title: Heart_Male_8 weeks_BS [207097260027_R01C02]

description:
Mouse_ID:ZM20
207097260027_R01C02


title: Heart_Male_8 weeks_bACE [207097260027_R06C01]

status: Public on Sep 26 2025

type: genomic

city: Phialdelphia

first: Wanding

last: Zhou

state: Pennsylvania

address: 3501 Civic Center Blvd, Philadelphia, PA 19104, Colket Translational Research Building, 9300, Colket Translational Research Building

department: Pathology & Lab Medicine

country: USA

institute: Children's Hospital of Philadelphia

description:
Mouse_ID:ZM19
207097260027_R06C01

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.20
20250221_GEO_processed_matrix_GPL30650.csv = Normalized average Beta
20250221_GEO_signal_intensity_matrix_GPL30650.csv = Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Mus musculus

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Phenol/Chloroform/Isoamyl alcohol

tag: tissue

value: Heart

tag: gender

value: Male

tag: age

value: 8 weeks

value: bACE

value: Normal


title: Heart_Male_8 weeks_bACE [207097260027_R02C02]

description:
Mouse_ID:ZM20
207097260027_R02C02


title: Heart_Female_8 weeks_BS [207097260027_R03C02]

description:
Mouse_ID:ZM21
207097260027_R03C02

value: Female

value: BS


title: Subcortical_Brain_Female_76 weeks_bACE [207097260027_R04C01]

description:
Mouse_ID:ZM25
207097260027_R04C01

value: 76 weeks


title: Subcortical_Brain_Female_76 weeks_BS [207097260027_R03C01]

description:
Mouse_ID:ZM25
207097260027_R03C01


title: Subcortical_Brain_Male_76 weeks_bACE [207097260027_R02C01]

description:
Mouse_ID:ZM24
207097260027_R02C01


title: Subcortical_Brain_Male_76 weeks_bACE [207115410020_R06C02]

description:
Mouse_ID:ZM23
207115410020_R06C02


title: Subcortical_Brain_Male_76 weeks_BS [207115410020_R05C02]

description:
Mouse_ID:ZM23
207115410020_R05C02


title: Eye_Female_8 weeks_bACE [207115410020_R04C02]

description:
Mouse_ID:ZM21
207115410020_R04C02

value: Eye


title: Brain_Cortex_Female_76 weeks_bACE [207115410020_R02C02]

description:
Mouse_ID:ZM26
207115410020_R02C02


title: Brain_Cortex_Female_76 weeks_BS [207115410020_R01C02]

description:
Mouse_ID:ZM26
207115410020_R01C02


title: Eye_Female_8 weeks_BS [207115410020_R03C02]

description:
Mouse_ID:ZM21
207115410020_R03C02


title: Lung_Male_8 weeks_bACE [207363410131_R02C01]

description:
Mouse_ID:ZM20
207363410131_R02C01

value: Lung


title: Cerebellum_Female_76 weeks_bACE [207115410020_R06C01]

description:
Mouse_ID:ZM25
207115410020_R06C01

value: Cerebellum


title: Eye_Male_8 weeks_bACE [207115410020_R04C01]

description:
Mouse_ID:ZM19
207115410020_R04C01


title: Optic_Nerve_Female_76 weeks_bACE [207115410020_R02C01]

description:
Mouse_ID:ZM25
207115410020_R02C01


title: Brain_Cortex_Female_76 weeks_bACE [207115410021_R06C02]

description:
Mouse_ID:ZM25
207115410021_R06C02


title: Subcortical_Brain_Male_76 weeks_BS [207097260027_R01C01]

description:
Mouse_ID:ZM24
207097260027_R01C01


title: Heart_Female_8 weeks_bACE [207097260027_R06C02]

description:
Mouse_ID:ZM22
207097260027_R06C02


title: Eye_Male_8 weeks_BS [207115410020_R03C01]

description:
Mouse_ID:ZM19
207115410020_R03C01


title: Brain_Cortex_Female_76 weeks_BS [207115410021_R05C02]

description:
Mouse_ID:ZM25
207115410021_R05C02


title: Heart_Male_8 weeks_BS [207097260027_R05C01]

description:
Mouse_ID:ZM19
207097260027_R05C01


title: Optic_Nerve_Female_76 weeks_BS [207115410020_R01C01]

description:
Mouse_ID:ZM25
207115410020_R01C01


title: Cerebellum_Male_76 weeks_bACE [207115410021_R04C02]

description:
Mouse_ID:ZM24
207115410021_R04C02


title: Heart_Male_76 weeks_BS [207097260043_R03C02]

description:
Mouse_ID:ZM24
207097260043_R03C02


title: Optic_Nerve_Male_76 weeks_bACE [207115410021_R06C01]

description:
Mouse_ID:ZM24
207115410021_R06C01


title: Spleen_Female_8 weeks_BS [207115410021_R01C02]

description:
Mouse_ID:ZM8
207115410021_R01C02

value: Spleen


title: Optic_Nerve_Male_76 weeks_BS [207115410021_R05C01]

description:
Mouse_ID:ZM24
207115410021_R05C01


title: Brain_Cortex_Male_76 weeks_bACE [207115410021_R04C01]

description:
Mouse_ID:ZM24
207115410021_R04C01


title: Cerebellum_Male_76 weeks_bACE [207115410021_R02C01]

description:
Mouse_ID:ZM23
207115410021_R02C01


title: Brain_Cortex_Male_76 weeks_BS [207115410021_R03C01]

description:
Mouse_ID:ZM24
207115410021_R03C01


title: Cerebellum_Male_76 weeks_BS [207115410021_R01C01]

description:
Mouse_ID:ZM23
207115410021_R01C01


title: Optic_Nerve_Male_76 weeks_bACE [206975990025_R04C02]

description:
Mouse_ID:ZM23
206975990025_R04C02


title: Optic_Nerve_Male_76 weeks_BS [206975990025_R03C02]

description:
Mouse_ID:ZM23
206975990025_R03C02


title: Cerebellum_Female_8 weeks_BS [206975990025_R01C02]

description:
Mouse_ID:ZM22
206975990025_R01C02


title: Cerebellum_Female_8 weeks_bACE [206975990025_R02C02]

description:
Mouse_ID:ZM22
206975990025_R02C02


title: Cerebellum_Female_76 weeks_BS [207115410020_R05C01]

description:
Mouse_ID:ZM25
207115410020_R05C01


title: Optic_Nerve_Female_8 weeks_BS [206975990025_R03C01]

description:
Mouse_ID:ZM22
206975990025_R03C01


title: Heart_Female_76 weeks_BS [207097260043_R05C02]

description:
Mouse_ID:ZM25
207097260043_R05C02


title: Brain_Cortex_Female_8 weeks_BS [206975990025_R01C01]

description:
Mouse_ID:ZM22
206975990025_R01C01


title: Cerebellum_Female_8 weeks_bACE [206975990054_R06C02]

description:
Mouse_ID:ZM21
206975990054_R06C02


title: Optic_Nerve_Female_8 weeks_BS [206975990054_R01C02]

description:
Mouse_ID:ZM21
206975990054_R01C02


title: Optic_Nerve_Female_8 weeks_bACE [206975990054_R02C02]

description:
Mouse_ID:ZM21
206975990054_R02C02


title: Brain_Cortex_Female_8 weeks_bACE [206975990054_R06C01]

description:
Mouse_ID:ZM21
206975990054_R06C01


title: Cerebellum_Female_8 weeks_BS [206975990054_R05C02]

description:
Mouse_ID:ZM21
206975990054_R05C02


title: Spleen_Female_8 weeks_bACE [207115410021_R02C02]

description:
Mouse_ID:ZM8
207115410021_R02C02


title: Brain_Cortex_Female_8 weeks_BS [206975990054_R05C01]

description:
Mouse_ID:ZM21
206975990054_R05C01


title: Cerebellum_Male_76 weeks_BS [207115410021_R03C02]

description:
Mouse_ID:ZM24
207115410021_R03C02


title: Optic_Nerve_Male_8 weeks_bACE [207115410019_R06C02]

description:
Mouse_ID:ZM20
207115410019_R06C02


title: Optic_Nerve_Male_8 weeks_BS [207115410019_R05C02]

description:
Mouse_ID:ZM20
207115410019_R05C02


title: Lung_Female_76 weeks_bACE [206975990054_R02C01]

description:
Mouse_ID:ZM25
206975990054_R02C01


title: Eye_Female_76 weeks_bACE [206975990054_R04C01]

description:
Mouse_ID:ZM26
206975990054_R04C01


title: Brain_Cortex_Male_8 weeks_BS [207115410019_R03C02]

description:
Mouse_ID:ZM20
207115410019_R03C02


title: Eye_Female_76 weeks_BS [206975990054_R03C01]

description:
Mouse_ID:ZM26
206975990054_R03C01


title: Lung_Male_8 weeks_bACE [207115410019_R02C02]

description:
Mouse_ID:ZM19
207115410019_R02C02


title: Brain_Cortex_Male_8 weeks_bACE [207115410019_R04C02]

description:
Mouse_ID:ZM20
207115410019_R04C02


title: Optic_Nerve_Female_8 weeks_bACE [206975990025_R04C01]

description:
Mouse_ID:ZM22
206975990025_R04C01


title: Subcortical_Brain_Female_8 weeks_bACE [206402260030_R06C02]

description:
Mouse_ID:ZM22
206402260030_R06C02


title: Brain_Cortex_Male_8 weeks_bACE [207115410019_R04C01]

description:
Mouse_ID:ZM19
207115410019_R04C01


title: Optic_Nerve_Male_8 weeks_BS [207115410019_R05C01]

description:
Mouse_ID:ZM19
207115410019_R05C01


title: Optic_Nerve_Male_8 weeks_bACE [207115410019_R06C01]

description:
Mouse_ID:ZM19
207115410019_R06C01


title: Brain_Cortex_Male_8 weeks_BS [207115410019_R03C01]

description:
Mouse_ID:ZM19
207115410019_R03C01


title: Subcortical_Brain_Male_8 weeks_bACE [206402260030_R02C02]

description:
Mouse_ID:ZM20
206402260030_R02C02


title: Brain_Cortex_Female_8 weeks_bACE [206975990025_R02C01]

description:
Mouse_ID:ZM22
206975990025_R02C01


title: Subcortical_Brain_Female_8 weeks_bACE [206402260030_R04C02]

description:
Mouse_ID:ZM21
206402260030_R04C02


title: Subcortical_Brain_Female_8 weeks_BS [206402260030_R05C02]

description:
Mouse_ID:ZM22
206402260030_R05C02


title: Subcortical_Brain_Male_8 weeks_BS [206402260030_R01C02]

description:
Mouse_ID:ZM20
206402260030_R01C02


title: Subcortical_Brain_Male_8 weeks_bACE [206402260030_R04C01]

description:
Mouse_ID:ZM19
206402260030_R04C01


title: Subcortical_Brain_Male_8 weeks_BS [206402260030_R03C01]

description:
Mouse_ID:ZM19
206402260030_R03C01


title: Lung_Female_76 weeks_BS [206975990054_R01C01]

description:
Mouse_ID:ZM25
206975990054_R01C01


title: Cerebellum_Male_8 weeks_BS_ACEseq [206402260030_R05C01]

description:
Mouse_ID:ZM20
206402260030_R05C01


title: Cerebellum_Male_8 weeks_BS [206402260030_R01C01]

description:
Mouse_ID:ZM19
206402260030_R01C01


title: Cerebellum_Male_8 weeks_bACE_ACEseq [206402260030_R06C01]

description:
Mouse_ID:ZM20
206402260030_R06C01


title: Cerebellum_Male_8 weeks_bACE [206402260030_R02C01]

description:
Mouse_ID:ZM19
206402260030_R02C01


title: Testis_Male_76 weeks_bACE [206402260037_R06C02]

description:
Mouse_ID:ZM17
206402260037_R06C02

value: Testis


title: Testis_Male_76 weeks_BS [206402260037_R05C02]

description:
Mouse_ID:ZM17
206402260037_R05C02


title: Spleen_Male_16 weeks_bACE [206402260037_R02C02]

description:
Mouse_ID:ZM2
206402260037_R02C02

value: 16 weeks


title: Lung_Male_8 weeks_BS [207115410019_R01C02]

description:
Mouse_ID:ZM19
207115410019_R01C02


title: Sciatic_Nerve_Male_8 weeks_bACE [206402260037_R04C02]

description:
Mouse_ID:ZM7
206402260037_R04C02


title: Spleen_Male_16 weeks_BS [206402260037_R01C02]

description:
Mouse_ID:ZM2
206402260037_R01C02


title: Liver_Male_16 weeks_bACE [206402260037_R06C01]

description:
Mouse_ID:ZM2
206402260037_R06C01

value: Liver


title: Tail_Female_8 weeks_BS [206402260019_R05C02]

description:
Mouse_ID:ZM8
206402260019_R05C02

value: Tail


title: Optic_Nerve_Male_8 weeks_bACE [206402260019_R04C02]

description:
Mouse_ID:ZM7
206402260019_R04C02


title: Optic_Nerve_Male_8 weeks_BS [206402260019_R03C02]

description:
Mouse_ID:ZM7
206402260019_R03C02


title: Subcortical_Brain_Female_8 weeks_BS [206402260030_R03C02]

description:
Mouse_ID:ZM21
206402260030_R03C02


title: Liver_Male_20 weeks_bACE [206402260019_R06C01]

description:
Mouse_ID:ZM6
206402260019_R06C01

value: 20 weeks


title: Tail_Female_8 weeks_bACE [206402260019_R06C02]

description:
Mouse_ID:ZM8
206402260019_R06C02


title: Kidney_Female_8 weeks_BS [206402260019_R01C02]

