nstd231 - Ali et al 2023 - dbVar Study

nstd231 (Ali et al. 2023)

Organism:: Human
Study Type:: Collection
Submitter:: Hassan Ali
Description:: To facilitate future clinical use of induced pluripotent stem cells (iPS), culturing protocols must be compliant with good manufacturing practice guidelines and devoid of xenogenic products. Hence, we aimed to compare the efficiency of using a xeno-free protocol (protocol utilizing platelet lysate in culture media) to a xenogenic one (protocol utilizing fetal bovine serum in culture media) for iPS generation. Chromosome microarray analysis was performed to determine the effect of each protocol on the genomic integrity of each generated iPS cell line. See Variant Summary counts for nstd231 in dbVar Variant Summary.

Links

Source: NCBI

Detailed Information: Download 133 Variant Regions, Download 146 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p14 (hg38)
Submitted: GRCh37 (hg19)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	105	106	Remapped	NC_000001.11
NC_000004.12	Chr4	2	2	Remapped	NC_000004.12
NC_000005.10	Chr5	4	5	Remapped	NC_000005.10
NC_000006.12	Chr6	2	2	Remapped	NC_000006.12
NC_000007.14	Chr7	2	2	Remapped	NC_000007.14
NC_000010.11	Chr10	1	1	Remapped	NC_000010.11
NC_000011.10	Chr11	2	5	Remapped	NC_000011.10
NC_000013.11	Chr13	6	9	Remapped	NC_000013.11
NC_000014.9	Chr14	1	1	Remapped	NC_000014.9
NC_000016.10	Chr16	2	2	Remapped	NC_000016.10
NC_000022.11	Chr22	1	1	Remapped	NC_000022.11
NC_000023.11	ChrX	4	9	Remapped	NC_000023.11
NW_014040926.1	Chr1\|NW_014040926.1	1	1	Remapped	NW_014040926.1
NT_187600.1	Chr14\|NT_187600.1	1	1	Remapped	NT_187600.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	106	107	Submitted	NC_000001.10
NC_000004.11	Chr4	2	2	Submitted	NC_000004.11
NC_000005.9	Chr5	4	5	Submitted	NC_000005.9
NC_000006.11	Chr6	2	2	Submitted	NC_000006.11
NC_000007.13	Chr7	2	2	Submitted	NC_000007.13
NC_000010.10	Chr10	1	1	Submitted	NC_000010.10
NC_000011.9	Chr11	2	5	Submitted	NC_000011.9
NC_000013.10	Chr13	6	9	Submitted	NC_000013.10
NC_000014.8	Chr14	1	1	Submitted	NC_000014.8
NC_000016.9	Chr16	2	2	Submitted	NC_000016.9
NC_000022.10	Chr22	1	1	Submitted	NC_000022.10
NC_000023.10	ChrX	4	9	Submitted	NC_000023.10

Remapping summary:

			Variant Region remap status						Variant Call remap status
Sequence ID	Chr	Variant Regions on source	Perfect	Good	Pass	Fail	Mult	Variant Calls on source	Perfect	Good	Pass	Fail	Mult
NC_000001.10	Chr1	106	84	16	4	1	1	107	85	16	4	1	1
NC_000004.11	Chr4	2	2	0	0	0	0	2	2	0	0	0	0
NC_000005.9	Chr5	4	4	0	0	0	0	5	5	0	0	0	0
NC_000006.11	Chr6	2	2	0	0	0	0	2	2	0	0	0	0
NC_000007.13	Chr7	2	2	0	0	0	0	2	2	0	0	0	0
NC_000010.10	Chr10	1	1	0	0	0	0	1	1	0	0	0	0
NC_000011.9	Chr11	2	2	0	0	0	0	5	5	0	0	0	0
NC_000013.10	Chr13	6	4	0	2	0	0	9	7	0	2	0	0
NC_000014.8	Chr14	1	0	0	0	0	1	1	0	0	0	0	1
NC_000016.9	Chr16	2	2	0	0	0	0	2	2	0	0	0	0
NC_000022.10	Chr22	1	0	1	0	0	0	1	0	1	0	0	0
NC_000023.10	ChrX	4	2	1	1	0	0	9	7	1	1	0	0

