-2: All Cell S2 100c:150 dil
GSM7471996
4858-AS-1: S1 Un fixed test (CP on crypts)
GSM7471997
4858-AS-2: S2 0.1X DSP fixed test
GSM7471998
4858-AS-3: S3 1% PFA fixed test
GSM7471999
4903-YX-1: S1F1 Tip loading
GSM7472000
4903-YX-3: S2 Tip loading
GSM7472001
4903-YX-4: S3 standard tubing (CP on crypts)
GSM7472002
4903-YX-5: S1 BHM frozen (tip load)
GSM7472003
4903-YX-6: S2 BHM normal (tip load)
GSM7472004
6690-yx-1: All Cell AC S1
GSM7472005
6690-yx-2: All Cell AC S2
GSM7472006
6690-yx-3: All Cell AC S3
GSM7472007
1172_AS_3: cell viability enrichment
GSM7472008
1291_AS_1_Coffey: cell viability enrichment
GSM7472009
1291_AS_3_Coffey: cell viability enrichment
GSM7472010
1291_AS_4_Coffey: cell viability enrichment
GSM7472011
1309_AS_1_Hughey: cell viability enrichment
GSM7472012
1309_AS_3_Hughey: cell viability enrichment
GSM7472013
2242_EC: Gastric Corpus
GSM7472014
MK6974_1: K562 Sample 2
GSM7472015
MK6974_2: K562 Sample 3
GSM7472016
5394-YX-2: Tipload S2 (CP but minced)
Relations
BioProject
PRJNA982142
Download family
Format
SOFT formatted family file(s)
SOFT
MINiML formatted family file(s)
MINiML
Series Matrix File(s)
TXT
Supplementary file
Size
Download
File type/resource
GSE234620_RAW.tar
1.1 Gb
(http)
(custom)
TAR (of H5AD)
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
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