title: Dog_MesentericLymphNode_Male_1001

description:
Dog_MesentericLymphNode_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Lung_Male_1005

status: Public on Dec 12 2022

type: SRA

city: North Chicago

first: Terry

last: Van Vleet

state: IL

address: 1 N Waukegan Rd

country: USA

institute: AbbVie

description:
Dog_Lung_Male_1005
Dog_FPKM_table_Jun22.xlsx

library_source: transcriptomic

data_processing:
ArrayStudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using ArrayStudio
Trimmed sequence reads were mapped to Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Read count extraction and normalization were performed using ArrayStudio
Assembly: Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Canis lupus familiaris

source_name: Lung

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 200-300ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit Gold following manufacturer's protocols.

treatment_protocol:
NA
NA

tag: breed

value: Beagle

tag: tissue

value: Lung

tag: Sex

value: Male

tag: treatment

value: untreated


title: Dog_MesentericLymphNode_Male_1003

description:
Dog_MesentericLymphNode_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Lymph Nodes

value: Lymph Nodes


title: Dog_LacrimalGland_Male_1005

description:
Dog_LacrimalGland_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Lacrimal Apparatus

value: Lacrimal Apparatus


title: Dog_Lung_Male_1003

description:
Dog_Lung_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Lung_Male_1001

description:
Dog_Lung_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_LacrimalGland_Male_1003

description:
Dog_LacrimalGland_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Kidney_Male_1005

description:
Dog_Kidney_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Kidney

value: Kidney


title: Dog_LacrimalGland_Male_1001

description:
Dog_LacrimalGland_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Jejunum_Male_1005

description:
Dog_Jejunum_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Jejunum

value: Jejunum


title: Dog_Kidney_Male_1003

description:
Dog_Kidney_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Ileum_Male_1003

description:
Dog_Ileum_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Ileum

value: Ileum


title: Dog_Kidney_Male_1001

description:
Dog_Kidney_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Jejunum_Male_1003

description:
Dog_Jejunum_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Ileum_Male_1001

description:
Dog_Ileum_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Jejunum_Male_1001

description:
Dog_Jejunum_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Ileum_Male_1005

description:
Dog_Ileum_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_Hippocampus_Male_1005

description:
Dog_Hippocampus_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Hippocampus

value: Hippocampus


title: Dog_Hippocampus_Male_1003

description:
Dog_Hippocampus_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Hippocampus_Male_1001

description:
Dog_Hippocampus_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Heart_Male_1003

description:
Dog_Heart_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Heart

value: Heart


title: Dog_Heart_Male_1005

description:
Dog_Heart_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_GastrocnemiusTendon_Male_1005

description:
Dog_GastrocnemiusTendon_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Tendons

value: Tendons


title: Dog_Gallbladder_Male_1005

description:
Dog_Gallbladder_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Gallbladder

value: Gallbladder


title: Dog_Gallbladder_Male_1001

description:
Dog_Gallbladder_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_FundicStomach_Male_1005

description:
Dog_FundicStomach_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Stomach

value: Stomach


title: Dog_GastrocnemiusTendon_Male_1003

description:
Dog_GastrocnemiusTendon_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Gallbladder_Male_1003

description:
Dog_Gallbladder_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_FundicStomach_Male_1001

description:
Dog_FundicStomach_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_FrontalLobe_Male_1003

description:
Dog_FrontalLobe_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Frontal Lobe

value: Frontal Lobe


title: Dog_FrontalLobe_Male_1005

description:
Dog_FrontalLobe_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_FemoralVein_Male_1005

description:
Dog_FemoralVein_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Femoral Vein

value: Femoral Vein


title: Dog_FrontalLobe_Male_1001

description:
Dog_FrontalLobe_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_FemoralVein_Male_1003

description:
Dog_FemoralVein_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_FemoralVein_Male_1001

description:
Dog_FemoralVein_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_EpididymisTail_Male_1005

description:
Dog_EpididymisTail_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Epididymis

value: Epididymis


title: Dog_EpididymisTail_Male_1003

description:
Dog_EpididymisTail_Male_1003
Dog_FPKM_table_Jun22.xlsx

value: Beagle


title: Dog_Heart_Male_1001

description:
Dog_Heart_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_FundicStomach_Male_1003

description:
Dog_FundicStomach_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_DorsalRootGanglia_Male_1003

description:
Dog_DorsalRootGanglia_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Ganglia, Spinal

value: Ganglia, Spinal


title: Dog_CorpusSpongiosum_Male_1003

description:
Dog_CorpusSpongiosum_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Penis

value: Penis

value: Male


title: Dog_DorsalRootGanglia_Male_1005

description:
Dog_DorsalRootGanglia_Male_1005
Dog_FPKM_table_Jun22.xlsx

value: untreated


title: Dog_CorpusSpongiosum_Male_1005

description:
Dog_CorpusSpongiosum_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_EpididymisHead_Male_1001

description:
Dog_EpididymisHead_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_EpididymisHead_Male_1003

description:
Dog_EpididymisHead_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_EpididymisHead_Male_1005

description:
Dog_EpididymisHead_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_DorsalRootGanglia_Male_1001

description:
Dog_DorsalRootGanglia_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Colon_Male_1001

description:
Dog_Colon_Male_1001
Dog_FPKM_table_Jun22.xlsx

source_name: Colon

value: Colon


title: Dog_Colon_Male_1003

description:
Dog_Colon_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_CervicalSpinalCord_Male_1003

description:
Dog_CervicalSpinalCord_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Cervical Cord

value: Cervical Cord


title: Dog_Cerebellum_Male_1005

description:
Dog_Cerebellum_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Cerebellum

value: Cerebellum


title: Dog_Cerebellum_Male_1003

description:
Dog_Cerebellum_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_CervicalSpinalCord_Male_1005

description:
Dog_CervicalSpinalCord_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_CervicalSpinalCord_Male_1001

description:
Dog_CervicalSpinalCord_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Cerebellum_Male_1001

description:
Dog_Cerebellum_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_CaudateNucleus_Male_1003

description:
Dog_CaudateNucleus_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Caudate Nucleus

value: Caudate Nucleus


title: Dog_BuccalMucosa_Male_1005

description:
Dog_BuccalMucosa_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Mouth Mucosa

value: Mouth Mucosa


title: Dog_BuccalMucosa_Male_1001

description:
Dog_BuccalMucosa_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_BuccalMucosa_Male_1003

description:
Dog_BuccalMucosa_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_EpididymisTail_Male_1001

description:
Dog_EpididymisTail_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Aorta_Male_1005

description:
Dog_Aorta_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Aorta

value: Aorta


title: Dog_BoneMarrow_Male_1003

description:
Dog_BoneMarrow_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Bone Marrow

value: Bone Marrow


title: Dog_Colon_Male_1005

description:
Dog_Colon_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_BoneMarrow_Male_1005

description:
Dog_BoneMarrow_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_CorpusSpongiosum_Male_1001

description:
Dog_CorpusSpongiosum_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Aorta_Male_1003

description:
Dog_Aorta_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_AdrenalGland_Male_1003

description:
Dog_AdrenalGland_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Adrenal Glands

value: Adrenal Glands


title: Dog_Aorta_Male_1001

description:
Dog_Aorta_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_CaudateNucleus_Male_1005

description:
Dog_CaudateNucleus_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_AdrenalGland_Male_1005

description:
Dog_AdrenalGland_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_CaudateNucleus_Male_1001

description:
Dog_CaudateNucleus_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Uterus_1006

description:
Dog_Female_Uterus_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Uterus

value: Uterus

value: Female


title: Dog_Female_Uvea_1006

description:
Dog_Female_Uvea_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Uvea

value: Uvea


title: Dog_Female_Uvea_1002

description:
Dog_Female_Uvea_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Vagina_1006

description:
Dog_Female_Vagina_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Vagina

value: Vagina


title: Dog_Female_WholeBlood_1004

description:
Dog_Female_WholeBlood_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Blood

value: Beagle

value: Blood


title: Dog_Female_Uvea_1004

description:
Dog_Female_Uvea_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_WholeBlood_1006

description:
Dog_Female_WholeBlood_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Vagina_1002

description:
Dog_Female_Vagina_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Vagina_1004

description:
Dog_Female_Vagina_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Uterus_1004

description:
Dog_Female_Uterus_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Uterus_1002

description:
Dog_Female_Uterus_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_WholeBlood_1002

description:
Dog_Female_WholeBlood_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_UrinaryBladder_1006

description:
Dog_Female_UrinaryBladder_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Urinary Bladder

value: Urinary Bladder


title: Dog_Female_Tongue_1006

description:
Dog_Female_Tongue_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Tongue

value: Tongue


title: Dog_Female_Tongue_1004

description:
Dog_Female_Tongue_1004
Dog_FPKM_table_Jun22.xlsx

value: untreated


title: Dog_Female_UrinaryBladder_1004

description:
Dog_Female_UrinaryBladder_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_UrinaryBladder_1002

description:
Dog_Female_UrinaryBladder_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Tongue_1002

description:
Dog_Female_Tongue_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Thyroid_1004

description:
Dog_Female_Thyroid_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Thyroid Gland

value: Thyroid Gland


title: Dog_Female_Thyroid_1002

description:
Dog_Female_Thyroid_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Thyroid_1006

description:
Dog_Female_Thyroid_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Thalamus_1006

description:
Dog_Female_Thalamus_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Thalamus

value: Thalamus


title: Dog_AdrenalGland_Male_1001

description:
Dog_AdrenalGland_Male_1001
Dog_FPKM_table_Jun22.xlsx

value: Male


title: Dog_Female_Thalamus_1004

description:
Dog_Female_Thalamus_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Synovium_1006

description:
Dog_Female_Synovium_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Synovial Membrane

value: Synovial Membrane


title: Dog_Female_Synovium_1004

description:
Dog_Female_Synovium_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_SubcorticalWhiteMatter_1004

description:
Dog_Female_SubcorticalWhiteMatter_1004
Dog_FPKM_table_Jun22.xlsx

source_name: White Matter

value: White Matter


title: Dog_Female_SubcorticalWhiteMatter_1006

description:
Dog_Female_SubcorticalWhiteMatter_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Thalamus_1002

description:
Dog_Female_Thalamus_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Synovium_1002

description:
Dog_Female_Synovium_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Soleus_1006

description:
Dog_Female_Soleus_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Muscle, Skeletal

value: Muscle, Skeletal


title: Dog_Female_Spleen_1004

description:
Dog_Female_Spleen_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Spleen

value: Spleen


title: Dog_Female_Soleus_1004

description:
Dog_Female_Soleus_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Retina_1004

description:
Dog_Female_Retina_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Retina

value: Retina


title: Dog_Female_Retina_1002

description:
Dog_Female_Retina_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_SubcorticalWhiteMatter_1002

description:
Dog_Female_SubcorticalWhiteMatter_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_SciaticNerve_1006

description:
Dog_Female_SciaticNerve_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Sciatic Nerve

value: Sciatic Nerve


title: Dog_Female_Spleen_1006

description:
Dog_Female_Spleen_1006
Dog_FPKM_table_Jun22.xlsx

value: Female


title: Dog_Female_SciaticNerve_1002

description:
Dog_Female_SciaticNerve_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Soleus_1002

description:
Dog_Female_Soleus_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Retina_1006

description:
Dog_Female_Retina_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Quadriceps_1002

description:
Dog_Female_Quadriceps_1002
Dog_FPKM_table_Jun22.xlsx

source_name: Quadriceps Muscle

value: Quadriceps Muscle


title: Dog_Female_PyloricStomach_1006

description:
Dog_Female_PyloricStomach_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Stomach

value: Stomach


title: Dog_Female_Quadriceps_1004

description:
Dog_Female_Quadriceps_1004
Dog_FPKM_table_Jun22.xlsx

value: Beagle


title: Dog_Female_PyloricStomach_1004

description:
Dog_Female_PyloricStomach_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Spleen_1002

description:
Dog_Female_Spleen_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_PyloricStomach_1002

description:
Dog_Female_PyloricStomach_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Quadriceps_1006

description:
Dog_Female_Quadriceps_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_PituitaryGland_1002

description:
Dog_Female_PituitaryGland_1002
Dog_FPKM_table_Jun22.xlsx

source_name: Pituitary Gland

value: Pituitary Gland


title: Dog_Female_PituitaryGland_1006

description:
Dog_Female_PituitaryGland_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_PeyersPatch_1006

description:
Dog_Female_PeyersPatch_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Peyer's Patches

value: Peyer's Patches


title: Dog_Female_PeyersPatch_1004

description:
Dog_Female_PeyersPatch_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_PeyersPatch_1002

description:
Dog_Female_PeyersPatch_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_ParotidGland_1006

description:
Dog_Female_ParotidGland_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Salivary Glands

value: Salivary Glands


title: Dog_Female_SciaticNerve_1004

description:
Dog_Female_SciaticNerve_1004
Dog_FPKM_table_Jun22.xlsx

value: untreated


title: Dog_Female_ParotidGland_1002

description:
Dog_Female_ParotidGland_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Parathyroid_1004

description:
Dog_Female_Parathyroid_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Parathyroid Glands

value: Parathyroid Glands


title: Dog_Female_Parathyroid_1006

description:
Dog_Female_Parathyroid_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_ParotidGland_1004

description:
Dog_Female_ParotidGland_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Pancreas_1002

description:
Dog_Female_Pancreas_1002
Dog_FPKM_table_Jun22.xlsx

source_name: Pancreas

value: Pancreas


title: Dog_Female_Ovaries_1002

description:
Dog_Female_Ovaries_1002
Dog_FPKM_table_Jun22.xlsx

source_name: Ovary

value: Ovary


title: Dog_Female_OlfactoryEpithelium_1004

description:
Dog_Female_OlfactoryEpithelium_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Olfactory Mucosa

value: Olfactory Mucosa


title: Dog_Female_PituitaryGland_1004

description:
Dog_Female_PituitaryGland_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_OlfactoryEpithelium_1002

description:
Dog_Female_OlfactoryEpithelium_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_OlfactoryEpithelium_1006

description:
Dog_Female_OlfactoryEpithelium_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_MesentericLymphNode_1006

description:
Dog_Female_MesentericLymphNode_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Lymph Nodes

value: Lymph Nodes


title: Dog_Female_Ovaries_1004

description:
Dog_Female_Ovaries_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_MesentericAdiposeTissue_1002

description:
Dog_Female_MesentericAdiposeTissue_1002
Dog_FPKM_table_Jun22.xlsx

source_name: Intra-Abdominal Fat

value: Intra-Abdominal Fat


description:
Dog_Female_SubmandibularSalivaryGland_1004
Dog_FPKM_table_Jun22.xlsx


description:
Dog_Female_SubmandibularSalivaryGland_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_MesentericLymphNode_1004

description:
Dog_Female_MesentericLymphNode_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_MammaryTissue_1006

description:
Dog_Female_MammaryTissue_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Mammary Glands, Animal

value: Mammary Glands, Animal


title: Dog_Female_MesentericAdiposeTissue_1004

description:
Dog_Female_MesentericAdiposeTissue_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Pancreas_1006

description:
Dog_Female_Pancreas_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_MesentericLymphNode_1002

description:
Dog_Female_MesentericLymphNode_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Pancreas_1004

description:
Dog_Female_Pancreas_1004
Dog_FPKM_table_Jun22.xlsx


description:
Dog_Female_SubmandibularSalivaryGland_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_MammaryTissue_1002

description:
Dog_Female_MammaryTissue_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_MammaryTissue_1004

description:
Dog_Female_MammaryTissue_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Lung_1006

description:
Dog_Female_Lung_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Lung

value: Lung


title: Dog_Female_MesentericAdiposeTissue_1006

description:
Dog_Female_MesentericAdiposeTissue_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Lung_1004

description:
Dog_Female_Lung_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Parathyroid_1002

description:
Dog_Female_Parathyroid_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Ovaries_1006

description:
Dog_Female_Ovaries_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Lung_1002

description:
Dog_Female_Lung_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Liver_1002

description:
Dog_Female_Liver_1002
Dog_FPKM_table_Jun22.xlsx

source_name: Liver

value: Liver


title: Dog_Female_Liver_1004

description:
Dog_Female_Liver_1004
Dog_FPKM_table_Jun22.xlsx

value: Female


title: Dog_Female_Lens_1006

description:
Dog_Female_Lens_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Lens, Crystalline

value: Lens, Crystalline


title: Dog_Female_Lens_1004

description:
Dog_Female_Lens_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_LacrimalGland_1002

description:
Dog_Female_LacrimalGland_1002
Dog_FPKM_table_Jun22.xlsx

source_name: Lacrimal Apparatus

value: Lacrimal Apparatus


title: Dog_Female_Lens_1002

description:
Dog_Female_Lens_1002
Dog_FPKM_table_Jun22.xlsx

value: Beagle


title: Dog_Female_LacrimalGland_1006

description:
Dog_Female_LacrimalGland_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_LacrimalGland_1004

description:
Dog_Female_LacrimalGland_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Kidney_1006

description:
Dog_Female_Kidney_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Kidney

value: Kidney


title: Dog_Female_Kidney_1004

description:
Dog_Female_Kidney_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Jejunum_1006

description:
Dog_Female_Jejunum_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Jejunum

value: Jejunum


title: Dog_Female_Kidney_1002

description:
Dog_Female_Kidney_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Hippocampus_1006

description:
Dog_Female_Hippocampus_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Hippocampus

value: Hippocampus


title: Dog_Female_Hippocampus_1004

description:
Dog_Female_Hippocampus_1004
Dog_FPKM_table_Jun22.xlsx

value: untreated


title: Dog_Female_Jejunum_1002

description:
Dog_Female_Jejunum_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Jejunum_1004

description:
Dog_Female_Jejunum_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Ileum_1004

description:
Dog_Female_Ileum_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Ileum

value: Ileum


title: Dog_Female_Hippocampus_1002

description:
Dog_Female_Hippocampus_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Ileum_1002

description:
Dog_Female_Ileum_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Heart_1004

description:
Dog_Female_Heart_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Heart

value: Heart


title: Dog_Female_Liver_1006

description:
Dog_Female_Liver_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_GastrocnemiusTendon_1006

description:
Dog_Female_GastrocnemiusTendon_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Tendons

value: Tendons


title: Dog_Female_Heart_1002

description:
Dog_Female_Heart_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_GastrocnemiusTendon_1004

description:
Dog_Female_GastrocnemiusTendon_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Ileum_1006

description:
Dog_Female_Ileum_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Gallbladder_1004

description:
Dog_Female_Gallbladder_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Gallbladder

value: Gallbladder


title: Dog_Female_Gallbladder_1002

description:
Dog_Female_Gallbladder_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Heart_1006

description:
Dog_Female_Heart_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_FrontalLobe_1004

description:
Dog_Female_FrontalLobe_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Frontal Lobe

value: Frontal Lobe


title: Dog_Female_FrontalLobe_1006

description:
Dog_Female_FrontalLobe_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_FundicStomach_1004

description:
Dog_Female_FundicStomach_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Stomach

value: Stomach


title: Dog_Female_Gallbladder_1006

description:
Dog_Female_Gallbladder_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_FrontalLobe_1002

description:
Dog_Female_FrontalLobe_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_FemoralVein_1006

description:
Dog_Female_FemoralVein_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Femoral Vein

value: Femoral Vein


title: Dog_Female_FundicStomach_1006

description:
Dog_Female_FundicStomach_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Duodenum_1006

description:
Dog_Female_Duodenum_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Duodenum

value: Duodenum


title: LCL_PSEN1_LC-26

type: RNA

city: Barcelona

first: Anna

last: Antonell

state: Barcelona

address: C/Casanova, 143

department: Neurosciences

country: Spain

institute: Fundacio Clinic per a la Recerca Biomèdica

hyb_protocol: Fragmentation, labelling and hybridization were performed according to the instructions described in the GeneChip WT Pico Reagent Kit Manual (from ThermoFisher Scientific). Instruments employed were a hybridization oven model 645 (Thermo Fisher) and a Fluidics Station 450 module. Arrays were washed before scanning using the FS450_0001 protocol, as stated in the aforementioned protocol.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 System according to the instructions detailed in the GeneChip Command Console User Guide.

data_processing:
The data were processed and analyzed separately for each tissue. Raw expression values were obtained directly from .CEL files and were processed using the Robust Multiarray Average (RMA) algorithm to get normalized expression values (log2 scale) summarized at the gene level. Different quality checks were performed before and after normalization to ensure that samples were suitable for differential expression analysis. Samples AD.MF.L3 and FTD.M2.B1 were identified as putative outliers during quality control and were therefore excluded from the analysis prior to normalization.  The analysis to select differentially expressed genes was based on adjusting a linear model with empirical Bayes moderation of the variance. Because batch effects were detected, a batch factor was included in the linear model used for differential expression analysis.  Statistical language R (version 3.6.0) and Bioconductor associated packages were used to process and analyze the data.
probe group file: Clariom_D_Human.r1.pgf
meta-probeset file: Clariom_D_Human.r1.mps

label: Biotin

organism: Homo sapiens

source_name: Immortalized lymphocyte B

label_protocol: In this procedure, the purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labling Reagent that is covalently linked to biotin. 5.5 ug of single-stranded cDNA is required for fragmentation and labeling.

growth_protocol: Human frozen prefrontal cortex from the Neurological Tissue Bank of IDIBAPS-Hospital Clínic of Barcelona. Lymphoblastoid cell lines immortalized with Epstein Barr virus, cultivated in suspension and maintained with RPMI-1640 GlutaMAX medium supplemented with 10% inactivated FBS and 1% penicillin/streptomycin.

extract_protocol: RNA extraction from frozen tissue was performed using RNeasy Lipid Tissue Mini Kit (Qiagen) using 20 mg of cortex samples. RNA extraction from LCLs was performed using Allprep DNA/RNA/Protein Mini Kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: Not applicable.

tag: gender

value: Male

tag: sample group

tag: tissue/cell type

value: Immortalized lymphocyte B


title: LCL_Control_LC-90

value: Control


title: Dog_Female_FundicStomach_1002

description:
Dog_Female_FundicStomach_1002
Dog_FPKM_table_Jun22.xlsx

value: Female


title: Dog_Female_Duodenum_1004

description:
Dog_Female_Duodenum_1004
Dog_FPKM_table_Jun22.xlsx

value: Beagle


title: LCL_GRN_LC-20

value: GRN


title: LCL_Control_LC-106


title: Dog_Female_Duodenum_1002

description:
Dog_Female_Duodenum_1002
Dog_FPKM_table_Jun22.xlsx


title: LCL_EOAD_LC-101

value: EOAD


title: Dog_Female_DorsalRootGanglia_1006

description:
Dog_Female_DorsalRootGanglia_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Ganglia, Spinal

value: Ganglia, Spinal


title: LCL_PSEN1_LC-31


title: Dog_Female_DorsalRootGanglia_1004

description:
Dog_Female_DorsalRootGanglia_1004
Dog_FPKM_table_Jun22.xlsx

value: untreated


title: LCL_EOAD_LC-45349


title: LCL_MAPT_LC-103

value: MAPT


title: LCL_EOAD_LC-45646


title: Dog_Female_DorsalRootGanglia_1002

description:
Dog_Female_DorsalRootGanglia_1002
Dog_FPKM_table_Jun22.xlsx


title: LCL_PSEN1_LC-16


title: Dog_Female_Cornea_1006

description:
Dog_Female_Cornea_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Cornea

value: Cornea


title: LCL_GRN_LC-27


title: LCL_Control_LC-82


title: LCL_Control_LC-24


title: LCL_PSEN1_LC-36


title: Dog_Female_Cornea_1004

description:
Dog_Female_Cornea_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Cornea_1002

description:
Dog_Female_Cornea_1002
Dog_FPKM_table_Jun22.xlsx


title: LCL_MAPT_LC-40


title: LCL_GRN_LC-21


title: Dog_Female_Colon_1006

description:
Dog_Female_Colon_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Colon

value: Colon


title: LCL_GRN_LC-89


title: LCL_MAPT_LC-6


title: LCL_PSEN1_LC-18


title: LCL_GRN_LC-19


title: Dog_Female_Colon_1004

description:
Dog_Female_Colon_1004
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Colon_1002

description:
Dog_Female_Colon_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Cervix_1004

description:
Dog_Female_Cervix_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Cervix Uteri

value: Cervix Uteri


title: Dog_Female_Cervix_1006

description:
Dog_Female_Cervix_1006
Dog_FPKM_table_Jun22.xlsx


title: Brain_MAPT_BK899

source_name: Frozen prefrontal cortex

value: Frozen prefrontal cortex


title: LCL_EOAD_LC-5


title: Dog_Female_CervicalSpinalCord_1006

description:
Dog_Female_CervicalSpinalCord_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Cervical Cord

value: Cervical Cord


title: Dog_Female_CervicalSpinalCord_1004

description:
Dog_Female_CervicalSpinalCord_1004
Dog_FPKM_table_Jun22.xlsx


title: LCL_Control_LC-28


title: Brain_C9orf72_BK1521


title: Dog_Female_CervicalSpinalCord_1002

description:
Dog_Female_CervicalSpinalCord_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Cervix_1002

description:
Dog_Female_Cervix_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Cerebellum_1004

description:
Dog_Female_Cerebellum_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Cerebellum

value: Cerebellum


title: Brain_TDP43_BK379


title: Dog_Female_Cerebellum_1006

description:
Dog_Female_Cerebellum_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_Cerebellum_1002

description:
Dog_Female_Cerebellum_1002
Dog_FPKM_table_Jun22.xlsx


title: Dog_Female_CaudateNucleus_1006

description:
Dog_Female_CaudateNucleus_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Caudate Nucleus

value: Caudate Nucleus


title: Brain_GRN_BK18002


title: rgs4_LL_2

city: Tulln

first: Miriam

last: Schalamun

address: Konrad Lorenz Strasse 24

country: Austria

institute: Austrian Institute of Technology

data_processing:
quality filtering and trimming bbduk version 38.18 (Q30)
Mapping using HISAT2 version 2.2.1
Read count extraction by feautreCounts version 2.0.1
normalization by DESeq2 function VST
Supplementary files format and content: tab-delimited text files include raw counts

organism: Trichoderma reesei

growth_protocol: Trichoderma reesei WT (QM6a) and deletion mutant QM6aΔrgs4 were grown in minimal medium with celluloseas carbon source at 28°C at for 96h

extract_protocol:
RNA was extracted using Rneasy plant mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using RNA stranded kit, NEB, rRNA depletion  by the Next Generation Sequencing Facility (Vienna Biocenter Core Facilities)

treatment_protocol: cultivation under at constant light or constant darkness

tag: cell line

tag: cell type

value: mycelium

tag: genotype

value: rgs4 deletion

value: growth on cellulose in light

tag: time


title: rgs4_LL_1


title: QM6a_LL_2

value: WT


title: rgs4_LL_3


title: Dog_Female_CaudateNucleus_1004

description:
Dog_Female_CaudateNucleus_1004
Dog_FPKM_table_Jun22.xlsx

value: Beagle

value: Female


title: Brain_C9orf72_BK1240

value: Male


title: QM6a_LL_1


title: Brain_PSEN1_BK929


title: Brain_Control_BK1074

value: Control


title: Brain_EOAD_BK1582

value: EOAD


title: Brain_TDP43_BK931


title: rgs4_DD_3

value: growth on cellulose in darkness


title: Brain_Tau_BK1312

value: Tau


title: Brain_Control_BK320


title: QM6a_DD_3


title: Dog_Female_CaudateNucleus_1002

description:
Dog_Female_CaudateNucleus_1002
Dog_FPKM_table_Jun22.xlsx

value: untreated


title: Brain_MAPT_BK922

value: MAPT


title: Brain_PSEN1_BK1134

value: Frozen prefrontal cortex


title: Dog_Female_BuccalMucosa_1006

description:
Dog_Female_BuccalMucosa_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Mouth Mucosa

value: Mouth Mucosa


title: rgs4_DD_2


title: QM6a_DD_1


title: Brain_MAPT_BK804


title: Brain_GRN_BK18001

value: GRN


title: Brain_C9orf72_BK1123


title: tbx5 enh3, enh5, exon knockout  - diff rep 2 - cellplex

city: Dallas

first: Daniel

last: Armendariz

state: TX

address: 5323 Harry Hines Boulevard

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

description:
DAA342
KO_SET2: Cellplex Library for tbx5 enh3, enh5, exon knockout  - diff rep 2

data_processing:
scRNA-seq libraries were demultiplexed, mapped to the human reference genome (hg38), and aggregated by experiment using the Cellranger software (ver 6.0.0, 10X Genomics). Cellplex barcodes and library assignments can be found in KO_SET2_cellplex_library_assignments.csv  supplementary file. Both knockout sequencing lanes were combined using Cellranger aggr and normalized for sequencing. Cells with higher than 20% mitochondrial content were removed, as well as genes with fewer than 1 counts. The count matrix was natural log transformed and saved as a separate layer for differential gene expression calling before scaling counts to unit variance and zero mean. Clusters were defined using the Louvain algorithm. Clusters which held fewer than 1% of all cells were removed. Dataset contained in KO_SET2_SC_DF.h5ad supplementary file.
Supplementary_files_format_and_content: CSV containing Cellplex barcode library assignments.
Assembly: hg38

molecule: polyA RNA

growth_protocol: H9 ESCs were maintained feeder-free in mTeSR Plus (Stemcell Tech. 100-0276) according to suggested manufacturer’s instructions on Matrigel (Corning 354277) coated plates, passaged every 3-4 days with DPBS/0.5 mM EDTA and plated in 2 uM thiazovivin (Sigma SML1045) supplemented mTeSR Plus overnight.

extract_protocol:
Library prepared following 10x v3.1 Dual Index with Cell Multiplexing protocol.
On day 8 post-differentiation, samples were washed with DPBS and dissociated to single cells with Accutase (Sigma SCR005) and resuspended in CDM3.

treatment_protocol: At 80-90% confluency, media was replaced with 3 uM CHIR99021 (Tocris 4423) supplemented CDM3 (RPMI 1640, Sigma R8758; 0.5 mg/ml human albumin, ScienCell OsrHSA; 211 ug/ml L-ascorbic acid 2-phosphate, Sigma A8960) for 48 hours followed by 2 uM Wnt-C59 (Cayman 16644) supplemented CDM3 for 48 hours with subsequent media changes every 2 days with CDM3 alone.

value: H9-derived cardiomyocytes

tag: differentiation day


title: QM6a_LL_3

value: mycelium


title: Dog_Female_BuccalMucosa_1002

description:
Dog_Female_BuccalMucosa_1002
Dog_FPKM_table_Jun22.xlsx


title: rgs4_DD_1

value: rgs4 deletion


title: Dog_Female_BuccalMucosa_1004

description:
Dog_Female_BuccalMucosa_1004
Dog_FPKM_table_Jun22.xlsx


title: Brain_Tau_BK1681


title: QM6a_DD_2


title: Brain_Tau_BK1751


title: Old transcriptome 2

city: New York

first: Vladimir

last: Despic

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

data_processing:
Removal of low quality reads and 3'-end adapter trimming was performed with flexbar v2.5.
Removal of duplicated reads was accomplished with pyFastqDuplicateRemover.py within the pyCRAC package v1.3.2.
Read trimming was performed using seqtk package v1.3.
Read alignement to fly, mouse or human genome was conducted using Bowtie v1.2.3.
5'-end read coverage was calculated per each genomic position using BEDTools v2.28.0.
Assembly: Drosohila melanogaster; dm6, Mus musculus; mm10, Homo sapiens; hg38.
Supplementary files format and content: Tag frequency and Cap1-2 tags in m7G-proximal dinucleotide
Library strategy: CapTag-seq

source_name: cell culture

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% FBS, 100 U Penicillin-Streptomycin at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  Poly(A)+ RNA was isolated from total RNA using magnetic oligo(dT)25 beads (NEB).

tag: cell line/tissue

value: wild-type

tag: purification

value: oligo(dT)25 beads


title: Dog_Female_Aorta_1004

description:
Dog_Female_Aorta_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Aorta

value: Beagle

value: Aorta


title: Dog_Female_BoneMarrow_1006

description:
Dog_Female_BoneMarrow_1006
Dog_FPKM_table_Jun22.xlsx

source_name: Bone Marrow

value: Bone Marrow

value: Female


title: Brain_EOAD_BK540

value: Male

value: EOAD


title: Brain_GRN_BK1544


title: tbx5 enh3, enh5, exon knockout  - diff rep 1 - cellplex

description:
DAA341
KO_SET2: Cellplex Library for tbx5 enh3, enh5, exon knockout  - diff rep 1


title: Brain_MAPT_BK760


title: Brain_Control_BK1694

value: Control


title: Old transcriptome 1


title: Dog_Female_Aorta_1002

description:
Dog_Female_Aorta_1002
Dog_FPKM_table_Jun22.xlsx

value: untreated


title: mRNA standard 2

value: knockout/wild-type CMTR2 OE=1/2

value: Wild type HEK293T cells were transfected with construct endocing for NeonGreen-tagged CMTR2. RNA was harvested 48 h after transfection.


title: Dog_Female_AdrenalGlands_1004

description:
Dog_Female_AdrenalGlands_1004
Dog_FPKM_table_Jun22.xlsx

source_name: Adrenal Glands

value: Adrenal Glands


title: mRNA standard 1

value: knockout


title: Young transcriptome 1

value: HEK293T cells were incubated in medium containing 200 uM 5-bromouridine (5-BrU) for 3 h. 5-BrU-containing medium was replaced with medium containing 2 mM Uridine and harvested for RNA extraction .


title: Dog_Female_AdrenalGlands_1006

description:
Dog_Female_AdrenalGlands_1006
Dog_FPKM_table_Jun22.xlsx


title: mRNA standard 4

value: knockout/wild-type CMTR2 OE=2:1


title: mRNA standard 3

value: knockout/wild-type CMTR2 OE=1:1


title: Dog_Female_Aorta_1006

description:
Dog_Female_Aorta_1006
Dog_FPKM_table_Jun22.xlsx


title: Dog_Liver_Male_1005

description:
Dog_Liver_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Liver

value: Liver


title: mRNA standard 5

value: wild-type CMTR2 OE

value: oligo(dT)25 beads


title: Dog_Female_AdrenalGlands_1002

description:
Dog_Female_AdrenalGlands_1002
Dog_FPKM_table_Jun22.xlsx

value: Beagle


title: TTg-MI_2

city: Shinjuku

first: Taketaro

last: Sadahiro

state: Tokyo

address: 35 Shinanomachi

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Raw data were processed with Affymetrix Expression Console software version 1.4 for normalization.

label: biotin

organism: Mus musculus

source_name: Whole heart

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Guide , Thermo Fisher Scientific Applied Biosystems).Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

extract_protocol: RNA was extracted from Ctrl-MI and TTg-MI hearts using the ReliaPrep RNA Cell Miniprep System (Promega, Z6012). The RNA quality was determined by the RNA Integrity Number (RIN) value with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)). Only specimens with RIN>7.0 were used in this study.

treatment_protocol: Experiments were performed in 8-week-old randomly allocated male mice. To generate the mouse MI model, mice were intubated and anesthetized with isoflurane gas. The chest cavity was exposed by cutting the intercostal muscle and then the left coronary artery was ligated with a 7-0 silk suture. The mouse surgeon was blinded to the study. Transthoracic echocardiography was performed after 2 days of MI, and mice with an ejection fraction (EF) > 45% were removed from the study.

value: heart harvested 3 months after MI

value: male


title: Dog_Liver_Male_1003

description:
Dog_Liver_Male_1003
Dog_FPKM_table_Jun22.xlsx

value: Male


title: TTg-MI_1


title: β-catenin ChIP-seq from Jurkat cell line in basal conditions 3

last: Bigas

address: Dr. Aiguader 88

department: Cancer Research

institute: Institut Hospital del Mar d'Investigacions Mèdiques

description: Basal Conditions

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads
Reads were aligned to the hg38 genome assembly using Bowtie2 (see materials and methods main paper)
peaks were called using MACS2 with the following setting: ChIP threshold FDR (0.1)
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph and bigWig files are generated from MACS2 peak calling output using bamtools

molecule: genomic DNA

source_name: Jurkat T-ALL cell line

extract_protocol:
Cells were crosslinked with 0.5% formaldehyde and lysated. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. DNA purification with GFX Kit [GE Healthcare Life Sciences Ref.28-9034-71]
Samples were digested with 0.1% collagenase and single-cell suspension was stained as described. Different subpopulations were directly sorted in a total volume of 10  ml of reaction buffer and processed for obtaining DNA following manufacture’s protocol. DNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified DNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total DNA was sequenced using an Illumina HiSeq 2000 sequencer.

treatment_protocol: Starting material was extracted directly from Jurkat cell cultures in basal conditions

value: Jurkat T-ALL cell line

tag: chip antibody

value: Beta-catenin, R&D Systems AF1329


title: β-catenin ChIP-seq from Jurkat cell line in basal conditions 2

description: Basal Conditions


title: Brain_C9orf72_BK811

value: Frozen prefrontal cortex


title: Ctrl-MI_2


title: β-catenin ChIP-seq from Jurkat cell line in basal conditions 1

description: Basal Conditions


title: Ctrl-MI_1


title: Brain_Tau_BK1587

value: Tau


title: Brain_TDP43_BK1137


title: Brain_EOAD_BK709

value: Female

value: EOAD


title: Brain_PSEN1_BK898


title: Brain_Control_BK365

value: Control


title: AGS

city: Daejeon

first: Bo-Kyung

last: Kim

address: Kwahag-ro

country: South Korea

institute: KRIBB

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: AGS*txt: tab-delimited text files include FPKM values
Supplementary files format and content: Expression_profile.GRCh38.gene.txt: raw counts

source_name: AGS

growth_protocol: cells were cultured in an atmosphere of 5% CO2 at 37 °C.

extract_protocol:
Total RNA from cell was isolated using Trizol Reagent (Molecular Research Center, Cincinnati, OH, USA), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AGS cells cocultured with RAW264.7 cells for 24 hours.

value: gastric cancer cells

value: only AGS cells cultured


title: Dog_Liver_Male_1001

description:
Dog_Liver_Male_1001
Dog_FPKM_table_Jun22.xlsx

value: untreated


title: AGS_RAW264.7

value: co-cultured AGS cells with Raw264.7 cells


title: Dog_Duodenum_Male_1003

description:
Dog_Duodenum_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Duodenum

value: Duodenum


title: Brain_PSEN1_BK335


title: Dog_Duodenum_Male_1001

description:
Dog_Duodenum_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: TCF1 ChIP-seq from RPMI8402 cell line in basal conditions T1R3

description:
TCF1 ChIP-seq from RPMI8402 cell line in basal conditions
Basal Conditions

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads
Reads were aligned to the mm10 genome assembly using Bowtie2 (see materials and methods main paper)
htseq software was used to estimate the raw gene counts
peaks were called using MACS2 with the following setting: ChIP threshold FDR (0.1)
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph and bigWig files are generated from MACS2 peak calling output using bamtools

source_name: RPMI8402 T-ALL cell line

treatment_protocol: Starting material was extracted directly from RPMI8402 cell cultures in basal conditions or on cells treated with LiCl 25mM for 16h

value: RPMI8402 T-ALL cell line

tag: strain

value: Cell line

value: TCF1, Cell Signalling 2206S


title: TCF1 ChIP-seq from RPMI8402 cell line in basal conditions T1R1


title: Dog_Duodenum_Male_1005

description:
Dog_Duodenum_Male_1005
Dog_FPKM_table_Jun22.xlsx

value: Beagle


title: Kaiso ChIP-seq from RPMI8402 cell line in basal conditions RKC3

description:
Kaiso ChIP-seq from RPMI8402 cell line in basal conditions
Basal Conditions

value: Kaiso, Santa Cruz sc-23871-X


title: Kaiso ChIP-seq from RPMI8402 cell line in basal conditions RKC2


title: Input from Jurkat cell line

description: Basal Conditions

value: Jurkat T-ALL cell line


title: Kaiso ChIP-seq from RPMI8402 cell line in basal conditions RKC1


title: Dog_WholeBlood_Male_1007

description:
Dog_WholeBlood_Male_1007
Dog_FPKM_table_Jun22.xlsx

source_name: Blood

value: Blood

value: Male


title: Brain_C9orf72_BK414

value: Frozen prefrontal cortex


title: LEF1 ChIP-seq from RPMI8402 cell line in basal conditions DL1

description:
LEF1 ChIP-seq from RPMI8402 cell line in basal conditions
Basal Conditions

value: LEF1, Abcam ab124271


title: Young transcriptome 2

value: wild-type

value: oligo(dT)25 beads


title: Dog_WholeBlood_Male_1011

description:
Dog_WholeBlood_Male_1011
Dog_FPKM_table_Jun22.xlsx


title: TCF1 ChIP-seq from RPMI8402 cell line in basal conditions T1R2


title: shPALI1_SUZ12 ChIP-seq_Rep2

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
Peak-calling by HOMER v4.2
Genome_build: hg19
Assembly: hg19
Supplementary files format and content: bigWig files and peak excel sheet

source_name: Human prostate cancer cells

growth_protocol: LNCaP cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin

extract_protocol:
For SUZ12 and G9a ChIP-Seq, Chromatin in nuclear fraction were sheared to 200-500bp using an Covaris M220 Focused-ultrasonicator, Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated using the indicated antibody. DNA was then reverse crosslinked from protein and purified.  For H3K27me3, H3K9me2 CUT&Tag and PALI1 CUT&RUN, 0.5x10^6 LNCaP cells bound to Concanavalin A-coated beads were incubated with indicated primary antibodies and secondary antibody. pA-Tn5 was used to induce DNA tagmentation in CUT&Tag while pA-MNase was used to digest chromatin/DNA bound by the antibodies-protein complex in CUT&RUN, followed by Proteinase K digestion and PCI extraction.
For CUT&Tag, the ethanol precipitated DNA was immediately subjected to PCR amplification by Universal and barcoded i7 primer using NEBNext HiFi 2x PCR Master mix. The amplified library was purified by using Agencourt AMPure XP beads without size selection. For ChIP-Seq and CUT&RUN, ChIP-seq libraries were prepared from 3-5ng ChIPped DNA while CUT&RUN libraries were prepared from 15-20ng DNA using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Postamplification libraries were size selected at 250–450 bp (ChIP-Seq) and 160-320bp (CUT&RUN) in length using Agencourt AMPure XP beads from Beckman Coulter and were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603). All CUT&Tag, CUT&RUN and ChIP-Seq Libraries were pooled to a final concentration of 10nM and sequenced single-end using the Illumina HiSeq 4000.

treatment_protocol: LNCaP cells were infected with control shRNA (pLKO), shRNA targeting G9a (shG9a), shRNA targeting PALI1 (shPALI1) or/and shRNA targeting JARID2 (shJARID2), lentiviruses for 4-5 days. For siRNA-mediated interference, LNCaP cells were transfected with control siRNA (siCtrl) or G9a siRNA (siG9a) for 4 days.

value: LNCaP

tag: treatment/infection

tag: antibody

tag: vendor

value: CST

tag: catalog number

tag: lot/batch number

value: Lot 8


title: Brain_MAPT_BK531

source_name: Frozen prefrontal cortex

tag: gender

value: MAPT


title: H3ac ChIP-seq from RPMI8402 cell line treated with LiCl RHL2

description:
H3ac ChIP-seq from RPMI8402 cell line treated with LiCl
16h treatment with LiCl 25mM

value: H3ac, Upstate 06-599


title: LEF1 ChIP-seq from RPMI8402 cell line in basal conditions DL3

value: RPMI8402 T-ALL cell line


title: LEF1 ChIP-seq from RPMI8402 cell line in basal conditions DL2

value: Cell line


title: Brain_Tau_BK1352

tag: sample group

value: Tau


title: Dog_Uvea_Male_1005

description:
Dog_Uvea_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Uvea

tag: breed

value: Beagle

tag: tissue

value: Uvea

tag: Sex

tag: treatment

value: untreated


title: pLKO_SUZ12 ChIP-seq

tag: cell line

value: pLKO


title: Brain_TDP43_BK1309

value: Male

tag: tissue/cell type


title: shPALI1_SUZ12 ChIP-seq_Rep1


title: Brain_TDP43_BK1243

value: Female

value: Frozen prefrontal cortex


title: H3ac ChIP-seq from RPMI8402 cell line in basal conditions RHC2

description:
H3ac ChIP-seq from RPMI8402 cell line in basal conditions
Basal Conditions

tag: cell type


title: H3ac ChIP-seq from RPMI8402 cell line treated with LiCl RHL1


title: Dog_Uvea_Male_1003

description:
Dog_Uvea_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: shPALI1_Jarid2_CUT&RUN

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
Peak-calling by HOMER v4.2
Genome_build: hg19
Assembly: hg19
Supplementary files format and content: bigWig files and peak excel sheet
Library strategy: CUT&RUN

value: Lot 1


title: H3ac ChIP-seq from RPMI8402 cell line in basal conditions RHC1


title: Brain_Control_BK499

value: Control


title: β-catenin ChIP-seq from RPMI8402 cell line treated with LiCl RBLS2

description:
β-catenin ChIP-seq from RPMI8402 cell line treated with LiCl
16h treatment with LiCl 25mM

value: β-catenin, Santa Cruz, sc-7199


title: Dog_UrinaryBladder_Male_1005

description:
Dog_UrinaryBladder_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Urinary Bladder

value: Urinary Bladder


title: pLKO_Jarid2_CUT&RUN

value: LNCaP

value: CST


title: Dog_UrinaryBladder_Male_1003

description:
Dog_UrinaryBladder_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: β-catenin ChIP-seq from RPMI8402 cell line in basal conditions RBCS2

description:
β-catenin ChIP-seq from RPMI8402 cell line in basal conditions
Basal Conditions


title: β-catenin ChIP-seq from RPMI8402 cell line treated with LiCl BRL2

value: β-catenin, R&D Systems AF1329


title: β-catenin ChIP-seq from RPMI8402 cell line treated with LiCl RBL2

value: RPMI8402 T-ALL cell line


title: β-catenin ChIP-seq from RPMI8402 cell line treated with LiCl RBLS1

value: Cell line


title: shPALI1_H3K27me3_CUTTag_Rep1

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
Peak-calling by HOMER v4.2
Genome_build: hg19
Assembly: hg19
Supplementary files format and content: bigWig files and peak excel sheet
Library strategy: CUT&Tag

value: Lot 16


title: Brain_EOAD_BK573

value: EOAD


title: β-catenin ChIP-seq from RPMI8402 cell line in basal conditions RBCS1


title: Dog_Uvea_Male_1001

description:
Dog_Uvea_Male_1001
Dog_FPKM_table_Jun22.xlsx

value: Beagle

value: Uvea


title: Dog_UrinaryBladder_Male_1001

description:
Dog_UrinaryBladder_Male_1001
Dog_FPKM_table_Jun22.xlsx

value: untreated


title: shPALI1_H3K27me3_CUTTag_Rep2


title: shPALI1_PALI1 CUT&RUN_Rep2

value: homemade


title: Dog_Tongue_Male_1005

description:
Dog_Tongue_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Tongue

value: Tongue

value: Male


title: β-catenin ChIP-seq from RPMI8402 cell line in basal conditions DB1


title: β-catenin ChIP-seq from RPMI8402 cell line in basal conditions BRC1


title: β-catenin ChIP-seq from RPMI8402 cell line in basal conditions DB3


title: Dog_Tongue_Male_1001

description:
Dog_Tongue_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Input from RPMI8402 cell line DIM

description:
Input from RPMI8402 cell line
Basal Conditions


title: Dog_Tongue_Male_1003

description:
Dog_Tongue_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: shG9a_H3K27me3 CUTTag_Rep2


title: shPALI1_PALI1 CUT&RUN_Rep1


title: TCRb-CD44+CD8+T cells from dLNs-2

first: Shan

last: Jiang

department: Taub Institute for Research on Alzheimer’s Disease and the Aging Brain

institute: Columbia University Irving Medical Center

data_processing:
decode: demultiplex barcode, VDJtools version 0.1
trim: trims ready by quality in order to enhance stitching chances, VDJtools version 0.1
pair: stitches read 1 and read 2; VDJtools version 0.1
map: maps germiline reference onto sequence reads; VDJtools version 0.1
cdr3: indeitfy CDR3 fragments from mapping results; VDJtools version 0.1
filterS: filter reads according to conserved motifs; VDJtools version 0.1
filter M: filter mosaic reads; VDJtools version 0.1
filter A: filter reads based on PCR error; VDJtools version 0.1
filterR: filter reads based on matches with references in the CDR3 region; VDJtools version 0.1
filterT: filter reads based on frequency; VDJtools version 0.1
condense: consolidate similar reads; VDJtools version 0.1
Assembly: As far as we know; VDJtools does not use any genome refefence.  It uses the manually curated reference sequences from IMGT. https://www.imgt.org/vquest/refseqh.html
Supplementary files format and content: Demultiplexed files are FASTQ, stitched files are FASTA, final analysis files are CSV/SQLite

source_name: dLNs

extract_protocol:
After 5~7days of rechallenge of GBM (DBT) cells in brain,leukocytes from brain and draining lymph nodes were stained with anti-CD3, anti-CD44, and anti-CD8 antibodies for 30 minutes at RT and washed twice. Then, live CD3+CD44+CD8+ T cells were sorted by using a FACSAria III flow cytometer (BD Biosciences) into 15-mL sterilized tubes containing 2 mL RPMI 1640 medium. After the samples were spun down, the supernatant was discarded. Next, the CD44+CD8+ T cells were resuspended in 1 mL RNAprotect Cell Reagent (Qiagen Inc.)
Library generated with iRepertoire’s reagent systems for a  specific chain and molecular barcode. Amplified libraries-TCRa, TCRb were used here.
Amplified libraries-TCRa, TCRb-RNA-seq

treatment_protocol: GBM (DBT) bearing mice treated with T cells transfected with an FGL2-blocking scFv vector. The long term survival mice were rechallenged to confirm the formation of Trm in brain.

value: dLNs

value: Balb/c

tag: genotype

value: WT

value: CD44+CD8+T cells

value: TCRb-CD44+CD8+T cells from dLNs


title: β-catenin ChIP-seq from RPMI8402 cell line in basal conditions DB2

tag: chip antibody


title: TCRa-CD8+TRM cells from brain-1

source_name: brain

value: brain

tag: strain

value: TCRa-CD8+TRM cells from brain


title: shG9a_PALI1 CUT&RUN_Rep1

value: LNCaP

tag: treatment/infection


title: TCRb-CD44+CD8+T cells from dLNs-1


title: TCRb-CD8+TRM cells from brain-2

value: TCRb-CD8+TRM cells from brain


title: shG9a_PALI1 CUT&RUN_Rep2

tag: antibody


title: shG9a_H3K27me3 CUTTag_Rep1

tag: vendor

value: CST

value: Lot 16


title: Dog_ThyroidParathyroid_Male_1003

description:
Dog_ThyroidParathyroid_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Thyroid Gland

value: Beagle

value: Thyroid Gland


title: β-catenin ChIP-seq from RPMI8402 cell line in basal conditions BRC2

value: RPMI8402 T-ALL cell line

value: Cell line

value: β-catenin, R&D Systems AF1329


title: TCRa-CD8+TRM cells from brain-2


title: Dog_Thalamus_Male_1005

description:
Dog_Thalamus_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Thalamus

value: Thalamus

value: Male

value: untreated


title: TCRb-CD8+TRM cells from brain-1

value: Balb/c

value: WT


title: Dog_ThyroidParathyroid_Male_1005

description:
Dog_ThyroidParathyroid_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: siG9a_G9a ChIP-seq_Rep1

value: bethyl laboratory

tag: catalog number

value: Lot 2


title: Dog_Thalamus_Male_1003

description:
Dog_Thalamus_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: FC00404: Control6_28

city: Wellington

first: Sotaro

last: Ochiai

address: Gate 7 Victoria University, Keburn Parade

country: New Zealand

institute: Malaghan Institute of Medical Research

description: FC00404: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 4

library_source: transcriptomic single cell

data_processing:
Detected number of molecules for each gene per cell was counted based on molecular barcodes
Number of molecules for each gene per cell was calculated using the detection efficiency of the spike-in RNAs which were measured together with every cell (total input number of spike-in RNA molecules per cell: 39000).
Assembly: mm10 assembly from the UCSC Genome Browser using STAR ver.2.7.3a
Supplementary files format and content: Tab-separated values files and matrix files

source_name: C1-C8 DRG

extract_protocol:
DRGs collected from Nav1.8-Cre R26CAG-floxStop-tdTomato mice were digested using 0.5 mg/mL liberase TL, 5 mg.mL dispase II, 0.33 mg/mL papain and 0.1mg/mL Dnase I in DMEM (with 2-ME). Samples were incubated for 20 min, mechanically agitated using glass Pasteur pipettes to prepare single cell suspension. tdTomato+ cells were single cell sorted using BD FACS Aria III into tubes containing 0.4uL of 10 x SingleCellProtect and immediiately frozen in LiqN2. Cell collection and sequencing was performed at four separate occasions from 6 naive Nav1.8-Cre R26CAG-floxStop-tdTomato mice . FC00029 contains cells from 2 mice (labelled blue and red), FC00185 contains samples from 1 mouse, FC00355 from 2 mice (Control1 and Control2) and FC00404 from 1 mouse (Control6).
Library was generated as previously described (Tenno et al, 2017,  J Exp Med 214, 2933-2946. 10.1084/jem.20170729.)
scRNA-seq using digital RNA sequencing method (Shiroguchi et al. 2012, Proc Natl Acad Sci U S A 109, 1347-1352. 10.1073/pnas.1118018109.)

value: Dorsal Root Ganglion

value: C1-C8 DRG

tag: age

value: 6-12 weeks old


title: FC00404: Control6_27


title: FC00404: Control6_32


title: FC00404: Control6_31


title: FC00404: Control6_30


title: siG9a_G9a ChIP-seq_Rep2

value: LNCaP

tag: lot/batch number


title: FC00404: Control6_25


title: Dog_ThyroidParathyroid_Male_1001

description:
Dog_ThyroidParathyroid_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: FC00404: Control6_24


title: FC00404: Control6_23


title: FC00404: Control6_29


title: pLKO_H3K27me3 CUTTag_Rep2

value: pLKO

value: CST

value: Lot 16


title: iCLIP_FLAG-PURA_overexpression_HeLa_antiPURA12D11_s4

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

country: Germany

institute: University Würzburg

data_processing:
library strategy: iCLIP-seq
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcode.fasta (using sample barcodes: PURA oe HeLa s1 NNNNNCGTGATNNNN, PURA oe HeLa s2 NNNNNACATCGNNNN, PURA oe HeLa s3 NNNNNGCCTAANNNN, PURA oe HeLa s4 NNNNNGATCTGNNNN)
Mapping: STAR (v2.7.3a) with parameters: --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --sjdbOverhang 84 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate
Duplicate removal: UMI-tools (v1.0.0) with parameters --extract-umi-method read_id --method unique
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: bigWig (crosslink event per position): BAM files were transformed to a BED files using bedtools bamtobed (v2.27.1) considering only the 5' mapping position of each read. The BED file was then sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream using bedtools genomecov. bedGraph files were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite (v365).

source_name: cell culture

growth_protocol: Cells were grown to confluence in DMEM media containing 10% FBS, 1% Penicilin/Streptomycin.

extract_protocol:
Immunoprecipitation of PURA from cell lysates was performed using anti-PURA12D11-coated Dynabeads protein G (Thermo Fisher Scientific). Subsequently, co-purified RNAs were dephosphorylated at the 3’ end, the 3’ adapter was ligated and the 5’ end was labeled with radioactive isotopes (γ-32P ATP; Hartmann Analytic). Samples were loaded onto a NuPAGE 4-12% Bis-Tris pre-cast SDS gradient gel (Thermo Fisher Scientific), transferred to a nitrocellulose membrane (GE Healthcare) and visualized using a Phosphoimager (Fujifilm). After cutting the correct region from the nitrocellulose membrane using a cutting mask, RNA was isolated by Phenol/Chloroform/Isoamylalkohol (pH=8.0, Sigma Aldrich) and the mix was transferred to a 2 ml Phase Lock Gel Heavy tube (Quantabio). After separation of the phases the RNA was precipitated by the addition of 0.75 μl GlycoBlueTM Coprecipitant (ThermoFisher), 40 μl 3 M sodium acetate pH 5.5 and 1 ml 100 % Ethanol. It was mixed and stored at -20 °C for at least two hours. Reverse transcription was performed on the resulting purified RNA using Superscript III (Thermo Fisher Scientific) according to manufacturer’s instructions. Then cDNA was immobilized on MyONE SILANE beads (Thermo Fisher Scientific) as described by the manufacturer and the second adapter was ligated.
The library was amplified for six PCR cycles with short primers followed by a ProNex size selection step (Promega) in a 1:2.95 (v/v) sample/bead ratio according to manufacturer’s instructions. The size-selected library was amplified for 12 cycles. Afterwards, a second size selection was performed using ProNex chemistry (Promega) at 1/2.4 (v/v) sample/bead ratio according to manufacturer’s instructions and cDNA was eluted in 20 μl MQ water.
The final library was analyzed using a D1000 Chip (Agilent) in a Bioanalyzer (Agilent). Samples were equimolarly mixed before sequencing on an Illumina HiSeq 1500 platform with 100-nt single-end reads and 26.6-29.5 million reads per sample

treatment_protocol: GFP-P2A-FLAG-PURA overexpression was induced by addition of doxycycline (1 μg/ml) for 24 hours. Cells were washed using PBS, crosslinked using Stratalinker 2400 (Vilber Lourmat) at 254 nm and at 300 mJ/cm2 and lysed.

tag: experiment

value: iCLIP anti-PURA12D11

value: doxycycline inducible FLAG-PURA overexpression HeLa cell line

tag: pura concentration

value: PURA overexpression


title: FC00404: Control6_22

tag: tissue


title: pLKO_H3K27me3 CUTTag_Rep1


title: FC00404: Control6_21


title: iCLIP_FLAG-PURA_overexpression_HeLa_antiPURA12D11_s3


title: FC00404: Control6_20


title: pLKO_SUZ12 ChIP-seq_Rep1

value: Lot 8


title: pLKO_SUZ12 ChIP-seq_Rep2


title: FC00404: Control6_19


title: H3K9me2_CUT&Tag_Rep2

value: Untreated


title: iCLIP_FLAG-PURA_overexpression_HeLa_antiPURA12D11_s2


title: FC00404: Control6_18


title: iCLIP_FLAG-PURA_overexpression_HeLa_antiPURA12D11_s1


title: Dog_Thalamus_Male_1001

description:
Dog_Thalamus_Male_1001
Dog_FPKM_table_Jun22.xlsx

tag: breed

value: Beagle

value: Thalamus

tag: Sex

value: Male

value: untreated


title: FC00404: Control6_17


title: FC00404: Control6_14


title: FC00404: Control6_16


title: pLKO_PALI1 CUT&RUN_Rep2

tag: cell line

value: homemade


title: FC00404: Control6_15

value: Dorsal Root Ganglion


title: iCLIP_FLAG-PURA_overexpression_HeLa_antiFLAG_s2

data_processing:
library strategy: iCLIP-seq
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcode.fasta (using sample barcodes: PURA oe HeLa s1 NNNNNTGGTCANNNN, PURA oe HeLa s2 NNNNNATTGGCNNNN)
Mapping: STAR (v2.7.3a) with parameters: --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --sjdbOverhang 59 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate
Duplicate removal: UMI-tools (v1.0.0) with parameters --extract-umi-method read_id --method unique
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: bigWig (crosslink event per position): BAM files were transformed to a BED files using bedtools bamtobed (v2.27.1) considering only the 5' mapping position of each read. The BED file was then sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream using bedtools genomecov. bedGraph files were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite (v365).

extract_protocol:
Immunoprecipitation of PURA from cell lysates was performed using FLAG M2 beads (Sigma Aldrich). Subsequently, co-purified RNAs were dephosphorylated at the 3’ end, the 3’ adapter was ligated and the 5’ end was labeled with radioactive isotopes (γ-32P ATP; Hartmann Analytic). Samples were loaded onto a NuPAGE 4-12% Bis-Tris pre-cast SDS gradient gel (Thermo Fisher Scientific), transferred to a nitrocellulose membrane (GE Healthcare) and visualized using a Phosphoimager (Fujifilm). After cutting the correct region from the nitrocellulose membrane using a cutting mask, RNA was isolated by Phenol/Chloroform/Isoamylalkohol (pH=8.0, Sigma Aldrich) and the mix was transferred to a 2 ml Phase Lock Gel Heavy tube (Quantabio). After separation of the phases the RNA was precipitated by the addition of 0.75 μl GlycoBlueTM Coprecipitant (ThermoFisher), 40 μl 3 M sodium acetate pH 5.5 and 1 ml 100 % Ethanol. It was mixed and stored at -20 °C for at least two hours. Reverse transcription was performed on the resulting purified RNA using Superscript III (Thermo Fisher Scientific) according to manufacturer’s instructions. Then cDNA was immobilized on MyONE SILANE beads (Thermo Fisher Scientific) as described by the manufacturer and the second adapter was ligated.
The library was amplified for six PCR cycles with short primers followed by a ProNex size selection step (Promega) in a 1:2.95 (v/v) sample/bead ratio according to manufacturer’s instructions. The size-selected library was amplified for 13/14 cycles (sample 1 and sample 2, respectively). Afterwards, a second size selection was performed using ProNex chemistry (Promega) at 1/2.4 (v/v) sample/bead ratio according to manufacturer’s instructions and cDNA was eluted in 20 μl MQ water.
The final library was analyzed using a D1000 Chip (Agilent) in a Bioanalyzer (Agilent). Samples were equimolarly mixed before sequencing on an Illumina HiSeq 1500 platform with 75-nt single-end reads and 20-23.8 million reads per sample

value: iCLIP anti-FLAG

tag: cell type/genotype


title: iCLIP_FLAG-PURA_overexpression_HeLa_antiFLAG_s1


title: H3K9me2_CUT&Tag_Rep1

value: LKO


title: FC00404: Control6_12

tag: cell type

value: C1-C8 DRG

value: 6-12 weeks old


title: FC00404: Control6_10


title: pLKO_PALI1 CUT&RUN_Rep1

value: LNCaP

value: pLKO


title: FC00404: Control6_13


title: FC00404: Control6_9


title: siCtrl_G9a ChIP-seq_Rep1

value: siCtrl

value: bethyl laboratory

value: Lot 2


title: iCLIP_endogenous_PURA_NPC_s4

data_processing:
library strategy: iCLIP-seq
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcode.fasta (using sample barcodes: PURA endo NPC s1 NNNNNCGTGATNNNN, PURA endo NPC s2 NNNNNACATCGNNNN, PURA endo NPC s3 NNNNNGCCTAANNNN, PURA endo NPC s4 NNNNNGATCTGNNNN)
Mapping: STAR (v2.7.3a) with parameters: --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --sjdbOverhang 59 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate
Duplicate removal: UMI-tools (v1.0.0) with parameters --extract-umi-method read_id --method unique
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: bigWig (crosslink event per position): BAM files were transformed to a BED files using bedtools bamtobed (v2.27.1) considering only the 5' mapping position of each read. The BED file was then sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream using bedtools genomecov. bedGraph files were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite (v365).

growth_protocol: The protocol for differentiation of neural progenitor cells was based on the generation of neurospheres {Reinhardt, 2013 #2503}. Briefly, the human induced pluripotent stem cell (hiPSC) line HMGU12 was harvested using StemMACS Passaging Solution (Miltenyi Biotec) and resuspended in DMEM/F-12 medium supplemented with 20% KSR, 1% NEAA, 1% GlutaMAX (Thermo Fisher Scientific), 10 μM SB431542, 5 μM dorsomorphin, 3 μM CHIR99021, 10 μM purmorphamine (Miltenyi Biotec), and 10 μM Y-27632 (Bio-Techne). The suspension was plated on an ultra-low attachment 6-well plate (Corning). Fresh medium was applied 24 h later without Y-27632. 48 h later, the basal medium was exchanged with N2B27-based medium containing a 1:1 mixture of DMEM-F-12 and Neurobasal A supplemented with 0.5% N-2, 1% B-27 minus vitamin A, 1% NEAA, and 1% GlutaMAX (Thermo Fisher Scientific), and the above-described small molecules. On day 5, N2B27-based medium was supplemented only with 50 μg/ml L-ascorbic acid, SB431542, and dorsomorphin. Approximately 24 h prior to replating, the medium was supplemented additionally with 5 ng/ml bFGF (Peprotech). On day 8, the neurospheres were mechanically dissociated and plated 1:6 on Matrigel-coated plates. Plated neurospheres were maintained for 7 days on N2B27 basal medium supplemented with Dual Smad inhibitors (Miltenyi Biotec (SB), Tocris (DM)), ascorbic acid and bFGF. On day 14, confluent neuroepithelial outgrowths were passaged in a 1:10 dilution using collagenase IV. The resulting neural progenitor cell (NPC) cultures were passaged every 7 days and maintained in N2B27 basal medium as described above with medium change every other day.

extract_protocol:
Immunoprecipitation of PURA from cell lysates was performed using anti-PURA12D11-coated Dynabeads protein G (Thermo Fisher Scientific). Subsequently, co-purified RNAs were dephosphorylated at the 3’ end, the 3’ adapter was ligated and the 5’ end was labeled with radioactive isotopes (γ-32P ATP; Hartmann Analytic). Samples were loaded onto a NuPAGE 4-12% Bis-Tris pre-cast SDS gradient gel (Thermo Fisher Scientific), transferred to a nitrocellulose membrane (GE Healthcare) and visualized using a Phosphoimager (Fujifilm). After cutting the correct region from the nitrocellulose membrane using a cutting mask, RNA was isolated by Phenol/Chloroform/Isoamylalkohol (pH=8.0, Sigma Aldrich) and the mix was transferred to a 2 ml Phase Lock Gel Heavy tube (Quantabio). After separation of the phases the RNA was precipitated by the addition of 0.75 μl GlycoBlueTM Coprecipitant (ThermoFisher), 40 μl 3 M sodium acetate pH 5.5 and 1 ml 100 % Ethanol. It was mixed and stored at -20 °C for at least two hours. Reverse transcription was performed on the resulting purified RNA using Superscript III (Thermo Fisher Scientific) according to manufacturer’s instructions. Then cDNA was immobilized on MyONE SILANE beads (Thermo Fisher Scientific) as described by the manufacturer and the second adapter was ligated.
The library was amplified for six PCR cycles with short primers followed by a ProNex size selection step (Promega) in a 1:2.95 (v/v) sample/bead ratio according to manufacturer’s instructions. The size-selected library was amplified for 22 cycles. Afterwards, a second size selection was performed using ProNex chemistry (Promega) at 1/2.4 (v/v) sample/bead ratio according to manufacturer’s instructions and cDNA was eluted in 20 μl MQ water.
The final library was analyzed using a D1000 Chip (Agilent) in a Bioanalyzer (Agilent). Samples were equimolarly mixed before sequencing on an Illumina HiSeq 1500 platform with 75-nt single-end reads and 6.7-7.9 million reads per sample

treatment_protocol: Cells were washed using PBS, crosslinked using Stratalinker 2400 (Vilber Lourmat) at 254 nm and at 300 mJ/cm2 and lysed.

value: iCLIP anti-PURA12D11

value: neuronal pecursor cells (NPC)

value: endogenous PURA


title: siCtrl_G9a ChIP-seq_Rep2


title: FC00404: Control6_8


title: pLKO_input

value: input


title: FC00404: Control6_6


title: FC00404: Control6_7


title: CUT&RUN_igG

value: igG

value: Sigma


title: FC00404: Control6_3


title: iCLIP_endogenous_PURA_NPC_s2


title: FC00404: Control6_4


title: iCLIP_endogenous_PURA_NPC_s1


title: iCLIP_endogenous_PURA_HeLa_s4

data_processing:
library strategy: iCLIP-seq
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcode.fasta (using sample barcodes: PURA endo HeLa s1 NNNNNCGTGATNNNN, PURA endo HeLa s2 NNNNNACATCGNNNN, PURA endo HeLa s3 NNNNNGCCTAANNNN, PURA endo HeLa s4 NNNNNGATCTGNNNN)
Mapping: STAR (v2.7.3a) with parameters: --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --sjdbOverhang 94 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate
Duplicate removal: UMI-tools (v1.0.0) with parameters --extract-umi-method read_id --method unique
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: bigWig (crosslink event per position): BAM files were transformed to a BED files using bedtools bamtobed (v2.27.1) considering only the 5' mapping position of each read. The BED file was then sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream using bedtools genomecov. bedGraph files were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite (v365).
Supplementary_files_format_and_content: bed (5nt wide PURA binding sites): BAM files were merged into two pseudo-replicates and subjected to peak calling by PureCLIP (v1.3.1) with default parameters. PureCLIP sites closer than 5 nt were merged into regions, and isolated PureCLIP sites without an adjacent site within 4 nt were discarded. Binding site centers were defined iteratively by the position with the highest number of crosslink events and enlarged by 2 nt on both sides to obtain 5-nt binding sites. Binding site centers were required to harbor the maximum PureCLIP score within the binding site. Furthermore, binding sites were filtered for reproducibility by requiring a binding site to be supported by a sufficient number of crosslink events in at least two out of four replicates. The threshold for sufficient crosslink event coverage, using the 0.05 percentile, was determined as described in Busch et al., 2020.

extract_protocol:
Immunoprecipitation of PURA from cell lysates was performed using anti-PURA12D11-coated Dynabeads protein G (Thermo Fisher Scientific). Subsequently, co-purified RNAs were dephosphorylated at the 3’ end, the 3’ adapter was ligated and the 5’ end was labeled with radioactive isotopes (γ-32P ATP; Hartmann Analytic). Samples were loaded onto a NuPAGE 4-12% Bis-Tris pre-cast SDS gradient gel (Thermo Fisher Scientific), transferred to a nitrocellulose membrane (GE Healthcare) and visualized using a Phosphoimager (Fujifilm). After cutting the correct region from the nitrocellulose membrane using a cutting mask, RNA was isolated by Phenol/Chloroform/Isoamylalkohol (pH=8.0, Sigma Aldrich) and the mix was transferred to a 2 ml Phase Lock Gel Heavy tube (Quantabio). After separation of the phases the RNA was precipitated by the addition of 0.75 μl GlycoBlueTM Coprecipitant (ThermoFisher), 40 μl 3 M sodium acetate pH 5.5 and 1 ml 100 % Ethanol. It was mixed and stored at -20 °C for at least two hours. Reverse transcription was performed on the resulting purified RNA using Superscript III (Thermo Fisher Scientific) according to manufacturer’s instructions. Then cDNA was immobilized on MyONE SILANE beads (Thermo Fisher Scientific) as described by the manufacturer and the second adapter was ligated.
The library was amplified for six PCR cycles with short primers followed by a ProNex size selection step (Promega) in a 1:2.95 (v/v) sample/bead ratio according to manufacturer’s instructions. The size-selected library was amplified for 13/16 cycles ( sample 1 & 4 and sample 2 & 3, respectively). Afterwards, a second size selection was performed using ProNex chemistry (Promega) at 1/2.4 (v/v) sample/bead ratio according to manufacturer’s instructions and cDNA was eluted in 20 μl MQ water.
The final library was analyzed using a D1000 Chip (Agilent) in a Bioanalyzer (Agilent). Samples were equimolarly mixed before sequencing on an Illumina HiSeq 1500 platform with 110-nt single-end reads and 23.7-27.4 million reads per sample

value: HeLa


title: FC00404: Control6_26

value: Dorsal Root Ganglion


title: Zebrafish CapQuant-seq 2

data_processing:
Removal of low quality reads and 3'-end adapter trimming was performed with flexbar v2.5.
Removal of duplicated reads was accomplished with pyFastqDuplicateRemover.py within the pyCRAC package v1.3.2.
Read trimming was performed using seqtk package v1.3.
Read alignement to fly, mouse or human genome was conducted using Bowtie v1.2.3.
5'-end read coverage was calculated per each genomic position using BEDTools v2.28.0.
Genome_build: Drosohila melanogaster; dm6, Mus musculus; mm10, Homo sapiens; hg38.

organism: Danio rerio

source_name: 48 hours old embryo

growth_protocol: Zebrafish (AB line) embryos were maintained in E3 medium at 28 degrees and staged as previously described (Kimmel et al., Developmental Dynamics, 1995).

extract_protocol:
CapTag-seq
Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  Poly(A)+ RNA was isolated from total RNA using magnetic oligo(dT)25 beads (NEB).

tag: cell line/tissue

value: whole

tag: genotype

value: wild type A/B

tag: purification

value: oligo(dT)25 beads


title: FC00404: Control6_2

value: C1-C8 DRG

tag: strain

value: 6-12 weeks old


title: FC00404: Control6_11


title: Zebrafish CapQuant-seq 1

growth_protocol: Zebrafish (AB line) embryos were maintained and staged as previously described (Kimmel et al., Developmental Dynamics, 1995).


title: iCLIP_endogenous_PURA_NPC_s3


title: FC00356: Control2_26

description: FC00355: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 3


title: FC00404: Control6_1


title: FC00356: Control2_27


title: FC00356: Control2_25


title: FC00356: Control2_22


title: FC00356: Control2_24


title: iCLIP_endogenous_PURA_HeLa_s2


title: Lung, PUUC 24 h, rep 1

first: Krishnendu

last: Roy

address: 950 Atlantic Dr NW

department: The Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory

institute: Georgia Institute of Technology

description:
polyA RNA + protein
ADT (protein) sequences are provided in supplementary file, ADT_sequences.csv

data_processing:
Further processing was done with Seurat v4.0 (cell and gene filtering, clustering, differential gene expression analysis, GSEA, cell-cell communication, RNA velocity).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, raw_feature_bc_matrix.h5 (for each sample)
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Lung

extract_protocol:
Mice were euthanized at 4 and 24 h, and lungs were processed into single-cell suspensions with a gentle MACS Octo Dissociator and Mouse Lung Dissociation Kit (Miltenyi Biotec, #130-095-297) according to manufacturer protocols. Cell suspensions were counted and evaluated for viability over 80%. Live cell enrichment (e.g., Miltenyi Biotech) was processed if the cell viability was less than 80%. Suspensions were centrifuged at 400 x g for 5 min and were washed immediately after diluting the samples in 10ml PBS + 0.1% BSA. Cells were counted using Nucleocounter (Cemometec) automated counters. Cells were blocked with 0.5 µL of TruStain FcX™ PLUS (anti-mouse CD16/32) antibody and were incubated at 4°C for 10 min. The antibody cocktail was added to stain the cells and incubated for 30 minutes before proceeding to the wash steps. Three wash steps were performed, followed by filtration.
Following cell viability confirmation, the 10x Genomics single cell 3’ v3.1 assay protocol was performed according to the manufacturer’s instructions (transcriptome: mm10-2020-A). To obtain sufficient read coverage for both libraries, we sequenced ADT libraries in 10% and cDNA library fraction at 90% of a lane (Novaseq6000 SP kit).

treatment_protocol: Female 9-10 wk old Balb/cJ mice were anesthetized with 5% isoflurane. Each treatment group contained three mice. For each group, 4 mg of PUUC NPs (5 µg PUUC per mg NP) or MPLA+PUUC NPs (6 µg MPLA + 5 µg PUUC per mg NP) were resuspended in 60 µL of normal saline (0.9% sodium chloride, Hanna Pharmaceutical, #0409488810) and administered dropwise into the bilateral nares. Mice were euthanized at 4 and 24 h after NP administration to collect lungs. Naive mice were used as an untreated control.

value: Lung

value: Whole Lung Tissue

value: Balb/cJ

tag: treatment

value: PUUC, 24 h


title: FC00356: Control2_21


title: iCLIP_endogenous_PURA_HeLa_s1

value: iCLIP anti-PURA12D11


title: FC00356: Control2_23


title: FC00356: Control2_20


title: Lung, naïve, rep 1

value: Untreated


title: FC00404: Control6_5


title: Lung, PUUC 4 h, rep 1

value: PUUC, 4 h


title: FC00356: Control2_19


title: RNAseq_HeLa_PURA_siRNA_s3

data_processing:
Quality Control: FastQC (v0.11.9)
Read alignment: STAR (v2.7.6a) with up to 4% mismatches and no multimapping allowed
Genome_build: hg38.p12 from GENCODE
Supplementary_files_format_and_content: Read counts: Reads per gene were counted using htseq-count (v 0.11.3)

growth_protocol: One day prior to transfection, HeLa cells were plated at 20% confluency in 6-well plates.

extract_protocol:
Cells were washed using PBS and subsequently collected in TRIzol Reagent (Thermo Fisher Scientific). Total RNA was extracted using Maxwell® RSC miRNA Tissue Kit (AS1460) on the Maxwell® RSC instrument according to the manufacturer’s instructions. Briefly, shock frozen cells were resuspended in 500 µl Trizol. 6 µl 1-Thioglycerol were added to 300 µl Trizol suspension. The suspension was mixed vigorously and total RNA extracted by phase separation using RSC SimplyRNA Tissue (AS1340) setup.
Libraries were generated with the Lexogen SENSE mRNA-seq Library Prep Kit V2 (Lexogen) as described in the manual. Briefly, 100 ng of total RNA were bound to oligo-dT beads, reverse-transcribed on the beads and the second strand of cDNA was synthesized after ligation of an adapter. The eluted and adapted cDNA was amplified with barcoded primers during 11 cycles of PCR with the following program: 98 °C for 10 s, 65 °C for 20 s, 72 °C for 30 s and a final extension at 72 °C for 1 min (hold at 10 °C). The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter). The quality of the libraries was validated with an Agilent Bioanalyzer (DNA 1,000 Kit).
Barcoded libraries were pooled and sequenced on an Illumina HiSeq1500 as 50 b single reads with an average sequencing depth of 20 x106 reads per sample. Each library yielded on average 35 million reads.

treatment_protocol: siRNA-mediated knockdown of PURA in HeLa cells was performed using a predesigned PURA siRNA pool (Dharmacon, M-012136-01-000). 20 μM siRNA pool was mixed with OptiMEM (Thermo Fisher Scientific) in one reaction and lipofectamine RNAiMAX was mixed with OptiMEM in a second reaction. Both reactions were incubated at room temperature (RT) for 5 min and mixed by flicking. Meanwhile, culture media on HeLa cells was changed to 1 ml DMEM + 10% FBS lacking antibiotics. Contents of both reactions were mixed and further incubated for 20 min at RT. Finally, 400 μl of lipofection mix were added drop-wise onto HeLa cells. As a control, siGENOME Non-Targeting Pool #1 (Dharmacon, D-001206-13-05) was used as described for the PURA siRNA pool. The transfected cells were incubated for 48 h at 37 °C and 5% CO2.

value: Poly A+ RNAseq

value: PURA siRNA knockdown


title: FC00356: Control2_18


title: RNAseq_HeLa_PURA_siRNA_s2


title: Lung, MPLA+PUUC 24 h, rep 1

value: MPLA+PUUC, 24 h


title: RNAseq_HeLa_PURA_siRNA_s1

value: HeLa


title: Lung, MPLA+PUUC 4 h, rep 1

value: MPLA+PUUC, 4 h


title: FC00356: Control2_17

value: Dorsal Root Ganglion


title: iCLIP_endogenous_PURA_HeLa_s3

value: endogenous PURA


title: FC00356: Control2_16


title: FC00356: Control2_15


title: FC00356: Control2_12


title: RNAseq_HeLa_ctrl_s3


title: FC00356: Control2_13


title: KLRG1+CD127+ replicate 3

city: Houston

first: William

last: Hudson

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Aligned with STAR aligner
Assembly: GRCm38

source_name: Spleen

extract_protocol:
Qiagen Rneasy kit
poly(A) selection

value: Spleen

tag: group

value: T cells


title: Naïve replicate 1

value: Naive


title: FC00356: Control2_11

value: C1-C8 DRG

value: 6-12 weeks old


title: RNAseq_HeLa_PURA_siRNA_s4


title: KLRG1+CD127+ replicate 2


title: FC00356: Control2_7


title: FC00356: Control2_9


title: RNAseq_HeLa_ctrl_s1


title: FC00356: Control2_6


title: RNAseq_HeLa_ctrl_s2


title: FC00356: Control2_4


title: KLRG1-CD127+ replicate 3


title: KLRG1-CD127+ replicate 2


title: Naïve replicate 2


title: FC00356: Control2_3


title: RNAseq_HeLa_ctrl_s4


title: KLRG1-CD127+ replicate 1


title: FC00356: Control2_1


title: FC00356: Control2_2


title: epidermis_32h_subject115

city: Berlin

first: Bharath

last: Ananthasubramaniam

address: Philippstr. 13, House 20, R. 209

institute: Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin

description: Gene expression at 8:00h the day after in human epidermis

hyb_protocol: Samples were hybridized to Agilent Whole Genome Oligo Microarrays 4x44k (Agilent Technologies).

scan_protocol: Agilent protocol

data_processing: The RMA algorithm was used to preprocess and extract expression profiles from the raw CEL files. Genes were annotated with ENSEMBL and ENTREZ IDs using Agilent “Human Genome, Whole” annotation data (hgug4112a.db, v3.2). Background correction was performed with the “normexp” function from R package “limma”; normalization between the different arrays was done with the “quantile” function from the same package. Non-annotated probes as well as control probes were filtered out. Genes were considered to be expressed if the signal across the 7 time points was well above the background signal in at least 50% of the samples. Averaged values of probes that mapped to the same gene were used for further analysis.

source_name: Skin biopsy from upper back, epidermis, subject P115, taken at 8:00h day after

label_protocol: For each of the samples, RNA was amplified and 1.2–1.65 μg of RNA were labelled with Cyanine 3-CTP according to the manufacturer's instruction (Miltenyi Biotec).

extract_protocol:
3 mm biopsies were obtained from the upper back for seven time points over a period of 24 h (8:00, 12:00, 16:00, 20:00, 00:00, 04:00 and 8:00 the following day).
RNA extraction and quality control was performed with TRIzol following manufacturer's instructions.

treatment_protocol: Skin biopsies were subsequently incubated in PBS at 55oC for 3 min to separate epidermis and dermis. Tissue samples were then frozen in liquid nitrogen and stored at -80oC.

tag: subject

value: Skin – epidermis

tag: time of collection

value: 8:00h day after

value: female


title: KLRG1+CD127- replicate 3


title: FC00356: Control1_20

tag: age


title: FC00356: Control2_8


title: KLRG1+CD127+ replicate 1


title: FC00356: Control1_19


title: KLRG1+CD127- replicate 2


title: FC00356: Control1_21


title: FC00356: Control1_18


title: FC00356: Control1_17


title: FC00356: Control2_5


title: KLRG1+CD127- replicate 1


title: epidermis_32h_subject113

source_name: Skin biopsy from upper back, epidermis, subject P113, taken at 8:00h day after

value: male


title: FC00356: Control1_16


title: FC00356: Control2_10


title: epidermis_32h_subject111

source_name: Skin biopsy from upper back, epidermis, subject P111, taken at 8:00h day after


title: FC00356: Control1_15


title: FC00356: Control1_14


title: epidermis_32h_subject108

source_name: Skin biopsy from upper back, epidermis, subject P108, taken at 8:00h day after


title: FC00356: Control1_13


title: Sample3_WT+Vehicle

city: San Francisco

first: Ilia

middle: D.

last: Vainchtein

state: California

address: 1550 4th street

department: Psychiatry

institute: UCSF

data_processing:
Sequenced libraries were processed using the Cell Ranger 5.0 pipeline and aligned to the GRCm38 (mm10) mouse reference genome.
Clustering and differential expression analysis were performed using Seurat version 4.0.1
Assembly: GRCm38, mm10
Supplementary files format and content: CSV; counts_scrnaseq_IL33.csv.gz (counts per gene per cell)
Supplementary files format and content: CSV; metadata_scrnaseq_IL33.csv (metadata for each barcode, cell)
Supplementary files format and content: Excel; scRNAseq_genes_all_clusters.xlsx (gene expression per cluster)

extract_protocol:
CD45+ cells were isolated using a tissue homogenizer followed by 22% Percoll gradient, all on ice or 4C, and collected with FACS.
10x Genomics Chromium Chip G (V3.1)

treatment_protocol: Mice were i.c.v. injected with IL-33 or vehicle and terminated after 4 hours.

tag: genotype +_injection

value: Cx3cr1-creER Heterozygous + Vehicle

value: Thalamus

tag: celltype


title: epidermis_32h_subject114

source_name: Skin biopsy from upper back, epidermis, subject P114, taken at 8:00h day after

tag: tissue


title: Sample2_cKO+IL33

value: Cx3cr1-creER Heterozygous:ST2 Flox homozygous + IL33


title: FC00356: Control1_11


title: FC00356: Control1_12


title: FC00356: Control1_9


title: Sample1_WT+IL33

value: Cx3cr1-creER Heterozygous + IL33


title: FC00356: Control1_8


title: FC00356: Control1_10


title: FC00356: Control1_7


title: epidermis_32h_subject107

source_name: Skin biopsy from upper back, epidermis, subject P107, taken at 8:00h day after


title: Neutrophils from AT3-gcsf tumor-bearing mice, hashtag library [GR20024-HTO]

city: Bar Harbor

first: Guangwen

last: Ren

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Hashtag-derived oligonucleotide (HTO)

data_processing:
The raw data (FASTQ file) of each library were produced and demultiplexed using Illumina bcl2fastq 2.20.0.422.
For all libraries, R1 contains a 16bp cell barcode + 12bp UMI barcode and R2 contains the biological reads. If present, I1 contains the index which is needed for 10X CellRanger pipelines.
An unfiltered digital gene expression matrix was generated for each gene expression library against the 10X Genomics mouse reference genome (mm10-2020-A) build using CellRanger v4.0.0
A digital counts matrix was generated for each hashtag library using CITE-Seq-Count. This produces a matrix of counts with hashtag labels for rows and cell barcodes for columns.
Assembly: mm10-2020-A
Supplementary files format and content: Transcriptomic and HashTag (HTO) counts matrices in Matrix Market sparse CSC matrix format. Rows correspond to genes in the order provided in features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

source_name: BM, PB, Lung

extract_protocol:
Neutrophils were sorted from BM, PB and lung, and then labeled with cell hashing antibodies. Around 24,000 cells (8,000 cells from each hashtagged sample) were loaded into one lane of a 10X Chromium microfluidic chip. Cells capture, lysis and RNA extraction were performed using the 10X V3 Chromium technology following the manufacturer’s protocol.
Single cell capture, barcoding and library preparation were performed with the 10x Chromium system using version 3 chemistry, following the manufacturer’s protocol. cDNA was synthesized and amplified as per manufacturer’s protocol and amplified to construct an Illumina sequencing library. cDNA and libraries were checked for quality on an Agilent 4200 TapeStation, quantified by KAPA qPCR.

value: BM, PB, Lung

value: Female

value: Neutrophils

value: Wild type


title: epidermis_32h_subject106

source_name: Skin biopsy from upper back, epidermis, subject P106, taken at 8:00h day after


title: FC00356: Control1_5

value: Dorsal Root Ganglion


title: FC00356: Control1_4


title: Neutrophils from AT3 tumor-bearing mice, gene expression library [GR20021]

description: polyA RNA


title: FC00356: Control1_2


title: epidermis_32h_subject103

source_name: Skin biopsy from upper back, epidermis, subject P103, taken at 8:00h day after


title: epidermis_32h_subject100

source_name: Skin biopsy from upper back, epidermis, subject P100, taken at 8:00h day after


title: FC00185: Control_64

description: FC00185: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 2


title: FC00356: Control1_3


title: epidermis_32h_subject102

source_name: Skin biopsy from upper back, epidermis, subject P102, taken at 8:00h day after


title: Neutrophils from naïve (C57BL/6J) and AT3 tumor-bearing mice, hashtag library [GR20020-HTO_GR20022-HTO]

description: Hashtag-derived oligonucleotide (HTO)


title: Neutrophils from naïve (C57BL/6J) mice, gene expression library [GR20019]

description: polyA RNA


title: FC00185: Control_63


title: FC00356: Control1_1


title: epidermis_28h_subject115

description: Gene expression at 4:00h the day after in human epidermis

source_name: Skin biopsy from upper back, epidermis, subject P115, taken at 4:00h day after

value: 4:00h day after


title: FC00356: Control2_14

source_name: C1-C8 DRG


title: Neutrophils from AT3-gcsf tumor-bearing mice, gene expression library [GR20023]

description: polyA RNA


title: FC00185: Control_61


title: FC00185: Control_62


title: epidermis_28h_subject114

source_name: Skin biopsy from upper back, epidermis, subject P114, taken at 4:00h day after


title: Primed wild type rep1

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

data_processing:
Quality control of FASTQ files was done using FastQC.
trimGalore was used for QC-aware trimming and adapter-removal.
Reads were aligned to a pre-compiled index of the mouse mm9 genome using HISAT2 v2.2.1
Duplicates were removed with Picard tools v2.21.9. Coverage tracks were generated with deepTools.
Peak calling was performed using MACS 2.2.71
Assembly: mm9
Supplementary files format and content: bigwig files (of coverage) at 25 bp resolution

source_name: mES V6.5

growth_protocol: mESCs were cultured on 0.1%-gelatin-coated 6-well plates in N2B27 medium supplemented with 50 μM β-mercaptoethanol, 2 mM L-glutamine, 0.1% Sodium bicarbonate, 0.11% bovine serum albumin fraction V, 1000 units/ml recombinant mouse leukemia inhibitory factor (LIF), 1 µM PD0325901 (MEK inhibitor) and 3 µM CHIR99021 (GSK3 inhibitor). Every two days, cells were passaged at a density of 1.4x105 cells/well.

extract_protocol:
ATAC-seq was performed on 1x105 primed mESCs at applying the ATAC-Seq Kit cat. 53150 (Active Motif) according to manufacturer instructions.
ATAC-Seq Kit Cat. 53150 (Active Motif) - transposase based

treatment_protocol: On differentiation day 0, naïve wild type and Hmg20a KO mESCs (2i+LIF) were adapted to primed state in differentiation media (DMEM, Sigma) supplemented with 10% FCS, 2 mM L-glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1000 U/mL leukemia inhibitory factor (LIF) for 2 days before harvesting.

value: mES V6.5

value: embryonic stem cell

value: Primed mouse embryonic stem cells


title: FC00185: Control_60

value: C1-C8 DRG

value: 6-12 weeks old


title: FC00356: Control1_6


title: FC00185: Control_59


title: epidermis_32h_subject109

source_name: Skin biopsy from upper back, epidermis, subject P109, taken at 8:00h day after

value: Skin – epidermis

value: 8:00h day after


title: Primed Hmg20a DP #26 rep2

value: Hmg20A DP


title: Primed wild type rep2


title: FC00185: Control_57


title: FC00185: Control_56


title: epidermis_28h_subject113

source_name: Skin biopsy from upper back, epidermis, subject P113, taken at 4:00h day after

value: male


title: FC00185: Control_55


title: FC00185: Control_54


title: epidermis_28h_subject111

source_name: Skin biopsy from upper back, epidermis, subject P111, taken at 4:00h day after

value: female


title: FC00185: Control_53


title: epidermis_28h_subject107

source_name: Skin biopsy from upper back, epidermis, subject P107, taken at 4:00h day after