description:
Mouse_ID:ZM8
206402260019_R01C02

value: Kidney


title: Liver_Male_16 weeks_BS [206402260037_R05C01]

description:
Mouse_ID:ZM2
206402260037_R05C01

value: Male


title: Colon_Male_20 weeks_BS [206402260019_R03C01]

description:
Mouse_ID:ZM6
206402260019_R03C01

value: Colon


title: Liver_Male_12 weeks_bACE [206402260019_R02C01]

description:
Mouse_ID:ZM5
206402260019_R02C01

value: 12 weeks

value: bACE


title: Colon_Male_20 weeks_bACE [206402260019_R04C01]

description:
Mouse_ID:ZM6
206402260019_R04C01

value: Normal


title: Liver_Male_12 weeks_BS [206402260019_R01C01]

description:
Mouse_ID:ZM5
206402260019_R01C01

value: BS


title: Liver_Male_20 weeks_BS [206402260019_R05C01]

description:
Mouse_ID:ZM6
206402260019_R05C01


title: Liver_Male_12 weeks_bACE [206130600024_R06C02]

description:
Mouse_ID:ZM4
206130600024_R06C02


title: Liver_Male_12 weeks_BS [206130600024_R05C02]

description:
Mouse_ID:ZM4
206130600024_R05C02


title: Femur_Male_8 weeks_bACE [206130600024_R04C02]

description:
Mouse_ID:ZM7
206130600024_R04C02

value: Femur

value: 8 weeks


title: Femur_Male_8 weeks_BS [206130600024_R03C02]

description:
Mouse_ID:ZM7
206130600024_R03C02


title: Sciatic_Nerve_Male_8 weeks_BS [206402260037_R03C02]

description:
Mouse_ID:ZM7
206402260037_R03C02


title: Kidney_Male_12 weeks_bACE [206130600024_R02C02]

description:
Mouse_ID:ZM5
206130600024_R02C02


title: Kidney_Male_12 weeks_BS [206130600024_R01C02]

description:
Mouse_ID:ZM5
206130600024_R01C02


title: Liver_Female_27 weeks_bACE [206130600024_R02C01]

description:
Mouse_ID:ZM3
206130600024_R02C01

source_name: C57BL/6J_Germ-Free, cecum twisted, the mouse is weak and dying

value: Female

value: 27 weeks


title: Colon_Male_12 weeks_bACE [206130600024_R04C01]

description:
Mouse_ID:ZM4
206130600024_R04C01


title: Colon_Female_27 weeks_bACE [206130600019_R06C02]

description:
Mouse_ID:ZM3
206130600019_R06C02


title: Liver_Female_27 weeks_BS [206130600024_R01C01]

description:
Mouse_ID:ZM3
206130600024_R01C01


title: Colon_Female_27 weeks_BS [206130600019_R05C02]

description:
Mouse_ID:ZM3
206130600019_R05C02


title: Blood_Female_36 weeks_BS [206130600019_R01C02]

description:
Mouse_ID:ZM14
206130600019_R01C02

value: Blood

value: 36 weeks


title: Blood_Female_36 weeks_bACE [206130600019_R02C02]

description:
Mouse_ID:ZM14
206130600019_R02C02


title: Kidney_Female_8 weeks_bACE [206402260019_R02C02]

description:
Mouse_ID:ZM8
206402260019_R02C02


title: Liver_Male_16 weeks_BS [206130600019_R03C02]

description:
Mouse_ID:ZM1
206130600019_R03C02

value: 16 weeks


title: Sciatic_Nerve_Female_8 weeks_bACE [206130600019_R02C01]

description:
Mouse_ID:ZM8
206130600019_R02C01


title: Optic_Nerve_Female_8 weeks_bACE [206130600019_R04C01]

description:
Mouse_ID:ZM8
206130600019_R04C01


title: Sciatic_Nerve_Female_8 weeks_BS [206130600019_R01C01]

description:
Mouse_ID:ZM8
206130600019_R01C01


title: Retina_Female_8 weeks_bACE [206130600021_R04C02]

description:
Mouse_ID:ZM8
206130600021_R04C02

value: Retina


title: Thymus_Female_8 weeks_bACE [206130600021_R06C02]

description:
Mouse_ID:ZM8
206130600021_R06C02

value: Thymus


title: Thymus_Female_8 weeks_BS [206130600021_R05C02]

description:
Mouse_ID:ZM8
206130600021_R05C02


title: Colon_Male_12 weeks_BS [206130600024_R03C01]

description:
Mouse_ID:ZM4
206130600024_R03C01


title: Retina_Female_8 weeks_BS [206130600021_R03C02]

description:
Mouse_ID:ZM8
206130600021_R03C02


title: Femur_Female_8 weeks_bACE [206130600021_R02C02]

description:
Mouse_ID:ZM8
206130600021_R02C02


title: Colon_Male_16 weeks_bACE [206130600021_R04C01]

description:
Mouse_ID:ZM1
206130600021_R04C01


title: Optic_Nerve_Female_8 weeks_BS [206130600019_R03C01]

description:
Mouse_ID:ZM8
206130600019_R03C01


title: Femur_Female_8 weeks_BS [206130600021_R01C02]

description:
Mouse_ID:ZM8
206130600021_R01C02


title: Bile_Duct_Female_8 weeks_bACE [206130600021_R06C01]

description:
Mouse_ID:ZM8
206130600021_R06C01


title: Liver_Male_16 weeks_bACE [206130600019_R04C02]

description:
Mouse_ID:ZM1
206130600019_R04C02

value: Liver


title: Liver_Male_52 weeks_bACE [206130600021_R02C01]

description:
Mouse_ID:ZM15
206130600021_R02C01

value: 52 weeks


title: Liver_Male_52 weeks_BS [206130600021_R01C01]

description:
Mouse_ID:ZM15
206130600021_R01C01

value: Male


title: Colon_Male_12 weeks_bACE [206130600039_R06C01]

description:
Mouse_ID:ZM5
206130600039_R06C01

value: Colon


title: Bile_Duct_Female_8 weeks_BS [206130600021_R05C01]

description:
Mouse_ID:ZM8
206130600021_R05C01


title: Colon_Male_16 weeks_BS [206130600021_R03C01]

description:
Mouse_ID:ZM1
206130600021_R03C01


title: Kidney_Female_27 weeks_BS [206130600039_R05C02]

description:
Mouse_ID:ZM3
206130600039_R05C02

value: Kidney


title: Kidney_Female_27 weeks_bACE [206130600039_R06C02]

description:
Mouse_ID:ZM3
206130600039_R06C02

value: bACE


title: Colon_Male_12 weeks_BS [206130600039_R05C01]

description:
Mouse_ID:ZM5
206130600039_R05C01

value: 12 weeks

value: Normal


title: Liver_Female_24 weeks_bACE [206130600039_R04C01]

description:
Mouse_ID:ZM12
206130600039_R04C01

value: 24 weeks


title: Adrenal_Male_8 weeks_BS [206130600039_R01C01]

description:
Mouse_ID:ZM7
206130600039_R01C01

value: Adrenal

value: 8 weeks

value: BS


title: Adrenal_Male_8 weeks_bACE [206130600039_R02C01]

description:
Mouse_ID:ZM7
206130600039_R02C01


title: Brain_Cortex_Male_12 weeks_bACE [206402260035_R06C02]

description:
Mouse_ID:ZM5
206402260035_R06C02


title: Tail_Male_16 weeks_bACE [206402260035_R04C02]

description:
Mouse_ID:ZM2
206402260035_R04C02

value: Tail


title: Tail_Male_16 weeks_BS [206402260035_R03C02]

description:
Mouse_ID:ZM2
206402260035_R03C02


title: Blood_Male_12 weeks_bACE [206402260035_R02C02]

description:
Mouse_ID:ZM9
206402260035_R02C02

value: Blood


title: Blood_Male_12 weeks_BS [206402260035_R01C02]

description:
Mouse_ID:ZM9
206402260035_R01C02


title: Mammary_Glands_Female_8 weeks_bACE [206402260035_R06C01]

description:
Mouse_ID:ZM8
206402260035_R06C01

value: Female


title: Mammary_Glands_Female_8 weeks_BS [206402260035_R05C01]

description:
Mouse_ID:ZM8
206402260035_R05C01


title: Heart_Female_8 weeks_BS [206402260035_R03C01]

description:
Mouse_ID:ZM8
206402260035_R03C01

value: Heart


title: Liver_Male_12 weeks_bACE [206402260035_R02C01]

description:
Mouse_ID:ZM9
206402260035_R02C01


title: Liver_Male_12 weeks_BS [206402260035_R01C01]

description:
Mouse_ID:ZM9
206402260035_R01C01


title: Blood_Male_76 weeks_bACE [206402260003_R06C02]

description:
Mouse_ID:ZM17
206402260003_R06C02

value: 76 weeks


title: Bile_Duct_Male_8 weeks_BS [206402260031_R01C01]

description:
Mouse_ID:ZM7
206402260031_R01C01


title: Liver_Female_8 weeks_bACE [206402260031_R04C01]

description:
Mouse_ID:ZM8
206402260031_R04C01

value: Liver


title: Spleen_Male_12 weeks_bACE [206402260031_R06C02]

description:
Mouse_ID:ZM5
206402260031_R06C02

value: Spleen


title: Testis_Male_8 weeks_bACE [206402260031_R06C01]

description:
Mouse_ID:ZM7
206402260031_R06C01

value: Testis

value: Male


title: Brain_Cortex_Male_16 weeks_BS [206402260031_R01C02]

description:
Mouse_ID:ZM2
206402260031_R01C02

value: 16 weeks


title: Tail_Female_27 weeks_BS [206402260031_R03C02]

description:
Mouse_ID:ZM3
206402260031_R03C02

value: 27 weeks


title: Testis_Male_8 weeks_BS [206402260031_R05C01]

description:
Mouse_ID:ZM7
206402260031_R05C01


title: Tail_Male_20 weeks_bACE [206402260003_R04C02]

description:
Mouse_ID:ZM6
206402260003_R04C02

value: 20 weeks

value: bACE


title: Spleen_Male_12 weeks_BS [206402260031_R05C02]

description:
Mouse_ID:ZM5
206402260031_R05C02

value: 12 weeks

value: Normal


title: Tail_Female_27 weeks_bACE [206402260031_R04C02]

description:
Mouse_ID:ZM3
206402260031_R04C02


title: Brain_Cortex_Male_16 weeks_bACE [206402260031_R02C02]

description:
Mouse_ID:ZM2
206402260031_R02C02


title: Blood_Male_76 weeks_BS [206402260003_R05C02]

description:
Mouse_ID:ZM17
206402260003_R05C02


title: Liver_Female_76 weeks_bACE [206402260003_R02C02]

description:
Mouse_ID:ZM18
206402260003_R02C02


title: Tail_Male_20 weeks_BS [206402260003_R03C02]

description:
Mouse_ID:ZM6
206402260003_R03C02


title: OCSCC patient 8, tumor, CD45+ cells

type: SRA

city: Bethesda

first: Clint

middle: Tanner

last: Allen

state: MD

address: 10 Center Drive, Room 7N240C

department: NIDCD

institute: NIH

description: Library name: HNSCC_8_Tumor

library_source: transcriptomic single cell

data_processing:
The quality of sequencing reads was assessed using FastQC and MultiQC. Demultiplexed FASTQ files were processed with Cell Ranger (v7.1.0, 10x Genomics) using default parameters to align reads to the human reference genome GRCh38 and generate per-sample gene expression matrices of unique molecular identifier (UMI) counts. The resulting gene-barcode matrices were imported into Seurat (v4.0.1, R package) for quality control and downstream analysis. Cells were excluded if they met any of the following criteria: (1) fewer than 200 or more than 5000 detected genes, (2) greater than 20% reads mapping to mitochondrial genes, or (3) fewer than 400 or more than 20,000 detected UMIs, indicating potential low-quality cells or doublets. Remaining high-quality cells were normalized using the NormalizeData function (method = "LogNormalize", scale.factor = 10,000). Highly variable genes (n = 2,000) were identified using the FindVariableFeatures function with the "vst" method. Data were scaled and centered with ScaleData. Dimensionality reduction was performed by principal component analysis (PCA) using the top 30 principal components. These components were used to construct a shared nearest-neighbor (SNN) graph (FindNeighbors) and define clusters (FindClusters). Cell type annotation was performed using SingleR (v1.8.1), referencing the MonacoImmuneData() datasets. Non-neutrophils were removed from downstream analysis. For visualization, the uniform manifold approximation and projection (UMAP) algorithm was applied to project the cells into two-dimensional space.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
Whole peripheral blood was collected via venipuncture into EDTA vacutainers (BD) and processed immediately. Blood was diluted 1:1 in PBS and layered onto 15 mL Ficoll-Paque (Cytiva) for density gradient centrifugation (400 × g, 30 min, room temperature, no acceleration or brake). The distal fraction containing red blood cells (RBCs) and high-density neutrophils was harvested and subjected to two rounds of RBC depletion (STEMCELL) followed by one round of RBC lysis (BioLegend), according to manufacturer instructions. The intermediate buffy coat layer containing low-density mononuclear cells and neutrophils was collected and subjected to two rounds of platelet removal by dilution in PBS with 2% fetal bovine serum (FBS) and centrifugation (120 × g, 10 min, room temperature, no acceleration or brake). CD11b⁺ cells were isolated from both high-density and low-density blood fractions using positive magnetic selection. Tumor biopsies were transported from the operating room to the laboratory and processed immediately. Tissues were minced into <1 mm fragments and enzymatically and mechanically dissociated into single-cell suspensions using the Human Tumor Dissociation Kit and gentleMACS Dissociator (Miltenyi Biotec) following manufacturer protocols. CD45⁺ leukocytes were isolated from dissociated tumor suspensions using positive magnetic selection. Isolated cells were washed in PBS, filtered through 70 μm strainers, and assessed for viability and concentration using acridine orange/propidium iodide (AO/PI) staining on a Cellometer Auto 2000 (Nexcelom). Cells were adjusted to 1,000 cells/μL and loaded onto the 10x Genomics Chromium Controller with a target recovery of 8,000 cells per sample.
Cells were mixed with 5’ v2 or 3’ v3 Next GEM Kit reagents (10X Genomics) and single cells were captured along with barcoded gelbeads. Following reverse transcription, cDNA was amplified, and gene expression libraries were constructed according to the manufacturer’s recommendations. Each DNA library was loaded into a sequencing lane on a NovaSeq system (Illumina) and was sequenced with paired-end reads of 75 bp.

value: Tumor

tag: cell line

value: tissue

tag: cell type

value: CD45+ cells


title: Liver_Female_76 weeks_BS [206402260003_R01C02]

description:
Mouse_ID:ZM18
206402260003_R01C02

value: BS


title: Liver_Female_24 weeks_BS [206130600039_R03C01]

description:
Mouse_ID:ZM12
206130600039_R03C01

value: Female

value: 24 weeks


title: Skin_Female_36 weeks_bACE [206402260003_R06C01]

description:
Mouse_ID:ZM14
206402260003_R06C01

value: Skin

value: 36 weeks


title: Skin_Female_36 weeks_BS [206402260003_R05C01]

description:
Mouse_ID:ZM14
206402260003_R05C01


title: Brain_Cortex_Male_12 weeks_BS [206402260035_R05C02]

description:
Mouse_ID:ZM5
206402260035_R05C02


title: OCSCC patient 6, tumor, CD45+ cells

description: Library name: HNSCC_6_Tumor


title: OCSCC patient 5, tumor, CD45+ cells

description: Library name: HNSCC_5_Tumor


title: OCSCC patient 7, tumor, CD45+ cells

description: Library name: HNSCC_7_Tumor


title: Heart_Female_8 weeks_bACE [206402260035_R04C01]

description:
Mouse_ID:ZM8
206402260035_R04C01

value: Heart

value: 8 weeks


title: Liver_Female_8 weeks_BS [206402260031_R03C01]

description:
Mouse_ID:ZM8
206402260031_R03C01

value: Liver


title: Bile_Duct_Male_8 weeks_bACE [206402260031_R02C01]

description:
Mouse_ID:ZM7
206402260031_R02C01

value: Male


title: Kidney_Male_20 weeks_BS [206402260003_R01C01]

description:
Mouse_ID:ZM6
206402260003_R01C01

value: Kidney


title: Pancreas_Male_8 weeks_bACE [206402260065_R06C02]

description:
Mouse_ID:ZM7
206402260065_R06C02

value: Pancreas


title: OCSCC patient 3, tumor, CD45+ cells

description: Library name: HNSCC_3_Tumor


title: Brain_Cortex_Male_16 weeks_BS [206402260065_R05C01]

description:
Mouse_ID:ZM1
206402260065_R05C01

value: 16 weeks


title: Kidney_Male_8 weeks_bACE_ACEseq [206402260065_R04C02]

description:
Mouse_ID:ZM7
206402260065_R04C02

value: bACE


title: OCSCC patient 2, tumor, CD45+ cells

description: Library name: HNSCC_2_Tumor


title: OCSCC patient 8, peripheral blood, high density CD11b+ cells

description: Library name: HNSCC_8_PBMC_High

source_name: Peripheral blood

value: Peripheral blood

value: CD11b+ cells


title: OCSCC patient 6, peripheral blood, high density CD11b+ cells

description: Library name: HNSCC_6_PBMC_High

value: tissue


title: Kidney_Male_8 weeks_BS_ACEseq [206402260065_R03C02]

description:
Mouse_ID:ZM7
206402260065_R03C02

value: Normal


title: Kidney_Male_20 weeks_bACE [206402260003_R02C01]

description:
Mouse_ID:ZM6
206402260003_R02C01

value: 20 weeks


title: OCSCC patient 5, peripheral blood, high density CD11b+ cells

description: Library name: HNSCC_5_PBMC_High


title: OCSCC patient 1, tumor, CD45+ cells

description: Library name: HNSCC_1_Tumor

value: Tumor

value: CD45+ cells


title: OCSCC patient 4, peripheral blood, high density CD11b+ cells

description: Library name: HNSCC_4_PBMC_High


title: Skin_Male_76 weeks_bACE [206402260065_R04C01]

description:
Mouse_ID:ZM17
206402260065_R04C01

value: Skin

value: 76 weeks


title: Skin_Male_76 weeks_BS [206402260065_R03C01]

description:
Mouse_ID:ZM17
206402260065_R03C01

value: BS


title: Skin_Male_36 weeks_bACE [206402260033_R06C02]

description:
Mouse_ID:ZM13
206402260033_R06C02

value: 36 weeks


title: OCSCC patient 3, peripheral blood, high density CD11b+ cells

description: Library name: HNSCC_3_PBMC_High


title: Ears_Female_8 weeks_bACE [206402260033_R04C02]

description:
Mouse_ID:ZM8
206402260033_R04C02

value: Ears

value: Female

value: 8 weeks


title: Skin_Male_36 weeks_BS [206402260033_R05C02]

description:
Mouse_ID:ZM13
206402260033_R05C02

value: Male


title: OCSCC patient 8, peripheral blood, low density CD11b+ cells

description: Library name: HNSCC_8_PBMC_Low


title: OCSCC patient 4, tumor, CD45+ cells

description: Library name: HNSCC_4_Tumor


title: OCSCC patient 1, peripheral blood, high density CD11b+ cells

description: Library name: HNSCC_1_PBMC_High


title: OCSCC patient 2, peripheral blood, high density CD11b+ cells

description: Library name: HNSCC_2_PBMC_High


title: OCSCC patient 7, peripheral blood, low density CD11b+ cells

description: Library name: HNSCC_7_PBMC_Low


title: Ears_Female_8 weeks_BS [206402260033_R03C02]

description:
Mouse_ID:ZM8
206402260033_R03C02


title: Pancreas_Male_8 weeks_BS [206402260065_R05C02]

description:
Mouse_ID:ZM7
206402260065_R05C02

value: Pancreas


title: Urinary_Bladder_Male_8 weeks_BS [206402260033_R01C02]

description:
Mouse_ID:ZM7
206402260033_R01C02


title: OCSCC patient 6, peripheral blood, low density CD11b+ cells

description: Library name: HNSCC_6_PBMC_Low


title: Brain_Cortex_Male_16 weeks_bACE [206402260065_R06C01]

description:
Mouse_ID:ZM1
206402260065_R06C01

value: 16 weeks

value: bACE


title: OCSCC patient 7, peripheral blood, high density CD11b+ cells

description: Library name: HNSCC_7_PBMC_High

value: Peripheral blood

value: CD11b+ cells


title: Urinary_Bladder_Male_8 weeks_bACE [206402260033_R02C02]

description:
Mouse_ID:ZM7
206402260033_R02C02

value: Normal


title: Brain_Cortex_Male_8 weeks_BS [206402260033_R05C01]

description:
Mouse_ID:ZM7
206402260033_R05C01


title: Brain_Cortex_Male_8 weeks_bACE [206402260033_R06C01]

description:
Mouse_ID:ZM7
206402260033_R06C01


title: OCSCC patient 4, peripheral blood, low density CD11b+ cells

description: Library name: HNSCC_4_PBMC_Low

value: tissue


title: Diaphragm_Female_8 weeks_bACE [206402260033_R04C01]

description:
Mouse_ID:ZM8
206402260033_R04C01

value: Diaphragm


title: OCSCC patient 3, peripheral blood, low density CD11b+ cells

description: Library name: HNSCC_3_PBMC_Low


title: Lung_Female_8 weeks_bACE [206402260033_R02C01]

description:
Mouse_ID:ZM8
206402260033_R02C01

value: Lung


title: Diaphragm_Female_8 weeks_BS [206402260033_R03C01]

description:
Mouse_ID:ZM8
206402260033_R03C01


title: OCSCC patient 2, peripheral blood, low density CD11b+ cells

description: Library name: HNSCC_2_PBMC_Low


title: OCSCC patient 1, peripheral blood, low density CD11b+ cells

description: Library name: HNSCC_1_PBMC_Low


title: Healthy donor 5, peripheral blood, high density CD11b+ cells

description: Library name: HD_5_PBMC_High


title: Lung_Female_8 weeks_BS [206402260033_R01C01]

description:
Mouse_ID:ZM8
206402260033_R01C01


title: Healthy donor 4, peripheral blood, high density CD11b+ cells

description: Library name: HD_4_PBMC_High


title: Healthy donor 3, peripheral blood, high density CD11b+ cells

description: Library name: HD_3_PBMC_High


title: Skin_Female_76 weeks_BS [206402260061_R05C02]

description:
Mouse_ID:ZM18
206402260061_R05C02

value: Skin


title: Skin_Female_76 weeks_bACE [206402260061_R06C02]

description:
Mouse_ID:ZM18
206402260061_R06C02

value: 76 weeks


title: Healthy donor 2, peripheral blood, high density CD11b+ cells

description: Library name: HD_2_PBMC_High


title: Healthy donor 1, peripheral blood, high density CD11b+ cells

description: Library name: HD_1_PBMC_High


title: Thymus_Male_8 weeks_bACE [206402260061_R04C02]

description:
Mouse_ID:ZM7
206402260061_R04C02

value: Thymus


title: Thymus_Male_8 weeks_BS [206402260061_R03C02]

description:
Mouse_ID:ZM7
206402260061_R03C02

value: BS


title: Healthy donor 5, peripheral blood, low density CD11b+ cells

description: Library name: HD_5_PBMC_Low


title: Diaphragm_Male_8 weeks_bACE [206402260061_R02C02]

description:
Mouse_ID:ZM7
206402260061_R02C02


title: Diaphragm_Male_8 weeks_BS [206402260061_R01C02]

description:
Mouse_ID:ZM7
206402260061_R01C02


title: Healthy donor 4, peripheral blood, low density CD11b+ cells

description: Library name: HD_4_PBMC_Low


title: Healthy donor 2, peripheral blood, low density CD11b+ cells

description: Library name: HD_2_PBMC_Low


title: Healthy donor 3, peripheral blood, low density CD11b+ cells

description: Library name: HD_3_PBMC_Low


title: OCSCC patient 5, peripheral blood, low density CD11b+ cells

description: Library name: HNSCC_5_PBMC_Low


title: Brain_Cortex_Male_12 weeks_BS [206402260061_R03C01]

description:
Mouse_ID:ZM4
206402260061_R03C01

value: 12 weeks


title: Blood_Female_52 weeks_bACE [206402260061_R02C01]

description:
Mouse_ID:ZM16
206402260061_R02C01

value: Blood

value: Female

value: 52 weeks


title: Brain_Cortex_Male_12 weeks_bACE [206402260061_R04C01]

description:
Mouse_ID:ZM4
206402260061_R04C01

value: Male


title: Healthy donor 1, peripheral blood, low density CD11b+ cells

description: Library name: HD_1_PBMC_Low


title: Spleen_Female_27 weeks_bACE [206402260051_R06C02]

description:
Mouse_ID:ZM3
206402260051_R06C02

value: Spleen

value: 27 weeks


title: Blood_Female_52 weeks_BS [206402260061_R01C01]

description:
Mouse_ID:ZM16
206402260061_R01C01


title: Spleen_Female_27 weeks_BS [206402260051_R05C02]

description:
Mouse_ID:ZM3
206402260051_R05C02


title: Brain_Cortex_Female_27 weeks_bACE [206402260051_R04C02]

description:
Mouse_ID:ZM3
206402260051_R04C02

value: bACE


title: Brain_Cortex_Female_27 weeks_BS [206402260051_R03C02]

description:
Mouse_ID:ZM3
206402260051_R03C02


title: Kidney_Male_16 weeks_BS [206402260051_R01C02]

description:
Mouse_ID:ZM2
206402260051_R01C02

value: Kidney

value: 16 weeks


title: Skin_Male_52 weeks_BS [206402260051_R05C01]

description:
Mouse_ID:ZM15
206402260051_R05C01

value: Normal


title: Testis_Male_52 weeks_bACE [206402260051_R04C01]

description:
Mouse_ID:ZM15
206402260051_R04C01

value: Testis


title: Testis_Male_52 weeks_BS [206402260051_R03C01]

description:
Mouse_ID:ZM15
206402260051_R03C01


title: Blood_Male_52 weeks_bACE [206402260051_R02C01]

description:
Mouse_ID:ZM15
206402260051_R02C01


title: Blood_Male_52 weeks_BS [206402260051_R01C01]

description:
Mouse_ID:ZM15
206402260051_R01C01


title: Tail_Male_16 weeks_bACE [206402260027_R06C02]

description:
Mouse_ID:ZM1
206402260027_R06C02

value: Tail


title: Kidney_Male_16 weeks_bACE [206402260027_R04C02]

description:
Mouse_ID:ZM1
206402260027_R04C02


title: Tail_Male_16 weeks_BS [206402260027_R05C02]

description:
Mouse_ID:ZM1
206402260027_R05C02


title: Kidney_Male_16 weeks_BS [206402260027_R03C02]

description:
Mouse_ID:ZM1
206402260027_R03C02


title: Skin_Male_24 weeks_bACE [206402260027_R06C01]

description:
Mouse_ID:ZM11
206402260027_R06C01

value: Skin

value: 24 weeks


title: Skin_Male_24 weeks_BS [206402260027_R05C01]

description:
Mouse_ID:ZM11
206402260027_R05C01


title: Testis_Male_24 weeks_bACE [206402260027_R04C01]

description:
Mouse_ID:ZM11
206402260027_R04C01


title: Blood_Female_24 weeks_BS [206402260027_R01C02]

description:
Mouse_ID:ZM12
206402260027_R01C02


title: Liver_Male_24 weeks_bACE [206402260027_R02C01]

description:
Mouse_ID:ZM11
206402260027_R02C01

value: Liver


title: Testis_Male_24 weeks_BS [206402260027_R03C01]

description:
Mouse_ID:ZM11
206402260027_R03C01

value: BS


title: Pancreas_Female_8 weeks_bACE [206402260036_R06C02]

description:
Mouse_ID:ZM8
206402260036_R06C02

value: Pancreas

value: 8 weeks


title: Liver_Male_24 weeks_BS [206402260027_R01C01]

description:
Mouse_ID:ZM11
206402260027_R01C01


title: Skin_Female_8 weeks_BS [206402260036_R03C02]

description:
Mouse_ID:ZM8
206402260036_R03C02

value: Female


title: Skin_Female_8 weeks_bACE [206402260036_R04C02]

description:
Mouse_ID:ZM8
206402260036_R04C02


title: Pancreas_Female_8 weeks_BS [206402260036_R05C02]

description:
Mouse_ID:ZM8
206402260036_R05C02


title: Spinal_Cord_Female_8 weeks_bACE [206402260036_R02C02]

description:
Mouse_ID:ZM8
206402260036_R02C02


title: Urinary_Bladder_Female_8 weeks_bACE [206402260036_R06C01]

description:
Mouse_ID:ZM8
206402260036_R06C01


title: Spinal_Cord_Female_8 weeks_BS [206402260036_R01C02]

description:
Mouse_ID:ZM8
206402260036_R01C02


title: Kidney_Male_16 weeks_bACE [206402260051_R02C02]

description:
Mouse_ID:ZM2
206402260051_R02C02


title: Skin_Male_52 weeks_bACE [206402260051_R06C01]

description:
Mouse_ID:ZM15
206402260051_R06C01

value: 52 weeks


title: Urinary_Bladder_Female_8 weeks_BS [206402260036_R05C01]

description:
Mouse_ID:ZM8
206402260036_R05C01


title: Brain_Cortex_Female_8 weeks_bACE [206402260036_R04C01]

description:
Mouse_ID:ZM8
206402260036_R04C01


title: Brain_Cortex_Female_8 weeks_BS [206402260036_R03C01]

description:
Mouse_ID:ZM8
206402260036_R03C01


title: Colon_Female_8 weeks_BS [206402260036_R01C01]

description:
Mouse_ID:ZM8
206402260036_R01C01

value: Colon


title: Blood_Female_8 weeks_BS [206250300028_R05C02]

description:
Mouse_ID:ZM8
206250300028_R05C02

value: Blood


title: Mammary_Glands_Male_8 weeks_BS [206250300028_R03C02]

description:
Mouse_ID:ZM7
206250300028_R03C02

value: Male


title: Blood_Female_8 weeks_bACE [206250300028_R06C02]

description:
Mouse_ID:ZM8
206250300028_R06C02

value: bACE


title: Colon_Female_8 weeks_bACE [206402260036_R02C01]

description:
Mouse_ID:ZM8
206402260036_R02C01


title: Tail_Male_8 weeks_bACE [206250300028_R02C02]

description:
Mouse_ID:ZM7
206250300028_R02C02


title: Mammary_Glands_Male_8 weeks_bACE [206250300028_R04C02]

description:
Mouse_ID:ZM7
206250300028_R04C02


title: Spleen_Male_8 weeks_BS [206250300028_R05C01]

description:
Mouse_ID:ZM7
206250300028_R05C01

value: Spleen


title: Lung_Male_8 weeks_bACE [206250300028_R04C01]

description:
Mouse_ID:ZM7
206250300028_R04C01

value: Lung


title: Lung_Male_8 weeks_BS [206250300028_R03C01]

description:
Mouse_ID:ZM7
206250300028_R03C01

value: Normal


title: Liver_Male_8 weeks_bACE [206250300028_R02C01]

description:
Mouse_ID:ZM7
206250300028_R02C01


title: Blood_Female_24 weeks_bACE [206402260027_R02C02]

description:
Mouse_ID:ZM12
206402260027_R02C02


title: Liver_Male_8 weeks_BS [206250300028_R01C01]

description:
Mouse_ID:ZM7
206250300028_R01C01


title: Tail_Male_8 weeks_BS [206250300028_R01C02]

description:
Mouse_ID:ZM7
206250300028_R01C02


title: Spleen_Male_16 weeks_bACE [206250300036_R06C02]

description:
Mouse_ID:ZM1
206250300036_R06C02

value: 16 weeks


title: Spleen_Male_16 weeks_BS [206250300036_R05C02]

description:
Mouse_ID:ZM1
206250300036_R05C02


title: Blood_Female_76 weeks_bACE [206250300036_R04C02]

description:
Mouse_ID:ZM18
206250300036_R04C02

value: 76 weeks


title: Blood_Female_76 weeks_BS [206250300036_R03C02]

description:
Mouse_ID:ZM18
206250300036_R03C02


title: Liver_Female_36 weeks_bACE [206250300036_R06C01]

description:
Mouse_ID:ZM14
206250300036_R06C01

value: 36 weeks


title: Liver_Female_36 weeks_BS [206250300036_R05C01]

description:
Mouse_ID:ZM14
206250300036_R05C01


title: Skin_Female_12 weeks_bACE [206250300036_R04C01]

description:
Mouse_ID:ZM10
206250300036_R04C01

value: Skin

value: 12 weeks


title: Skin_Female_12 weeks_BS [206250300036_R03C01]

description:
Mouse_ID:ZM10
206250300036_R03C01

value: BS


title: Eye_Female_8 weeks_bACE [206250300036_R02C01]

description:
Mouse_ID:ZM8
206250300036_R02C01

value: Eye


title: Brain_Cortex_Male_20 weeks_bACE [206250300029_R06C02]

description:
Mouse_ID:ZM6
206250300029_R06C02

value: 20 weeks


title: Eye_Female_8 weeks_BS [206250300036_R01C01]

description:
Mouse_ID:ZM8
206250300036_R01C01

value: Female

value: 8 weeks


title: Liver_Male_76 weeks_bACE [206250300029_R02C02]

description:
Mouse_ID:ZM17
206250300029_R02C02

value: Liver


title: Brain_Cortex_Male_20 weeks_BS [206250300029_R05C02]

description:
Mouse_ID:ZM6
206250300029_R05C02


title: Tail_Male_12 weeks_BS [206250300029_R03C02]

description:
Mouse_ID:ZM4
206250300029_R03C02

value: Tail


title: Testis_Male_36 weeks_bACE [206250300029_R06C01]

description:
Mouse_ID:ZM13
206250300029_R06C01

value: Testis

value: Male


title: Spleen_Male_8 weeks_bACE [206250300028_R06C01]

description:
Mouse_ID:ZM7
206250300028_R06C01

value: Spleen

value: bACE


title: Liver_Male_76 weeks_BS [206250300029_R01C02]

description:
Mouse_ID:ZM17
206250300029_R01C02

value: Normal


title: Testis_Male_36 weeks_BS [206250300029_R05C01]

description:
Mouse_ID:ZM13
206250300029_R05C01


title: Skin_Male_8 weeks_bACE [206250300029_R04C01]

description:
Mouse_ID:ZM7
206250300029_R04C01


title: Heart_Male_8 weeks_bACE_ACEseq [206250300029_R02C01]

description:
Mouse_ID:ZM7
206250300029_R02C01

value: Heart


title: Skin_Male_8 weeks_BS [206250300029_R03C01]

description:
Mouse_ID:ZM7
206250300029_R03C01


title: Heart_Male_8 weeks_BS_ACEseq [206250300029_R01C01]

description:
Mouse_ID:ZM7
206250300029_R01C01


title: Tail_Male_12 weeks_bACE [206250300032_R06C02]

description:
Mouse_ID:ZM5
206250300032_R06C02


title: Tail_Male_12 weeks_BS [206250300032_R05C02]

description:
Mouse_ID:ZM5
206250300032_R05C02


title: Kidney_Male_12 weeks_bACE [206250300032_R04C02]

description:
Mouse_ID:ZM4
206250300032_R04C02

value: Kidney


title: Blood_Female_12 weeks_bACE [206250300032_R02C02]

description:
Mouse_ID:ZM10
206250300032_R02C02

value: Blood


title: Eye_Male_8 weeks_bACE [206250300032_R04C01]

description:
Mouse_ID:ZM7
206250300032_R04C01


title: Adrenal_Female_8 weeks_bACE [206250300032_R06C01]

description:
Mouse_ID:ZM8
206250300032_R06C01

value: Adrenal


title: Adrenal_Female_8 weeks_BS [206250300032_R05C01]

description:
Mouse_ID:ZM8
206250300032_R05C01


title: Colon_Male_8 weeks_BS [206250300032_R01C01]

description:
Mouse_ID:ZM7
206250300032_R01C01

value: Colon


title: Eye_Male_8 weeks_BS [206250300032_R03C01]

description:
Mouse_ID:ZM7
206250300032_R03C01

value: BS


title: Colon_Male_8 weeks_bACE [206250300032_R02C01]

description:
Mouse_ID:ZM7
206250300032_R02C01


title: Tail_Male_12 weeks_bACE [206250300029_R04C02]

description:
Mouse_ID:ZM4
206250300029_R04C02

value: 12 weeks


title: Spleen_Male_20 weeks_BS [206250300033_R05C02]

description:
Mouse_ID:ZM6
206250300033_R05C02

value: 20 weeks


title: Ears_Male_8 weeks_bACE [206250300033_R04C02]

description:
Mouse_ID:ZM7
206250300033_R04C02

value: Ears


title: Ears_Male_8 weeks_BS [206250300033_R03C02]

description:
Mouse_ID:ZM7
206250300033_R03C02

value: 8 weeks


title: Spleen_Male_20 weeks_bACE [206250300033_R06C02]

description:
Mouse_ID:ZM6
206250300033_R06C02


title: Skin_Female_52 weeks_BS [206250300033_R01C02]

description:
Mouse_ID:ZM16
206250300033_R01C02

value: Skin

value: Female

value: 52 weeks


title: Liver_Male_36 weeks_bACE [206250300033_R06C01]

description:
Mouse_ID:ZM13
206250300033_R06C01

value: Liver

value: Male

value: 36 weeks


title: Skin_Female_52 weeks_bACE [206250300033_R02C02]

description:
Mouse_ID:ZM16
206250300033_R02C02

value: bACE

value: Normal


title: Liver_Male_36 weeks_BS [206250300033_R05C01]

description:
Mouse_ID:ZM13
206250300033_R05C01


title: Skin_Female_24 weeks_bACE [206250300033_R04C01]

description:
Mouse_ID:ZM12
206250300033_R04C01

value: 24 weeks


title: Skin_Female_24 weeks_BS [206250300033_R03C01]

description:
Mouse_ID:ZM12
206250300033_R03C01


title: Testis_Male_12 weeks_BS [206250300033_R01C01]

description:
Mouse_ID:ZM9
206250300033_R01C01

value: Testis


title: Blood_Female_12 weeks_BS [206250300032_R01C02]

description:
Mouse_ID:ZM10
206250300032_R01C02

value: Blood


title: Testis_Male_12 weeks_bACE [206250300033_R02C01]

description:
Mouse_ID:ZM9
206250300033_R02C01


title: Blood_Male_8 weeks_bACE_ACEseq [206102340052_R04C02]

description:
Mouse_ID:ZM7
206102340052_R04C02


title: Liver_Female_52 weeks_bACE [206102340052_R02C02]

description:
Mouse_ID:ZM16
206102340052_R02C02


title: Kidney_Male_12 weeks_BS [206250300032_R03C02]

description:
Mouse_ID:ZM4
206250300032_R03C02

value: Kidney


title: Blood_Male_36 weeks_bACE [206102340052_R06C01]

description:
Mouse_ID:ZM13
206102340052_R06C01


title: Liver_Female_52 weeks_BS [206102340052_R01C02]

description:
Mouse_ID:ZM16
206102340052_R01C02

value: BS


title: Blood_Male_24 weeks_bACE [206102340052_R04C01]

description:
Mouse_ID:ZM11
206102340052_R04C01


title: Liver_Female_12 weeks_bACE [206102340052_R02C01]

description:
Mouse_ID:ZM10
206102340052_R02C01

value: 12 weeks


title: Blood_Male_24 weeks_BS [206102340052_R03C01]

description:
Mouse_ID:ZM11
206102340052_R03C01


title: Liver_Female_12 weeks_BS [206102340052_R01C01]

description:
Mouse_ID:ZM10
206102340052_R01C01


title: Male_Con_3_RNA

status: Public on Sep 25 2025

city: Bronx

first: Marija

last: Kundakovic

state: NY

address: 441 E. Fordham Road

department: Biological Sciences

institute: Fordham University

description: Library name: Male_Con_3_RNA

library_source: transcriptomic

data_processing:
Sequences were adapter-trimmed and aligned to the mouse reference genome (mm39) with the GENCODE M36 gtf file using STAR Aligner.
The aligned reads were assigned to gene counts using featureCounts and were collated into a count matrix.
Differential gene expression analysis was then performed using DESeq2 at significance level p-adj < 0.05.
Assembly: mm39
Supplementary files format and content: featureCounts output is a tab-separated file with columns correspondeng to gene id, chromosome, start  position, end position, strand, gene length, and the counts for the gene in the given sample.

molecule: nuclear RNA

source_name: bilateral ventral hippocampus

extract_protocol:
Animals were sacrificed by cervical dislocation and bilateral ventral hippocampi were rapidly dissected then flash frozen in liquid nitrogen. Total nuclei were extracted using sucrose gradient centrifugation. Neuronal (NeuN+) nuclei were isolated by fluorescence-activated nuclei sorting with anti-NeuN antibody conjugated to AlexaFluor 488 on a FACSAria instrument. Nuclei were direclty sorted into TRIzol. Following sorting of nuclei, chloroform was added to the sample and the aqueous phase was recovered. nucRNA was then isolated and purified using the RNeasy Micro kit (Qiagen). The quality of nucRNA was assessed using the Fragment Analyzer (Agilent), with each sample having RQN>7. nucRNA quantity was determined using the Qubit RNA High-Sensitivity assay (Thermo Fisher Scientific, Q32852).
All purified nucRNA was used to construct cDNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KK8560, KAPA Biosystems), following the manufacturer's instructions. rRNA was depleted from nucRNA samples using hybridization of DNA oligonucleotides complementary to rRNA followed by RNase H and DNase treatment. The efficiency of rRNA depletion was confirmed using the Bioanalyzer (Agilent) and with qRT-PCR amplification of the 28S rRNA transcript before and after RiboErase treatment using the following primers: Forward, 5'-CCCATATCCGCAGCAGGTC-3'; Reverse, 5'-CCAGCCCTTAGAGCCAATCC-3';. rRNA-depleted nucRNA was then fragmented at 94°C for 5 minutes in the presence of Mg2+, followed by first and second strand cDNA synthesis and A-tailing. After ligation of KAPA dual-indexed adapters (KK8722), each library was amplified using 13-15 PCR cycles. Following a bead-based clean-up, the length of the libraries (365bp, on average) and their quality was assessed using the Bioanalyzer High-Sensitivity DNA Assay. The libraries were quantified with the Qubit HS DNA kit (Life Technologies, Q32851) and by qPCR (KAPA Biosystems, KK4873) prior to sequencing.

value: bilateral ventral hippocampus

tag: Sex

value: male

value: neuronal (NeuN+) nuclei

tag: genotype

tag: treatment

value: Scramble shRNA AAV


title: Male_Con_2_RNA

description: Library name: Male_Con_2_RNA


title: Male_KD_3_RNA

description: Library name: Male_KD_3_RNA

value: Egr1 shRNA AAV


title: Male_KD_2_RNA

description: Library name: Male_KD_2_RNA


title: Male_KD_1_RNA

description: Library name: Male_KD_1_RNA


title: Proestrus_Con_2_RNA

description: Library name: Proestrus_Con_2_RNA

value: proestrus female


title: Proestrus_KD_3_RNA

description: Library name: Proestrus_KD_3_RNA


title: Proestrus_Con_3_RNA

description: Library name: Proestrus_Con_3_RNA


title: Proestrus_KD_2_RNA

description: Library name: Proestrus_KD_2_RNA


title: Male_Con_3_ATAC

description: Library name: Male_Con_3_ATAC

library_source: genomic

data_processing:
Sequences were adapter trimmed and aligned to the mouse reference genome (mm39) using BWA-MEM software
The peak-calling was performed using MACS2.
Reads in peaks were counted using DiffBind
Differential accessibility analysis was performed using DESeq2
Assembly: mm39
Supplementary files format and content: Processed ATAC-seq data are supplied as .narrowPeak files. This is a 6 + 4 BED format with first 6 columns identical to BED format (chromosome, start coordinate, end coordinate, name, score, strand). The last 4 columns are narrowPeak-specific and contain the following information: Col 7 - signalValue (overall enrichment measure); Col 8 - pValue (-log10); Col 9 - qValue (-log10); Col 10 - point-source called for peak

extract_protocol:
Animals were sacrificed by cervical dislocation and bilateral ventral hippocampi were rapidly dissected then flash frozen in liquid nitrogen. Total nuclei were extracted using sucrose gradient centrifugation. Neuronal (NeuN+) nuclei were isolated by fluorescence-activated nuclei sorting with anti-NeuN antibody conjugated to AlexaFluor 488 on a FACSAria instrument.
Following FANS, nuclei were pelleted and resuspended in 50 µL of the transposase reaction mix including 25 µL of the 2xTD reaction buffer, 5 µL of transposase enzyme (Illumina Tagment DNA TDE1 kit, 20034197). We also included additional components: 16.5µl 0.1M PBS, 0.5µl 1% digitonin, and 0.5 µl 10% Tween-20, which were previously shown to enhance transposition efficiency. Transposition occurred at 37°C for 30 minutes and transposed DNA was purified using the MinElute PCR Purification Kit (Qiagen, 28004). Indexing libraries using Nextera i5 and i7 indexed amplification primers (Illumina XT index kit, 15055290) occurred alongside library amplification with NEBNext High-Fidelity PCR Master Mix (New England Biolabs, M0541S). The PCR reaction was carried out with the following conditions: 1 cycle of 72°C for 5 minutes and 98°C for 30 seconds; followed by 10 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. Amplified libraries were then purified using the MinElute PCR Purification Kit. Library quality was then assessed using the Bioanalyzer High-Sensitivity DNA Assay. The ATAC-seq libraries were quantified by Qubit HS DNA kit and by qPCR prior to sequencing.


title: Male_Con_2_ATAC

description: Library name: Male_Con_2_ATAC


title: Male_KD_3_ATAC

description: Library name: Male_KD_3_ATAC


title: Male_KD_2_ATAC

description: Library name: Male_KD_2_ATAC


title: Proestrus_Con_3_ATAC

description: Library name: Proestrus_Con_3_ATAC

tag: reproductive cycle_sex


title: Male_KD_1_ATAC

description: Library name: Male_KD_1_ATAC


title: Blood_Male_8 weeks_BS_ACEseq [206102340052_R03C02]

description:
Mouse_ID:ZM7
206102340052_R03C02

value: 8 weeks


title: Proestrus_Con_2_ATAC

description: Library name: Proestrus_Con_2_ATAC


title: Blood_Male_36 weeks_BS [206102340052_R05C01]

description:
Mouse_ID:ZM13
206102340052_R05C01

value: Male


title: Proestrus_Con_1_ATAC

description: Library name: Proestrus_Con_1_ATAC


title: Proestrus_KD_3_ATAC

description: Library name: Proestrus_KD_3_ATAC


title: Proestrus_KD_1_ATAC

description: Library name: Proestrus_KD_1_ATAC


title: Male_eGFP_3

data_processing:
Sequences were adapter-trimmed and aligned to the mouse reference genome (mm39) with the GENCODE M32 gtf file using STAR Aligner.
The gene counts produced by STAR were collated into a count matrix.
Differential gene expression analysis was then performed using DESeq2 at significance level p-adj < 0.05.
Assembly: mm39
Supplementary files format and content: .TAB files are tab-separated output files from STAR aligner with the following information: column 1- ensembl gene ID; column 2- counts for unstranded RNA-seq; column 3- counts for reads from forward strand of RNA; column 4-: counts for reads from reverse strand of RNA. Our RNA-seq libraries are strand-specific, and therefore column 4 was used as read counts per gene.

extract_protocol:
Animals were sacrificed by cervical dislocation and bilateral ventral hippocampi were rapidly dissected then flash frozen in liquid nitrogen. Total nuclei were extracted using sucrose gradient centrifugation. Neuronal (NeuN+) nuclei were isolated by fluorescence-activated nuclei sorting with anti-NeuN antibody conjugated to AlexaFluor 488 on a FACSAria instrument. Nuclei were direclty sorted into TRIzol. Following sorting of nuclei, chloroform was added to the sample and the aqueous phase was recovered. nucRNA was then isolated and purified using the RNeasy Micro kit (Qiagen). The quality of nucRNA was assessed using the Fragment Analyzer (Agilent), with each sample having RQN>7. nucRNA quantity was determined using the Qubit RNA High-Sensitivity assay (Thermo Fisher Scientific, Q32852).
All purified nucRNA (9-20 ng/sample) was used to construct cDNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KK8560, KAPA Biosystems), following the manufacturer's instructions. rRNA was depleted from nucRNA samples using hybridization of DNA oligonucleotides complementary to rRNA followed by RNase H and DNase treatment. The efficiency of rRNA depletion was confirmed using the Bioanalyzer (Agilent) and with qRT-PCR amplification of the 28S rRNA transcript before and after RiboErase treatment using the following primers: Forward, 5'-CCCATATCCGCAGCAGGTC-3'; Reverse, 5'-CCAGCCCTTAGAGCCAATCC-3';. rRNA-depleted nucRNA was then fragmented at 94°C for 5 minutes in the presence of Mg2+, followed by first and second strand cDNA synthesis and A-tailing. After ligation of KAPA dual-indexed adapters (KK8722), each library was amplified using 13-14 PCR cycles. Following a bead-based clean-up, the length of the libraries (365bp, on average) and their quality was assessed using the Bioanalyzer High-Sensitivity DNA Assay. The libraries were quantified with the Qubit HS DNA kit (Life Technologies, Q32851) and by qPCR (KAPA Biosystems, KK4873) prior to sequencing.

value: NeuN+ Nuclei

tag: strain

value: 10 weeks

tag: gonadal-status

value: Intact


title: Female_Egr1_3

value: Female

value: Ovariectomized at 4 weeks


title: Male_Egr1_3


title: Male_Con_1_RNA

description: Library name: Male_Con_1_RNA


title: Female_eGFP_3


title: Female_Egr1_2


title: Proestrus_Con_1_RNA

description: Library name: Proestrus_Con_1_RNA


title: Proestrus_KD_1_RNA

description: Library name: Proestrus_KD_1_RNA


title: Male_eGFP_1


title: Female_eGFP_2


title: Female_Egr1_1


title: Male_Egr1_2


title: Male_Con_1_ATAC

description: Library name: Male_Con_1_ATAC


title: Male_Egr1_1


title: eGFP_Male_4

data_processing:
Sequences were adapter trimmed and aligned to the mouse reference genome (mm39) using BWA-MEM software
Bam files were down-sampled prior to peak-calling to ensure a comparable number of reads for each sample.
The peak-calling was performed using MACS2.
High confidence peaks were then selected for downstream analysis by overlapping the replicates in each group (n = 4/group/sex) and continuing the analysis with peaks that were called in at least 3/4 replicates.
Peak annotation was performed using the annotatePeakInBatch function on UCSC.mm39.refGene annotation, and we identified overlapping peaks using the findOverlapsOfPeaks function of ChIPpeakAnno.
Assembly: mm39
Supplementary files format and content: Processed ATAC-seq data are supplied as .narrowPeak files. This is a 6 + 4 BED format with first 6 columns identical to BED format (chromosome, start coordinate, end coordinate, name, score, strand). The last 4 columns are narrowPeak-specific and contain the following information: Col 7 - signalValue (overall enrichment measure); Col 8 - pValue (-log10); Col 9 - qValue (-log10); Col 10 - point-source called for peak


title: Female_eGFP_1


title: Egr1_Male_4


title: eGFP_Female_3


title: Egr1_Male_3


title: Egr1_Female_3


title: Egr1_Female_4


title: eGFP_Male_3


title: Proestrus_KD_2_ATAC

description: Library name: Proestrus_KD_2_ATAC


title: Egr1_Male_2


title: eGFP_Male_2


title: Egr1_Female_2


title: eGFP_Female_2


title: eGFP_Male_1


title: Male_eGFP_2


title: Egr1_Female_1


title: scRNA-seq of tumor-infiltrating neutrophils from Egr1 knockout mice

description:
Library name: Sample_4_Egr1_KO
10x Genomics

data_processing:
The quality of sequencing reads was assessed using FastQC and MultiQC. Demultiplexed FASTQ files were processed with Cell Ranger (v8.0.1, 10x Genomics) using default parameters to align reads to the Mus musculus reference genome (mm10) and generate per-sample gene expression matrices of unique molecular identifier (UMI) counts. Due to the low RNA content of neutrophils, adjusted cell calling thresholds (--force-cells) were applied based on barcode knee plots to recover low-UMI neutrophil populations. The resulting gene-barcode matrices were imported into Seurat (v4.0.1, R package) for quality control and downstream analysis. Cells were excluded if they met any of the following criteria: (1) fewer than 200 or more than 5000 detected genes, (2) greater than 20% reads mapping to mitochondrial genes, or (3) fewer than 400 or more than 20,000 detected UMIs, indicating potential low-quality cells or doublets. Remaining high-quality cells were normalized using the NormalizeData function (method = "LogNormalize", scale.factor = 10,000). Highly variable genes (n = 2,000) were identified using the FindVariableFeatures function with the "vst" method. Data were scaled and centered with ScaleData. Dimensionality reduction was performed by principal component analysis (PCA) using the top 30 principal components. These components were used to construct a shared nearest-neighbor (SNN) graph (FindNeighbors) and define clusters (FindClusters). For visualization, the uniform manifold approximation and projection (UMAP) algorithm was applied to project the cells into two-dimensional space. Cell type annotation was performed using SingleR (v1.8.1), referencing the MouseRNAseq() datasets. Non-granulocytes were removed from downstream analysis.
Assembly: Mouse mm10
Supplementary files format and content: Gene–cell count matrix is included as an HDF5 file (raw_feature_bc_matrix.h5).
Supplementary files format and content: To ease downstream analysis and facilitate future re-analysis, a merged Seurat object (.rds file) containing filtered neutrophils and processed data from all samples is provided on the Series record.

extract_protocol:
Neutrophils were isolated from tumors by fluorescence-activated cell sorting (FACS). Cells were concentrated to 1,000 cells/μL in 1× PBS with 1% BSA and loaded into the Chromium Controller (10x Genomics) with a target recovery of ~8,000 cells per sample. Cells were partitioned with barcoded gel beads and reagents from the Chromium Next GEM Single Cell 3′ v3.1 chemistry (10x Genomics).
Following reverse transcription, cDNA was amplified, and gene expression libraries were constructed according to the Chromium Next GEM Single Cell 3′ v3.1 protocol (10x Genomics). Single-cell libraries were pooled and sequenced on an Illumina NextSeq 2000 P1 flowcell using a non-symmetric 28-cycle + 90-cycle paired-end configuration. All samples yielded >9 million reads per sample. Sequencing quality was high, with >93.9% of bases in the barcode regions, >92.2% of bases in the reads, and >95.6% of bases in the UMI regions reaching Q30 or above. Demultiplexing was performed allowing one mismatch in barcodes. Raw data were processed with Cell Ranger v8.0.1 using default parameters, with adjusted cell calling thresholds applied for neutrophils.

treatment_protocol: Mice were assigned to experimental groups representing vehicle control, trametinib treatment, Egr1 wild-type, or Egr1 knockout backgrounds. Trametinib-treated animals received pharmacologic MEK inhibition prior to tumor harvest.

value: Tumor

value: Neutrophils

value: Egr1 knock out


title: scRNA-seq of tumor-infiltrating neutrophils from Egr1 wild-type mice

description:
Library name: Sample_3_Egr1_WT
10x Genomics

value: wild type


title: scRNA-seq of tumor-infiltrating neutrophils from trametinib-treated mice

description:
Library name: Sample_2_WT_Trame
10x Genomics

value: Trametinib treatment


title: primary human hepatocytes,IL-1β 20ng/ml, bio rep 2 [S_24]

status: Public on Sep 22 2025

city: Cleveland

first: Xianfang

last: Wu

state: Ohio

address: 9500 Euclid Avenue/NE20, Office NE2-308, Office NE2-308

department: Infection Biology

institute: Cleveland Clinic

data_processing:
Fastq files containing reads were quality-controlled with fastQC (https://bioinformatics.babraham.ac.uk/projects/fastqc/).
Assembly: The raw sequence reads from each replicate were aligned to the human genome GRCh38 with GENCODE annotation v30 using STAR aligner with quantMode mode to generate gene counts.
Supplementary files format and content: Gene and transcript expression levels (TPM and estimated counts) were quantified by pseudo-alignment using Salmon (v0.13.1) using the annotation from Ensembl v95 as the reference transcriptome. Differential gene expression analysis was then performed by the R software (v4.2.3) DESeq2 package according to its user guide.

molecule: total RNA

source_name: primary human hepatocytes,

extract_protocol:
Total RNA was extracted using PureLink RNA Mini Kit (Thermo Fisher) according to the manufacturer’s instruction.
RNA integrity and quantitation were determined using Agilent 2100 bioanalyzer. Oligo(dT) purified RNAs were used to construct stranded libraries, followed by quality control using Agilent 2100 bioanalyzer. Approximately 200ng of total RNA was used as input. Libraries were prepared according to Illumina's instructions for the TruSeq long Stranded mRNA LT Sample Prep Kit (Catalog IDs: RS-122-2101, RS-122-2102).
Paired-end Illumina sequencing was performed on the Illumina NovaSeq 6000 system to generate approximately 20 million reads per sample.

treatment_protocol: Experiments were performed in duplicates.

value: primary human hepatocytes,

value: IL-1beta 20ng/ml


title: primary human hepatocytes,IL-1β 20ng/ml, bio rep 1 [S_23]


title: primary human hepatocytes,IL-1β 10ng/ml, bio rep 1 [S_21]

value: IL-1beta 10ng/ml


title: primary human hepatocytes, BSA control, bio rep 1 [S_19]

value: BSA control


title: human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes,IL-1β 20ng/ml, bio rep 1 [S_17]


title: human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes,IL-1β 10ng/ml, bio rep 2 [S_16]


title: human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes,IL-1β 20ng/ml, bio rep 2 [S_18]


title: eGFP_Female_4

value: bilateral ventral hippocampus


title: primary human hepatocytes,IL-1β 10ng/ml, bio rep 2 [S_22]


title: primary human hepatocytes, BSA control, bio rep 2 [S_20]


title: human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes, BSA control, bio rep 1 [S_13]


title: scRNA-seq of tumor-infiltrating neutrophils from untreated control mice

description:
Library name: Sample_1_WT_Ctl
10x Genomics

value: control


title: Kidney, UUO 3d, ligated, SK1440

city: Zürich

first: Olga

middle: Maria

last: Lempke

address: Winterthurerstrasse 190

country: Switzerland

institute: Univeristy of Zurich

description:
Library name: Exp36_3d_SK1440_LIG
Fresh frozen tissue for Spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ranger to generate FASTQ files from BCL files.
Sequences were aligned to the mouse reference genome (mm10) using Space Ranger’s default settings.
Gene expression counts for RefSeq-annotated coding genes were quantified per cell using Space Ranger’s default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in matrix market exchange format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: aligned_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_impage.png: high-resolution image of tissue
Supplementary files format and content: tissue_lowres_impage.png: low-resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Kidney

extract_protocol:
Fixed kidney tissues were OCT embedded and frozen, 10 μm cryosections were cut using crytostat
Spatial transriptomics of mouse kidneys was performed according to the manufacturer's recommendations (Visium CytAssist for fixed frozen tissue; 10x Genomics, Pleasanton, CA, USA).

value: Kidney

tag: condition

value: Limb injury

value: roxadustat


title: Kidney, UUO 3d, ligated, SK1441

description:
Library name: Exp36_3d_SK1441_LIG
Fresh frozen tissue for Spatial transcriptomics sequencing


title: Kidney, UUO 7d, ligated, FG-4592/roxadustat, SK3753

description:
Library name: Exp44_7d_SK3753_LIG
Fresh frozen tissue for Spatial transcriptomics sequencing


title: Kidney, UUO 7d, ligated, FG-4592/roxadustat, SK3747

description:
Library name: Exp44_7d_SK3747_LIG
Fresh frozen tissue for Spatial transcriptomics sequencing


title: eGFP_Female_1

value: NeuN+ Nuclei

value: 10 weeks


title: Egr1_Male_1

value: Male

value: Intact


title: TacHetNeg_P14_BL_10Hz_2h_Exp2_OP115

status: Public on Sep 14 2025

city: Ramat Gan

first: Nissan

last: Yissachar

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

description: Library name: op 115

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt (v2.7); resulting reads shorter than 30 bp were discarded. Reads were mapped to the M. musculus reference genome GRCm39 using STAR (v2.7.3a), supplied with gene annotations downloaded from Ensembl (https://www.ensembl.org/index.html) (with the EndToEnd option and outFilterMismatchNoverLmax set to 0.04). Reads with the same UMI were removed with the PICARD MarkDuplicate tool using the BARCODE_TAG parameter. Expression levels for each gene were quantified using htseq-count (v0.11.2), using the gtf mentioned above. The pipeline was run using snakemake. The output was ~4 million reads per sample per Illumina NextSeq run. All three counts tables from the 3 independent sequencing runs were merged together, for a final sequencing depth of ~10-12 million reads per sample. All gene reads were converted from Ensembl ID to gene symbol (in case of multiple Ensembl ID that were assigned to the same gene, the sum of total counts was calculated and assigned to the corresponding gene symbol). Differential gene expression analysis was performed using DESeq2 (v1.36.0) R/bioconductor package.
Assembly: GRCm39
Supplementary files format and content: deseq2_normalized_count_2_10_Hz_BL_YL.csv
Supplementary files format and content: deseq2_normalized_count_10_Hz_BL_BL+Cram_YL.csv
Supplementary files format and content: deseq2_normalized_count_10_Hz_Tac_Het_Pos_Neg.csv

source_name: colon

extract_protocol:
Bulk RNA was extracted using the RNeasy Plus Universal Mini QIAGEN kit.
Libraries were prepared using a modified SMART-Seq2 protocol. In brief, 1 ng of purified RNA was taken for reverse transcription with Maxima Reverse Transcriptase (Life Technologies) and whole-transcription amplification (WTA) with KAPA HotStart HIFI 2× ReadyMix (Kapa Biosystems) for 20 cycles. WTA products were purified with Ampure XP beads (Beckman Coulter), quantified with the Qubit dsDNA HS Assay Kit (ThermoFisher), and assessed with a high-sensitivity DNA chip (Agilent). RNA-seq libraries were constructed from purified WTA products using the Nextera XT DNA Library Preparation Kit (Illumina).

value: colon

value: ChR2-EYFP +/- TAC-cre -/-

tag: time

value: 2 hours experiment

tag: freq (hrz)

value: 10 hz

tag: light

value: Blue light

value: M

tag: experiment


title: human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes, BSA control, bio rep 2 [S_14]


title: N991

description: Library name: S7

data_processing:
Sequencing reads were merged across lanes per sample and decompressed to obtain single FASTQ files using custom shell scripts. Quality control was performed with FastQC, and results were summarized using MultiQC. STAR was used to generate a genome index and align reads to the mouse reference genome (GRCm39). BAM files were sorted and indexed, and alignment quality was assessed with BamQC and MultiQC. Gene-level counts were obtained using HTSeq-count with the corresponding GTF annotation.
Assembly: GRCm39
Supplementary files format and content: deseq2_normalized_count_YL_NL.csv

extract_protocol:
Bulk RNA was extracted using the RNeasy Plus Universal Mini QIAGEN kit.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced on an Illumina NextSeq 500 using the High Output v2 kit (#FC-404-2005).

value: ChR2-EYFP +/+ ChAT-cre +/+

value: Yellow light

value: F


title: N993

description: Library name: S9


title: N998

description: Library name: S14

value: No light


title: N992

description: Library name: S8


title: N997

description: Library name: S13


title: Kidney, UUO 7d, contralateral, FG-4592/roxadustat, SK3753

description:
Library name: Exp44_7d_SK3753_CL
Fresh frozen tissue for Spatial transcriptomics sequencing

value: Kidney

value: Contralateral limb


title: TacHetPos_P14_BL_10Hz_2h_Exp2_OP112

description: Library name: op 112

value: ChR2-EYFP +/- TAC-cre +/-


title: TacHetPos_P14_BL_10Hz_2h_Exp2_OP110

description: Library name: op 110


title: TacHetNeg_P14_BL_10Hz_2h_Exp2_OP113

description: Library name: op 113


title: TacHetNeg_P14_BL_10Hz_2h_Exp2_OP111

description: Library name: op 111


title: TacHetPos_P14_BL_10Hz_2h_Exp2_OP109

description: Library name: op 109


title: TacHetNeg_P14_BL_10Hz_2h_Exp1_OP108

description: Library name: op 108


title: N999

description: Library name: S15


title: TacHetNeg_P14_BL_10Hz_2h_Exp1_OP104

description: Library name: op 104


title: ChATHomo_P14_BL_Med_10Hz_2h_Exp2_OP61

description: Library name: op 61

value: Media


title: TacHetPos_P14_BL_10Hz_2h_Exp1_OP107

description: Library name: op 107


title: TacHetPos_P14_BL_10Hz_2h_Exp1_OP105

description: Library name: op 105


title: human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes,IL-1β 10ng/ml, bio rep 1 [S_15]

value: IL-1beta 10ng/ml


title: ChATHomo_P14_BL_Med_10Hz_2h_Exp2_OP60

description: Library name: op 60


title: ChATHomo_P14_BL_Cram_10Hz_2h_Exp2_OP58

description: Library name: op 58

value: C. ramosum


title: ChATHomo_P14_YL_Med_10Hz_2h_Exp2_OP55

description: Library name: op 55


title: ChATHomo_P14_YL_Med_10Hz_2h_Exp2_OP56

description: Library name: op 56


title: ChATHomo_P14_BL_Cram_10Hz_2h_Exp2_OP59

description: Library name: op 59


title: ChATHomo_P14_BL_Cram_10Hz_2h_Exp2_OP57

description: Library name: op 57


title: ChATHomo_P14_BL_Cram_10Hz_2h_Exp1_OP51

description: Library name: op 51


title: ChATHomo_P14_BL_Cram_10Hz_2h_Exp1_OP50

description: Library name: op 50


title: ChATHomo_P14_BL_Med_10Hz_2h_Exp1_OP49

description: Library name: op 49


title: ChATHomo_P14_BL_Med_10Hz_2h_Exp1_OP48

description: Library name: op 48


title: ChATHomo_P14_BL_2Hz_2h_Exp2_OP29

description: Library name: op 29

value: 2 hz


title: ChATHomo_P14_YL_Med_10Hz_2h_Exp1_OP42

description: Library name: op 42

value: colon


title: ChATHomo_P14_BL_Med_10Hz_2h_Exp1_OP47

description: Library name: op 47


title: ChATHomo_P14_YL_Med_10Hz_2h_Exp1_OP41

description: Library name: op 41


title: ChATHomo_P14_BL_2Hz_2h_Exp2_OP28

description: Library name: op 28


title: ChATHomo_P14_BL_Cram_10Hz_2h_Exp1_OP52

description: Library name: op 52


title: ChATHomo_P14_BL_2Hz_2h_Exp2_OP27

description: Library name: op 27


title: ChATHomo_P14_BL_2Hz_2h_Exp2_OP26

description: Library name: op 26


title: ChATHomo_P14_YL_2Hz_2h_Exp2_OP24

description: Library name: op 24


title: ChATHomo_P14_YL_2Hz_2h_Exp2_OP23

description: Library name: op 23


title: ChATHomo_P14_YL_2Hz_2h_Exp2_OP22

description: Library name: op 22


title: ChATHomo_P14_YL_2Hz_2h_Exp2_OP21

description: Library name: op 21


title: ChATHomo_P14_BL_2Hz_2h_Exp1_OP19

description: Library name: op 19


title: ChATHomo_P14_BL_2Hz_2h_Exp1_OP20

description: Library name: op 20


title: ChATHomo_P14_BL_2Hz_2h_Exp1_OP18

description: Library name: op 18


title: ChATHomo_P14_BL_2Hz_2h_Exp2_OP25

description: Library name: op 25


title: ChATHomo_P14_YL_Med_10Hz_2h_Exp1_OP43

description: Library name: op 43


title: ChATHomo_P14_YL_2Hz_2h_Exp1_OP17

description: Library name: op 17


title: ChATHomo_P14_YL_2Hz_2h_Exp1_OP16

description: Library name: op 16


title: 604021_HS014_12_Yellow_light

description: Library name: 604021_HS014_12

data_processing:
Raw FASTQ files containing 16S rRNA gene sequences were processed using the QIIME2 pipeline (v2023.7.0). Sequences were imported into QIIME2 and were denoised using the DADA2 algorithm. For quality trimming, forward reads were truncated at 221 bp, reverse reads at 241 bp, and 13 bp were removed from the left of both forward and reverse reads. ASVs were aligned using the MAFFT program, and a phylogenetic tree was constructed with the FastTree algorithm. ASVs with fewer than 20 reads in total were removed. Taxonomic assignment was performed with the classify-sklearn naïve Bayes classifier in QIIME2, using the GreenGenes2 (v2022.10) reference database.
Assembly: Green Genes 2 database
Supplementary files format and content: species_level_relative_abundance.csv
Library strategy: 16S rRNA-seq

organism: feces metagenome

source_name: Feces

extract_protocol:
DNA was extracted from colonic content using the PureLink™ Microbiome DNA Purification Kit, as described by the manufacturer (A29790, Invitrogen).
Library preparation and sequencing were performed by HyLabs Ltd (Israel), using MiSeq platform (Illumina).

treatment_protocol: Luminal contents from ChAT-ChR2 colonic tissues were collected following 10Hz blue or yellow light stimulation in the ex vivo culture system. After two hours, microbial composition was profiled using 16S rDNA sequencing

value: Feces

tag: biology sample

value: mouse fecal sample

tag: frequency

tag: light activation

value: Yellow Light

tag: time (hr)

value: ChAT homo ChR2 homo

tag: littermates

value: B


title: 604021_HS014_11_Yellow_light

description: Library name: 604021_HS014_11

tag: tissue

tag: gender


title: 604021_HS014_9_Yellow_light

description: Library name: 604021_HS014_9

value: M

tag: genotype

value: A


title: 604021_HS014_8_Yellow_light

description: Library name: 604021_HS014_8

value: F


title: 604021_HS014_5_Blue_light

description: Library name: 604021_HS014_5

value: Blue Light


title: 604021_HS014_6_Blue_light

description: Library name: 604021_HS014_6


title: 604021_HS014_7_Yellow_light

description: Library name: 604021_HS014_7


title: 604021_HS014_3_Blue_light

description: Library name: 604021_HS014_3


title: 604021_HS014_1_Blue_light

description: Library name: 604021_HS014_1


title: Donor2

status: Public on Sep 04 2025

city: Chicago

first: Yudai

last: Miyashita

state: IL

address: Simpson Querrey 5-402-C 303 E Superior Street

department: Thoracic Surgery

institute: Northwestern Univesity

description: Library name: AB-23-16

data_processing:
Raw sequencing data were processed using Cell Ranger (version 8.0.1) for demultiplexing, alignment to the GRCh38 reference genome, and generation of gene-barcode matrices.
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: The processed data files include gene-barcode matrices (barcodes.tsv, features.tsv, matrix.mtx) and Seurat objects (RDS files) for downstream analysis.
Supplementary files format and content: Data are provided in TSV format for raw counts and RDS format for processed Seurat objects, including metadata, clustering information, and expression matrices.

source_name: Lung

extract_protocol:
Single-cell suspensions were prepared from human lung tissues using enzymatic digestion (collagenase and DNase) and mechanical dissociation to isolate viable single cells for downstream processing.
Single-cell RNA libraries were prepared using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3.1 following the manufacturer's protocols.

treatment_protocol: No specific treatments were applied for the study purpose. Patients received routine post-transplant clinical care, including immunosuppressive therapy, antibiotics, and other medications as clinically indicated.

value: Lung


title: CLAD2

description: Library name: AB-23-17


title: 604021_HS014_10_Yellow_light

description: Library name: 604021_HS014_10


title: E59 human metatarsal, digit 2, rep 6, MiSeq

status: Public on Aug 20 2025

city: Cambridge

first: Terence

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

description: Library name: FM2_early_rep6_miseq

data_processing:
concatenate reads
adapter trimming with NGmerge v0.3 -e 30
ribosomal read filtering with RiboDetector v0.2.7 -e rrna --chunk_size 512
Alignment to hg38 with STAR v2.7.1
Read counts generated with RSEM v1.3.3 --forward-prob 0
Differential expression calculated with DESeq2 v1.36.0
Assembly: hg38
Supplementary files format and content: RSEM output tab-delimited file with gene expression data, TPM, and FPKM

source_name: Metatarsal, digit II

growth_protocol: in vivo collected human autopod chondrocytes from E53-E74

extract_protocol:
Embryos were microdissected under a light microscope in 10% fetal bovine serum (FBS) in Dulbecco’s Modified Eagle Medium (DMEM) on ice. The pooled phalanges (proximal and distal for digit I; proximal, intermediate, and distal for digits II-V) and metapodials were collected separately for all digits in both the fore- and hind limbs. The right and left sides of each element were pooled together.. Each element was stripped of soft tissue and collected in a 2-ml tube containing 200 ul of TRIzol  and one 5-mm stainless steel bead. Each sample was then homogenized at 50 Hz for 2 min, followed by 1 min on ice, and a second homogenization at 50 Hz for 2 min. Samples were stored at -80˚C until RNA extraction was performed.  For each RNA extraction, samples were incubated at room temperature for 5 min and then centrifuged at 4˚C for 5 minutes at 12,000 x g. The supernatant was collected and transferred to a clean tube, to which 200 ul of chloroform was added per 1 ml of TRIzol. Each sample was then vortexed briefly and incubated at room temperature for 2 minutes before being transferred to a MaXtract tube  and centrifuged at 4˚C for 5 minutes at 12,000 x g. Following centrifugation, the aqueous phase was removed and transferred to a new microcentrifuge Eppendorf tube and an equal volume of 100% ethanol was added. After completion of this phenol-chloroform step, the RNA extraction continued using the Direct-zol RNA MicroPrep kit  following the manufacturer’s protocols and eluted in 15 ul of nuclease-free water. Samples were stored at -80˚C until library preparation. Aliquots of the samples were nanodropped to quantify the extracted RNA and to determine 260/230 and 260/280 values and then run on a HS RNA Tapestation tape to their determined their RNA integrity number (RIN) value. Only samples with RIN scores higher than 6 were used for subsequent steps so long as the average RIN for all tissues from that sample was greater than 7. Samples were then sent out for 7 rounds of sequencing on an Illumina MiSeq/NovaSeq 6000 at the Harvard Bauer Core in order to obtain ~30 million reads per sample.
Kapa mRNA HyperPrep Kit with 25 ng input volume

treatment_protocol: Human products of conception were collected from late first-trimester terminations through the Laboratory of Developmental Biology in full compliance with the ethical guidelines of the National Institutes of Health and with the approval of the University of Washington Institutional Review Boards for the collection and distribution of human tissues for research, and Harvard University for the receipt and use of such materials. The Laboratory of Developmental Biology obtained written consent from all tissue donors.

value: Metatarsal, digit II

tag: cell type

value: chondrocytes

tag: Sex

value: Female


title: E59 human foot phalanges, digit 3, rep 6, MiSeq

description: Library name: FP3_early_rep6_miseq

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: E59 human metatarsal, digit 5, rep 6, MiSeq

description: Library name: FM5_early_rep6_miseq

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: E59 human metatarsal, digit 3, rep 6, MiSeq

description: Library name: FM3_early_rep6_miseq

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: E59 human metatarsal, digit 4, rep 6, MiSeq

description: Library name: FM4_early_rep6_miseq

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E59 human metacarpal, digit 5, rep 6, MiSeq

description: Library name: HM5_early_rep6_miseq

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: E59 human foot phalanges, digit 4, rep 6, MiSeq

description: Library name: FP4_early_rep6_miseq

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: E59 human hand phalanges, digit 3, rep 6, MiSeq

description: Library name: HP3_early_rep6_miseq

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


title: E59 human metatarsal, digit 1, rep 6, MiSeq

description: Library name: FM1_early_rep6_miseq

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: E59 human metacarpal, digit 3, rep 6, MiSeq

description: Library name: HM3_early_rep6_miseq

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: E59 human foot phalanges, digit 1, rep 6, MiSeq

description: Library name: FP1_early_rep6_miseq

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: E59 human hand phalanges, digit 5, rep 6, MiSeq

description: Library name: HP5_early_rep6_miseq

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


title: E59 human foot phalanges, digit 5, rep 6, MiSeq

description: Library name: FP5_early_rep6_miseq

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: E59 human metacarpal, digit 1, rep 6, MiSeq

description: Library name: HM1_early_rep6_miseq

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: E59 human foot phalanges, digit 2, rep 6, MiSeq

description: Library name: FP2_early_rep6_miseq

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: E57 human metatarsal, digit 5, rep 5, MiSeq

description: Library name: FM5_early_rep5_miseq

value: Male


title: 604021_HS014_4_Blue_light

description: Library name: 604021_HS014_4

source_name: Feces

value: Feces

value: mouse fecal sample

value: Blue Light

value: M

value: ChAT homo ChR2 homo

value: B


title: 604021_HS014_2_Blue_light

description: Library name: 604021_HS014_2

value: A


title: E59 human hand phalanges, digit 4, rep 6, MiSeq

description: Library name: HP4_early_rep6_miseq

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV

value: chondrocytes

value: Female


title: E59 human hand phalanges, digit 1, rep 6, MiSeq

description: Library name: HP1_early_rep6_miseq

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I


title: E57 human metatarsal, digit 4, rep 5, MiSeq

description: Library name: FM4_early_rep5_miseq

value: Metatarsal, digit IV


title: E57 human metatarsal, digit 2, rep 5, MiSeq

description: Library name: FM2_early_rep5_miseq

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: E57 human metatarsal, digit 3, rep 5, MiSeq

description: Library name: FM3_early_rep5_miseq

value: Metatarsal, digit III


title: E57 human metatarsal, digit 1, rep 5, MiSeq

description: Library name: FM1_early_rep5_miseq

value: Metatarsal, digit I


title: E57 human foot phalanges, digit 5, rep 5, MiSeq

description: Library name: FP5_early_rep5_miseq

value: Foot phalanges, digit V


title: E59 human metacarpal, digit 4, rep 6, MiSeq

description: Library name: HM4_early_rep6_miseq

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: E59 human metacarpal, digit 2, rep 6, MiSeq

description: Library name: HM2_early_rep6_miseq

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: E59 human hand phalanges, digit 2, rep 6, MiSeq

description: Library name: HP2_early_rep6_miseq

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: E57 human foot phalanges, digit 4, rep 5, MiSeq

description: Library name: FP4_early_rep5_miseq

value: Footphalanges, digit IV

value: Male


title: E57 human foot phalanges, digit 2, rep 5, MiSeq

description: Library name: FP2_early_rep5_miseq

value: Foot phalanges, digit II


title: E57 human metacarpal, digit 4, rep 5, MiSeq

description: Library name: HM4_early_rep5_miseq


title: E57 human metacarpal, digit 2, rep 5, MiSeq

description: Library name: HM2_early_rep5_miseq


title: E57 human foot phalanges, digit 1, rep 5, MiSeq

description: Library name: FP1_early_rep5_miseq

value: Foot phalanges, digit I


title: E57 human hand phalanges, digit 3, rep 5, MiSeq

description: Library name: HP3_early_rep5_miseq

value: Hand phalanges, digit III


title: E57 human metacarpal, digit 5, rep 5, MiSeq

description: Library name: HM5_early_rep5_miseq

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: E54 human metatarsal, digit 3, rep 4, MiSeq

description: Library name: FM3_early_rep4_miseq

source_name: Metatarsal, digit III

value: chondrocytes


title: E57 human metacarpal, digit 1, rep 5, MiSeq

description: Library name: HM1_early_rep5_miseq

value: Metacarpal, digit I


title: E54 human foot phalanges, digit 4, rep 4, MiSeq

description: Library name: FP4_early_rep4_miseq

source_name: Footphalanges, digit IV


title: E54 human metatarsal, digit 1, rep 4, MiSeq

description: Library name: FM1_early_rep4_miseq

source_name: Metatarsal, digit I


title: E57 human hand phalanges, digit 4, rep 5, MiSeq

description: Library name: HP4_early_rep5_miseq

value: Hand phalanges, digit IV


title: E54 human foot phalanges, digit 5, rep 4, MiSeq

description: Library name: FP5_early_rep4_miseq


title: E57 human hand phalanges, digit 2, rep 5, MiSeq

description: Library name: HP2_early_rep5_miseq


title: E57 human hand phalanges, digit 1, rep 5, MiSeq

description: Library name: HP1_early_rep5_miseq

value: Hand phalanges, digit I


title: E57 human hand phalanges, digit 5, rep 5, MiSeq

description: Library name: HP5_early_rep5_miseq

value: Hand phalanges, digit V


title: E54 human metatarsal, digit 2, rep 4, MiSeq

description: Library name: FM2_early_rep4_miseq

value: Metatarsal, digit II


title: E54 human metacarpal, digit 5, rep 4, MiSeq

description: Library name: HM5_early_rep4_miseq


title: E54 human metacarpal, digit 4, rep 4, MiSeq

description: Library name: HM4_early_rep4_miseq


title: E54 human metatarsal, digit 5, rep 4, MiSeq

description: Library name: FM5_early_rep4_miseq

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: E54 human foot phalanges, digit 1, rep 4, MiSeq

