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GEO accession:
Series GSE153520
Query DataSets for GSE153520
Status
Public on Jun 30, 2020
Title
Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection [ATAC-seq]
Organism
Homo sapiens
Experiment type
Genome binding/occupancy profiling by high throughput sequencing
Summary
ATAC-seq and RNA-seq of primary human neutrophils challenged with multiple pathogen mimicking ligands and whole organisms.
Overall design
ATAC-seq profiles of neutrophils in response to various pathogen ligands and whole organisms
**Please note that the processed *bed files were replaced on March 1, 2021**
Contributor(s)
Yang S
,
Ram Mohan N
,
Thair S
Citation(s)
34145026
BioProject
PRJNA636835
Submission date
Jun 29, 2020
Last update date
Aug 11, 2021
Contact name
Samuel Yang
Organization name
Stanford University School of Medicine
Department
Emergency Medicine
Street address
1201 Welch Road
City
Palo Alto
State/province
CA
ZIP/Postal code
94305
Country
USA
Platforms (1)
GPL20795
HiSeq X Ten (Homo sapiens)
Samples (76)
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GSM4646355
BGP challenge Donor 1-1
GSM4646356
BGP challenge Donor 1-2
GSM4646357
Control Donor 1-1
GSM4646358
Control Donor 1-2
GSM4646359
FLAG challenge Donor 1-1
GSM4646360
FLAG challenge Donor 1-2
GSM4646361
HMGB1 challenge Donor 1-1
GSM4646362
HMGB1 challenge Donor 1-2
GSM4646363
LPS challenge Donor 1-1
GSM4646364
LPS challenge Donor 1-2
GSM4646365
LTA challenge Donor 1-1
GSM4646366
LTA challenge Donor 1-2
GSM4646367
R848 challenge Donor 1-1
GSM4646368
R848 challenge Donor 1-2
GSM4646369
Whole Blood Donor 1-1
GSM4646370
Whole Blood Donor 1-2
GSM4646371
SA challenge 10^1 Donor 1-1
GSM4646372
SA challenge 10^1 Donor 1-2
GSM4646373
SA challenge 10^3 Donor 1-1
GSM4646374
SA challenge 10^3 Donor 1-2
GSM4646375
SA challenge 10^5 Donor 1-1
GSM4646376
SA challenge 10^5 Donor 1-2
GSM4646377
EC 1h challenge Donor 1-1
GSM4646378
EC 1h challenge Donor 1-2
GSM4646379
EC 4h challenge Donor 1-1
GSM4646380
EC 4h challenge Donor 1-2
GSM4646381
noEC 1h challenge Donor 1-1
GSM4646382
noEC 1h challenge Donor 1-2
GSM4646383
noEC 4h challenge Donor 1-1
GSM4646384
noEC 4h challenge Donor 1-2
GSM4646385
BGP challenge Donor 2-1
GSM4646386
BGP challenge Donor 2-2
GSM4646387
Control Donor 2-1
GSM4646388
Control Donor 2-2
GSM4646389
FLAG challenge Donor 2-1
GSM4646390
FLAG challenge Donor 2-2
GSM4646391
HMGB1 challenge Donor 2-1
GSM4646392
HMGB1 challenge Donor 2-2
GSM4646393
LPS challenge Donor 2-1
GSM4646394
LPS challenge Donor 2-2
GSM4646395
LTA challenge Donor 2-1
GSM4646396
LTA challenge Donor 2-2
GSM4646397
R848 challenge Donor 2-1
GSM4646398
R848 challenge Donor 2-2
GSM4646399
Whole Blood Donor 2-1
GSM4646400
Whole Blood Donor 2-2
GSM4646401
SA challenge 10^3 Donor 2-1
GSM4646402
SA challenge 10^3 Donor 2-2
GSM4646403
BGP challenge Donor 3-1
GSM4646404
BGP challenge Donor 3-2
GSM4646405
Control Donor 3-1
GSM4646406
Control Donor 3-2
GSM4646407
FLAG challenge Donor 3-1
GSM4646408
FLAG challenge Donor 3-2
GSM4646409
HMGB1 challenge Donor 3-1
GSM4646410
HMGB1 challenge Donor 3-2
GSM4646411
LPS challenge Donor 3-1
GSM4646412
LPS challenge Donor 3-2
GSM4646413
LTA challenge Donor 3-1
GSM4646414
LTA challenge Donor 3-2
GSM4646415
R848 challenge Donor 3-1
GSM4646416
R848 challenge Donor 3-2
GSM4646417
BGP challenge Donor 4-1
GSM4646418
BGP challenge Donor 4-2
GSM4646419
Control Donor 4-1
GSM4646420
Control Donor 4-2
GSM4646421
FLAG challenge Donor 4-1
GSM4646422
FLAG challenge Donor 4-2
GSM4646423
HMGB1 challenge Donor 4-1
GSM4646424
HMGB1 challenge Donor 4-2
GSM4646425
LPS challenge Donor 4-1
GSM4646426
LPS challenge Donor 4-2
GSM4646427
LTA challenge Donor 4-1
GSM4646428
LTA challenge Donor 4-2
GSM4646429
R848 challenge Donor 4-1
GSM4646430
R848 challenge Donor 4-2
This SubSeries is part of SuperSeries:
GSE153522
Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection
Relations
SRA
SRP265675
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
GSE153520_BGP_Merged_peaks_coverage.bed.gz
246.1 Kb
(ftp)
(http)
BED
GSE153520_CL_Merged_peaks_coverage.bed.gz
311.2 Kb
(ftp)
(http)
BED
GSE153520_EC_1h_peaks_coverage.bed.gz
227.5 Kb
(ftp)
(http)
BED
GSE153520_EC_4h_peaks_coverage.bed.gz
141.1 Kb
(ftp)
(http)
BED
GSE153520_FLAG_Donor_Merged_peaks_coverage.bed.gz
438.0 Kb
(ftp)
(http)
BED
GSE153520_HMGB_Merged_peaks_coverage.bed.gz
545.0 Kb
(ftp)
(http)
BED
GSE153520_LPS_Merged_peaks_coverage.bed.gz
262.9 Kb
(ftp)
(http)
BED
GSE153520_LTA_Merged_peaks_coverage.bed.gz
279.0 Kb
(ftp)
(http)
BED
GSE153520_R848_Merged_peaks_coverage.bed.gz
434.4 Kb
(ftp)
(http)
BED
GSE153520_SA_peaks_coverage.bed.gz
127.5 Kb
(ftp)
(http)
BED
GSE153520_WB-SA_peaks_coverage.bed.gz
56.8 Kb
(ftp)
(http)
BED
GSE153520_noEC_1h_peaks_coverage.bed.gz
161.5 Kb
(ftp)
(http)
BED
GSE153520_noEC_4h_peaks_coverage.bed.gz
109.2 Kb
(ftp)
(http)
BED
SRA Run Selector
Raw data are available in SRA
Processed data are available on Series record
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