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11107 items
PKBFI5947MIIA
- joyce-niland:IIDP_scRNAseq_SRR22775801_no_treatment_Alignment_Aligned.sortedByCoord.out.bam
GRCh38
filtered alignments
alignments
bam
/analysis-sets/PKBDS9867LLDH/
Joyce Niland, CoH
/reference-files/PKBFI0723SUOK/, /reference-files/PKBFI6475GTLH/
released
GRCh38 filtered alignments
validated
fff3adf3-3d79-473c-b1c8-4c7bbd51a26a
PKBFI7657TECG
- joyce-niland:IIDP_scRNAseq_SRR10751500_DMSO_Control_72Hr_Tabular_barcodes.tsv
barcode to element mapping
tsv
/analysis-sets/PKBDS6543THTF/
Joyce Niland, CoH
released
barcode to element mapping
validated
ffef3e2f-e7bb-4e7f-865b-671a56f76003
PKBDO6190OSXB
- joyce-niland:SAMN08786556
IIDP
Human donor SAMN08786556 in the IIDP database
IIDP:SAMN08786556
Joyce Niland, CoH
male
released
male
Homo sapiens
ffee93ae-664e-4a09-a333-caa4873392af
PKBFI4277VOLY
- klaus-kaestner:HPAP_scRNAseq_HPAP-092_no_treatment_doubletFiinderMatrix_matrix.mtx
gene by cell sparse gene count matrix
sparse gene count matrix
mtx
/analysis-sets/PKBDS2848ZCYL/
Klaus Kaestner, UPenn
/reference-files/PKBFI0723SUOK/, /reference-files/PKBFI6475GTLH/
released
gene by cell sparse gene count matrix
validated
ffecee3b-04a1-48c1-82bc-38c2d76aa178
PKBDO2390DHUQ
- prodo:HP-19242-01
Prodo
Human donor HP-19242-01 in the Prodo Laboratories database
Prodo:HP-19242-01
Prodo Laboratories, PRODO
male
released
male
Homo sapiens
ffeb6903-ab11-453f-84a1-ff7a21746f97
PKBFI2061GCSI
- klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-051_RSEM-gene
GRCh38
element quantifications
This file contains gene-level expression quantification, including gene IDs, expected counts, TPM, FPKM, and posterior mean estimates.
tsv
/analysis-sets/PKBDS5408EAEI/
Klaus Kaestner, UPenn
released
GRCh38 element quantifications
validated
ffeab1d5-912b-4405-afb8-8b9d9229c5aa
PKBDS0823AWQO
- klaus-kaestner:HPAP_MeasurementSet_scRNAseq_HPAP-032_no_treatment
Measurement set of scRNA-seq for islet biosample of human donor HPAP-032 from HPAP with no_treatment (HPAP-032)
experimental data
Klaus Kaestner, UPenn
scRNA-seq
released
single-cell RNA sequencing assay (scRNA-seq)
Homo sapiens
ffe812fd-7f27-46a7-a098-4289cef00007
PKBFI4280YUSM
- klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-040_STAR-Transbam
GENCODE 39
PanKbase
filtered transcriptome alignments
transcriptome alignments
The file contains RNA-seq reads aligned to a reference transcriptome in BAM format, used for gene expression and transcript analysis.
bam
/analysis-sets/PKBDS4203KSNH/
Klaus Kaestner, UPenn
/reference-files/PKBFI0723SUOK/, /reference-files/PKBFI6475GTLH/
released
GENCODE 39 filtered transcriptome alignments
validated
ffe61c06-93d7-4c34-bf24-e9516c5356f0
PKBDO1238GOVB
- joyce-niland:SAMN08784602
IIDP, Prodo
Human donor SAMN08784602 in the IIDP database
IIDP:SAMN08784602, Prodo:12280-01
Joyce Niland, CoH
female
released
female
Homo sapiens
ffe6074a-af93-49da-b3df-70f9b1084f8a
PKBFI9279XNCC
- klaus-kaestner:HPAP_scRNAseq_HPAP-072_no_treatment_Tabular_barcodes.tsv
barcode to element mapping
tsv
/analysis-sets/PKBDS6939NVNR/
Klaus Kaestner, UPenn
released
barcode to element mapping
validated
ffe3a326-8b82-4b93-aa40-d15202754071
PKBFI6884NSUP
- klaus-kaestner:HPAP_scRNAseq_HPAP-074_no_treatment_Matrix_cellbender_FPR_0.1_filtered.h5
gene by cell sparse gene count matrix
sparse gene count matrix
h5ad
/analysis-sets/PKBDS1578ODWO/
Klaus Kaestner, UPenn
/reference-files/PKBFI0723SUOK/, /reference-files/PKBFI6475GTLH/
released
gene by cell sparse gene count matrix
validated
ffe12001-6bb8-444f-a5c8-a39b0d7377a9
PKBFI8100OWRD
- joyce-niland:IIDP_scRNAseq_SRR22775817_no_treatment_Matrix_cellbender_FPR_0.1.h5
gene by cell sparse gene count matrix
sparse gene count matrix
h5ad
/analysis-sets/PKBDS5522YXVV/
Joyce Niland, CoH
/reference-files/PKBFI0723SUOK/, /reference-files/PKBFI6475GTLH/
released
gene by cell sparse gene count matrix
validated
ffe0085d-8826-455c-b45c-6c3d80f1f7a5
PKBDO7764MJRA
- joyce-niland:SAMN08768701
IIDP
Human donor SAMN08768701 in the IIDP database
HIPP:HIPP56, IIDP:SAMN08768701
Joyce Niland, CoH
male
released
male
Homo sapiens
ffdb740d-5f9d-4ae4-a5c0-38dffa9ba096
PKBDO1170ATLC
- atkinson:6477
nPOD
Human donor SAMN15879530 in the nPOD database
nPOD_portal:6477
Mark Atkinson, UFHealth
female
released
female /phenotype-terms/MONDO_0005147/
Homo sapiens
ffd97d16-af9b-4113-afc5-626decf53e2a
PKBFI4604NUMN
- joyce-niland:IIDP_scRNAseq_SRR22775837_no_treatment_Tabular_cellbender_FPR_0.05_metrics.csv
QC metrics
csv
/analysis-sets/PKBDS3380PKTA/
Joyce Niland, CoH
released
QC metrics
validated
ffc9bd20-2441-4015-89bb-5843931bfbea
PKBFI7751UVNI
- klaus-kaestner:HPAP_scRNAseq_HPAP-052_no_treatment_Matrix_matrix.mtx
cell by gene sparse gene count matrix
sparse gene count matrix
mtx
/analysis-sets/PKBDS5847QGPP/
Klaus Kaestner, UPenn
/reference-files/PKBFI0723SUOK/, /reference-files/PKBFI6475GTLH/
released
cell by gene sparse gene count matrix
validated
ffc99899-f02c-489e-ae57-f1f46c648eef
PKBDS6276JJRU
- joyce-niland:SAMN10737781_scRNAseq_assay_untreated
experimental data
Joyce Niland, CoH
scRNA-seq
polyA enriched
released
single-cell RNA sequencing assay (scRNA-seq)
Homo sapiens
ffc214b6-7594-4ed7-abeb-213afb07724c
PKBFI9821TPGV
- joyce-niland:IIDP_scRNAseq_SRR22775808_no_treatment_Tabular_Log.progress.out
QC metrics
txt
/analysis-sets/PKBDS6939TCMH/
Joyce Niland, CoH
released
QC metrics
validated
ffb86e72-62e7-477f-a4ca-137b82e59b7b
PKBFI8769YPUJ
- joyce-niland:IIDP_scRNAseq_SRR22775812_no_treatment_Tabular_cellbender_FPR_0.05_metrics.csv
QC metrics
csv
/analysis-sets/PKBDS4530RFYP/
Joyce Niland, CoH
released
QC metrics
validated
ffb3195e-6edf-4332-9c75-22cdfe6f83fb
- kyle-gaulton:phenotype_amyotrophicLateralSclerosisType15
amyotrophic lateral sclerosis 15, with or without frontotemporal dementia, X-linked dominant,amyotrophic lateral sclerosis caused by mutation in UBQLN2,ALS15,amyotrophic lateral sclerosis 15, with or without frontotemporal dementia,UBQLN2 amyotrophic lateral sclerosis,amyotrophic lateral sclerosis 15,amyotrophic lateral sclerosis type 15
MONDO_0010459
released
amyotrophic lateral sclerosis type 15
ALS15, amyotrophic lateral sclerosis 15, amyotrophic lateral sclerosis 15, with or without frontotemporal dementia, amyotrophic lateral sclerosis 15, with or without frontotemporal dementia, X-linked dominant, amyotrophic lateral sclerosis caused by mutation in UBQLN2, amyotrophic lateral sclerosis type 15, UBQLN2 amyotrophic lateral sclerosis
MONDO:0010459
amyotrophic lateral sclerosis type 15
ffac462a-1554-402c-9018-5e906e0f4cff
PKBFI2134DKYX
- klaus-kaestner:HPAP_scRNAseq_HPAP-026_no_treatment_Alignment_.before-dedup.bam
GRCh38
filtered alignments
alignments
bam
/analysis-sets/PKBDS7481RHDC/
Klaus Kaestner, UPenn
/reference-files/PKBFI0723SUOK/, /reference-files/PKBFI6475GTLH/
released
GRCh38 filtered alignments
validated
ffa462b8-dfdb-4f51-91b1-2147befd381a
PKBDO0633JCCW
- joyce-niland:SAMN11578544
IIDP
Human donor SAMN11578544 in the IIDP database
HIPP:HIPP233, IIDP:SAMN11578544
Joyce Niland, CoH
female
released
female
Homo sapiens
ffa38713-8cb1-4c25-9aa9-8d033e637a6a
PKBFI3999YYUM
- joyce-niland:Prodo_scRNAseq_HP-23135-01__18_hr_NMMA_18_hr_NMMA_Tabular_cellbender_FPR_0.15_report.html
QC metrics
txt
/analysis-sets/PKBDS3609OQGX/
Joyce Niland, CoH
released
QC metrics
validated
ff9d30eb-3621-4cf1-9312-1a5284958b9a
PKBSM1653KRSJ
- joyce-niland:SAMN08768784_scRNAseq_secondaryBiosample_untreated
primary islet
Islet biosample from human donor SAMN08768784, untreated
/human-donors/PKBDO6951KCYY/
Joyce Niland, CoH
female
released
islet of Langerhans cell, female, Homo sapiens
/human-donors/PKBDO6951KCYY/
Homo sapiens
ff8bf8c1-5a9d-466f-a811-c1d1f1d9498e
PKBDS6113LMCM
- klaus-kaestner:scATAC_isletCells_HPAP-044
HPAP
experimental data
Klaus Kaestner, UPenn
snATAC-seq
https://hpap.pmacs.upenn.edu/explore/workflow/islet-molecular-phenotyping-studies?protocol=5
PMID:31127054, PMID:36206763
accessible DNA
released
single-cell ATAC-seq (snATAC-seq)
Homo sapiens
ff84d1c0-4b3c-472b-af65-8b3827f7d01d
Supported by National Institutes of Health (NIH) grants U24 DK138515, U24 DK138512
Supplemental funds from the NIH Office of Data Science Strategies
Supplemental funds from the NIH Office of Data Science Strategies