description: Library name: FP1_early_rep4_miseq

source_name: Foot phalanges, digit I


title: E54 human foot phalanges, digit 2, rep 4, MiSeq

description: Library name: FP2_early_rep4_miseq


title: E54 human metacarpal, digit 3, rep 4, MiSeq

description: Library name: HM3_early_rep4_miseq


title: E54 human metacarpal, digit 2, rep 4, MiSeq

description: Library name: HM2_early_rep4_miseq


title: E54 human metacarpal, digit 1, rep 4, MiSeq

description: Library name: HM1_early_rep4_miseq


title: E54 human hand phalanges, digit 5, rep 4, MiSeq

description: Library name: HP5_early_rep4_miseq

source_name: Hand phalanges, digit V


title: E57 human foot phalanges, digit 3, rep 5, MiSeq

description: Library name: FP3_early_rep5_miseq

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: E57 human metacarpal, digit 3, rep 5, MiSeq

description: Library name: HM3_early_rep5_miseq

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: E54 human metatarsal, digit 4, rep 4, MiSeq

description: Library name: FM4_early_rep4_miseq

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E54 human foot phalanges, digit 3, rep 4, MiSeq

description: Library name: FP3_early_rep4_miseq


title: E54 human hand phalanges, digit 3, rep 4, MiSeq

description: Library name: HP3_early_rep4_miseq

source_name: Hand phalanges, digit III


title: E54 human hand phalanges, digit 2, rep 4, MiSeq

description: Library name: HP2_early_rep4_miseq

value: Hand phalanges, digit II


title: E54 human hand phalanges, digit 1, rep 4, MiSeq

description: Library name: HP1_early_rep4_miseq


title: E54 human hand phalanges, digit 4, rep 4, MiSeq

description: Library name: HP4_early_rep4_miseq

source_name: Hand phalanges, digit IV


title: E54 human metatarsal, digit 4, rep 3, MiSeq

description: Library name: FM4_early_rep3_miseq


title: E54 human metatarsal, digit 1, rep 3, MiSeq

description: Library name: FM1_early_rep3_miseq

value: Metatarsal, digit I


title: E54 human foot phalanges, digit 4, rep 3, MiSeq

description: Library name: FP4_early_rep3_miseq

value: Footphalanges, digit IV

value: Male


title: E54 human metatarsal, digit 5, rep 3, MiSeq

description: Library name: FM5_early_rep3_miseq


title: E54 human metacarpal, digit 5, rep 3, MiSeq

description: Library name: HM5_early_rep3_miseq


title: E54 human foot phalanges, digit 3, rep 3, MiSeq

description: Library name: FP3_early_rep3_miseq


title: E54 human foot phalanges, digit 5, rep 3, MiSeq

description: Library name: FP5_early_rep3_miseq

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: E54 human metatarsal, digit 3, rep 3, MiSeq

description: Library name: FM3_early_rep3_miseq

value: Metatarsal, digit III


title: E54 human metatarsal, digit 2, rep 3, MiSeq

description: Library name: FM2_early_rep3_miseq

source_name: Metatarsal, digit II


title: E54 human metacarpal, digit 3, rep 3, MiSeq

description: Library name: HM3_early_rep3_miseq


title: E54 human metacarpal, digit 2, rep 3, MiSeq

description: Library name: HM2_early_rep3_miseq

value: Metacarpal, digit II


title: E54 human metacarpal, digit 4, rep 3, MiSeq

description: Library name: HM4_early_rep3_miseq

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV

value: chondrocytes


title: E54 human hand phalanges, digit 4, rep 3, MiSeq

description: Library name: HP4_early_rep3_miseq

value: Hand phalanges, digit IV


title: E54 human hand phalanges, digit 5, rep 3, MiSeq

description: Library name: HP5_early_rep3_miseq


title: E54 human hand phalanges, digit 3, rep 3, MiSeq

description: Library name: HP3_early_rep3_miseq

value: Hand phalanges, digit III


title: E54 human hand phalanges, digit 2, rep 3, MiSeq

description: Library name: HP2_early_rep3_miseq


title: E54 human foot phalanges, digit 1, rep 3, MiSeq

description: Library name: FP1_early_rep3_miseq

value: Foot phalanges, digit I


title: E53 human metatarsal, digit 5, rep 2, MiSeq

description: Library name: FM5_early_rep2_miseq


title: E53 human metatarsal, digit 3, rep 2, MiSeq

description: Library name: FM3_early_rep2_miseq


title: E53 human metatarsal, digit 2, rep 2, MiSeq

description: Library name: FM2_early_rep2_miseq

value: Metatarsal, digit II


title: E53 human metatarsal, digit 1, rep 2, MiSeq

description: Library name: FM1_early_rep2_miseq


title: E54 human metacarpal, digit 1, rep 3, MiSeq

description: Library name: HM1_early_rep3_miseq

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: E54 human hand phalanges, digit 1, rep 3, MiSeq

description: Library name: HP1_early_rep3_miseq

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I


title: E53 human metatarsal, digit 4, rep 2, MiSeq

description: Library name: FM4_early_rep2_miseq


title: E54 human foot phalanges, digit 2, rep 3, MiSeq

description: Library name: FP2_early_rep3_miseq

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: E53 human foot phalanges, digit 5, rep 2, MiSeq

description: Library name: FP5_early_rep2_miseq


title: E53 human foot phalanges, digit 3, rep 2, MiSeq

description: Library name: FP3_early_rep2_miseq

value: Foot phalanges, digit III


title: E53 human foot phalanges, digit 1, rep 2, MiSeq

description: Library name: FP1_early_rep2_miseq


title: E53 human foot phalanges, digit 2, rep 2, MiSeq

description: Library name: FP2_early_rep2_miseq


title: E53 human metacarpal, digit 3, rep 2, MiSeq

description: Library name: HM3_early_rep2_miseq

value: Metacarpal, digit III


title: E53 human metacarpal, digit 2, rep 2, MiSeq

description: Library name: HM2_early_rep2_miseq

source_name: Metacarpal, digit II


title: E53 human metacarpal, digit 1, rep 2, MiSeq

description: Library name: HM1_early_rep2_miseq


title: E53 human metacarpal, digit 5, rep 2, MiSeq

description: Library name: HM5_early_rep2_miseq

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: E53 human metacarpal, digit 4, rep 2, MiSeq

description: Library name: HM4_early_rep2_miseq


title: E53 human hand phalanges, digit 5, rep 2, MiSeq

description: Library name: HP5_early_rep2_miseq

value: Hand phalanges, digit V


title: E53 human hand phalanges, digit 4, rep 2, MiSeq

description: Library name: HP4_early_rep2_miseq

value: Male


title: Kidney, UUO 7d, contralateral, FG-4592/roxadustat, SK3747

description:
Library name: Exp44_7d_SK3747_CL
Fresh frozen tissue for Spatial transcriptomics sequencing

source_name: Kidney

value: Kidney

value: Contralateral limb

tag: treatment

value: roxadustat


title: E57 human metatarsal, digit 5, rep 1, MiSeq

description: Library name: FM5_early_rep1_miseq

source_name: Metatarsal, digit V

value: Metatarsal, digit V

value: Female


title: E53 human hand phalanges, digit 2, rep 2, MiSeq

description: Library name: HP2_early_rep2_miseq

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II

value: chondrocytes


title: E57 human metatarsal, digit 2, rep 1, MiSeq

description: Library name: FM2_early_rep1_miseq


title: E57 human metatarsal, digit 3, rep 1, MiSeq

description: Library name: FM3_early_rep1_miseq

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: E57 human metatarsal, digit 4, rep 1, MiSeq

description: Library name: FM4_early_rep1_miseq

value: Metatarsal, digit IV


title: E57 human metatarsal, digit 1, rep 1, MiSeq

description: Library name: FM1_early_rep1_miseq

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: E57 human foot phalanges, digit 5, rep 1, MiSeq

description: Library name: FP5_early_rep1_miseq

value: Foot phalanges, digit V


title: E57 human foot phalanges, digit 4, rep 1, MiSeq

description: Library name: FP4_early_rep1_miseq

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: E57 human foot phalanges, digit 3, rep 1, MiSeq

description: Library name: FP3_early_rep1_miseq

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: E57 human foot phalanges, digit 2, rep 1, MiSeq

description: Library name: FP2_early_rep1_miseq

value: Foot phalanges, digit II


title: E57 human foot phalanges, digit 1, rep 1, MiSeq

description: Library name: FP1_early_rep1_miseq

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: E57 human metacarpal, digit 5, rep 1, MiSeq

description: Library name: HM5_early_rep1_miseq

value: Metacarpal, digit V


title: E57 human metacarpal, digit 4, rep 1, MiSeq

description: Library name: HM4_early_rep1_miseq

value: Metacarpal, digit IV


title: E53 human foot phalanges, digit 4, rep 2, MiSeq

description: Library name: FP4_early_rep2_miseq

value: Male


title: E57 human metacarpal, digit 3, rep 1, MiSeq

description: Library name: HM3_early_rep1_miseq

value: Metacarpal, digit II


title: E57 human metacarpal, digit 2, rep 1, MiSeq

description: Library name: HM2_early_rep1_miseq


title: E57 human metacarpal, digit 1, rep 1, MiSeq

description: Library name: HM1_early_rep1_miseq

value: Metacarpal, digit I


title: E57 human hand phalanges, digit 5, rep 1, MiSeq

description: Library name: HP5_early_rep1_miseq

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


title: E57 human hand phalanges, digit 4, rep 1, MiSeq

description: Library name: HP4_early_rep1_miseq

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV

value: Female


title: E53 human hand phalanges, digit 3, rep 2, MiSeq

description: Library name: HP3_early_rep2_miseq

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III

value: chondrocytes


title: E53 human hand phalanges, digit 1, rep 2, MiSeq

description: Library name: HP1_early_rep2_miseq

value: Hand phalanges, digit I


title: E57 human hand phalanges, digit 3, rep 1, MiSeq

description: Library name: HP3_early_rep1_miseq


title: E57 human hand phalanges, digit 1, rep 1, MiSeq

description: Library name: HP1_early_rep1_miseq


title: E74 human metatarsal, digit 3, rep 6, MiSeq

description: Library name: FM3_late_rep6_miseq

value: Metatarsal, digit III


title: E74 human metatarsal, digit 5, rep 6, MiSeq

description: Library name: FM5_late_rep6_miseq

value: Metatarsal, digit V


title: E74 human metatarsal, digit 2, rep 6, MiSeq

description: Library name: FM2_late_rep6_miseq

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: E57 human hand phalanges, digit 2, rep 1, MiSeq

description: Library name: HP2_early_rep1_miseq

value: Hand phalanges, digit II


title: E74 human metatarsal, digit 4, rep 6, MiSeq

description: Library name: FM4_late_rep6_miseq

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E74 human metatarsal, digit 1, rep 6, MiSeq

description: Library name: FM1_late_rep6_miseq

value: Metatarsal, digit I


title: E74 human foot phalanges, digit 3, rep 6, MiSeq

description: Library name: FP3_late_rep6_miseq

value: Foot phalanges, digit III


title: E74 human foot phalanges, digit 5, rep 6, MiSeq

description: Library name: FP5_late_rep6_miseq

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: E74 human foot phalanges, digit 4, rep 6, MiSeq

description: Library name: FP4_late_rep6_miseq

value: Footphalanges, digit IV

value: Male


title: E74 human foot phalanges, digit 2, rep 6, MiSeq

description: Library name: FP2_late_rep6_miseq

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: E74 human metacarpal, digit 5, rep 6, MiSeq

description: Library name: HM5_late_rep6_miseq

value: Metacarpal, digit V


title: E74 human metacarpal, digit 4, rep 6, MiSeq

description: Library name: HM4_late_rep6_miseq

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: E74 human foot phalanges, digit 1, rep 6, MiSeq

description: Library name: FP1_late_rep6_miseq

value: Foot phalanges, digit I


title: E74 human metacarpal, digit 3, rep 6, MiSeq

description: Library name: HM3_late_rep6_miseq

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: E74 human metacarpal, digit 2, rep 6, MiSeq

description: Library name: HM2_late_rep6_miseq

source_name: Metacarpal, digit II

value: Metacarpal, digit II

value: chondrocytes


title: E74 human metacarpal, digit 1, rep 6, MiSeq

description: Library name: HM1_late_rep6_miseq

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: E74 human hand phalanges, digit 5, rep 6, MiSeq

description: Library name: HP5_late_rep6_miseq

value: Hand phalanges, digit V


title: E74 human hand phalanges, digit 4, rep 6, MiSeq

description: Library name: HP4_late_rep6_miseq

value: Hand phalanges, digit IV


title: E74 human hand phalanges, digit 3, rep 6, MiSeq

description: Library name: HP3_late_rep6_miseq

value: Hand phalanges, digit III