Samplesets

Number of Samplesets: 12

Sampleset ID:: 1
Name:: Dermal fibroblasts_FBS
Description:: Donor-matched dermal fibroblasts expanded in FBS media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
D_Fibs_FBS	Dermal fibroblasts	D_Fibs_FBS	Female	Human	Not reported

Sampleset ID:: 2
Name:: Buccal fibroblasts_FBS
Description:: Donor-matched buccal fibroblasts expanded in FBS media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 2
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
B_Fibs_FBS	Buccal fibroblasts	B_Fibs_FBS	Female	Human	Not reported

Sampleset ID:: 3
Name:: Gingival fibroblasts_FBS
Description:: Donor-matched gingival fibroblasts expanded in FBS media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 3
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
G_Fibs_FBS	Gingival fibroblasts	G_Fibs_FBS	Female	Human	Not reported

Sampleset ID:: 4
Name:: Dermal fibroblasts_PL
Description:: Donor-matched dermal fibroblasts expanded in PL media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 4
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
D_Fibs_PL	Dermal fibroblasts	D_Fibs_PL	Female	Human	Not reported

Sampleset ID:: 5
Name:: Buccal fibroblasts_PL
Description:: Donor-matched buccal fibroblasts expanded in PL media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 5
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
B_Fibs_PL	Buccal fibroblasts	B_Fibs_PL	Female	Human	Not reported

Sampleset ID:: 6
Name:: Gingival fibroblasts_PL
Description:: Donor-matched gingival fibroblasts expanded in PL media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 6
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
G_Fibs_PL	Gingival fibroblasts	G_Fibs_PL	Female	Human	Not reported

Sampleset ID:: 7
Name:: Dermal induced pluripotent stem cells_FBS
Sampleset Type:: Case
Description:: Donor-matched induced pluripotent stem cells generated from dermal fibroblasts expanded in FBS media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 7
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
D_iPS_FBS	Induced pluripotent stem cells generated from dermal fibroblasts	D_iPS_FBS	Female	Human	Not reported

Sampleset ID:: 8
Name:: Buccal induced pluripotent stem cells_FBS
Description:: Donor-matched induced pluripotent stem cells generated from buccal fibroblasts expanded in FBS media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 8
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
B_iPS_FBS	Induced pluripotent stem cells generated from buccal fibroblasts	B_iPS_FBS	Female	Human	Not reported

Sampleset ID:: 9
Name:: Gingival induced pluripotent stem cells_FBS
Description:: Donor-matched induced pluripotent stem cells generated from gingival fibroblasts expanded in FBS media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 9
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
G_iPS_FBS	Induced pluripotent stem cells generated from gingival fibroblasts	G_iPS_FBS	Female	Human	Not reported

Sampleset ID:: 10
Name:: Dermal induced pluripotent stem cells_PL
Description:: Donor-matched induced pluripotent stem cells generated from dermal fibroblasts expanded in PL media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 10
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
D_iPS_PL	Induced pluripotent stem cells generated from dermal fibroblasts	D_iPS_PL	Female	Human	Not reported

Sampleset ID:: 11
Name:: Buccal induced pluripotent stem cells_PL
Description:: Donor-matched induced pluripotent stem cells generated from buccal fibroblasts expanded in PL media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 11
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
B_iPS_PL	Induced pluripotent stem cells generated from buccal fibroblasts	B_iPS_PL	Female	Human	Not reported

Sampleset ID:: 12
Name:: Gingival induced pluripotent stem cells_PL
Description:: Donor-matched induced pluripotent stem cells generated from gingival fibroblasts expanded in PL media
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Female

Samples for sampleset 12
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
G_iPS_PL	Induced pluripotent stem cells generated from gingival fibroblasts	G_iPS_PL	Female	Human	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	146

dbVar

Database of genomic structural variation

nstd231 (Ali et al. 2023)

Links

Detailed Information: Download 133 Variant Regions, Download 146 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p14 (hg38)
Submitted: GRCh37 (hg19)

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 12

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd231 (Ali et al. 2023)

Links

Detailed Information: Download 133 Variant Regions, Download 146 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p14 (hg38)GRCh37 (hg19)

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 12

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: